tag:blogger.com,1999:blog-45066138219285679342012-01-27T22:44:58.110-06:00Considerations on the Genetic Development of PF11 via RecombinationNS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comBlogger1561100tag:blogger.com,1999:blog-4506613821928567934.post-39901987666461677642011-12-21T22:49:00.064-06:002012-01-27T22:44:58.136-06:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_12_20_NIMR_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><span style="font-size: small;"><br />Publish Date : 2011-12-21<br />Last Update : 2012-01-27</span><br /><br />On 2011-12-20, the <strong><span style="color: #783f04;">UK National Institute of Medical Research</span></strong> released a group of human <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences at <strong>GISAID</strong> including 46 full&nbsp;<strong><span style="color: #274e13;">HA</span></strong> and 45 full <strong><span style="color: #274e13;">NA</span></strong> segments.&nbsp; The sample dates&nbsp;cover 2010-12-15 to 2011-08-11 (44 during 2011).&nbsp; <strong><span style="color: #783f04;">Fifteen originating labs</span></strong> provided the samples&nbsp;though no specification of clinical outcome is notated within the <strong>NIMR</strong> deposit.&nbsp; The cases produced 968 total polymorphisms on the&nbsp;Hemagglutinin and Neuraminidase&nbsp;gene segments (<strong><span style="color: #274e13;">HA</span></strong> 638 / <strong><span style="color: #274e13;">NA</span></strong> 330) averaging <strong><span style="color: #783f04;">over 20 polymorphisms</span></strong> per full sequence (<strong><span style="color: #274e13;">HA</span></strong> 13.9 / <strong><span style="color: #274e13;">NA</span></strong> 7.3).<br /><br />The superset of polymorphisms demonstrates notable non-swine, zoonotic homology according to the <strong><span style="color: #783f04;">GeneWurx Zoonoses Listing (GZL)</span></strong> <a href="http://genewurx.com/data/GeneWurx_GZL_2011_12_20_NIMR_v1.xls" target="_blank">assessment</a>&nbsp;with an <strong><span style="color: #783f04;">85% minimum</span></strong> of the 350 combined distinct <strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> polymorphisms being found on <strong><span style="color: #783f04;">non-swine, animal</span></strong> sequences (primarily avian).&nbsp; <strong><span style="color: #783f04;">Trans-Zoonotic Serotype Analyses (TZSA)</span></strong>, [<a href="http://genewurx.com/data/genewurx_tzsa_2011_12_20_nimr_ha_v1.xls" target="_blank">HA</a>] / [<a href="http://genewurx.com/data/genewurx_tzsa_2011_12_20_nimr_na_v1.xls" target="_blank">NA</a>], provide the detail beneath the&nbsp;<strong><span style="color: #783f04;">GZL</span></strong>.&nbsp; Additionally, <strong><span style="color: #783f04;">GeneWurx LookAside</span></strong> analysis (Upstream &amp; Downstream Distances of 1 Amino Acid each) demonstrates potential <strong><span style="color: #783f04;">influencer relationships</span></strong> for <strong><span style="color: #741b47;">pH1N1</span></strong>&nbsp;<strong><span style="color: #274e13;">HA</span></strong> polymorphisms&nbsp;that have&nbsp;not yet&nbsp;shown&nbsp;<strong><span style="color: #783f04;">direct</span></strong> <strong><span style="color: #660000;">zoonotic</span></strong> homology.<br /><br />The volume and span of the deposit demonstrates the ongoing significant rate of genetic acquisition onto 4 of the established clades, alongside several uncladed sequences.&nbsp; Four sequences carry <strong><span style="color: #783f04;">clade-defining</span></strong> elements from <strong><span style="color: #783f04;">multiple clades</span></strong>.&nbsp; <strong><span style="color: #783f04;">Ambiguity</span></strong> in the traces is high with <strong><span style="color: #783f04;">44 mixed</span></strong> traces, 34 <strong><span style="color: #274e13;">HA</span></strong> and 10 <strong><span style="color: #274e13;">NA</span></strong>.&nbsp; <br /><br />A certain population of geographically-dispersed sequences shows a combined <strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> total of <strong><span style="color: #783f04;">25 or more revisions</span></strong> (10 sequences, 22% of the deposit).&nbsp; This deposit brings&nbsp;the first <strong><span style="color: #4c1130;">pH1N1</span></strong> sequence with a combined <strong><span style="color: #783f04;">40 polymorphisms</span></strong> (<strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong>)&nbsp;on the <strong><span style="color: #660000;">highly avian-influenced</span></strong>,&nbsp;<strong><span style="color: #783f04;">SenegalDakar14_1x_2011_04_14</span></strong> (<strong><span style="color: #274e13;">HA</span></strong> 29 / <strong><span style="color: #274e13;">NA</span></strong> 11) [<a href="http://pf11.blogspot.com/2011/12/avian-homology-on-high-diversity.html#EPI346724">EPI346724</a>].&nbsp; On that Dakar <strong><span style="color: #274e13;">HA</span></strong>,&nbsp;23 of 29 polymorphisms <strong><span style="color: #783f04;">(79%)</span></strong> are found&nbsp;within <strong><span style="color: #783f04;">Avian H1N1</span></strong>, while at least&nbsp;<strong><span style="color: #783f04;">90% are identifiable in non-swine</span></strong> zoonotic reservoirs (26 of 29 <strong><span style="color: #274e13;">HA</span></strong>).&nbsp; This single human sequence from a very young child carries 13 amino homologies to <strong><span style="color: #660000;">H5N1</span></strong> (9 <strong><span style="color: #274e13;">HA</span></strong> / 4 <strong><span style="color: #274e13;">NA</span></strong>), 13 to <strong><span style="color: #783f04;">H9N2</span></strong> (9 <strong><span style="color: #274e13;">HA</span></strong> / 4 <strong><span style="color: #274e13;">NA</span></strong>) and 18 to <strong><span style="color: #783f04;">H6N1</span></strong> (10 <strong><span style="color: #274e13;">HA</span></strong> / 8 <strong><span style="color: #274e13;">NA</span></strong>). Dakar homology to <strong><span style="color: #660000;">TamiFlu Resistant</span></strong> strains due to <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">247N</span></strong> is significant with 14 matches (8 <strong><span style="color: #274e13;">HA</span></strong> /&nbsp;6 <strong><span style="color: #274e13;">NA</span></strong>). <br /><br />Enhanced acquisition of <strong><span style="color: #783f04;">avian genetic data</span></strong> and convergence of polymorphisms found on <strong><span style="color: #660000;">High-CFR</span></strong> and highly-zoonotic <strong><span style="color: #4c1130;">pH1N1</span></strong> strains&nbsp;are quantified.&nbsp; Variant clades appear to be gaining data from the same sources as the <strong><span style="color: #4c1130;">pH1N1</span></strong> <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">230I</span></strong> strains (24 <strong><span style="color: #274e13;">HA</span></strong> / 12 <strong><span style="color: #274e13;">NA</span></strong> matches) and the <strong><span style="color: #4c1130;">Upsilon</span></strong> series (31 <strong><span style="color: #274e13;">HA</span></strong>&nbsp;/ 23 <strong><span style="color: #274e13;">NA</span></strong> matches)&nbsp;of 84 sequences (<strong><span style="color: #660000;">5.33% CFR</span></strong>).&nbsp; <br /><br />Five countries (Cameroon, France, England, Iceland and Hungary) produced a subset of 9 sequences bearing 12 total polymorphisms within the <strong><span style="color: #783f04;">aa156-aa159</span></strong> range,&nbsp;a domain documented to produce <strong><span style="color: #660000;">Vaccine Escape</span></strong>. &nbsp;<strong><span style="color: #783f04;">Hungary7_xM_2011_01_31</span></strong> (<strong><span style="color: #274e13;">HA</span></strong> 11 / <strong><span style="color: #274e13;">NA</span></strong> 06) [<a href="http://pf11.blogspot.com/2011/12/avian-homology-on-high-diversity.html#EPI346709">EPI346709</a>] on <strong><span style="color: blue;">Clade2: 188T</span></strong> with <strong><span style="color: #783f04;">RBS</span></strong> <strong><span style="color: blue;">226R</span></strong> (<strong>Vaccine Match</strong>) applies polymorphic behaviour at 3 consecutive <strong><span style="color: #660000;">Vaccine Escape</span></strong> locations in this domain (<strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">157E</span></strong> mix wt, <strong><span style="color: blue;">158E</span></strong> mix wt and <strong><span style="color: blue;">159D</span></strong> mix wt).<br /><br />One sequence is <strong><span style="color: #660000;">TamiFlu Resistant</span></strong> with <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">275Y</span></strong>.&nbsp; More importantly a strong gravity is indicated in the polymorphic pattern suggestive that more <strong><span style="color: #660000;">TmX</span></strong> due to <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">247N</span></strong> will be seen in the future on these types of strains.&nbsp; Considering the <strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> distinct polymorphic supersets on these human pandemic sequences,&nbsp;96 (52 <strong><span style="color: #274e13;">HA</span></strong> and 44 <strong><span style="color: #274e13;">NA</span></strong>) changes (27%) appear on earlier pandemic sequences with <strong><span style="color: #660000;">TmX</span></strong> due to <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">247N</span></strong> and 85 (52 <strong><span style="color: #274e13;">HA</span></strong> and 33 <strong><span style="color: #274e13;">NA</span></strong>)&nbsp;changes (24%) appear on the subset of <strong><span style="color: #783f04;">H5N1</span></strong> sequences that carry the <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">247N</span></strong> marker. <br /><br />Evaluating the 229 distinct <strong><span style="color: #274e13;">HA</span></strong> changes derived from these 46 human pandemic sequences against fractional <strong><span style="color: #274e13;">HA</span></strong> subsets of several <strong><span style="color: #660000;">animal serotypes</span></strong>, a <strong><span style="color: #783f04;">minimum of 84%</span></strong> <a href="http://genewurx.com/data/GeneWurx_GZL_2011_12_20_NIMR_v1.xls" target="_blank">share homology</a>.&nbsp; <strong><span style="color: #783f04;">Avian H1N1</span></strong> leads the match count at <strong><span style="color: #783f04;">140 polymorphic&nbsp;values</span></strong>&nbsp;(<strong>103</strong> <strong><span style="color: #783f04;">Farm Avian H1N1</span></strong>), while <strong><span style="color: #783f04;">H6N1</span></strong> continues to participate at a significant level (88 matches).&nbsp; Homology to <strong><span style="color: #783f04;">Avian H9N2</span></strong> (65), <strong><span style="color: #783f04;">H13</span></strong> (53) and the <strong><span style="color: #660000;">High-CFR</span></strong> <strong><span style="color: #783f04;">H5N1</span></strong> (<strong>104</strong>) demonstrates that this pandemic has ample opportunity <strong><span style="color: #783f04;">for genetic input from the extant reservoirs</span></strong> to amplify clinical conditions.&nbsp; <strong><span style="color: #783f04;">GeneWurx LookAside</span></strong> analysis shows that <strong>109</strong> of the 229 distinct&nbsp;<strong><span style="color: #741b47;">pH1N1</span></strong> <strong><span style="color: #274e13;">HA </span></strong>polymorphisms demonstrate an amino acid homology <strong><span style="color: #783f04;">within 1 position</span></strong> upstream or downstream in a <strong><span style="color: #660000;">zoonotic</span></strong> reservoir for a total of <strong>311</strong> <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: #783f04;">LookAside</span></strong> <strong><span style="color: #783f04;">influencers</span></strong>.<br /><br />Of 121 distinct <strong><span style="color: #274e13;">NA</span></strong> polymorphisms, <strong>104</strong> are <strong><span style="color: #783f04;">non-swine, zoonotic</span></strong> (86%) and a <strong>minimum of 89</strong> are found on <strong><span style="color: #783f04;">Avian H1N1</span></strong> (74%) with <strong>74 (61%)</strong> of those found on a subset of a dozen <strong><span style="color: #783f04;">Farm Avian H1N1</span></strong> sequences that have <strong><span style="color: #783f04;">consistently matched</span></strong> polymorphisms coming onto the human <strong><span style="color: #4c1130;">H1N1</span></strong> pandemic background since 2009.&nbsp; <strong><span style="color: #274e13;">NA</span></strong> homology with other&nbsp;<strong><span style="color: #783f04;">non-swine</span></strong>, zoonotic reservoirs remains significant: <strong><span style="color: #783f04;">Avian H6N1</span></strong> (<strong><span style="color: #660000;">88 / 73%</span></strong>), <strong><span style="color: #783f04;">Avian H9N2</span></strong> (30) and the <strong><span style="color: #660000;">High-CFR</span></strong> <strong><span style="color: #783f04;">H5N1</span></strong> (54).<br /><br />Though the <strong><span style="color: #660000;">zoonotic serotype backgrounds</span></strong> profiled against these human polymorphisms are entirely variant, these <strong><span style="color: #783f04;">many codon-level homologies</span></strong> crossing <strong><span style="color: #783f04;">multiple</span></strong> zoonotic reservoirs into the human&nbsp;pandemic illuminates the <strong><span style="color: #783f04;">GeneWurx </span></strong>premise that the <strong><span style="color: #783f04;">origin</span></strong> of the human H1N1 pandemic be reconsidered as <strong><span style="color: #783f04;">avian</span></strong>. <br /><br /><span style="font-size: x-large;"><strong>Cladistics</strong></span><br /><br /><strong><span style="color: blue;">Clade1: 189T</span></strong> - 07 Sequences<br /><strong><span style="color: blue;">Clade2: 188T</span></strong> - 23 Sequences<br /><strong><span style="color: blue;">Clade3: 186P</span></strong> - 05 Sequences<br /><strong><span style="color: blue;">Clade5: 208K_219V</span></strong>&nbsp;- 06 Sequences <br /><br /><strong><span style="color: #274e13;">HA</span></strong>&nbsp;638 Polymorphisms Averaging ~<strong><span style="color: #783f04;">13.9 per Segment </span></strong><br /><strong><span style="color: #274e13;">NA</span></strong>&nbsp;330 Polymorphisms Averaging ~ <strong><span style="color: #783f04;">7.3 per Segment</span></strong><br /><br /><strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong>&nbsp;968 Total Polymorphisms Averaging ~<strong><span style="color: #783f04;">20.0&nbsp;across 45&nbsp;w/ HA &amp; NA</span></strong><br /><br /><span style="font-size: x-large;"><strong>TamiFlu Resistance</strong></span><br /><br />One&nbsp;<strong><span style="color: #660000;">TamiFlu Resistant</span></strong> sequence (<strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">275Y</span></strong>) features on a&nbsp;<strong><span style="color: blue;">Clade2: 188T</span></strong> background and carries <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: #783f04;">RBS</span></strong> <strong><span style="color: blue;">227G</span></strong> with the <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">158E</span></strong> (mixture with wild type) that has repeatedly been observed to promote <strong><span style="color: #660000;">Vaccine Escape</span></strong>.&nbsp; <strong><span style="color: #783f04;">Avian H1N1</span></strong> carries homology with&nbsp;9 of the 11 <strong><span style="color: #274e13;">HA</span></strong> and 100% of <strong><span style="color: #274e13;">NA</span></strong> polymorphisms on the <strong><span style="color: #660000;">TamiFlu Resistant</span></strong> French case.&nbsp; One small population of <strong><span style="color: #660000;">Farm Avian H1N1</span></strong> sequences matches on 7 of these 11 <strong><span style="color: #274e13;">HA</span></strong> and 5 of 6 <strong><span style="color: #274e13;">NA</span></strong> revisions.&nbsp; <strong><span style="color: #660000;">TamiFlu Resistance Confluence</span></strong> (multiple <strong><span style="color: #660000;">TmX</span></strong> markers) is correlated due to 8 of the 11 <strong><span style="color: #274e13;">HA</span></strong> markers sharing homology to the superset of <strong><span style="color: #4c1130;">pH1N1</span></strong> <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">247N</span></strong> <strong><span style="color: #660000;">TamiFlu Resistant</span></strong> sequences and 100% of the <strong><span style="color: #274e13;">NA</span></strong> changes.&nbsp;&nbsp;Fourteen revisions (8 <strong><span style="color: #274e13;">HA</span></strong> / 6 <strong><span style="color: #274e13;">NA</span></strong>) pattern to the <strong><span style="color: #4c1130;">pH1N1</span></strong> superset of <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">230I</span></strong>-bearing sequences.&nbsp;&nbsp;Eleven&nbsp;changes (8&nbsp;<strong><span style="color: #274e13;">HA</span></strong>&nbsp;/ 3 <strong><span style="color: #274e13;">NA</span></strong>)&nbsp;equate to the <strong><span style="color: #660000;">High-CFR</span></strong> human pandemic <strong><span style="color: #741b47;">Upsilon</span></strong> sub-clade.<br /><ul><li>[<a href="http://pf11.blogspot.com/2011/12/avian-homology-on-high-diversity.html#EPI346699">EPI346699</a>] <strong><span style="color: #783f04;">FranceLorraine1176_50x_2011_02_23</span><span style="color: #660000;">_TmX</span></strong></li></ul><br /><span style="font-size: x-large;"><strong>Sequences</strong></span><br /><br /><br />. . . . Madagascar9274_7M_2011_08_11 (<br />. . . . . . . . GISAID HA EPI346721<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 22 Polymorphisms (12 Amino and 10 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . #4C,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn49G (GGa),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 141Q,<br />. . . . . . . . 146G,<br />. . . . . . . . 169S,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 216G,<br />. . . . . . . . 259P,<br />. . . . . . . . syn304G (GGg),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 388R,<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn473K (AAg),<br />. . . . . . . . syn512R (AGa),<br />. . . . . . . . syn538F (TTt),<br />. . . . . . . . syn546L (tTA))<br /><br />. . . . Madagascar9252_23F_2011_08_10 (<br />. . . . . . . . GISAID HA EPI346717<br />. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . #6M,<br />. . . . . . . . #4C,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn49G (GGa),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 141Q,<br />. . . . . . . . 146G,<br />. . . . . . . . 169S,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn301I (ATa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 364S,<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn473K (AAg),<br />. . . . . . . . syn496A (GCg),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . Madagascar9252_23F_2011_08_10 (<br />. . . . . . . . GISAID NA EPI346718<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . 126S,<br />. . . . . . . . syn152R (AGa),<br />. . . . . . . . syn225R (AGg),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn295N (AAt),<br />. . . . . . . . syn313Q (CAa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 416N)<br /><br />. . . . Madagascar8753_xF_2011_08_02 (<br />. . . . . . . . GISAID HA EPI346715<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . #4C,<br />. . . . . . . . syn1A (GCt),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn49G (GGa),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 141Q,<br />. . . . . . . . 146G,<br />. . . . . . . . 169S,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 400S,<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn473K (AAg),<br />. . . . . . . . syn514Y (TAt),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . Madagascar8753_xF_2011_08_02 (<br />. . . . . . . . GISAID NA EPI346716<br />. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 56C,<br />. . . . . . . . 126S,<br />. . . . . . . . syn225R (AGg),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn295N (AAt),<br />. . . . . . . . syn307N (AAt),<br />. . . . . . . . syn313Q (CAa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . SouthAfricaJohannesburg150_46F_2011_07_10 (<br />. . . . . . . . GISAID HA EPI346655<br />. . . . . . . . Clade5: 208K_219V<br />. . . . . . . . 16 Polymorphisms (8 Amino and 8 Silent)<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . syn82I (ATc),<br />. . . . . . . . syn93C (TGc),<br />. . . . . . . . 100N,<br />. . . . . . . . syn131S (TCa),<br />. . . . . . . . 141Q,<br />. . . . . . . . 142D,<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . 252L,<br />. . . . . . . . syn307P (CCc),<br />. . . . . . . . 359A,<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa),<br />. . . . . . . . syn512R (AGa))<br /><br />. . . . SouthAfricaJohannesburg150_46F_2011_07_10 (<br />. . . . . . . . GISAID NA EPI346656<br />. . . . . . . . 9 Polymorphisms (2 Amino and 7 Silent)<br />. . . . . . . . syn79S (TCg),<br />. . . . . . . . syn89S (TCt),<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . syn229S (TCc),<br />. . . . . . . . syn236G (GGc),<br />. . . . . . . . 269I mix wt,<br />. . . . . . . . 299A,<br />. . . . . . . . syn378N (AAt),<br />. . . . . . . . syn405S (AGc))<br /><br />. . . . CameroonLEID07111870_24F_2011_07_07 (<br />. . . . . . . . GISAID HA EPI346647<br />. . . . . . . . Clade1: 189T<br />. . . . . . . . 13 Polymorphisms (8 Amino and 5 Silent)<br />. . . . . . . . 1T,<br />. . . . . . . . syn168Y (TAt),<br />. . . . . . . . syn176V (GTt),<br />. . . . . . . . 189T,<br />. . . . . . . . 205E,<br />. . . . . . . . syn238E (GAa),<br />. . . . . . . . 275A,<br />. . . . . . . . syn286K (AAa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn413K (AAg),<br />. . . . . . . . 476D,<br />. . . . . . . . 477K,<br />. . . . . . . . 523A)<br /><br />. . . . CameroonLEID07111870_24F_2011_07_07 (<br />. . . . . . . . GISAID NA EPI346648<br />. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)<br />. . . . . . . . syn22L (cTA),<br />. . . . . . . . syn135T (ACc),<br />. . . . . . . . syn262K (AAa),<br />. . . . . . . . syn398E (GAa))<br /><br />. . . . SenegalDakar18_4x_2011_07_07 (<br />. . . . . . . . GISAID HA EPI346685<br />. . . . . . . . 25 Polymorphisms (8 Amino and 17 Silent)<br />. . . . . . . . 10H mix wt,<br />. . . . . . . . 35I,<br />. . . . . . . . 51V,<br />. . . . . . . . syn99I (ATt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 131T,<br />. . . . . . . . syn152I (ATt),<br />. . . . . . . . syn154L (CTg),<br />. . . . . . . . 206S,<br />. . . . . . . . syn214K (AAa),<br />. . . . . . . . syn219I (ATt),<br />. . . . . . . . syn254P (CCa),<br />. . . . . . . . 262K,<br />. . . . . . . . syn276H (CAt),<br />. . . . . . . . syn295F (TTc),<br />. . . . . . . . syn301I (ATt),<br />. . . . . . . . syn331G (GGt),<br />. . . . . . . . syn337A (GCt),<br />. . . . . . . . syn379T (ACc),<br />. . . . . . . . syn433E (GAg),<br />. . . . . . . . syn451K (AAa),<br />. . . . . . . . syn456L (cTA),<br />. . . . . . . . 463V,<br />. . . . . . . . syn475D (GAc),<br />. . . . . . . . 523A)<br /><br />. . . . SenegalDakar18_4x_2011_07_07 (<br />. . . . . . . . GISAID NA EPI346686<br />. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)<br />. . . . . . . . syn20A (GCc),<br />. . . . . . . . 74V,<br />. . . . . . . . syn89S (TCt),<br />. . . . . . . . 106V,<br />. . . . . . . . syn160S (AGt),<br />. . . . . . . . 166I mix wt,<br />. . . . . . . . syn275H (CAt),<br />. . . . . . . . syn304V (GTt),<br />. . . . . . . . syn382G (GGa),<br />. . . . . . . . 385T,<br />. . . . . . . . 386K,<br />. . . . . . . . syn433E (GAa))<br /><br />. . . . SouthAfricaJohannesburg146_xM_2011_06_29 (<br />. . . . . . . . GISAID HA EPI346653<br />. . . . . . . . Clade5: 208K_219V<br />. . . . . . . . 16 Polymorphisms (9 Amino and 7 Silent)<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . syn75T (ACc),<br />. . . . . . . . syn82I (ATc),<br />. . . . . . . . syn93C (TGc),<br />. . . . . . . . 100N,<br />. . . . . . . . 141Q,<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 218V mix wt,<br />. . . . . . . . 219V,<br />. . . . . . . . 252L,<br />. . . . . . . . 301V mix wt,<br />. . . . . . . . syn307P (CCc),<br />. . . . . . . . 359A,<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa))<br /><br />. . . . SouthAfricaJohannesburg146_xM_2011_06_29 (<br />. . . . . . . . GISAID NA EPI346654<br />. . . . . . . . 8 Polymorphisms (1 Amino and 7 Silent)<br />. . . . . . . . syn89S (TCt),<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . syn229S (TCc),<br />. . . . . . . . syn236G (GGc),<br />. . . . . . . . 299A,<br />. . . . . . . . syn355N (AAc),<br />. . . . . . . . syn405S (AGc),<br />. . . . . . . . syn427I (ATt))<br /><br />. . . . Madagascar3520_52M_2011_06_17 (<br />. . . . . . . . GISAID HA EPI346719<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn44L (tTA),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 132D,<br />. . . . . . . . 145R,<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 237I,<br />. . . . . . . . syn265G (GGg),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 397S,<br />. . . . . . . . 452I,<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn496A (GCc),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . Madagascar3520_52M_2011_06_17 (<br />. . . . . . . . GISAID NA EPI346720<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 151N mix wt,<br />. . . . . . . . syn177V (GTt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 339P,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt))<br /><br />. . . . CameroonLEID06111809_33M_2011_06_16 (<br />. . . . . . . . GISAID HA EPI346645<br />. . . . . . . . Clade1: 189T<br />. . . . . . . . 15 Polymorphisms (10 Amino and 5 Silent)<br />. . . . . . . . 1T,<br />. . . . . . . . 189T,<br />. . . . . . . . syn210S (AGt),<br />. . . . . . . . syn238E (GAa),<br />. . . . . . . . 275A,<br />. . . . . . . . syn286K (AAa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn403L (tTG),<br />. . . . . . . . 437I mix wt,<br />. . . . . . . . 439N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . 476D,<br />. . . . . . . . 477K,<br />. . . . . . . . 523A,<br />. . . . . . . . 531I)<br /><br />. . . . CameroonLEID06111809_33M_2011_06_16 (<br />. . . . . . . . GISAID NA EPI346646<br />. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)<br />. . . . . . . . syn22L (cTA),<br />. . . . . . . . syn161C (TGc),<br />. . . . . . . . 262R,<br />. . . . . . . . syn368R (AGg),<br />. . . . . . . . syn398E (GAa))<br /><br />. . . . ThailandNonthaburi78_2011_06_08 (<br />. . . . . . . . GISAID HA EPI346707<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 14 Polymorphisms (8 Amino and 6 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . syn178V (GTa),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 218E mix wt,<br />. . . . . . . . 218V mix wt,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 375V,<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . ThailandNonthaburi78_2011_06_08 (<br />. . . . . . . . GISAID NA EPI346708<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn14C (TGc),<br />. . . . . . . . 26T,<br />. . . . . . . . syn41G (GGa),<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt))<br /><br />. . . . SouthAfricaJohannesburg128_1F_2011_06_07 (<br />. . . . . . . . GISAID HA EPI346651<br />. . . . . . . . Clade5: 208K_219V<br />. . . . . . . . 19 Polymorphisms (9 Amino and 10 Silent)<br />. . . . . . . . syn#6L (tTG),<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 51T,<br />. . . . . . . . syn74S (TCt),<br />. . . . . . . . syn82I (ATc),<br />. . . . . . . . syn93C (TGc),<br />. . . . . . . . 100N,<br />. . . . . . . . 141Q,<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . 252L,<br />. . . . . . . . syn307P (CCc),<br />. . . . . . . . 359A,<br />. . . . . . . . syn366A (GCa),<br />. . . . . . . . 377K,<br />. . . . . . . . 404D,<br />. . . . . . . . syn446K (AAa),<br />. . . . . . . . syn477T (ACa))<br /><br />. . . . SouthAfricaJohannesburg128_1F_2011_06_07 (<br />. . . . . . . . GISAID NA EPI346652<br />. . . . . . . . 10 Polymorphisms (2 Amino and 8 Silent)<br />. . . . . . . . syn89S (TCt),<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . 157A mix wt,<br />. . . . . . . . syn163I (ATc),<br />. . . . . . . . syn229S (TCc),<br />. . . . . . . . syn236G (GGc),<br />. . . . . . . . syn241V (GTg),<br />. . . . . . . . syn298G (GGa),<br />. . . . . . . . 299A,<br />. . . . . . . . syn342G (GGg))<br /><br />. . . . HongKong3960_2M_2011_04_21 (<br />. . . . . . . . GISAID HA EPI346726<br />. . . . . . . . Clade1.Upsilon (5.33% CFR)<br />. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)<br />. . . . . . . . #12E [Novel to Upsilon],<br />. . . . . . . . #8I,<br />. . . . . . . . 34D,<br />. . . . . . . . syn118E (GAa),<br />. . . . . . . . 144E,<br />. . . . . . . . 165N,<br />. . . . . . . . 189T,<br />. . . . . . . . syn213F (TTt),<br />. . . . . . . . 275I,<br />. . . . . . . . syn287G (GGg),<br />. . . . . . . . syn305K (AAg),<br />. . . . . . . . syn346G (GGa),<br />. . . . . . . . syn397G (GGc),<br />. . . . . . . . 453K,<br />. . . . . . . . 502K)<br /><br />. . . . HongKong3960_2M_2011_04_21 (<br />. . . . . . . . GISAID NA EPI346727<br />. . . . . . . . 6 Polymorphisms (1 Amino and 5 Silent)<br />. . . . . . . . syn20A (GCc),<br />. . . . . . . . 82P,<br />. . . . . . . . syn139L (TTa),<br />. . . . . . . . syn300N (AAc),<br />. . . . . . . . syn327R (CGt),<br />. . . . . . . . syn330D (GAc))<br /><br /><a href="http://www.blogger.com/" name="EPI346724"></a><br />. . . . SenegalDakar14_1x_2011_04_14 (<br />. . . . . . . . GISAID HA EPI346724<br />. . . . . . . . 29 Polymorphisms (10 Amino and 19 Silent)<br />. . . . . . . . 16I,<br />. . . . . . . . 35I [H5N1 TmX247],<br />. . . . . . . . 89E [H1N1 Avian],<br />. . . . . . . . syn99I (ATt) [H1N1 Avian],<br />. . . . . . . . syn122K (AAa) [H5N1 Avian],<br />. . . . . . . . 131T [H5N1 Avian],<br />. . . . . . . . syn152I (ATt),<br />. . . . . . . . syn154L (CTg) [H9N2 Avian],<br />. . . . . . . . 206S,<br />. . . . . . . . syn214K (AAa) [H9N2 Avian],<br />. . . . . . . . syn219I (ATt),<br />. . . . . . . . syn254P (CCa) [H9N2 Avian],<br />. . . . . . . . 262K [H5N1 Avian],<br />. . . . . . . . 266A,<br />. . . . . . . . syn276H (CAt) [H1N1 Avian],<br />. . . . . . . . syn295F (TTc) [H9N2 Avian],<br />. . . . . . . . syn301I (ATt),<br />. . . . . . . . syn331G (GGt) [H1N1 Avian],<br />. . . . . . . . syn337A (GCt) [H9N2 Avian],<br />. . . . . . . . syn338G (GGc) [H6N1 Avian],<br />. . . . . . . . 377K [H9N2 Avian],<br />. . . . . . . . syn379T (ACc) [H6N1 Avian],<br />. . . . . . . . syn433E (GAg) [H6N1 Avian],<br />. . . . . . . . syn451K (AAa) [H6N1 Avian],<br />. . . . . . . . syn456L (cTA) [H6N1 Avian],<br />. . . . . . . . 463V,<br />. . . . . . . . syn475D (GAc) [H6N1 Avian],<br />. . . . . . . . 523A [H1N1 Avian],<br />. . . . . . . . syn527L (TTa))<br /><br />. . . . SenegalDakar14_1x_2011_04_14 (<br />. . . . . . . . GISAID NA EPI346725<br />. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)<br />. . . . . . . . syn20A (GCc) [H1N1 Avian],<br />. . . . . . . . 74V [H1N1 Avian],<br />. . . . . . . . syn89S (TCt),<br />. . . . . . . . 106V [H1N1 Avian],<br />. . . . . . . . syn127L (cTG) [H1N1 Avian],<br />. . . . . . . . syn183A (GCc) [H1N1 Avian],<br />. . . . . . . . syn304V (GTt) [H1N1 Avian],<br />. . . . . . . . syn382G (GGa) [H1N1 Avian (Gaa)],<br />. . . . . . . . 385T,<br />. . . . . . . . 386K,<br />. . . . . . . . syn433E (GAa) [H1N1 Avian])<br /><br />. . . . CameroonLEID04111671_1F_2011_04_12 (<br />. . . . . . . . GISAID HA EPI346691<br />. . . . . . . . Clade1: 189T<br />. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)<br />. . . . . . . . 1T,<br />. . . . . . . . syn97D (GAc),<br />. . . . . . . . syn130D (GAt),<br />. . . . . . . . 155I,<br />. . . . . . . . 189T,<br />. . . . . . . . syn238E (GAa),<br />. . . . . . . . 275A,<br />. . . . . . . . syn286K (AAa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn403L (tTG),<br />. . . . . . . . 476D,<br />. . . . . . . . 477K,<br />. . . . . . . . 509D,<br />. . . . . . . . 523A)<br /><br />. . . . CameroonLEID04111671_1F_2011_04_12 (<br />. . . . . . . . GISAID NA EPI346692<br />. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)<br />. . . . . . . . syn22L (cTA),<br />. . . . . . . . syn170Y (TAt),<br />. . . . . . . . syn262K (AAa),<br />. . . . . . . . syn398E (GAa),<br />. . . . . . . . syn421C (TGt))<br /><br />. . . . SenegalDakar11_4x_2011_04_06 (<br />. . . . . . . . GISAID HA EPI346683<br />. . . . . . . . Clade3: 186P, novel sub-clade<br />. . . . . . . . 22 Polymorphisms (8 Amino and 14 Silent)<br />. . . . . . . . 12T,<br />. . . . . . . . 35I,<br />. . . . . . . . syn99I (ATt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 131T,<br />. . . . . . . . syn152I (ATt),<br />. . . . . . . . syn154L (CTg),<br />. . . . . . . . 186P,<br />. . . . . . . . 206S,<br />. . . . . . . . syn214K (AAa),<br />. . . . . . . . syn219I (ATt),<br />. . . . . . . . syn254P (CCa),<br />. . . . . . . . 262K,<br />. . . . . . . . syn276H (CAt),<br />. . . . . . . . syn301I (ATt),<br />. . . . . . . . syn331G (GGt),<br />. . . . . . . . syn337A (GCt),<br />. . . . . . . . syn379T (ACc),<br />. . . . . . . . syn433E (GAg),<br />. . . . . . . . syn456L (cTA),<br />. . . . . . . . 463V,<br />. . . . . . . . 523A)<br /><br />. . . . SenegalDakar11_4x_2011_04_06 (<br />. . . . . . . . GISAID NA EPI346684<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . syn20A (GCc),<br />. . . . . . . . syn89S (TCt),<br />. . . . . . . . 106V,<br />. . . . . . . . syn172S (TCt),<br />. . . . . . . . 259D,<br />. . . . . . . . syn304V (GTt),<br />. . . . . . . . syn382G (GGa),<br />. . . . . . . . 385T,<br />. . . . . . . . 386K,<br />. . . . . . . . syn415L (tTG))<br /><br />. . . . SenegalDakar09_3x_2011_03_25 (<br />. . . . . . . . GISAID HA EPI346703<br />. . . . . . . . 24 Polymorphisms (8 Amino and 16 Silent)<br />. . . . . . . . 35I,<br />. . . . . . . . 47I,<br />. . . . . . . . syn99I (ATt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 131T,<br />. . . . . . . . syn152I (ATt),<br />. . . . . . . . syn154L (CTg),<br />. . . . . . . . 206S,<br />. . . . . . . . syn214K (AAa),<br />. . . . . . . . syn219I (ATt),<br />. . . . . . . . syn254P (CCa),<br />. . . . . . . . 262K,<br />. . . . . . . . syn276H (CAt),<br />. . . . . . . . syn288A (GCc),<br />. . . . . . . . syn301I (ATt),<br />. . . . . . . . syn325P (CCt),<br />. . . . . . . . syn331G (GGt),<br />. . . . . . . . syn337A (GCt),<br />. . . . . . . . syn379T (ACc),<br />. . . . . . . . syn433E (GAg),<br />. . . . . . . . syn456L (cTA),<br />. . . . . . . . 463V,<br />. . . . . . . . 481N,<br />. . . . . . . . 523A)<br /><br />. . . . SenegalDakar09_3x_2011_03_25 (<br />. . . . . . . . GISAID NA EPI346704<br />. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)<br />. . . . . . . . syn20A (GCc),<br />. . . . . . . . syn89S (TCt),<br />. . . . . . . . 106V,<br />. . . . . . . . syn281C (TGc),<br />. . . . . . . . syn304V (GTt),<br />. . . . . . . . syn370G (GGc),<br />. . . . . . . . syn371F (TTc),<br />. . . . . . . . syn382G (GGa),<br />. . . . . . . . 385T,<br />. . . . . . . . 386K)<br /><br />. . . . Iceland59_xF_2011_03_24 (<br />. . . . . . . . GISAID HA EPI346697<br />. . . . . . . . Clade3: 186P<br />. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)<br />. . . . . . . . 137T mix wt,<br />. . . . . . . . 144S,<br />. . . . . . . . syn163K (AAa),<br />. . . . . . . . 186P,<br />. . . . . . . . syn251L (CTg),<br />. . . . . . . . syn287G (GGg),<br />. . . . . . . . syn293L (CTt),<br />. . . . . . . . 298V,<br />. . . . . . . . syn363G (GGg),<br />. . . . . . . . 377K,<br />. . . . . . . . syn455Q (CAa),<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . 482I)<br /><br />. . . . Iceland59_xF_2011_03_24 (<br />. . . . . . . . GISAID NA EPI346698<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 46T,<br />. . . . . . . . syn187G (GGt),<br />. . . . . . . . 313R,<br />. . . . . . . . 321V,<br />. . . . . . . . 394I,<br />. . . . . . . . syn412L (tTA),<br />. . . . . . . . syn430R (CGg),<br />. . . . . . . . 467V)<br /><br />. . . . CameroonLEID03111616_xM_2011_03_22 (<br />. . . . . . . . GISAID HA EPI346689<br />. . . . . . . . Clade1: 189T<br />. . . . . . . . 12 Polymorphisms (8 Amino and 4 Silent)<br />. . . . . . . . 1T,<br />. . . . . . . . 167F,<br />. . . . . . . . 189T,<br />. . . . . . . . syn238E (GAa),<br />. . . . . . . . 275A,<br />. . . . . . . . syn286K (AAa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn403L (tTG),<br />. . . . . . . . 476D,<br />. . . . . . . . 477K,<br />. . . . . . . . 523A,<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . CameroonLEID03111616_xM_2011_03_22 (<br />. . . . . . . . GISAID NA EPI346690<br />. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)<br />. . . . . . . . syn22L (cTA),<br />. . . . . . . . syn118R (AGa),<br />. . . . . . . . syn262K (AAa),<br />. . . . . . . . 386D,<br />. . . . . . . . syn398E (GAa))<br /><br />. . . . FrancePaysdeLoire1347_12x_2011_03_22 (<br />. . . . . . . . GISAID HA EPI346701<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 12 Polymorphisms (4 Amino and 8 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn135V (GTg),<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn321L (cTG),<br />. . . . . . . . syn336I (ATc),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn400F (TTt),<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn482V (GTt))<br /><br />. . . . FrancePaysdeLoire1347_12x_2011_03_22 (<br />. . . . . . . . GISAID NA EPI346702<br />. . . . . . . . 8 Polymorphisms (2 Amino and 6 Silent)<br />. . . . . . . . syn162P (CCc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn313Q (CAa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn401G (GGg),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . Iceland52_xM_2011_03_18 (<br />. . . . . . . . GISAID HA EPI346643<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 12 Polymorphisms (9 Amino and 3 Silent)<br />. . . . . . . . 87I,<br />. . . . . . . . 100N,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 212N mix wt,<br />. . . . . . . . syn304G (GGg),<br />. . . . . . . . syn319T (ACg),<br />. . . . . . . . 324I,<br />. . . . . . . . 377K,<br />. . . . . . . . 440H mix wt,<br />. . . . . . . . syn441H (CAt),<br />. . . . . . . . 454N)<br /><br />. . . . Iceland52_xM_2011_03_18 (<br />. . . . . . . . GISAID NA EPI346644<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . UkraineDnipropetrovsk4929_21F_2011_03_10 (<br />. . . . . . . . GISAID HA EPI346637<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N)<br /><br />. . . . UkraineDnipropetrovsk4929_21F_2011_03_10 (<br />. . . . . . . . GISAID NA EPI346638<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . UkraineZaporizhzhya5200_31F_2011_03_09 (<br />. . . . . . . . GISAID HA EPI346663<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 326F,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 415E,<br />. . . . . . . . syn441H (CAt),<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N)<br /><br />. . . . UkraineZaporizhzhya5200_31F_2011_03_09 (<br />. . . . . . . . GISAID NA EPI346664<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 96R mix wt,<br />. . . . . . . . 127F,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . UkraineLuhansk5192_xF_2011_03_07 (<br />. . . . . . . . GISAID HA EPI346639<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . . . . . crossing Clade3: 186P<br />. . . . . . . . 16 Polymorphisms (6 Amino and 10 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn118E (GAa),<br />. . . . . . . . syn130D (GAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 186P mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . syn358N (Aac) mix,<br />. . . . . . . . syn358T mix,<br />. . . . . . . . 377K,<br />. . . . . . . . syn412K (AAg),<br />. . . . . . . . syn418F (TTt),<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . UkraineLuhansk5192_xF_2011_03_07 (<br />. . . . . . . . GISAID NA EPI346640<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 83G,<br />. . . . . . . . syn206L (cTA),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . CameroonLEID03111573_xM_2011_03_01 (<br />. . . . . . . . GISAID HA EPI346687<br />. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)<br />. . . . . . . . 1T,<br />. . . . . . . . syn157K (AAg),<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . syn173G (GGa),<br />. . . . . . . . 190G,<br />. . . . . . . . 205E mix wt,<br />. . . . . . . . syn238E (GAa),<br />. . . . . . . . 275A,<br />. . . . . . . . syn286K (AAa),<br />. . . . . . . . syn334G (GGa),<br />. . . . . . . . 377K,<br />. . . . . . . . 476D,<br />. . . . . . . . 477K,<br />. . . . . . . . 523A)<br /><br />. . . . CameroonLEID03111573_xM_2011_03_01 (<br />. . . . . . . . GISAID NA EPI346688<br />. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)<br />. . . . . . . . syn6K (AAa),<br />. . . . . . . . syn22L (cTA),<br />. . . . . . . . syn262K (AAa),<br />. . . . . . . . syn398E (GAa))<br /><br />. . . . UkraineOdessa5197_24F_2011_03_01 (<br />. . . . . . . . GISAID HA EPI346641<br />. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)<br />. . . . . . . . syn391T (ACc),<br />. . . . . . . . syn413K (AAg),<br />. . . . . . . . 415E mix wt)<br /><br />. . . . UkraineOdessa5197_24F_2011_03_01 (<br />. . . . . . . . GISAID NA EPI346642<br />. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)<br />. . . . . . . . syn330D (GAc),<br />. . . . . . . . syn407V (GTc))<br /><br /><a href="http://www.blogger.com/" name="EPI346699"></a><br />. . . . FranceLorraine1176_50x_2011_02_23_TmX (<br />. . . . . . . . GISAID HA EPI346699<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 227G,<br />. . . . . . . . syn245F (TTt),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn461K (AAa),<br />. . . . . . . . syn470F (TTc),<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . FranceLorraine1176_50x_2011_02_23_TmX (<br />. . . . . . . . GISAID NA EPI346700<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . LithuaniaKlaipeda1067_xF_2011_02_22 (<br />. . . . . . . . GISAID HA EPI346673<br />. . . . . . . . Clade3: 186P<br />. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)<br />. . . . . . . . 137T,<br />. . . . . . . . 186P,<br />. . . . . . . . syn279N (AAc),<br />. . . . . . . . syn288A (GCc),<br />. . . . . . . . syn352Y (TAt),<br />. . . . . . . . 377G,<br />. . . . . . . . syn408E (GAa),<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn475D (GAc),<br />. . . . . . . . 512M,<br />. . . . . . . . 530I)<br /><br />. . . . LithuaniaKlaipeda1067_xF_2011_02_22 (<br />. . . . . . . . GISAID NA EPI346674<br />. . . . . . . . 14 Polymorphisms (3 Amino and 11 Silent)<br />. . . . . . . . syn20A (GCc),<br />. . . . . . . . syn66Y (TAc),<br />. . . . . . . . syn124C (TGt),<br />. . . . . . . . syn130R (AGg),<br />. . . . . . . . syn157T (ACt),<br />. . . . . . . . syn175E (GAa),<br />. . . . . . . . 232V,<br />. . . . . . . . syn302P (CCa),<br />. . . . . . . . syn382G (GGa),<br />. . . . . . . . 389V,<br />. . . . . . . . 394I,<br />. . . . . . . . syn425E (GAg),<br />. . . . . . . . syn428R (AGg),<br />. . . . . . . . syn430R (CGg))<br /><br />. . . . LithuaniaTelsiai1038_xM_2011_02_19 (<br />. . . . . . . . GISAID HA EPI346671<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn#6L (CTa),<br />. . . . . . . . 100N,<br />. . . . . . . . 188T,<br />. . . . . . . . syn245F (TTt),<br />. . . . . . . . syn321L (cTG),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . LithuaniaTelsiai1038_xM_2011_02_19 (<br />. . . . . . . . GISAID NA EPI346672<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . syn436I (ATa))<br /><br />. . . . LithuaniaTelsiai1037_xM_2011_02_19 (<br />. . . . . . . . GISAID HA EPI346669<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn#6L (CTa),<br />. . . . . . . . 100N,<br />. . . . . . . . 188T,<br />. . . . . . . . syn245F (TTt),<br />. . . . . . . . syn321L (cTG),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . LithuaniaTelsiai1037_xM_2011_02_19 (<br />. . . . . . . . GISAID NA EPI346670<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . syn436I (ATa))<br /><br />. . . . LithuaniaKaunas146s_xM_2011_02_17 (<br />. . . . . . . . GISAID HA EPI346675<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . 152M,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N)<br /><br />. . . . LithuaniaKaunas146s_xM_2011_02_17 (<br />. . . . . . . . GISAID NA EPI346676<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn162P (CCc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . 453M)<br /><br />. . . . LithuaniaKaunas988_xM_2011_02_15 (<br />. . . . . . . . GISAID HA EPI346667<br />. . . . . . . . Clade2: 188T <br />. . . . . . . . . . . . crossed with Clade4:128D<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 59S,<br />. . . . . . . . syn69E (GAa) [Upsilon?],<br />. . . . . . . . 100N,<br />. . . . . . . . 128D,<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . LithuaniaKaunas988_xM_2011_02_15 (<br />. . . . . . . . GISAID NA EPI346668<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . FranceParis940_16x_2011_02_11 (<br />. . . . . . . . GISAID HA EPI346722<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 15 Polymorphisms (8 Amino and 7 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 76T,<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 205E mix wt,<br />. . . . . . . . 277N,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . syn358N (AAc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn418F (TTt),<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . FranceParis940_16x_2011_02_11 (<br />. . . . . . . . GISAID NA EPI346723<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . FranceCentre869_60x_2011_02_08 (<br />. . . . . . . . GISAID HA EPI346681<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . syn31H (CAt),<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 205E,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N)<br /><br />. . . . FranceCentre869_60x_2011_02_08 (<br />. . . . . . . . GISAID NA EPI346682<br />. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)<br />. . . . . . . . syn162P (CCc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn316Y (TAt),<br />. . . . . . . . 344K,<br />. . . . . . . . syn365I (ATc),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn390K (AAa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . FranceHauteNormandie774_3x_2011_02_01 (<br />. . . . . . . . GISAID HA EPI346679<br />. . . . . . . . Clade5: 208K_219V<br />. . . . . . . . 14 Polymorphisms (7 Amino and 7 Silent)<br />. . . . . . . . syn41N (AAt),<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . 133E,<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . syn221P (CCt),<br />. . . . . . . . 252L,<br />. . . . . . . . syn319T (ACg),<br />. . . . . . . . 352F,<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa))<br /><br />. . . . FranceHauteNormandie774_3x_2011_02_01 (<br />. . . . . . . . GISAID NA EPI346680<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . syn60T (ACc),<br />. . . . . . . . 81A,<br />. . . . . . . . syn138A (GCt),<br />. . . . . . . . 151N mix wt,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . Hungary13_xM_2011_01_31 (<br />. . . . . . . . GISAID HA EPI346711<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . 157E,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 226R,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N)<br /><br />. . . . Hungary13_xM_2011_01_31 (<br />. . . . . . . . GISAID NA EPI346712<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . syn162P (CCc),<br />. . . . . . . . syn191L (tTA),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br /><a href="http://www.blogger.com/" name="EPI346709"></a><br />. . . . Hungary7_xM_2011_01_31 (<br />. . . . . . . . GISAID HA EPI346709<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 11 Polymorphisms (8 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . 157E mix wt,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 159D mix wt,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 226R,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N)<br /><br />. . . . Hungary7_xM_2011_01_31 (<br />. . . . . . . . GISAID NA EPI346710<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn162P (CCc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . TurkeyMalatyaTR_29_28M_2011_01_28 (<br />. . . . . . . . GISAID HA EPI346659<br />. . . . . . . . Clade3: 186P<br />. . . . . . . . 11 Polymorphisms (8 Amino and 3 Silent)<br />. . . . . . . . syn16T (ACg),<br />. . . . . . . . 137T,<br />. . . . . . . . 167F,<br />. . . . . . . . 186P,<br />. . . . . . . . 263K,<br />. . . . . . . . 377G,<br />. . . . . . . . syn408E (GAa),<br />. . . . . . . . 413R mix wt,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . 512M,<br />. . . . . . . . 530I)<br /><br />. . . . TurkeyMalatyaTR_29_28M_2011_01_28 (<br />. . . . . . . . GISAID NA EPI346660<br />. . . . . . . . 13 Polymorphisms (4 Amino and 9 Silent)<br />. . . . . . . . syn20A (GCc),<br />. . . . . . . . syn66Y (TAc),<br />. . . . . . . . syn124C (TGt),<br />. . . . . . . . syn130R (AGg),<br />. . . . . . . . syn157T (ACt),<br />. . . . . . . . syn175E (GAa),<br />. . . . . . . . 232V,<br />. . . . . . . . 267I,<br />. . . . . . . . syn382G (GGa),<br />. . . . . . . . 389V,<br />. . . . . . . . 394I,<br />. . . . . . . . syn425E (GAg),<br />. . . . . . . . syn430R (CGg))<br /><br />. . . . CameroonLEID01111467_28F_2011_01_27 (<br />. . . . . . . . GISAID HA EPI346705<br />. . . . . . . . Clade1: 189T<br />. . . . . . . . 11 Polymorphisms (7 Amino and 4 Silent)<br />. . . . . . . . 1T,<br />. . . . . . . . 189T,<br />. . . . . . . . syn238E (GAa),<br />. . . . . . . . 275A,<br />. . . . . . . . syn286K (AAa),<br />. . . . . . . . syn340I (ATc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn403L (tTG),<br />. . . . . . . . 476D,<br />. . . . . . . . 477K,<br />. . . . . . . . 523A)<br /><br />. . . . CameroonLEID01111467_28F_2011_01_27 (<br />. . . . . . . . GISAID NA EPI346706<br />. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)<br />. . . . . . . . syn22L (cTA),<br />. . . . . . . . syn262K (AAa),<br />. . . . . . . . syn271A (GCt),<br />. . . . . . . . syn398E (GAa))<br /><br />. . . . Kazakhstan2081_xF_2011_01_23 (<br />. . . . . . . . GISAID HA EPI346713<br />. . . . . . . . Clade3: 186P<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . 137T,<br />. . . . . . . . 186P,<br />. . . . . . . . syn297N (AAc),<br />. . . . . . . . syn316R (AGg),<br />. . . . . . . . syn326S (TCc),<br />. . . . . . . . syn383N (AAc),<br />. . . . . . . . syn388K (AAa),<br />. . . . . . . . 433K,<br />. . . . . . . . 444K,<br />. . . . . . . . syn474C (TGt))<br /><br />. . . . Kazakhstan2081_xF_2011_01_23 (<br />. . . . . . . . GISAID NA EPI346714<br />. . . . . . . . 7 Polymorphisms (1 Amino and 6 Silent)<br />. . . . . . . . syn6K (AAa),<br />. . . . . . . . syn139L (cTG),<br />. . . . . . . . syn202A (GCt),<br />. . . . . . . . syn274Y (TAc),<br />. . . . . . . . syn275H (CAt),<br />. . . . . . . . syn372E (GAa),<br />. . . . . . . . 394I)<br /><br />. . . . CameroonLEID01111450_3F_2011_01_19 (<br />. . . . . . . . GISAID HA EPI346649<br />. . . . . . . . Clade1: 189T<br />. . . . . . . . 12 Polymorphisms (9 Amino and 3 Silent)<br />. . . . . . . . 1T,<br />. . . . . . . . 159S,<br />. . . . . . . . 189T,<br />. . . . . . . . 205E,<br />. . . . . . . . syn238E (GAa),<br />. . . . . . . . 275A,<br />. . . . . . . . syn286K (AAa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn403L (tTG),<br />. . . . . . . . 476D,<br />. . . . . . . . 477K,<br />. . . . . . . . 523A)<br /><br />. . . . CameroonLEID01111450_3F_2011_01_19 (<br />. . . . . . . . GISAID NA EPI346650<br />. . . . . . . . 4 Polymorphisms (1 Amino and 3 Silent)<br />. . . . . . . . syn22L (cTA),<br />. . . . . . . . 59R,<br />. . . . . . . . syn262K (AAa),<br />. . . . . . . . syn398E (GAa))<br /><br />. . . . Iceland9_xF_2011_01_19 (<br />. . . . . . . . GISAID HA EPI346695<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 15 Polymorphisms (10 Amino and 5 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . 159D,<br />. . . . . . . . syn179L (tTA),<br />. . . . . . . . 188T,<br />. . . . . . . . 225N,<br />. . . . . . . . syn245F (TTt),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 437I (Atc) mix wt,<br />. . . . . . . . 437I (Att) mix wt,<br />. . . . . . . . 437N (Aac) mix wt,<br />. . . . . . . . 437N (Aat) mix wt,<br />. . . . . . . . syn437T (Acc) mix wt,<br />. . . . . . . . 454N,<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . Iceland9_xF_2011_01_19 (<br />. . . . . . . . GISAID NA EPI346696<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . TurkeyTokatTR_26_26M_2011_01_19 (<br />. . . . . . . . GISAID HA EPI346657<br />. . . . . . . . Clade5: 208K_219V<br />. . . . . . . . . . . . crossing Clade4: 128D<br />. . . . . . . . 14 Polymorphisms (8 Amino and 6 Silent)<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . 128D,<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 210I mix wt,<br />. . . . . . . . 219V,<br />. . . . . . . . syn221P (CCt),<br />. . . . . . . . 252L,<br />. . . . . . . . syn319T (ACg),<br />. . . . . . . . 377K,<br />. . . . . . . . 431Q mix wt,<br />. . . . . . . . syn446K (AAa))<br /><br />. . . . TurkeyTokatTR_26_26M_2011_01_19 (<br />. . . . . . . . GISAID NA EPI346658<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . syn60T (ACc),<br />. . . . . . . . 81A,<br />. . . . . . . . syn138A (GCt),<br />. . . . . . . . 211T mix wt,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . Iceland7_xM_2011_01_16 (<br />. . . . . . . . GISAID HA EPI346661<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)<br />. . . . . . . . #7I,<br />. . . . . . . . 100N,<br />. . . . . . . . 157N mix wt,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 449C mix wt,<br />. . . . . . . . 454N)<br /><br />. . . . Iceland7_xM_2011_01_16 (<br />. . . . . . . . GISAID NA EPI346662<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . 117M,<br />. . . . . . . . syn162P (CCc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . Iceland3_xM_2011_01_10 (<br />. . . . . . . . GISAID HA EPI346677<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn379T (ACc),<br />. . . . . . . . 440H,<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . Iceland3_xM_2011_01_10 (<br />. . . . . . . . GISAID NA EPI346678<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . syn38I (ATc),<br />. . . . . . . . 44S,<br />. . . . . . . . 151E mix wt,<br />. . . . . . . . 151K mix wt,<br />. . . . . . . . 151N mix wt,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn274Y (TAc),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . TurkeyAnkaraTR_23_20M_2010_12_30 (<br />. . . . . . . . GISAID HA EPI346693<br />. . . . . . . . Clade5: 208K_219V<br />. . . . . . . . . . . . crossing Clade3: 186P<br />. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . 159D mix wt,<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 186P mix wt,<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . 252L,<br />. . . . . . . . syn346G (GGa),<br />. . . . . . . . 377K,<br />. . . . . . . . 426V,<br />. . . . . . . . syn446K (AAa),<br />. . . . . . . . syn507K (AAa), <br />. . . . . . . . 530I)<br /><br />. . . . TurkeyAnkaraTR_23_20M_2010_12_30 (<br />. . . . . . . . GISAID NA EPI346694<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn238C (TGt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . UKEngland687_2010_12_15 (<br />. . . . . . . . GISAID HA EPI346665<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . 11 Polymorphisms (7 Amino and 4 Silent)<br />. . . . . . . . syn#7V (GTc),<br />. . . . . . . . 59S,<br />. . . . . . . . syn69E (GAa),<br />. . . . . . . . 100N,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 179I,<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . UKEngland687_2010_12_15 (<br />. . . . . . . . GISAID NA EPI346666<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . syn161C (TGc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn398E (GAa),<br />. . . . . . . . syn416D (GAc))<br /><br /><br />This analysis catalysed&nbsp;with <strong><span style="color: #783f04;">ingenuity</span></strong> from 2 lead Professors of <strong><span style="color: #783f04;">Group10</span></strong> at <strong><span style="color: #783f04;">Ion</span>₂₀₃</strong>.&nbsp; We never cease to find inspiration in your halls of instruction.<br /><br /></sub><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-3990198766646167764?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-32383511437940983662011-11-05T23:45:00.003-05:002011-11-05T23:54:53.162-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_10_31_Greece_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br /><span style="color: black;">Last Update</span><br />2011-11-05<br /><br />On 2011-10-31, the <strong><span style="color: #783f04;">Institut Pasteur Hellenique</span></strong> deposited one human <strong><span style="color: #4c1130;">pH1N1</span></strong> <strong><span style="color: #274e13;">HA</span></strong> fragment sequence at <strong>GISAID</strong> of 216 amino acids (aa35 to aa220), documenting roughly 38% of a full <strong><span style="color: #4c1130;">pH1N1</span></strong> Hemagglutinin segment.&nbsp; <strong><span style="color: #783f04;">GreeceAthens7033_75M_2011_02_22_s</span></strong> was sampled from a 75 year old male, <strong><span style="color: #783f04;">hospital inpatient</span></strong>.&nbsp; This hypermorphic fragment patterns onto <strong><span style="color: blue;">Clade5: 208K_219V</span></strong>, a highly zoonotic, recently emergent series with a sequence count that has quickly accumulated to triple digits. <br /><br />Two dispersed polymorphisms, each <strong><span style="color: #660000;">novel</span></strong> to <strong><span style="color: #4c1130;">pH1N1</span></strong>.<strong><span style="color: blue;">Clade5</span></strong>, appear on this Greek sequence.&nbsp; <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">77R</span></strong>, a <strong><span style="color: #660000;">novel</span></strong> <strong><span style="color: blue;">Clade5</span></strong> revision, is rare to the human pandemic and is <strong><span style="color: #783f04;">emergent</span></strong> on <strong><span style="color: blue;">Clade2</span></strong> (<a href="http://pf11.blogspot.com/2011/11/greece-deposits-ph1n1-clade5-from-2011.html#Clade2_77R">3 instances</a>).&nbsp; Those 3 <strong><span style="color: blue;">Clade2</span></strong>, <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">77R</span></strong>-bearing <strong><span style="color: #274e13;">HA</span></strong> segment sequences are hypermorphic (accounting for 48 total <strong><span style="color: #274e13;">HA</span></strong> changes); however, no <strong><span style="color: #274e13;">HA</span></strong> cross-over onto this Greek sequence occurs from the full superset of polymorphisms with <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">77R</span></strong>.&nbsp; <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">169T</span></strong>, also <strong><span style="color: #660000;">novel</span></strong> to <strong><span style="color: blue;">Clade5</span></strong>, is rare to the human pandemic and is found once on <strong><span style="color: blue;">Clade2</span></strong>, the numerically dominant series for human <strong><span style="color: #4c1130;">pH1N1</span></strong>. <br /><br />Avian H13 serotypes share <strong><span style="color: #783f04;">significant homology</span></strong> with <strong><span style="color: #4c1130;">pH1N1</span></strong>.<strong><span style="color: blue;">Clade5</span></strong> and this Greek sequence.&nbsp; Given the serology background of the more recently discovered Hemagglutinin forms above H12 (~30 years for H13 to ~6 years for H16), question arise <strong><span style="color: #783f04;">concerning cross-serotype compatibility</span></strong>.&nbsp; Returning to the archives after these recent discoveries, investigators repeatedly found that H16 samples from the past had been <strong><span style="color: #783f04;">mis-typed on first inspection</span></strong> to various Hemagglutinin forms (H1, H7, H13) due to <strong><span style="color: #783f04;">cross-reactive serology</span></strong> on various inhibition panels.&nbsp; Serotypes <strong><span style="color: #783f04;">known to infect humans</span></strong>, including H1 and H7, featured in those earlier mistaken categorisations.&nbsp; <br /><br />Precise discernment of the exact relationship between the current <strong><span style="color: #4c1130;">human pandemic H1N1</span></strong> and the more recently discovered Hemagglutinin forms (H13 to H16) merits evaluation due to the significant <strong><span style="color: #783f04;">H13 homology</span></strong> with the heavily zoonotic and rapidly emergent <strong><span style="color: #4c1130;">pH1N1</span></strong>.<strong><span style="color: blue;">Clade5</span></strong> and the <strong><span style="color: #660000;">High CFR</span></strong> <strong><span style="color: #4c1130;">pH1N1</span></strong>.<strong><span style="color: blue;">Clade1.Upsilon</span></strong>.<br /><br /><span style="font-size: x-large;"><strong>Sequence</strong></span><br /><br />. . . . GreeceAthens7033_75M_2011_02_22_s (<br />. . . . . . . . Clade5: <a href="http://pf11.blogspot.com/2011/06/sweden-signals-rapid-zoonosis-from.html" target="_blank">208K_219V</a> <br />. . . . . . . . GISAID HA EPI340964<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . HA Truncated before aa35,<br />. . . . . . . . syn47L (CTg) [H1N1 Avian],<br />. . . . . . . . 77R (AGa) [<strong><span style="color: #660000;">Rare </span></strong>to Human pH1N1 (11 Total / 5 Asia)],<br />. . . . . . . . . . . . . . . [<strong><span style="color: #660000;">Novel </span></strong>to pH1N1.<strong><span style="color: blue;">Clade5</span></strong>],<br />. . . . . . . . . . . . . . . [<strong><span style="color: #660000;">Emergent</span></strong> pH1N1.<strong><span style="color: blue;">Clade2</span></strong> (3)],<br />. . . . . . . . . . . . . . . [H9N2 Avian and Human wt<br />. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms],<br />. . . . . . . . . . . . . . . [H13N2 Mammal<br />. . . . . . . . . . . . . . . . . . . with 188T, 225G &amp; 252L],<br />. . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],<br />. . . . . . . . . . . . . . . [WSN_1933, WSZ_1933],<br />. . . . . . . . 100N [H5N1 Egypt Avian 2009-2010 <br />. . . . . . . . . . . . . . . . . with syn40H, syn55L, 192I, 196K],<br />. . . . . . . . . . . . [H5N1 Egypt Avian 2008 with syn40H, syn55L],<br />. . . . . . . . . . . . [H5N2 Italy Avian 2005-2007],<br />. . . . . . . . . . . . [H7N3, H7N7, H9N2],<br />. . . . . . . . . . . . [H13N2 Mammal],<br />. . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],<br />. . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . syn102E (GAa) [H5N1 wt],<br />. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],<br />. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],<br />. . . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . 169T [<strong><span style="color: #660000;">Rare</span></strong> to Human pH1N1 (6 Total / 3 <a href="http://pf11.blogspot.com/2011/11/greece-deposits-ph1n1-clade5-from-2011.html#EPI256314">Asia</a>)],<br />. . . . . . . . . . . [<strong><span style="color: #660000;">Novel</span></strong> to pH1N1.<strong><span style="color: blue;">Clade5</span></strong>],<br />. . . . . . . . . . . [<a href="http://pf11.blogspot.com/2011/11/greece-deposits-ph1n1-clade5-from-2011.html#EPI310031">Singular</a> to pH1N1.<strong><span style="color: blue;">Clade2</span></strong>],<br />. . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . . . . [H1N1 swine],<br />. . . . . . . . syn170N (AAc) [H5N1 Egypt Human 2009],<br />. . . . . . . . . . . . . . . . . . [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . . . with 188T, 225G &amp; 252L],<br />. . . . . . . . . . . . . . . . . . [H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . . . with 225G &amp; 252L],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . 208K (AaA) [pH1N1 Canine 2009],<br />. . . . . . . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . [H3N2 Avian 2006, 2009],<br />. . . . . . . . 219V (gTA) [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . with 188T, 225G &amp; 252L],<br />. . . . . . . . . . . . . . . . [H13N2, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . with 188T, 225G &amp; 252L],<br />. . . . . . . . syn221P (CCt) [H3N2 Avian <br />. . . . . . . . . . . . . . . . . . . . . with 157S, 159S, syn287G],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human and Avian (tCt)],<br />. . . . . . . . . . . . . . . . . . [H5N1 Nigeria Avian (tCt)],<br />. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . [H13N2 Mammal],<br />. . . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . HA Truncated after aa250)<br /><br /><span style="font-size: x-large;"><strong>Supporting Sequences</strong></span><br /><br /><strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">169T</span></strong><br /><a href="http://www.blogger.com/" name="EPI310031"></a><br />. . . . Montana03_2011_02_02 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI310031<br />. . . . . . . . 8 Polymorphisms (6 Amino and 2 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . 169T,<br />. . . . . . . . 188T,<br />. . . . . . . . 213S,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . Lebanon09L_29_2009_11_05 (<br />. . . . . . . . GISAID HA EPI320624<br />. . . . . . . . 4 Polymorphisms (4 Amino and 0 Silent)<br />. . . . . . . . #1T,<br />. . . . . . . . 169T,<br />. . . . . . . . 225E,<br />. . . . . . . . 300S,<br />. . . . . . . . HA Truncated after aa355)<br /><a href="http://www.blogger.com/" name="EPI256314"></a><br />. . . . ShanxiChengquSWL547_2009_10_19 (<br />. . . . . . . . GISAID HA EPI256314<br />. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)<br />. . . . . . . . 57N,<br />. . . . . . . . 131P,<br />. . . . . . . . 169T,<br />. . . . . . . . syn238E (GAa))<br /><br />. . . . TianjinTangguSWL1110_2009_10_13 (<br />. . . . . . . . GISAID HA EPI256126<br />. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)<br />. . . . . . . . 169T,<br />. . . . . . . . 206S,<br />. . . . . . . . 447K,<br />. . . . . . . . syn455Q (CAa))<br /><br />. . . . BeijingHuairouSWL1805_2009_10_01 (<br />. . . . . . . . GISAID HA EPI256274<br />. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)<br />. . . . . . . . 169T,<br />. . . . . . . . 206S,<br />. . . . . . . . 447K,<br />. . . . . . . . syn455Q (CAa))<br /><br />. . . . Russia01_MA_2009 (<br />. . . . . . . . GISAID HA EPI297205<br />. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)<br />. . . . . . . . 169T,<br />. . . . . . . . 208K,<br />. . . . . . . . syn359E (GAa))<br /><a href="http://www.blogger.com/" name="Clade2_77R"></a><br /><strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">77R</span></strong> on <strong><span style="color: blue;">Clade2</span></strong><br /><br />. . . . OzBrisbane500_2011_06_22 (<br />. . . . . . . . GISAID HA EPI333109<br />. . . . . . . . 18 Polymorphisms (8 Amino and 10 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn33V (GTc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 77R,<br />. . . . . . . . syn99I (ATt),<br />. . . . . . . . syn115E (GAg),<br />. . . . . . . . 146G,<br />. . . . . . . . 171G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . syn346G (GGa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn413K (AAg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn508L (tTG),<br />. . . . . . . . 523A,<br />. . . . . . . . HA Truncated after aa552)<br /><br />. . . . OzNewcastle1_2011_04_11 (<br />. . . . . . . . GISAID HA EPI331558<br />. . . . . . . . 21 Polymorphisms (9 Amino and 12 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn33V (GTc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 77R,<br />. . . . . . . . syn99I (ATt),<br />. . . . . . . . syn115E (GAg),<br />. . . . . . . . 146G,<br />. . . . . . . . 157Q mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . syn346G (GGa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn413K (AAg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn508L (tTG),<br />. . . . . . . . 523A,<br />. . . . . . . . syn538F (TTt),<br />. . . . . . . . syn549R (AGg),<br />. . . . . . . . 550S,<br />. . . . . . . . HA Truncated after aa550)<br /><br />. . . . JapanHiroshimaC2_2011_01_05 (<br />. . . . . . . . GISAID HA EPI305466<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 71D,<br />. . . . . . . . 77R,<br />. . . . . . . . 102G mix wt,<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-3238351143794098366?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-21666286711213084052011-11-03T21:47:00.003-05:002011-11-03T21:55:12.478-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_11_02_Mexico_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br /><span style="color: black;">Last Update</span><br />2011-11-03<br /><br />On 2011-10-27, the <strong><span style="color: #783f04;">Instituto Nacional de Enfermedades Respiratorias</span></strong> from the <strong><span style="color: #783f04;">Centro de Investigacion en Enfermedades Infecciosas</span></strong> of <strong><span style="color: #783f04;">Mexico</span></strong> deposited a group of human <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences at <strong>GenBank</strong> and <strong>GISAID.</strong>&nbsp; The deposit is composed of <strong><span style="color: #274e13;">HA</span></strong> segments, 14 sequence fragments of 232 amino acids (aa38 to aa269), each documenting roughly 41% of a full <strong><span style="color: #4c1130;">pH1N1</span></strong> Hemagglutinin segment.&nbsp; Various homology to <strong><span style="color: blue;">Clade1.Upsilon</span></strong> exists on 5 of the sequences.<br /><br />This Mexican genetic data supports an investigation entitled, <strong><em>H1N1pdm HA D222 variants associated with severity and mortality in patients during a second wave in Mexico and their pathogenicity in mouse model</em></strong>.&nbsp; Mexico City, Mexico is the geography indicated on the sequence names.&nbsp; Each sequence is annotated with gender and isolation source (<strong><span style="color: #783f04;">nasopharyngeal swab</span></strong>), while 12 of the 14 also indicate the subject age.&nbsp; Subject ages range from <strong><span style="color: #783f04;">23 to 54 years old,</span></strong> all outside the general severity range for seasonal influenza (under 2 years old or over 60 years old).&nbsp; The sample dates span 2009-10-01 to 2010-04-05 with <strong><span style="color: #783f04;">no case-level specification</span></strong> of treatment protocol, clinical progression or clinical outcome.<br /><br />The severity and fatality correlation in cases with polymorphisms at amino acid position 222 (<strong><span style="color: #783f04;">aa225 in H3 numbering</span></strong>) was established very early in the pandemic.&nbsp; The issue of sample location has been repeatedly posed, with ongoing discussion that samples taken from the <strong><span style="color: #783f04;">lower respiratory tract</span></strong> are more probable to produce valid evidence of aa225 revisions.&nbsp; This <strong><span style="color: #783f04;">INER</span></strong> deposit, relying entirely on <strong><span style="color: #783f04;">upper respiratory swabs</span></strong>, documents cases where aa225 revisions are found in the upper airway.&nbsp; The individual details of clinical progression and outcome (<strong><span style="color: #783f04;">severe v. fatal</span></strong>) will establish measurable correlation to the upper respiratory sample location. <br /><br />Four of the samples show <strong><span style="color: #783f04;">multi-nucleotide ambiguity</span></strong> at amino acid position 225 (contiguous mixed traces, residues 715 and 716) producing a codon of <strong><span style="color: blue;">rrT</span></strong>.&nbsp; That sequencing outcome of <strong><span style="color: blue;">rrT</span></strong> demonstrates the presence of wild type D225 with both <strong><span style="color: blue;">225G</span></strong> and <strong><span style="color: blue;">225N</span></strong>, hypermorphism at a single amino acid position.&nbsp; Overall, <strong><span style="color: #783f04;">ten of the fourteen</span></strong> sequences demonstrate a mixed peak (ambiguity) at one or more nucleotides that build aa225.&nbsp; <strong><span style="color: #783f04;">MexicoCityINER3_NP_47M_2009_10_15</span></strong> [<a href="http://pf11.blogspot.com/2011/11/mexico-evaluates-upper-respiratory.html#EPI341034">EPI341034</a>] illustrates the <strong><span style="color: #783f04;">highly variant</span></strong> nature of the <strong><span style="color: #4c1130;">pH1N1</span></strong> reservoir Receptor Binding Site aa225 with two rare values, <strong><span style="color: blue;">225A</span></strong> and <strong><span style="color: blue;">225V</span></strong>, in a mixture <strong><span style="color: #783f04;">without wild type</span></strong> (D225) and with no additional polymorphisms.<br /><br /><span style="font-size: x-large;"><strong>Sequences</strong></span><br /><br />. . . . MexicoCityINER14_NP_xF_2010_04_05 (<br />. . . . . . . . Clade1.Upsilon Potential Precursor<br />. . . . . . . . GISAID HA EPI341023<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . syn71E (GAg) mix wt [H6N1],<br />. . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . syn100D (GAc) [H1N1 Avian Farm],<br />. . . . . . . . 165N,<br />. . . . . . . . 181S,<br />. . . . . . . . 189T,<br />. . . . . . . . syn198A (GCg) mix wt,<br />. . . . . . . . syn213F (TTt),<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER13_NP_48F_2010_03_25 (<br />. . . . . . . . Clade1.Upsilon Potential Precursor<br />. . . . . . . . GISAID HA EPI341024<br />. . . . . . . . 6 Polymorphisms (5 Amino and 1 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . 165N,<br />. . . . . . . . 189T,<br />. . . . . . . . syn213F (TTt),<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . 225N mix wt,<br />. . . . . . . . 225S mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER12_NP_37M_2010_03_23 (<br />. . . . . . . . GISAID HA EPI341025<br />. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . 122R,<br />. . . . . . . . 225N,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER11_NP_34F_2010_02_09 (<br />. . . . . . . . GISAID HA EPI341026<br />. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . syn214K (AAa) [H9N2],<br />. . . . . . . . . . . . . . . . . . [H13N2 Avian],<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER10_NP_39M_2010_02_09 (<br />. . . . . . . . Clade1.Upsilon Potential Precursor<br />. . . . . . . . GISAID HA EPI341027<br />. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . syn58C (TGc) [H2N3, H3N8, H4, H6],<br />. . . . . . . . . . . . . . . . . [H7N3, H7N7], <br />. . . . . . . . . . . . . . . . . [H9N2, H11],<br />. . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . 189T,<br />. . . . . . . . syn213F (TTt),<br />. . . . . . . . 225G,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER8_NP_23F_2009_11_23 (<br />. . . . . . . . GISAID HA EPI341029<br />. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . syn106E (GAa) [H1N1 Avian],<br />. . . . . . . . syn189A (GCc),<br />. . . . . . . . 225G,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER9_NP_49M_2010_01_18 (<br />. . . . . . . . GISAID HA EPI341028<br />. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER7_NP_54F_2009_11_09 (<br />. . . . . . . . Clade1.Upsilon Potential Precursor<br />. . . . . . . . GISAID HA EPI341030<br />. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . 157T,<br />. . . . . . . . 165N,<br />. . . . . . . . 225G,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER6_NP_22F_2009_11_06 (<br />. . . . . . . . GISAID HA EPI341031<br />. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . syn106E (GAa) [H1N1 Avian],<br />. . . . . . . . syn189A (GCc),<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER5_NP_52F_2009_10_27 (<br />. . . . . . . . GISAID HA EPI341032<br />. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER4_NP_xM_2009_10_16 (<br />. . . . . . . . GISAID HA EPI341033<br />. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . syn145K (AAg),<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . 225N mix wt,<br />. . . . . . . . 225S mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><a href="http://www.blogger.com/" name="EPI341034"></a><br />. . . . MexicoCityINER3_NP_47M_2009_10_15 (<br />. . . . . . . . GISAID HA EPI341034<br />. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . 225A mix,<br />. . . . . . . . 225V mix,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER2_NP_44F_2009_10_12 (<br />. . . . . . . . GISAID HA EPI341035<br />. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . 225N mix wt,<br />. . . . . . . . 225S mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><br />. . . . MexicoCityINER1_NP_40M_2009_10_01 (<br />. . . . . . . . Clade1.Upsilon Potential Precursor<br />. . . . . . . . GISAID HA EPI341036<br />. . . . . . . . 4 Polymorphisms (4 Amino and 0 Silent)<br />. . . . . . . . HA Truncated before aa38,<br />. . . . . . . . 165N,<br />. . . . . . . . 225G mix wt,<br />. . . . . . . . 225N mix wt,<br />. . . . . . . . 225S mix wt,<br />. . . . . . . . HA Truncated after aa269)<br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-2166628671121308405?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-70575956218252519472011-10-28T21:34:00.044-05:002011-11-03T22:46:11.712-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_10_27_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br /><span style="color: black;">Last Update</span><br />2011-11-03<br /><br />On 2011-10-25, the <strong><span style="color: #783f04;">Institute Pasteur of Morocco</span></strong> deposited a group of human <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences at <strong>GenBank</strong> and <strong>GISAID.</strong>&nbsp; <strong><span style="color: #274e13;">HA</span></strong> segments include 14 fragments.&nbsp; The <strong><span style="color: #274e13;">NA</span></strong> segment is represented with 15 fragments, 7 that are related to a deposited <strong><span style="color: #274e13;">HA</span></strong> fragment.&nbsp; All sequences are marked geographically as Casablanca.&nbsp; The <strong><span style="color: #783f04;">sample dates</span></strong> span 2010-12-20 to 2011-04-01 with no specification of treatment protocol, clinical progression or clinical outcome.<br /><br />Hypermorphic behaviour is found on <strong><span style="color: #783f04;">71%</span></strong> of the sequences that have both <strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA </span></strong>segments, notwithstanding the fact that <strong><span style="color: #783f04;">both segments are fragments</span></strong> across this deposit.&nbsp; These 5 hypermorphic representatives are on <strong><span style="color: #783f04;">two separate lineages</span></strong>. Additionally, the <strong><span style="color: #274e13;">NA</span></strong> fragment of &nbsp;<strong><span style="color: #783f04;">MoroccoCasablanca69_11F_2011_01_26</span></strong> &nbsp;[<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340865">EPI340865</a>] demonstrates significant, <strong><span style="color: #660000;">rare zoonotic</span></strong> homology to <span style="color: #783f04;"><strong>Avian H1N1, H5N1</strong></span>&nbsp;and <strong><span style="color: #660000;">Avian H9N2</span></strong>.<br /><br /><strong><span style="color: #783f04;">Multi-clade</span></strong> hypermorphism in a <strong><span style="color: #783f04;">single geography</span></strong> and within a contemporaneous time span merits careful evaluation.<br /><br /><span style="font-size: x-large;"><strong>Zoonoses of Polymorphisms</strong></span><br /><br />The mammal and avian database of <strong><span style="color: #783f04;">Influenza A H13</span></strong> covering all Neuraminidase forms comprises only 93 sequences, yet <strong><span style="color: #783f04;">shares homology</span></strong> to <strong><span style="color: #4c1130;">pH1N1</span></strong> human polymorphisms on <strong><span style="color: blue;">Clade1.Upsilon</span></strong> as well as <strong><span style="color: #660000;">rare and novel</span></strong> <strong><span style="color: #4c1130;">pH1N1</span></strong> human polymorphisms on <strong><span style="color: blue;">Clade2, Clade4</span></strong> and <strong><span style="color: blue;">Clade5</span></strong> sequences in this Moroccan deposit.&nbsp; Several of these shared polymorphisms, e.g. markers for <strong><span style="color: blue;">Clade5</span></strong> (<strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">219V</span></strong> and <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">252L</span></strong>), are <strong><span style="color: #783f04;">previously uncharacterised</span></strong> as to potential <strong><span style="color: #783f04;">Ultimate Origin</span></strong>.&nbsp; The identification of multi-clade hypermorphism in this geography with <strong><span style="color: #783f04;">wide homology to a single candidate animal reservoir</span></strong> (<strong><span style="color: #783f04;">A/H13</span></strong>) solidifies the clear requirement for <strong><span style="color: #783f04;">higher levels of avian surveillance</span></strong>. <br /><br /><span style="font-size: x-large;"><strong>Cladistics</strong></span><br /><br />10 - <strong><span style="color: blue;">Clade2: 188T</span></strong> <br />01 - <strong><span style="color: blue;">Clade4: 128D</span></strong> [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340861">EPI340861</a>]<br />03 - <strong><span style="color: blue;">Clade5: 208K_219V</span></strong> [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340881">EPI340881</a>], [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340860">EPI340860</a>], [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340876">EPI340876</a>] <br /><br /><strong><span style="color: #274e13;">HA</span></strong>&nbsp;&nbsp; 84 Polymorphisms Averaging ~<strong><span style="color: #783f04;">6.0 per Segment Fragment</span></strong><br /><strong><span style="color: #274e13;">NA</span></strong>&nbsp;118 Polymorphisms Averaging ~<strong><span style="color: #783f04;">7.9 per Segment Fragment</span></strong><br /><br /><strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> 202 Total Polymorphisms Averaging ~<strong><span style="color: #783f04;">13.9 per Sequence (Fragments)</span></strong><br /><br /><strong><span style="font-size: x-large;">Diversity</span></strong><br /><br /><strong><span style="color: #274e13;">HA</span></strong> Superset – <strong><span style="color: #783f04;">36 Distinct Values</span></strong><br /><strong><span style="color: #274e13;">NA</span></strong> Superset - <strong><span style="color: #783f04;">47 Distinct Values</span></strong><br /><br />Two <strong><span style="color: #783f04;">Receptor Binding Site</span></strong> items of interest are <strong><span style="color: blue;">syn221P</span></strong> and <strong><span style="color: blue;">224K</span></strong>.&nbsp; No indication is found of revisions at aa225, aa226 or aa230.&nbsp; The <strong><span style="color: blue;">Clade5</span></strong> sequence bearing <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">syn221P</span></strong> is contemporary in timing and homology to a small group of European <strong><span style="color: blue;">Clade5</span></strong> sequences.&nbsp; A hypermorphic, <strong><span style="color: blue;">Clade2</span></strong> Moroccan sequence bears <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">224K</span></strong>, a polymorphism previously found in <strong><span style="color: #4c1130;">pH1N1</span></strong> swine <strong><span style="color: blue;">Clade5</span></strong>, suggesting a potential <strong><span style="color: #783f04;">cross-clade transfer</span></strong> or compatibility.&nbsp; The <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">224K</span></strong> may signal <strong><span style="color: #783f04;">tissue tropism</span></strong> issues, having been documented on a <strong><span style="color: #783f04;">lethal, neurotropic experimental</span></strong> strain (<strong><span style="color: #783f04;">WSN_1933</span></strong>).<br /><ul><li>[<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340860">EPI340860</a>] <strong><span style="color: #783f04;">MoroccoCasablanca91_15mM_2011_02_02</span></strong> – <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">syn221P</span></strong></li><li>[<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340866">EPI340866</a>] <strong><span style="color: #783f04;">MoroccoCasablanca69_11F_2011_01_26</span></strong>&nbsp;&nbsp;&nbsp;&nbsp;– <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">224K</span></strong> </li></ul><br /><span style="font-size: x-large;"><strong>Hypermorphic Behaviour</strong></span> <br /><br />04 <strong><span style="color: #274e13;">HA</span></strong> Fragments &gt;=&nbsp;7 polymorphisms (29%)<br />13 <strong><span style="color: #274e13;">NA</span></strong> Segments&nbsp; &gt;=&nbsp;7 polymorphisms <strong><span style="color: #783f04;">(87%)</span></strong><br /><br /><span style="font-size: x-large;">Combined Polymorphic Count &gt;= 15</span><br />5 of 7 Sequences with <strong><span style="color: #274e13;">HA</span></strong> and <span style="color: #274e13;"><strong>NA</strong></span> Fragments <strong><span style="color: #783f04;">(71%)</span></strong><br />Total (HA / NA)<br /><ul><li>16 (HA 09 / NA 07): [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340881">EPI340881</a>] <strong><span style="color: #783f04;">MoroccoCasablanca117_10m_2011_02_15</span></strong></li><li>16 (HA 07 / NA 09): [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340860">EPI340860</a>] <strong><span style="color: #783f04;">MoroccoCasablanca91_15mM_2011_02_02</span></strong></li><li>16 (HA 05 / NA 11): [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340866">EPI340866</a>] <strong><span style="color: #783f04;">MoroccoCasablanca69_11F_2011_01_26</span></strong></li><li>16 (HA 09 / NA 07): [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340876">EPI340876</a>] <strong><span style="color: #783f04;">MoroccoCasablanca23_3F_2011_01_13</span></strong></li><li>15 (HA 09 / NA 07): [<a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#EPI340868">EPI340868</a>] <strong><span style="color: #783f04;">MoroccoCasablanca63_47F_2011_01_20</span></strong></li></ul><span style="font-size: x-large;"><strong>Sequences</strong></span><br /><a href="http://www.blogger.com/" name="EPI340879"></a><br />. . . . MoroccoCasablanca124_5M_2011_04_01 (<br />. . . . . . . . GISAID NA EPI340879<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . NA Truncated before aa36,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . NA Truncated after aa453)<br /><a href="http://www.blogger.com/" name="EPI340885"></a><br />. . . . MoroccoCasablanca211_15M_2010_12_20 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340885<br />. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa354)<br /><a href="http://www.blogger.com/" name="EPI340881"></a><br />. . . . MoroccoCasablanca117_10m_2011_02_15 (<br />. . . . . . . . Clade5: <a href="http://pf11.blogspot.com/2011/06/sweden-signals-rapid-zoonosis-from.html" target="_blank">208K_219V</a> crossing with<br />. . . . . . . . . . . Clade2: 188T Defining Marker syn338G<br />. . . . . . . . GISAID HA EPI340881<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn47L (CTg) [H1N1 Avian],<br />. . . . . . . . syn82I (ATc) [H5N2 Avian],<br />. . . . . . . . syn93C (TGc) [H5N1 Avian Domestic & Wild],<br />. . . . . . . . . . . . . . . . . [H9N2 Avian Emergent 2009],<br />. . . . . . . . . . . . . . . . . [H13N2 Mammal],<br />. . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . 100N [H5N1 Egypt Avian 2009-2010 <br />. . . . . . . . . . . . . . . with syn40H, syn55L, 192I, 196K],<br />. . . . . . . . . . . . [H5N1 Egypt Avian 2008 with syn40H, syn55L],<br />. . . . . . . . . . . . [H5N2 Italy Avian 2005-2007],<br />. . . . . . . . . . . . [H7N3, H7N7, H9N2],<br />. . . . . . . . . . . . [H13N2 Mammal],<br />. . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],<br />. . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . 141Q (CAa) [H13 Avian (gAa, gga)],<br />. . . . . . . . syn170N (AAc) [H5N1 Egypt Human 2009],<br />. . . . . . . . . . . . . . . . . . [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . . . . . . . . . . . [H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . . . with 225G & 252L],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . 208K (AaA) [pH1N1 Canine 2009],<br />. . . . . . . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . [H3N2 Avian 2006, 2009],<br />. . . . . . . . 219V (gTA) [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . . . . . . . . . [H13N2, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . syn338G (GGc) [Clade2, Rare to Clade5],<br />. . . . . . . . HA Truncated after aa342)<br /><br />. . . . MoroccoCasablanca117_10m_2011_02_15 (<br />. . . . . . . . GISAID NA EPI340880<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . NA Truncated before aa33,<br />. . . . . . . . syn89S (TCt) [H1N1 Avian],<br />. . . . . . . . syn126P (CCt) [H1N1 Avian (Cat)],<br />. . . . . . . . . . . . . . . . . .[H9N2 Avian (Ctt)],<br />. . . . . . . . syn229S (TCc) [H1N1 Avian],<br />. . . . . . . . syn236G (GGc) [H1N1 Avian],<br />. . . . . . . . syn241V (GTg) [H1N1 Avian],<br />. . . . . . . . 299A,<br />. . . . . . . . 454V [Rare to pH1N1 (1)],<br />. . . . . . . . NA Truncated after aa454)<br /><a href="http://www.blogger.com/" name="EPI340882"></a><br />. . . . MoroccoCasablanca110_3F_2011_02_09 (<br />. . . . . . . . GISAID NA EPI340882<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . NA Truncated before aa38,<br />. . . . . . . . 38V [H9N2 Avian],<br />. . . . . . . . syn60T (ACc) [H1N1 Avian Farm],<br />. . . . . . . . 81A [H1N1 Avian],<br />. . . . . . . . syn138A (GCt) [H1N1 Avian],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian],<br />. . . . . . . . 192N [H9N2 Avian (cac)],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . NA Truncated after aa453)<br /><br />. . . . MoroccoCasablanca107_xF_2011_02_09 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340883<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa#4,<br />. . . . . . . . 100N,<br />. . . . . . . . 173R,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa341)<br /><br />. . . . MoroccoCasablanca103_5M_2011_02_07 (<br />. . . . . . . . GISAID HA EPI340884<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa#7,<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 324D [Novel to pH1N1],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa350)<br /><a href="http://www.blogger.com/" name="EPI340858"></a><br />. . . . MoroccoCasablanca92_52F_2011_02_02 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340858<br />. . . . . . . . 8 Polymorphisms (6 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa#3,<br />. . . . . . . . 22E [Novel to pH1N1],<br />. . . . . . . . 34T [Novel to pH1N1 2011],<br />. . . . . . . . 47Q [Novel to pH1N1],<br />. . . . . . . . 60V [H1N1 Avian],<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa341)<br /><a href="http://www.blogger.com/" name="EPI340860"></a><br />. . . . MoroccoCasablanca91_15mM_2011_02_02 (<br />. . . . . . . . Clade5: <a href="http://pf11.blogspot.com/2011/06/sweden-signals-rapid-zoonosis-from.html" target="_blank">208K_219V</a> <br />. . . . . . . . GISAID HA EPI340860<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . HA Truncated before aa82,<br />. . . . . . . . 100F [Novel to pH1N1],<br />. . . . . . . . syn102E (GAa) [H5N1 wt],<br />. . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],<br />. . . . . . . . . . . . . . . . . [H9N2 Avian wt],<br />. . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . syn170N (AAc) [H5N1 Egypt Human 2009],<br />. . . . . . . . . . . . . . . . . . [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . . . . . . . . . . . [H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . . . with 225G & 252L],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . 208K (AaA) [pH1N1 Canine 2009],<br />. . . . . . . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . [H3N2 Avian 2006, 2009],<br />. . . . . . . . 219V (gTA) [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . . . . . . . . . [H13N2, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . syn221P (CCt) [H3N2 Avian <br />. . . . . . . . . . . . . . . . . . . . . with 157S, 159S, syn287G],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human and Avian (tCt)],<br />. . . . . . . . . . . . . . . . . . [H5N1 Nigeria Avian (tCt)],<br />. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],<br />. . . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . with extensive Upsilon polymorphisms],<br />. . . . . . . . 252L (tTG) [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],<br />. . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],<br />. . . . . . . . HA Truncated after aa352)<br /><br />. . . . MoroccoCasablanca91_15mM_2011_02_02 (<br />. . . . . . . . GISAID NA EPI340859<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . NA Truncated before aa36,<br />. . . . . . . . 69V [H1N1 Avian],<br />. . . . . . . . 81A [H1N1 Avian],<br />. . . . . . . . 106M,<br />. . . . . . . . syn138A (GCt) [H1N1 Avian],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn395G (GGg),<br />. . . . . . . . NA Truncated after aa452)<br /><a href="http://www.blogger.com/" name="EPI340861"></a><br />. . . . MoroccoCasablanca76_13M_2011_01_26 (<br />. . . . . . . . Clade4: 128D<br />. . . . . . . . GISAID HA EPI340861<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa13,<br />. . . . . . . . 28P [Novel to pH1N1.Clade4],<br />. . . . . . . . . . . [pH1N1 with Avian Influence (3)],<br />. . . . . . . . . . . [H13N2 Mammal <br />. . . . . . . . . . . . . . with 188T, syn210S, 225G & 252L],<br />. . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . with 188T, syn210S, 225G & 252L],<br />. . . . . . . . syn60I (ATc) [H9N2 Human and Avian Emergent],<br />. . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, <br />. . . . . . . . . . . . . . . . . . . H13N8, H13N9 Avian (tTc) <br />. . . . . . . . . . . . . . . . . . . . . . with 28P, 188T, syn210S],<br />. . . . . . . . . . . . . . . . [1918],<br />. . . . . . . . 128D,<br />. . . . . . . . syn210S (AGt) [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . . . with 28P, 188T, 225G & 252L],<br />. . . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . . . with 28P, 188T, 225G & 252L],<br />. . . . . . . . 298V [H3N2 Avian, Canine, Feline & Mink],<br />. . . . . . . . . . . [H3N8], <br />. . . . . . . . . . . [H5 Avian, H6 Avian], <br />. . . . . . . . . . . [H9N2],<br />. . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . HA Truncated after aa341)<br /><br />. . . . MoroccoCasablanca73_43F_2011_01_26 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340863<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa0,<br />. . . . . . . . 11L [Novel to pH1N1],<br />. . . . . . . . . . . [H13N2 Mammal <br />. . . . . . . . . . . . . . with 28P, 188T, syn210S, 225G & 252L],<br />. . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . with 28P, 188T, syn210S, 225G & 252L], <br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 259T [Recently Novel to pH1N1υ],<br />. . . . . . . . . . . . [H9N2 Avian and Human (att) <br />. . . . . . . . . . . . . . . . with syn40H],<br />. . . . . . . . . . . . [Not Found in H1N1 Swine with 124N],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa338)<br /><br />. . . . MoroccoCasablanca73_43F_2011_01_26 (<br />. . . . . . . . GISAID NA EPI340862<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . NA Truncated before aa44,<br />. . . . . . . . syn126P (CCa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn293R (AGa) [H1N1 Avian Farm],<br />. . . . . . . . . . . . . . . . . . . [H5N1 Avian],<br />. . . . . . . . . . . . . . . . . . . [H9N2 Avian],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . NA Truncated after aa453)<br /><a href="http://www.blogger.com/" name="EPI340866"></a><br />. . . . MoroccoCasablanca69_11F_2011_01_26 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340866<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa#5,<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 224K [swine pH1N1.Clade5]<br />. . . . . . . . . . . . [WSN_1933],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa339)<br /><a href="http://www.blogger.com/" name="EPI340865"></a><br />. . . . MoroccoCasablanca69_11F_2011_01_26 (<br />. . . . . . . . GISAID NA EPI340865<br />. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)<br />. . . . . . . . NA Truncated before aa35,<br />. . . . . . . . 70N [H1N1 Avian],<br />. . . . . . . . syn137G (GGa) [H1N1 Avian],<br />. . . . . . . . syn215T (ACa) [H1N1 Avian],<br />. . . . . . . . 235D [H9N2 Avian],<br />. . . . . . . . syn240T (ACc) [H1N1 Avian],<br />. . . . . . . . 241I [H1N1 Avian],<br />. . . . . . . . 260R [H1N1 Avian],<br />. . . . . . . . 369K [H1N1 Avian],<br />. . . . . . . . syn377P (CCa) [H1N1 Avian],<br />. . . . . . . . syn386N (AAt) [H1N1 Environment],<br />. . . . . . . . syn416D (GAc) [H5N1 wt],<br />. . . . . . . . NA Truncated after aa453)<br /><a href="http://www.blogger.com/" name="EPI340868"></a><br />. . . . MoroccoCasablanca63_47F_2011_01_20 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340868<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . HA Truncated before aa3,<br />. . . . . . . . syn90N (AAc) [Rare to pH1N1],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa339)<br /><br />. . . . MoroccoCasablanca63_47F_2011_01_20 (<br />. . . . . . . . GISAID NA EPI340867<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . NA Truncated before aa20,<br />. . . . . . . . syn89S (TCt) [H1N1 Avian],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 262N,<br />. . . . . . . . 263V [H1N1 Avian],<br />. . . . . . . . . . . . [H5N1 wt], <br />. . . . . . . . . . . . [H9N2 Avian],<br />. . . . . . . . 269I [H5N1 (tTa)],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . 420C,<br />. . . . . . . . NA Truncated after aa453)<br /><br />. . . . MoroccoCasablanca60_43F_2011_01_20 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340869<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . HA Truncated before aa#3,<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn205G (GGa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa338)<br /><a href="http://www.blogger.com/" name="EPI340870"></a><br />. . . . MoroccoCasablanca54_23F_2011_01_20 (<br />. . . . . . . . GISAID NA EPI340870<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . NA Truncated before aa17,<br />. . . . . . . . 54L,<br />. . . . . . . . 81A [H1N1 Avian],<br />. . . . . . . . syn138A (GCt) [H1N1 Avian],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn395G (GGg),<br />. . . . . . . . NA Truncated after aa454)<br /><a href="http://www.blogger.com/" name="EPI340871"></a><br />. . . . MoroccoCasablanca52_25F_2011_01_20 (<br />. . . . . . . . GISAID NA EPI340871<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . NA Truncated before aa19,<br />. . . . . . . . 43R,<br />. . . . . . . . 44T,<br />. . . . . . . . 45L,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . NA Truncated after aa452)<br /><br />. . . . MoroccoCasablanca28_10M_2011_01_13 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340873<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . HA Truncated before aa#6,<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 340M,<br />. . . . . . . . HA Truncated after aa340)<br /><br />. . . . MoroccoCasablanca28_10M_2011_01_13 (<br />. . . . . . . . GISAID NA EPI340872<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . NA Truncated before aa21,<br />. . . . . . . . 54V [H1N1 Avian],<br />. . . . . . . . . . [H9N2 Avian],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . 454V [Rare to pH1N1 (1)],<br />. . . . . . . . NA Truncated after aa454)<br /><br />. . . . MoroccoCasablanca26_24M_2011_01_13 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340874<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn136T (ACt),<br />. . . . . . . . 176I,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa353)<br /><a href="http://www.blogger.com/" name="EPI340876"></a><br />. . . . MoroccoCasablanca23_3F_2011_01_13 (<br />. . . . . . . . Clade5: <a href="http://pf11.blogspot.com/2011/06/sweden-signals-rapid-zoonosis-from.html" target="_blank">208K_219V</a> <br />. . . . . . . . GISAID HA EPI340876<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . HA Truncated before aa#7,<br />. . . . . . . . syn36L (tTA) [H5N1 Avian (tTg)],<br />. . . . . . . . syn47L (CTg) [H1N1 Avian],<br />. . . . . . . . 100N [H5N1 Egypt Avian 2009-2010 <br />. . . . . . . . . . . . . . . . . with syn40H, syn55L, 192I, 196K],<br />. . . . . . . . . . . . [H5N1 Egypt Avian 2008 with syn40H, syn55L],<br />. . . . . . . . . . . . [H5N2 Italy Avian 2005-2007],<br />. . . . . . . . . . . . [H7N3, H7N7, H9N2],<br />. . . . . . . . . . . . [H13N2 Mammal],<br />. . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],<br />. . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . syn102E (GAa) [H5N1 wt],<br />. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],<br />. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],<br />. . . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . syn170N (AAc) [H5N1 Egypt Human 2009],<br />. . . . . . . . . . . . . . . . . . [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . . . . . . . . . . . [H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . . . with 225G & 252L],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . syn184H (CAc) [Early pH1N1 <a href="http://pf11.blogspot.com/2011/10/morocco-reports-hypermorphism-on-ph1n1.html#syn184H">Highly Zoonotic</a>]<br />. . . . . . . . . . . . . . . . . . [swine pH1N1.Clade5],<br />. . . . . . . . . . . . . . . . . . [H2N3, H3N8],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Fatality 2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009],<br />. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],<br />. . . . . . . . . . . . . . . . . . [H13N2 Mammal],<br />. . . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . 208K (AaA) [pH1N1 Canine 2009],<br />. . . . . . . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . [H3N2 Avian 2006, 2009],<br />. . . . . . . . 219V (gTA) [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . . . . . . . . . [H13N2, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],<br />. . . . . . . . 252L (tTG) [H13N2 Mammal <br />. . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],<br />. . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian<br />. . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],<br />. . . . . . . . HA Truncated after aa335)<br /><br />. . . . MoroccoCasablanca23_3F_2011_01_13 (<br />. . . . . . . . GISAID NA EPI340875<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . NA Truncated before aa39,<br />. . . . . . . . syn87G (GGg) [H9N2 Avian (aag)],<br />. . . . . . . . syn138A (GCt) [H1N1 Avian],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 242V [H9N2 Avian],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . NA Truncated after aa455)<br /><a href="http://www.blogger.com/" name="EPI340877"></a><br />. . . . MoroccoCasablanca17_12F_2011_01_07 (<br />. . . . . . . . GISAID NA EPI340877<br />. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)<br />. . . . . . . . NA Truncated before aa35,<br />. . . . . . . . syn176S (TCg) [H1N1 Avian],<br />. . . . . . . . 213K,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn338V (GTg) [H1N1 Avian],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . NA Truncated after aa453)<br /><br />. . . . MoroccoCasablanca15_35F_2011_01_06 (<br />. . . . . . . . GISAID NA EPI340878<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . NA Truncated before aa35,<br />. . . . . . . . syn126P (CCa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 263V [H1N1 Avian],<br />. . . . . . . . . . . . [H5N1 wt], <br />. . . . . . . . . . . . [H9N2 Avian],<br />. . . . . . . . 269I [H5N1 (tTa)],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . NA Truncated after aa454)<br /><a href="http://www.blogger.com/" name="EPI340864"></a><br />. . . . MoroccoCasablanca07_23F_2011_01_05 (<br />. . . . . . . . GISAID NA EPI340864<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . NA Truncated before aa34,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . 419S,<br />. . . . . . . . 420A,<br />. . . . . . . . 428I,<br />. . . . . . . . NA Truncated after aa453)<br /><a href="http://www.blogger.com/" name="EPI340886"></a><br />. . . . MoroccoCasablanca210_2010_12_20 (<br />. . . . . . . . GISAID NA EPI340886<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . NA Truncated before aa17,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn273N (AAc) [H1N1 Avian],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . NA Truncated after aa457)<br /><br /><span style="font-size: x-large;"><strong>Supporting Sequences</strong></span><br /><a href="http://www.blogger.com/" name="syn184H"></a><br />. . . . NewYork7420_2010_01_02 (<br />. . . . . . . . GenBank HA CY065067<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . 35I [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . syn80S (TCt) [H5N1 Egypt Human 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H6N1, H7N3, H9N2, H11],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn31H, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn40H, syn42G, 72L,<br />. . . . . . . . . . . . . . . . . . . . . . . . syn81Y, syn82I, 87N<br />. . . . . . . . . . . . . . . . . . . . . . . . syn118E, 144E, 158E, <br />. . . . . . . . . . . . . . . . . . . . . . . . 189T, 200T, 218S, 218V, <br />. . . . . . . . . . . . . . . . . . . . . . . . 237I, syn287G, syn346G,<br />. . . . . . . . . . . . . . . . . . . . . . . . 453K, 502K, 523A, 523I],<br />. . . . . . . . syn159N (AAc) [H3N8 Avian &amp; Equine],<br />. . . . . . . . . . . . . . . [H9N2],<br />. . . . . . . . syn184H (CAc) [Early pH1N1 Highly Zoonotic]<br />. . . . . . . . . . . . . . . . . . [swine pH1N1.Clade5],<br />. . . . . . . . . . . . . . . . . . [H2N3, H3N8],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Fatality 2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009],<br />. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],<br />. . . . . . . . 236I [H3N8],<br />. . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],<br />. . . . . . . . . . . . [H6, H7N7, H9N2 2009, H11],<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . syn441H (CAt) [H1N1 Avian, H2, H5N1, H6, H9N2, H11])<br /><br />. . . . NewYork7425_2009_12_20 (<br />. . . . . . . . GenBank HA CY065091<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . 35I [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . syn113S (TCg) [1918],<br />. . . . . . . . syn159N (AAc) [H3N8 Avian &amp; Equine],<br />. . . . . . . . . . . . . . . [H9N2],<br />. . . . . . . . syn184H (CAc) [Early pH1N1 Highly Zoonotic]<br />. . . . . . . . . . . . . . . . . . [swine pH1N1.Clade5],<br />. . . . . . . . . . . . . . . . . . [H2N3, H3N8],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Fatality 2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009],<br />. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],<br />. . . . . . . . 236I [H3N8],<br />. . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],<br />. . . . . . . . . . . . [H6, H7N7, H9N2 2009, H11],<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . syn441H (CAt) [H1N1 Avian, H2, H5N1, H6, H9N2, H11])<br /><br />. . . . Texas43242018_2009_07_24 (<br />. . . . . . . . GenBank HA CY051823<br />. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)<br />. . . . . . . . syn184H (CAc) [Early pH1N1 Highly Zoonotic]<br />. . . . . . . . . . . . . . . . . . [swine pH1N1.Clade5],<br />. . . . . . . . . . . . . . . . . . [H2N3, H3N8],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Fatality 2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009],<br />. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],<br />. . . . . . . . syn239P (CCt) [H1N1 Avian],<br />. . . . . . . . syn297N (AAc) [H3N2 Asia Avian 1975-1977 with 159S, 453K],<br />. . . . . . . . . . . . . . . . . . [H3N8 Avian],<br />. . . . . . . . . . . . . . . . . . [H5N1],<br />. . . . . . . . . . . . . . . . . . [H9N2 Human, Avian, Equine and Seal wt],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian 2009],<br />. . . . . . . . syn453R (AGg) [H1N1 Avian],<br />. . . . . . . . syn525S (AGc) [H1N1 Avian])<br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-7057595621825251947?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-72273459723361272702011-10-26T23:52:00.021-05:002011-10-27T22:55:32.379-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_10_25_Japan_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br /><span style="color: black;">Last Update</span><br />2011-10-27<br /><br />On 2011-10-19, the <strong><span style="color: #783f04;">Japanese Influenza Collaborative Study Group</span></strong> based at <strong><span style="color: #783f04;">Niigata University</span></strong> released a group of human <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences at <strong>GenBank</strong> and <strong>GISAID</strong> including 46 <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: #783f04;">fragments</span></strong> and 46 full <strong><span style="color: #274e13;">NA</span></strong> segments.&nbsp; The sample dates span 2011-01-04 to 2011-03-08.&nbsp; <strong><span style="color: #783f04;">Seven geographic</span></strong> areas of Japan are covered with no specification of subject age, subject gender, treatment protocol, clinical progression or clinical outcome notated.<br /><br /><span style="font-size: x-large;"><strong>Cladistics</strong></span><br /><br /><strong><span style="color: blue;">Clade2: 188T</span></strong> is represented on 44 sequences crossing all geographic divisions and <strong><span style="color: blue;">Clade3: 186P</span></strong> is found once each in Niigata and Osaka.&nbsp; Although cladding is clear, <strong><span style="color: #783f04;">perhaps due to publication bias</span></strong>, overall <strong><span style="color: #783f04;">diversity is high</span></strong>. That diversity and the sheer polymorphic count demonstrate the <strong><span style="color: #783f04;">instability </span></strong>of human <strong><span style="color: #4c1130;">pH1N1</span></strong> as the reservoir <strong><span style="color: #783f04;">continues to undergo revision</span></strong>. <br /><br /><strong><span style="color: #274e13;">HA</span></strong> 320 Polymorphisms Averaging ~<strong><span style="color: #783f04;">7.0 per Segment Fragment</span></strong><br /><strong><span style="color: #274e13;">NA</span></strong> 352 Polymorphisms Averaging ~<strong><span style="color: #783f04;">7.6 per Segment</span></strong><br /><br /><strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> 672 Total Polymorphisms Averaging ~<strong><span style="color: #783f04;">14.6 per Sequence (HA Fragments)</span></strong><br /><br /><span style="font-size: x-large;"><strong>Diversity</strong></span><br /><br />The <strong><span style="color: #274e13;">HA</span></strong> superset&nbsp;producing <strong><span style="color: #783f04;">77 distinct values</span></strong> includes 4 polymorphisms (<strong><span style="color: blue;">syn31H, syn42G, 189T, syn287G</span></strong>) that appear on the <strong><span style="color: #660000;">High CFR</span></strong> <strong><span style="color: blue;">Clade1.Upsilon</span></strong> revision set.&nbsp; Polymorphic sets shared across <strong><span style="color: #4c1130;">pH1N1</span></strong> clades suggest <strong><span style="color: #783f04;">cross-clade compatibility</span></strong>.&nbsp; <strong><span style="color: #660000;">H5N1 involvement</span></strong> is notated on <strong><span style="color: #783f04;">JapanOsaka10K362_2011_02_15</span></strong>, [<a href="http://www.blogger.com/post-edit.g?blogID=4506613821928567934&amp;postID=7227345972336127270#EPI340541">EPI340541</a>].&nbsp; Notably absent in this deposit are&nbsp;Receptor Binding Site changes at <strong><span style="color: #274e13;">HA</span></strong> aa225.&nbsp; The <strong><span style="color: #274e13;">NA</span></strong> superset produces <strong><span style="color: #783f04;">85 distinct values</span></strong>.&nbsp; No mixed peaks (ambiguity) are found on any segment though <strong><span style="color: #783f04;">significant zoonoses</span></strong> are represented. <br /><br /><span style="font-size: x-large;"><strong>Hypermorphic Behaviour</strong></span> <br /><br />14 <strong><span style="color: #274e13;">HA</span></strong> Fragments &gt;= 8 polymorphisms (30%)<br />20 <strong><span style="color: #274e13;">NA</span></strong> Segments &gt;= 8 polymorphisms (43%)<br /><br /><span style="font-size: x-large;">Combined Polymorphic Count &gt;= 17</span><br />Total (HA / NA)<br /><br /><ul><li>21 (HA 11 / NA 10): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340579">EPI340579</a>] <strong><span style="color: #783f04;">JapanHokkaido10H054_2011_02_07</span></strong></li><li>21 (HA 11 / NA 10): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340574">EPI340574</a>] <strong><span style="color: #783f04;">JapanHyogo10K055_2011_01_24</span></strong> </li><li>19 (HA 11 / NA 08): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340549">EPI340549</a>] <strong><span style="color: #783f04;">JapanNiigata10F257_2011_02_03</span></strong></li><li>18 (HA 10 / NA 08): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340551">EPI340551</a>] <strong><span style="color: #783f04;">JapanNiigata10F202_2011_01_31</span></strong></li><li>18 (HA 10 / NA 08): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340552">EPI340552</a>] <strong><span style="color: #783f04;">JapanNiigata10F117_2011_01_25</span></strong></li><li>18 (HA 07 / NA 11): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340548">EPI340548</a>] <strong><span style="color: #783f04;">JapanNiigata10F306_2011_02_05</span></strong></li><li>18 (HA 11 / NA 07): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340543">EPI340543</a>] <strong><span style="color: #783f04;">JapanOsaka10K346_2011_02_07</span></strong></li><li>17 (HA 07 / NA 10): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340555">EPI340555</a>] <strong><span style="color: #783f04;">JapanNagasaki10N103_2011_02_10</span></strong></li><li>17 (HA 08 / NA 09): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340561">EPI340561</a>] <strong><span style="color: #783f04;">JapanKyoto10K385_2011_02_22</span></strong></li><li>17 (HA 09 / NA 08): [<a href="http://pf11.blogspot.com/2011/10/japan-demonstrates-2011-ph1n1-multi.html#EPI340568">EPI340568</a>] <strong><span style="color: #783f04;">JapanHyogo10K308_2011_02_14</span></strong></li></ul><span style="font-size: x-large;"><strong>TamiFlu Resistance</strong></span><br /><br />Two <strong><span style="color: #660000;">TamiFlu Resistant</span></strong> sequences (<strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">275Y</span></strong>) each feature on <strong><span style="color: blue;">Clade2: 188T</span></strong> backgrounds having significant <strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> homology with <strong><span style="color: #660000;">Avian H1N1</span></strong>. <br /><ul><li>[<a href="http://www.blogger.com/post-edit.g?blogID=4506613821928567934&amp;postID=7227345972336127270#EPI340570">EPI340570</a>] <strong><span style="color: #783f04;">JapanHyogo10K291_2011_02_07</span><span style="color: #660000;">_TmX</span></strong></li><li>[<a href="http://www.blogger.com/post-edit.g?blogID=4506613821928567934&amp;postID=7227345972336127270#EPI340564">EPI340564</a>] <strong><span style="color: #783f04;">JapanKyoto10K124_2011_01_28</span><span style="color: #660000;">_TmX</span></strong></li></ul><br /><span style="font-size: x-large;"><strong>Sequences</strong></span><br /><br />. . . . JapanNiigata10F557_2011_03_08 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340547<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNiigata10F557_2011_03_08 (<br />. . . . . . . . GISAID NA EPI340662<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanKyoto10K393_2011_02_25 (<br />. . . . . . . . GISAID HA EPI340560<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . syn#6L (tTG),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn53L (TTa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanKyoto10K393_2011_02_25 (<br />. . . . . . . . GISAID NA EPI340675<br />. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 62I,<br />. . . . . . . . syn237S (TCa),<br />. . . . . . . . 240I,<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><a href="http://www.blogger.com/" name="EPI340561"></a><br />. . . . JapanKyoto10K385_2011_02_22 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340561<br />. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn130D (GAt),<br />. . . . . . . . 146G,<br />. . . . . . . . syn162P (CCg),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn321L (TTa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanKyoto10K385_2011_02_22 (<br />. . . . . . . . GISAID NA EPI340676<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 62L,<br />. . . . . . . . 127S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn427I (ATa),<br />. . . . . . . . 431S)<br /><br />. . . . JapanOsaka10K366_2011_02_21 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340539<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . syn#12K (AAa),<br />. . . . . . . . #6M,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 156T,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanOsaka10K366_2011_02_21 (<br />. . . . . . . . GISAID NA EPI340654<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 13A,<br />. . . . . . . . 44S,<br />. . . . . . . . syn64Q (CAa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt))<br /><br />. . . . JapanNagasaki10N088_2011_02_19 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340556<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn258F (TTt),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNagasaki10N088_2011_02_19 (<br />. . . . . . . . GISAID NA EPI340671<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 86T,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt))<br /><br />. . . . JapanOsaka10K363_2011_02_16 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340540<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 288S,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanOsaka10K363_2011_02_16 (<br />. . . . . . . . GISAID NA EPI340655<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn157T (ACa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><a href="http://www.blogger.com/" name="EPI340541"></a><br />. . . . JapanOsaka10K362_2011_02_15 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340541<br />. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . 33I,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 305E [<strong><span style="color: #660000;">H5N1 wt</span></strong>],<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanOsaka10K362_2011_02_15 (<br />. . . . . . . . GISAID NA EPI340656<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn121F (TTt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><a href="http://www.blogger.com/" name="EPI340568"></a><br />. . . . JapanHyogo10K308_2011_02_14 (<br />. . . . . . . . Clade2: 188T crossed with 189T from Clade1<br />. . . . . . . . GISAID HA EPI340568<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc) [H1N1 Avian],<br />. . . . . . . . syn34N (AAt) [H1N1 Avian],<br />. . . . . . . . syn98F (TTt) [H1N1 Avian],<br />. . . . . . . . syn122K (AAa) [H1N1 Avian],<br />. . . . . . . . 146G,<br />. . . . . . . . 166T,<br />. . . . . . . . 188T [H1N1 Avian],<br />. . . . . . . . 189T [pH1N1 Clade1.Upsilon],<br />. . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . 200T [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K308_2011_02_14 (<br />. . . . . . . . GISAID NA EPI340683<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn104N (AAt) [H1N1 Avian],<br />. . . . . . . . syn240T [H1N1 Avian],<br />. . . . . . . . 241I [H1N1 Avian],<br />. . . . . . . . syn287E (GAg) [H1N1 Avian],<br />. . . . . . . . 369K [H1N1 Avian],<br />. . . . . . . . syn377P (CCa) [H1N1 Avian],<br />. . . . . . . . 451N [H3N8 Equine, Canine, Swine (aAa)])<br /><br />. . . . JapanHokkaido10H073_2011_02_14 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340578<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn223V (GTa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHokkaido10H073_2011_02_14 (<br />. . . . . . . . GISAID NA EPI340693<br />. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 140V,<br />. . . . . . . . 224F,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 309D,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 392N)<br /><br />. . . . JapanOsaka10K358_2011_02_12 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340542<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanOsaka10K358_2011_02_12 (<br />. . . . . . . . GISAID NA EPI340657<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanHyogo10K302_2011_02_12 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340569<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn#12K (AAa),<br />. . . . . . . . syn31H (CAt) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K302_2011_02_12 (<br />. . . . . . . . GISAID NA EPI340684<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn301R (CGg),<br />. . . . . . . . syn326P (CCg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M,<br />. . . . . . . . 454D)<br /><a href="http://www.blogger.com/" name="EPI340555"></a><br />. . . . JapanNagasaki10N103_2011_02_10 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340555<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . syn50V (GTt),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . 297D,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNagasaki10N103_2011_02_10 (<br />. . . . . . . . GISAID NA EPI340670<br />. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)<br />. . . . . . . . syn42N (AAc),<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 257K,<br />. . . . . . . . 351Y,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M,<br />. . . . . . . . 416G)<br /><br />. . . . JapanNagasaki10N073_2011_02_09 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340557<br />. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNagasaki10N073_2011_02_09 (<br />. . . . . . . . GISAID NA EPI340672<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn28N (AAt),<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><a href="http://www.blogger.com/" name="EPI340543"></a><br />. . . . JapanOsaka10K346_2011_02_07 (<br />. . . . . . . . Clade3: 186P<br />. . . . . . . . GISAID HA EPI340543<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . syn#12K (AAa),<br />. . . . . . . . 41T,<br />. . . . . . . . 135A,<br />. . . . . . . . 137T,<br />. . . . . . . . 144S,<br />. . . . . . . . syn163K (AAa),<br />. . . . . . . . 186P,<br />. . . . . . . . syn251L (CTg),<br />. . . . . . . . syn287G (GGg) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . syn293L (CTt),<br />. . . . . . . . 298V,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanOsaka10K346_2011_02_07 (<br />. . . . . . . . GISAID NA EPI340658<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 46T,<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . syn187G (GGt),<br />. . . . . . . . 313R,<br />. . . . . . . . 394I,<br />. . . . . . . . syn430R (CGg),<br />. . . . . . . . 467V)<br /><a href="http://www.blogger.com/" name="EPI340570"></a><br />. . . . <strong><span style="color: #783f04;">JapanHyogo10K291_2011_02_07</span><span style="color: #660000;">_TmX</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340570 <br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . 17G,<br />. . . . . . . . syn34N (AAt) [H1N1 Avian],<br />. . . . . . . . 188T [H1N1 Avian],<br />. . . . . . . . 200T [H1N1 Avian],<br />. . . . . . . . syn296Q [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . <strong><span style="color: #783f04;">JapanHyogo10K291_2011_02_07</span><span style="color: #660000;">_TmX</span></strong> (<br />. . . . . . . . GISAID NA EPI340685<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 47G [H1N1 Avian Farm],<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . syn240T [H1N1 Avian],<br />. . . . . . . . 241I [H1N1 Avian],<br />. . . . . . . . 275Y,<br />. . . . . . . . 369K [H1N1 Avian],<br />. . . . . . . . syn377P (CCa) [H1N1 Avian],<br />. . . . . . . . 415M [H1N1 Avian Farm])<br /><a href="http://www.blogger.com/" name="EPI340579"></a><br />. . . . JapanHokkaido10H054_2011_02_07 (<br />. . . . . . . . Clade 2: 188T<br />. . . . . . . . GISAID HA EPI340579<br />. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . syn174K (AAg),<br />. . . . . . . . syn177L (CTt),<br />. . . . . . . . syn185P (CCg),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 218E,<br />. . . . . . . . 253A,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHokkaido10H054_2011_02_07 (<br />. . . . . . . . GISAID NA EPI340694<br />. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn152R (AGa),<br />. . . . . . . . syn234V (GTg),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn392D (GAc),<br />. . . . . . . . 396T,<br />. . . . . . . . 469N)<br /><a href="http://www.blogger.com/" name="EPI340548"></a><br />. . . . JapanNiigata10F306_2011_02_05 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340548<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn22V (GTc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . 297D,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNiigata10F306_2011_02_05 (<br />. . . . . . . . GISAID NA EPI340663<br />. . . . . . . . 11 Polymorphisms (8 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 58Y,<br />. . . . . . . . 67I,<br />. . . . . . . . 86V,<br />. . . . . . . . syn224L (cTG),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . 371Y,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanOsaka10K340_2011_02_04 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340544<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn239P (CCa),<br />. . . . . . . . syn259A (GCg),<br />. . . . . . . . 264T,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanOsaka10K340_2011_02_04 (<br />. . . . . . . . GISAID NA EPI340659<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 62I,<br />. . . . . . . . 77V,<br />. . . . . . . . 90T,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn366S (AGc),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanHyogo10K283_2011_02_04 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340571<br />. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 205E,<br />. . . . . . . . 276Q,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K283_2011_02_04 (<br />. . . . . . . . GISAID NA EPI340686<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 38F,<br />. . . . . . . . 44S,<br />. . . . . . . . 143N,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn251A (GCt),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanKyoto10K250_2011_02_04 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340562<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanKyoto10K250_2011_02_04 (<br />. . . . . . . . GISAID NA EPI340677<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt),<br />. . . . . . . . 415M)<br /><a href="http://www.blogger.com/" name="EPI340549"></a><br />. . . . JapanNiigata10F257_2011_02_03 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340549<br />. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn50V (GTg),<br />. . . . . . . . 89N,<br />. . . . . . . . syn98F (TTt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn214K (AAa),<br />. . . . . . . . syn293L (CTt),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNiigata10F257_2011_02_03 (<br />. . . . . . . . GISAID NA EPI340664<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 13I,<br />. . . . . . . . 44S,<br />. . . . . . . . syn104N (AAt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 451N)<br /><br />. . . . JapanKyoto10K243_2011_02_02 (<br />. . . . . . . . GISAID HA EPI340563<br />. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)<br />. . . . . . . . syn33V (GTc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . syn96G (GGg),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn205G (GGa),<br />. . . . . . . . syn214K (AAa),<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . 297D,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanKyoto10K243_2011_02_02 (<br />. . . . . . . . GISAID NA EPI340678<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanNiigata10F228_2011_02_01 (<br />. . . . . . . . GISAID HA EPI340550<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . syn162P (CCt),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNiigata10F228_2011_02_01 (<br />. . . . . . . . GISAID NA EPI340665<br />. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)<br />. . . . . . . . syn12S (TCa),<br />. . . . . . . . 44S,<br />. . . . . . . . syn148T (ACt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt))<br /><br />. . . . JapanGunma10G021_2011_02_01 (<br />. . . . . . . . GISAID HA EPI340582<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn211K (AAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanGunma10G021_2011_02_01 (<br />. . . . . . . . GISAID NA EPI340697<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanOsaka10K332_2011_01_31 (<br />. . . . . . . . GISAID HA EPI340545<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanOsaka10K332_2011_01_31 (<br />. . . . . . . . GISAID NA EPI340660<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn382G (GGa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanHyogo10K275_2011_01_31 (<br />. . . . . . . . GISAID HA EPI340572<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 205E,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K275_2011_01_31 (<br />. . . . . . . . GISAID NA EPI340687<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 143N,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 364N,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><a href="http://www.blogger.com/" name="EPI340551"></a><br />. . . . JapanNiigata10F202_2011_01_31 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340551<br />. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn50V (GTg),<br />. . . . . . . . syn98F (TTt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn214K (AAa),<br />. . . . . . . . syn293L (CTt),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNiigata10F202_2011_01_31 (<br />. . . . . . . . GISAID NA EPI340666<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn104N (AAt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn243T (ACa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 451N)<br /><br />. . . . JapanHokkaido10H041_2011_01_31 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340580<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHokkaido10H041_2011_01_31 (<br />. . . . . . . . GISAID NA EPI340695<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 100H,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn252S (TCg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><a href="http://www.blogger.com/" name="EPI340564"></a><br />. . . . <strong><span style="color: #783f04;">JapanKyoto10K124_2011_01_28</span><span style="color: #660000;">_TmX</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340564<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt) [H1N1 Avian],<br />. . . . . . . . syn37E (GAg) [H1N1 Avian Farm],<br />. . . . . . . . 146G [H3N8 Avian],<br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline <br />. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],<br />. . . . . . . . 188T [H1N1 Avian],<br />. . . . . . . . 200T [H1N1 Avian],<br />. . . . . . . . syn259A (GCg) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . <strong><span style="color: #783f04;">JapanKyoto10K124_2011_01_28</span><span style="color: #660000;">_TmX</span></strong> (<br />. . . . . . . . GISAID NA EPI340679<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 43H [H1N1 Avian],<br />. . . . . . . . 44S [H1N1 Avian],<br />. . . . . . . . syn240T [H1N1 Avian],<br />. . . . . . . . 241I [H1N1 Avian],<br />. . . . . . . . 275Y,<br />. . . . . . . . syn366S (AGc) [H1N1 Avian],<br />. . . . . . . . 369K [H1N1 Avian],<br />. . . . . . . . syn377P (CCa) [H1N1 Avian],<br />. . . . . . . . 381A)<br /><a href="http://www.blogger.com/" name="EPI340552"></a><br />. . . . JapanNiigata10F117_2011_01_25 (<br />. . . . . . . . Clade3: 186P<br />. . . . . . . . GISAID HA EPI340552<br />. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 137T,<br />. . . . . . . . 144S,<br />. . . . . . . . 146G,<br />. . . . . . . . syn163K (AAa),<br />. . . . . . . . 186P,<br />. . . . . . . . syn251L (CTg),<br />. . . . . . . . syn287G (GGg) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . syn293L (CTt),<br />. . . . . . . . 298V,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNiigata10F117_2011_01_25 (<br />. . . . . . . . GISAID NA EPI340667<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 32V,<br />. . . . . . . . 46T,<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . syn187G (GGt),<br />. . . . . . . . 313R,<br />. . . . . . . . 394I,<br />. . . . . . . . syn430R (CGg),<br />. . . . . . . . 467V)<br /><br />. . . . JapanHyogo10K061_2011_01_25 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340573<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 166N,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 288S,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K061_2011_01_25 (<br />. . . . . . . . GISAID NA EPI340688<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn157T (ACa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanGunma10G013_2011_01_25 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340583<br />. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanGunma10G013_2011_01_25 (<br />. . . . . . . . GISAID NA EPI340698<br />. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 288V,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanOsaka10K323_2011_01_24 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340546<br />. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)<br />. . . . . . . . syn#8V (GTg),<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn130D (GAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn280T (ACc),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanOsaka10K323_2011_01_24 (<br />. . . . . . . . GISAID NA EPI340661<br />. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 127S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn315G (GGg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn382G (GGa),<br />. . . . . . . . 432T,<br />. . . . . . . . syn436I (ATt))<br /><a href="http://www.blogger.com/" name="EPI340574"></a><br />. . . . JapanHyogo10K055_2011_01_24 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340574<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn33V (GTc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 86F,<br />. . . . . . . . syn99I (ATt),<br />. . . . . . . . syn116R (AGa),<br />. . . . . . . . 123A,<br />. . . . . . . . 146G,<br />. . . . . . . . 169V,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K055_2011_01_24 (<br />. . . . . . . . GISAID NA EPI340689<br />. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn139L (cTG),<br />. . . . . . . . syn158L (tTA),<br />. . . . . . . . syn183A (GCc),<br />. . . . . . . . syn195I (ATc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn246P (CCg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanGunma10G004_2011_01_21 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340584<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanGunma10G004_2011_01_21 (<br />. . . . . . . . GISAID NA EPI340699<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanHyogo10K045_2011_01_20 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340575<br />. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn205G (GGa),<br />. . . . . . . . syn214K (AAa),<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . 297D,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K045_2011_01_20 (<br />. . . . . . . . GISAID NA EPI340690<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanKyoto10K025_2011_01_18 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340565<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn#4Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanKyoto10K025_2011_01_18 (<br />. . . . . . . . GISAID NA EPI340680<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanNiigata10F025_2011_01_18 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340553<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . 297D,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNiigata10F025_2011_01_18 (<br />. . . . . . . . GISAID NA EPI340668<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanHyogo10K037_2011_01_17 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340576<br />. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)<br />. . . . . . . . syn33V (GTc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn205G (GGa),<br />. . . . . . . . syn214K (AAa),<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . 297D,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K037_2011_01_17 (<br />. . . . . . . . GISAID NA EPI340691<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M,<br />. . . . . . . . syn460G (GGc))<br /><br />. . . . JapanHokkaido10H031_2011_01_17 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340581<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . #1E,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHokkaido10H031_2011_01_17 (<br />. . . . . . . . GISAID NA EPI340696<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn330D (GAc),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanNiigata10F012_2011_01_17 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340554<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn240G (GGg),<br />. . . . . . . . syn258F (TTt),<br />. . . . . . . . syn299H (CAc),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNiigata10F012_2011_01_17 (<br />. . . . . . . . GISAID NA EPI340669<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn210G (GGa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt))<br /><br />. . . . JapanKyoto10K012_2011_01_15 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340566<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn212K (AAa),<br />. . . . . . . . 289M,<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanKyoto10K012_2011_01_15 (<br />. . . . . . . . GISAID NA EPI340681<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 46V,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn449N (AAt))<br /><br />. . . . JapanHyogo10K029_2011_01_13 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340577<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanHyogo10K029_2011_01_13 (<br />. . . . . . . . GISAID NA EPI340692<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanKyoto10K002_2011_01_12 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340567<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn31H (CAt) [pH1N1 Clade1.Upsilon],<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanKyoto10K002_2011_01_12 (<br />. . . . . . . . GISAID NA EPI340682<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanNagasaki10N010_2011_01_11 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340558<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 143E,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNagasaki10N010_2011_01_11 (<br />. . . . . . . . GISAID NA EPI340673<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn28N (AAt),<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanNagasaki10N005_2011_01_04 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI340559<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn36L (tTA),<br />. . . . . . . . 163M,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 238K,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . HA Truncated after aa329)<br /><br />. . . . JapanNagasaki10N005_2011_01_04 (<br />. . . . . . . . GISAID NA EPI340674<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn28N (AAt),<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-7227345972336127270?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-51478908258891401232011-10-24T22:58:00.012-05:002011-10-25T21:28:38.611-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_HA_142V_FatalityMarker_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br /><span style="color: black;">Last Update</span><br />2011-10-25<br /><br /><strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong> appears on 22 <strong><span style="color: #4c1130;">pH1N1</span></strong> human sequences geographically spanning 5 countries covering 16 cases documented from 2009-07-20 (Italy) to 2011-02-04 (Russia).&nbsp; Researchers produced multiple sequences for 5 cases.&nbsp; These 22 sequences <strong><span style="color: #783f04;">delineate</span></strong> on the last day of 2010 from low polymorphic count genetics onto <strong><span style="color: #783f04;">highly polymorphic Clade2: 188T</span></strong> backgrounds.&nbsp; The 9 most current <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong> sequences share 6 HA revisions and 5 NA revisions demonstrating <strong><span style="color: #783f04;">capable transmission</span></strong>. <br /><br />At a minimum, 7 of those sequences represent <strong><span style="color: #660000;">fatalities</span></strong>.&nbsp; These fatality sequences were generated from 2 independent labs.&nbsp; The subjects were <strong><span style="color: #783f04;">geographically dispersed</span></strong> (Nizhnii Novgorod and Vladimir: &gt;100 miles distant).&nbsp; Non-fatality sequences (2) with <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong> on similar Clade2 backgrounds are on file in a similar region of the world (Tula, Russia and Slovenia).&nbsp; Of 9 Clade2 sequences with <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong>, 7 are noted as <strong><span style="color: #660000;">fatal</span></strong> (<strong><span style="color: #660000;">78% Case Fatality Rate</span></strong>).&nbsp; 5 of those 9 Clade2 sequences carry <strong><span style="color: #783f04;">Receptor Binding Site</span></strong> revisions between <strong><span style="color: #274e13;">HA</span></strong> aa225 and aa230, including <strong><span style="color: blue;">225G, 225N</span></strong> and <strong><span style="color: blue;">230I</span></strong>.&nbsp; Although the amino-level <strong><span style="color: #783f04;">Ultimate Origin</span></strong> investigation for Valine at aa142 continues, many H5N1 sequences demonstrate the <strong><span style="color: #783f04;">2nd Base Codon</span></strong> donation potential (atg, ctt, ctg, ttg) to create the <strong><span style="color: #4c1130;">pH1N1</span></strong> <strong><span style="color: blue;">142V (GtT).</span></strong><br /><br />An examination of the Neuraminidase segments provides additional sectioning to the fatalities.&nbsp; The NA segments are <strong><span style="color: #783f04;">hyper-morphic and zoonotic</span></strong>.&nbsp; Each Clade2 fatality with <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong> carries <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">syn204A</span></strong>. The 2 Clade2 <strong><span style="color: #783f04;">non-fatality</span></strong> <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong>-bearing sequences do <strong>not</strong> demonstrate the <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">syn204A</span></strong>.&nbsp; All <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">syn204A (GCa)</span></strong> <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences (7) are in <strong><span style="color: #783f04;">cross-segment combination</span></strong> with <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong> on a very <strong><span style="color: #783f04;">common Clade2: 188T</span></strong> background.&nbsp; <br /><br /><strong><span style="color: #783f04;">Potential animal</span></strong> progenitors are found on 18 sequences in Avian and Mink hosts across several serotypes (<strong>H4N4, H5N4, H7N1, H8N4, H10N4</strong>).&nbsp; The databases do not yet appear to demonstrate <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">syn204A (GCa)</span></strong> on an Avian H1N1 sequence.&nbsp; Future Avian H1N1 deposits may very well demonstrate that this value has crossed to human <strong><span style="color: #4c1130;">pH1N1</span></strong> via an <strong><span style="color: #783f04;">Avian H1N1 bridge</span></strong> (intermediate) from one of the noted H4N4, H5N4, H7N1, H8N4 or H10N4 serotypes.<br /><br /><strong><span style="color: #660000;">7 human fatalities on 7 cases</span></strong> across 2 cities and 2 labs each bearing the rare <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong> and the rarer <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">syn204A</span></strong> merit attention as a potential “<strong><span style="color: #783f04;">flashfire</span></strong>” candidate due to the <strong><span style="color: #660000;">100% Case Fatality Rate</span></strong> (CFR) of this transmissible combination found on the <strong><span style="color: #783f04;">most dominant</span></strong> pH1N1 Clade.&nbsp; Furthermore, this group of sequences demonstrates a <strong><span style="color: #783f04;">superset of revisions</span></strong> (HA and NA) with <strong><span style="color: #660000;">significant homology to the Avian</span></strong> H1N1 pool.&nbsp; Each <strong><span style="color: #4c1130;">pH1N1</span></strong> <strong><span style="color: #783f04;">chimera strain</span></strong> that is in mid-stride between host species, that is “<strong><span style="color: #783f04;">confused</span></strong>”, holds the potential for <strong><span style="color: #783f04;">variant</span></strong> clinical symptoms and outcomes. &nbsp; Early detection of "<strong><span style="color: #783f04;">flashfire</span></strong>" strains (High CFR) via increased surveillance is essential to public health planning.<br /><br /><span style="font-size: x-large;">Case Fatality Rates for HA 142V</span><br /><br />44% CFR Overall (7 of 16)<br />78% CFR on Clade2 (2010-12-31 to 2011-02-14) (7 of 9)<br />78% CFR in Northern Hemisphere from 2010-12-31 to 2011-02-14 (7 of 9)<br /><strong>100% CFR with NA syn204A (7 of 7)</strong><br /><br /><span style="font-size: x-large;">Hemagglutinin Statistics for HA 142V</span><br /><br />Total HA: 123 Polymorphisms (2 to 14) on 22 HA Segments <br />. . . . . . . . with 30 Distinct Values<br />. . . . . . . . Averaging <strong><span style="color: #783f04;">~5.6 Polymorphisms per HA Segment</span></strong><br /><br />Total HA Clade2: 88 Polymorphisms (8 to 14) on 9 Segments<br />. . . . . . . . . . . . with 24 Distinct Values<br />. . . . . . . . . . . . Averaging<strong><span style="color: #783f04;"> ~9.8 Polymorphisms</span></strong> per Clade2 HA Segment<br /><br /><strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong> is not found as a singleton polymorphism, even on short fragments. 100% of <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">142V</span></strong>-bearing <strong><span style="color: #4c1130;">pH1N1</span></strong> human sequences (22) also carry either <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">188T</span></strong> (9), <strong><span style="color: blue;">syn194L</span></strong> (12) or <strong><span style="color: blue;">225E</span></strong> (1, <strong><span style="color: #783f04;">Origin pH1N1</span></strong>). <br /><br /><span style="font-size: x-large;">Neuraminidase Statistics for HA 142V</span><br /><br />Total NA: 94 Polymorphisms (1 to 12) on 20 Segments<br />. . . . . . . . with 20 Distinct Values <br />. . . . . . . . Averaging <strong><span style="color: #783f04;">~4.7 Polymorphisms per HA Segment</span></strong><br /><br />Total NA Clade2: 81 Polymorphisms (7 to 12) on 9 Segments <br />. . . . . . . . . . . . with 19 Distinct Values<br />. . . . . . . . . . . . Averaging <strong><span style="color: #783f04;">~9.0 Polymorphisms per Clade2 NA Segment</span></strong><br /><br />100% of the available related <strong><span style="color: #274e13;">NA</span></strong> segments (20) carries <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">syn416D</span></strong>.<br /><br /><span style="font-size: x-large;">Clade2 Shared Polymorphisms</span><br /><br /><strong><span style="color: #274e13;">HA</span></strong> Background: <strong><span style="color: blue;">100N, 142V, 188T, syn338G, 377K, 454N</span></strong> (6 common)<br /><strong><span style="color: #274e13;">NA</span></strong> Background: [<strong><span style="color: blue;">76S</span></strong> (8), <strong><span style="color: blue;">77E</span></strong> (1)], <strong><span style="color: blue;">syn240T, 241I, 369K, syn377P, syn416D</span></strong> (5 common)<br /><br /><span style="font-size: x-large;">Sequences</span><br /><br />. . . . RussiaTulaCRIE_KEE_2011_02_04 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI335282<br />. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn154L (CTg) [Rare to pH1N1 Human (3 Total: 2 on Clade2)]<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with #1T, syn202V <br />. . . . . . . . . . . . . . . . . . . . . . . . &amp; extensive pH1N1υ polymorphisms],<br />. . . . . . . . . . . . . . . . . . [H1N1 swine],<br />. . . . . . . . . . . . . . . . . . [H7N7 Avian and Human (tcg)],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian 2009 &amp; Human 2009<br />. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms],<br />. . . . . . . . . . . . . . . . . . [S9, M9, S7],<br />. . . . . . . . . . . . . . . . . . [WSN1933, WSZ1933], <br />. . . . . . . . . . . . . . . . . . [1918],<br />. . . . . . . . 188T,<br />. . . . . . . . syn202V (GTc) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . . . . . . . . . . . [H6N1 Avian],<br />. . . . . . . . . . . . . . . . . . [S9],<br />. . . . . . . . . . . . . . . . . . [H1N1 Human 1943, 1946, 1951],<br />. . . . . . . . . . . . . . . . . . [WSN1933, WSZ1933], <br />. . . . . . . . . . . . . . . . . . [1918],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaTulaCRIE_KEE_2011_02_04 (<br />. . . . . . . . GISAID NA EPI335288<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaVladimirIIV35_T_27M_2011_01_31<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI324794<br />. . . . . . . . 14 Polymorphisms (10 Amino and 4 Silent)<br />. . . . . . . . 1T [42 pH1N1, <br />. . . . . . . . . . . . . only 9 from 2010-2011 Season (NH)],<br />. . . . . . . . . . [H1N1 Avian Farm<br />. . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . . . [H6N1 Avian (agc)]<br />. . . . . . . . . . [H7N7 Avian &amp; Human Fatality],<br />. . . . . . . . . . [H9N2 Avian &amp; Human (agc, agt, atc)],<br />. . . . . . . . . . [Netherlands2457b_2009_11_07_xL <br />. . . . . . . . . . . . . . . . . . with 225N,<br />. . . . . . . . . . IndiaHyderabad51_2009_05 <br />. . . . . . . . . . . . . . . . . . with syn144A],<br />. . . . . . . . . . [H1N1 swine],<br />. . . . . . . . . . [S9, M9, S7],<br />. . . . . . . . . . [1976],<br />. . . . . . . . . . [WSN1933, WSZ1933], <br />. . . . . . . . . . [1918],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . 157Q mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . <strong><span style="color: blue;">225G mix wt,</span></strong><br />. . . . . . . . <strong><span style="color: blue;">225N mix wt,</span></strong><br />. . . . . . . . <strong><span style="color: blue;">225S mix wt,</span></strong><br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn515Q (CAa) [H5N1 Avian &amp; Human wt],<br />. . . . . . . . syn527L (TTa) [H5N1 Avian])<br /><br />. . . . RussiaVladimirIIV35_T_27M_2011_01_31<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI324795<br />. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn291V (GTa) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_BLM_L_2011_01_26<strong><span style="color: #660000;">_TmX_f</span></strong> (<br />. . . . . . . . Clade2: 188T with 230I<br />. . . . . . . . GISAID HA EPI339320<br />. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)<br />. . . . . . . . <strong><span style="color: blue;">77N</span></strong> [Recently Novel to Clade1.Upsilon],<br />. . . . . . . . . . . . [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 124N, 233H, 275A],<br />. . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . with syn42G, 159T, <br />. . . . . . . . . . . . . . . . . . . . 188T, 189T, syn346G, 453K],<br />. . . . . . . . . . . . [Rare to H1N1 US Swine with 124N (6)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong> [H5N1 Avian (atg, ctg)],<br />. . . . . . . . 188T,<br />. . . . . . . . <strong><span style="color: blue;">230I (ATt)</span></strong> [H9N2 Avian &amp; Human wt],<br />. . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt) [H2 2009], <br />. . . . . . . . . . . . . . . . . . [H3N8 Canine 2007, Equine 2009, Swine],<br />. . . . . . . . . . . . . . . . . . [H5N1 wt],<br />. . . . . . . . . . . . . . . . . . [H5N2 Avian],<br />. . . . . . . . . . . . . . . . . . [H9N2 2009], <br />. . . . . . . . . . . . . . . . . . [H1N1 Avian 2010],<br />. . . . . . . . . . . . . . . . . . [H1N1 swine 2010],<br />. . . . . . . . syn542S (TCc) [H2, H5, H9N2],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms])<br /><br />. . . . RussiaNizhniiNovgorodCRIE_BLM_L_2011_01_26<strong><span style="color: #660000;">_TmX_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339322<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . syn111K (AAa) [H1N1 Avian Farm],<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc) [H1N1 Avian Farm],<br />. . . . . . . . 241I [H1N1 Avian Farm],<br />. . . . . . . . <strong><span style="color: blue;">275Y mix wt,</span></strong><br />. . . . . . . . 369K [H1N1 Avian <br />. . . . . . . . . . . . . . . . with syn111K, syn240T, 241I],<br />. . . . . . . . syn377P (CCa) [H5N1 Avian], <br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with 241I],<br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . exclusive of syn240T (ACc)],<br />. . . . . . . . syn416D (GAc) [H5N1 Avian Emergent 2011],<br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with syn51Q, syn240T, 241I],<br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with syn111K, syn377P])<br /><br />. . . . RussiaNizhniiNovgorodCRIE_LAV_L_2011_01_24<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI335268<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . 188T,<br />. . . . . . . . <strong><span style="color: blue;">225G,</span></strong><br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_LAV_L_2011_01_24<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI335295<br />. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_OAV_L_2011_01_24<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI335280<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_OAV_L_2011_01_24<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI335294<br />. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_UBA_L_2011_01_23<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI335274<br />. . . . . . . . 12 Polymorphisms (9 Amino and 3 Silent)<br />. . . . . . . . 50I,<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . 188T,<br />. . . . . . . . <strong><span style="color: blue;">225G mix wt,</span></strong><br />. . . . . . . . <strong><span style="color: blue;">225N mix wt,</span></strong><br />. . . . . . . . <strong><span style="color: blue;">225S mix wt,</span></strong><br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_UBA_L_2011_01_23<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI335301<br />. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 149F,<br />. . . . . . . . syn152R (AGa) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn291V (GTa) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 305A,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . Slovenia414_75F_2011_01_19 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI331063<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn467C (TGt) mix wt [H1N1 Avian Farm])<br /><br />. . . . Slovenia414_75F_2011_01_19 (<br />. . . . . . . . GISAID NA EPI331064<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 77E [H1N1 Avian],<br />. . . . . . . . syn162P (CCc) [H1N1 Avian],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 242I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_PAV_L_2011_01_10<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339341<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_PAV_L_2011_01_10<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339342<br />. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 115L,<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 322L [H1N1 Avian with syn240T, 241I],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_NGV_L_2010_12_31<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339312<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_NGV_L_2010_12_31<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339314<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 115L,<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . Moldova93_CS_2010_01_05 (<br />. . . . . . . . GISAID HA EPI278150<br />. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . 324I (aTC) [H1N1 Avian],<br />. . . . . . . . . . . . . . [H3N2 Avian with 159S],<br />. . . . . . . . . . . . . . [H3N2 Canine with syn287G],<br />. . . . . . . . . . . . . . [H3N8 Avian Emergent],<br />. . . . . . . . . . . . . . [H6 Avian], <br />. . . . . . . . . . . . . . [S8],<br />. . . . . . . . HA Truncated after aa396)<br /><br />. . . . Moldova93_CS_2010_01_05 (<br />. . . . . . . . GISAID NA EPI278149<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanTaraz01_2009_12 (<br />. . . . . . . . GISAID HA EPI235349<br />. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)<br />. . . . . . . . 4Y,<br />. . . . . . . . syn111V (GTa) [H1N1 Avian],<br />. . . . . . . . . . . . . . . . [H9N2 Human (Gca)],<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . <strong><span style="color: blue;">225G</span></strong>,<br />. . . . . . . . 324I (aTC) [H1N1 Avian],<br />. . . . . . . . . . . . . . [H3N2 Avian with 159S],<br />. . . . . . . . . . . . . . [H3N2 Canine with syn287G],<br />. . . . . . . . . . . . . . [H3N8 Avian Emergent],<br />. . . . . . . . . . . . . . [H6 Avian], <br />. . . . . . . . . . . . . . [S8])<br /><br />. . . . KazakhstanAlmaty373_9M_2009_11_28 (<br />. . . . . . . . GISAID HA EPI277103<br />. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty373M_9M_2009_11_28 (<br />. . . . . . . . GISAID NA EPI277104<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . NA Truncated before aa193,<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty373CX_9M_2009_11_28 (<br />. . . . . . . . GISAID HA EPI271067<br />. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty373CX_9M_2009_11_28 (<br />. . . . . . . . GISAID NA EPI271068<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . NA Truncated before aa193,<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty352M_9M_2009_11_23 (<br />. . . . . . . . GISAID HA EPI277101<br />. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty352M_9M_2009_11_23 (<br />. . . . . . . . GISAID NA EPI277102<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . NA Truncated before aa184,<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty352CX_9M_2009_11_23 (<br />. . . . . . . . GISAID HA EPI271065<br />. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty352CX_9M_2009_11_23 (<br />. . . . . . . . GISAID NA EPI271066<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . NA Truncated before aa184,<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty347M_18M_2009_11_19 (<br />. . . . . . . . GISAID HA EPI277098<br />. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)<br />. . . . . . . . 124I [H1N1 Avian],<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty347M_18M_2009_11_19 (<br />. . . . . . . . GISAID NA EPI277099<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . NA Truncated before aa184,<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty347_NP_18M_2009_11_19 (<br />. . . . . . . . GISAID HA EPI277097<br />. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)<br />. . . . . . . . 124I [H1N1 Avian],<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty347_NP_18M_2009_11_19 (<br />. . . . . . . . GISAID NA EPI277100<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . NA Truncated before aa184,<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty347CX_18M_2009_11_19 (<br />. . . . . . . . GISAID HA EPI271063<br />. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)<br />. . . . . . . . 124I [H1N1 Avian],<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty347CX_18M_2009_11_19 (<br />. . . . . . . . GISAID NA EPI271064<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . NA Truncated before aa184,<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty347_18M_2009_11_19 (<br />. . . . . . . . GISAID HA EPI271061<br />. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)<br />. . . . . . . . 124I [H1N1 Avian],<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty347_18M_2009_11_19 (<br />. . . . . . . . GISAID NA EPI271062<br />. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)<br />. . . . . . . . NA Truncated before aa184,<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty330_NP_4M_2009_11_17 (<br />. . . . . . . . GISAID HA EPI277095<br />. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty330_NP_4M_2009_11_17 (<br />. . . . . . . . GISAID NA EPI277096<br />. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)<br />. . . . . . . . NA Truncated before aa186,<br />. . . . . . . . syn259E (GAg)[H1N1 Avian],<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . KazakhstanAlmaty330_4M_2009_11_17 (<br />. . . . . . . . GISAID HA EPI271059<br />. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)<br />. . . . . . . . <strong><span style="color: blue;">142V,</span></strong><br />. . . . . . . . syn194L (CTt) [H1N1 Avian],<br />. . . . . . . . HA Truncated after aa293)<br /><br />. . . . KazakhstanAlmaty330_4M_2009_11_17 (<br />. . . . . . . . GISAID NA EPI271060<br />. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)<br />. . . . . . . . NA Truncated before aa186,<br />. . . . . . . . syn259E (GAg) [H1N1 Avian],<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . ItalyPavia15_2009_07_20 (<br />. . . . . . . . GISAID HA EPI240761<br />. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)<br />. . . . . . . . HA Truncated before aa83,<br />. . . . . . . . <strong><span style="color: blue;">142V</span></strong>,<br />. . . . . . . . 225E,<br />. . . . . . . . HA Truncated after aa338)<br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-5147890825889140123?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-60376257948819202302011-10-24T22:51:00.014-05:002011-10-25T01:51:07.276-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_10_19_Russia_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br />Last Update<br />2011-10-25<br /><br />On 2011-10-17, the <strong><span style="color: #783f04;">Central Research Institute for Epidemiology</span></strong> under the <strong><span style="color: #783f04;">Federal Budget Institute of Science (Moscow, Russia)</span></strong> released a series of human <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences at <strong>GenBank and GISAID</strong> with no specified subject age or gender.&nbsp; The samples cover <strong><span style="color: #783f04;">7 distinct geographic</span></strong> areas spanning 2010-12-31 to 2011-03-14 with the largest group in January 2010 and demonstrate <strong><span style="color: #783f04;">avian influence</span></strong>. <br /><br /><strong><span style="color: #274e13;">HA</span></strong> 253 Total Polymorphisms Averaging <strong><span style="color: #783f04;">~11.0 per Segment</span></strong><br /><strong><span style="color: #274e13;">NA</span></strong> 142 Total Polymorphisms Averaging <strong><span style="color: #783f04;">~6.2 per Segment</span></strong><br /><br /><strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> Total 395 Polymorphisms Averaging <strong><span style="color: #783f04;">~17.2 per Sequence</span></strong><br /><br />Of the 23 sequences, <strong><span style="color: #783f04;">Clade2: 188T</span></strong> is predominant with 20 enlistments.&nbsp; <strong><span style="color: #783f04;">Clade4: 128D</span></strong> and <strong><span style="color: #783f04;">Clade5: 208K_219V</span></strong> are respectively represented with 1 and 2 entries.&nbsp; 5 sequences carry polymorphisms at the critical <strong><span style="color: #783f04;">Receptor Binding Site</span></strong> aa225, including the fatality markers of <strong><span style="color: blue;">225G</span></strong> and <strong><span style="color: blue;">225N</span></strong>.&nbsp; 9 of the sequences (all Moscow Oblast) carry <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">73F</span></strong>, an Asian marker that is&nbsp;rare to European&nbsp;<strong><span style="color: #4c1130;">pH1N1</span></strong> and domains near the <strong><span style="color: #660000;">emergent</span></strong> <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">77N</span></strong>.&nbsp; 10 sequences from the Russian deposit are <strong><span style="color: #660000;">fatalities</span></strong>, isolated from “<strong><span style="color: #660000;">lung autopsy tissue</span></strong>”.&nbsp;&nbsp; The fatalities sequence primarily onto <strong><span style="color: #783f04;">Clade2: 188T</span></strong> (9 sequences) with 1 fatality falling&nbsp;on <strong><span style="color: #783f04;">Clade4: 128D</span></strong>.&nbsp; <strong><span style="color: #783f04;">TamiFlu Resistance</span></strong> is genetically indicated with <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">275Y</span></strong> on 2 sequences, both <strong><span style="color: #783f04;">Clade2: 188T</span></strong> <strong><span style="color: #660000;">fatalities</span></strong>.<br /><br />One <strong><span style="color: #660000;">fatal </span></strong>sequence, <strong><span style="color: #783f04;">RussiaNizhniiNovgorodCRIE_BLM_L_2011_01_26</span><span style="color: #660000;">_TmX_f</span></strong>, carries the <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">230I</span></strong> paired with an emergent <strong><span style="color: blue;">77N</span></strong>, similar to the previous regional <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">230I</span></strong>-bearing sequence, <strong><span style="color: #783f04;">RussiaBelgorod2_2010_03_15</span></strong>.&nbsp; The Nizhnii Novgorod <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">230I (ATt)</span></strong> becomes the <strong><span style="color: #783f04;">second coding</span></strong> of Isoleucine at aa230 on a <strong><span style="color: #783f04;">Clade2: 188T</span></strong> background after <strong><span style="color: #783f04;">SwedenHalmstad1_23F_2010_12_21</span></strong> coded as <strong><span style="color: blue;">ATa</span></strong>.&nbsp; The <strong><span style="color: #660000;">TamiFlu Resistant</span></strong> Nizhnii Novgorod sequence is <strong><span style="color: #783f04;">hypermorphic</span></strong> with 10 revisions each on the <strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> gene segments for a total of <strong><span style="color: #783f04;">20 revisions</span></strong>.&nbsp; The <strong><span style="color: #783f04;">Clade2</span></strong> underpinning is <strong><span style="color: #783f04;">commonly circulating</span></strong>, but has 3 <strong><span style="color: #660000;">uncommon</span></strong> additions: <strong><span style="color: blue;">77N, 142V</span></strong> and <strong><span style="color: blue;">230I</span></strong>. <br /><br />. . . . RussiaStPeterCRIE_GoVM_L_2011_03_14<strong><span style="color: #660000;">_TmX_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339343<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . <strong><span style="color: blue;">225G,</span></strong><br />. . . . . . . . 286N,<br />. . . . . . . . syn332L (tTA),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaStPeterCRIE_GoVM_L_2011_03_14<strong><span style="color: #660000;">_TmX_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339344<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . 11S,<br />. . . . . . . . syn86A (GCt),<br />. . . . . . . . 222K,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaJoshkarOlaCRIE_BLP_L_2011_02_22<span style="color: #660000;"><strong>_f</strong></span> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339328<br />. . . . . . . . 16 Polymorphisms (8 Amino and 8 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn118E (GAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . <strong><span style="color: blue;">225G mix wt,</span></strong><br />. . . . . . . . <strong><span style="color: blue;">225N mix wt,</span></strong><br />. . . . . . . . <strong><span style="color: blue;">225S mix wt,</span></strong><br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . syn358N (AAc) [H1N1 Avian],<br />. . . . . . . . 377K,<br />. . . . . . . . syn418F (TTt),<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaJoshkarOlaCRIE_BLP_L_2011_02_22<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339330<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn140L (tTA) mix wt,<br />. . . . . . . . syn206L (cTA) [H1N1 Avian Farm],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . RussiaTulaCRIE_STA_2011_02_11 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339347<br />. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)<br />. . . . . . . . syn15S (TCg),<br />. . . . . . . . syn39K (AAa),<br />. . . . . . . . syn69E (GAa),<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 442V mix wt,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaTulaCRIE_STA_2011_02_11 (<br />. . . . . . . . GISAID NA EPI339348<br />. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)<br />. . . . . . . . syn18G (GGg),<br />. . . . . . . . syn177V (GTa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 386S,<br />. . . . . . . . syn410P (CCt),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaTulaCRIE_GSYu_2011_02_08 (<br />. . . . . . . . Clade5: 208K_219V<br />. . . . . . . . GISAID HA EPI339349<br />. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)<br />. . . . . . . . syn36L (tTA),<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . syn161Y (TAt),<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . 252L,<br />. . . . . . . . 359G,<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaTulaCRIE_GSYu_2011_02_08 (<br />. . . . . . . . GISAID NA EPI339350<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn18G (GGg),<br />. . . . . . . . syn138A (GCt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . RussiaVolgogradCRIE_DMV_L_2011_02_05<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade4: 128D<br />. . . . . . . . GISAID HA EPI339336<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn60I (ATc) [H9N2 Human and Avian Emergent],<br />. . . . . . . . . . . . . . . . [1918],<br />. . . . . . . . <strong><span style="color: blue;">128D</span></strong>,<br />. . . . . . . . <strong><span style="color: blue;">225G</span></strong>,<br />. . . . . . . . 377K,<br />. . . . . . . . syn392Q (CAa) [H1N1 Avian wt],<br />. . . . . . . . syn469E (GAg) [pH1N1 Upsilon <br />. . . . . . . . . . . . . . . . . . . . . Estonia55236_30M_2011_03_02<br />. . . . . . . . . . . . . . . . . . . . . . . . with 42W, syn87S and 397G,<br />. . . . . . . . . . . . . . . . . . . . . Denmark111_2010_12_07<br />. . . . . . . . . . . . . . . . . . . . . . . . with syn87S and 397G]<br />. . . . . . . . . . . . . . . . . . [pH1N1 Australia VxX with 128D],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Azerbaijan Human 2006],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Feline with syn40H, syn55L],<br />. . . . . . . . . . . . . . . . . . [H5N2 Avian],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian wt],<br />. . . . . . . . . . . . . . . . . . [H9N2 Human with 39E, syn40H, syn42G],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian tn],<br />. . . . . . . . . . . . . . . . . . [H1N1 Swine],<br />. . . . . . . . . . . . . . . . . . [1918],<br />. . . . . . . . . . . . . . . . . . [H1N2 Swine],<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaVolgogradCRIE_DMV_L_2011_02_05<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339338<br />. . . . . . . . 8 Polymorphisms (6 Amino and 2 Silent)<br />. . . . . . . . 78H,<br />. . . . . . . . 249E,<br />. . . . . . . . 264I,<br />. . . . . . . . syn327R (CGt),<br />. . . . . . . . syn339S (TCa),<br />. . . . . . . . 359V,<br />. . . . . . . . 397K,<br />. . . . . . . . 442I)<br /><br />. . . . RussiaTulaCRIE_SYuP_2011_02_04 (<br />. . . . . . . . Clade5: 208K_219V<br />. . . . . . . . GISAID HA EPI339351<br />. . . . . . . . 15 Polymorphisms (7 Amino and 8 Silent)<br />. . . . . . . . syn36L (tTA),<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . syn161Y (TAt),<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . 252L,<br />. . . . . . . . 359G,<br />. . . . . . . . 377K,<br />. . . . . . . . 397D mix wt,<br />. . . . . . . . syn446K (AAa),<br />. . . . . . . . syn533L (tTG) mix wt,<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaTulaCRIE_SYuP_2011_02_04 (<br />. . . . . . . . GISAID NA EPI339352<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn18G (GGg),<br />. . . . . . . . syn138A (GCt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . RussiaArchangelskCRIE_PE_2011_02_01 (<br />. . . . . . . . Clade2: 188T with H5N1 Homology<br />. . . . . . . . GISAID HA EPI339345<br />. . . . . . . . 14 Polymorphisms (5 Amino and 9 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . syn376D (GAt) [H2, H3N8, H4],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine],<br />. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],<br />. . . . . . . . 377K,<br />. . . . . . . . syn379T (ACc) [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine],<br />. . . . . . . . . . . . . . . . . . [H5N1 North America Avian],<br />. . . . . . . . . . . . . . . . . . [H1N1 Europe Avian 2010<br />. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],<br />. . . . . . . . syn425N (AAc) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . . . . with syn376D <br />. . . . . . . . . . . . . . . . . . . . . . . . . . . &amp; extensive pH1N1υ polymorphisms],<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn538F (TTt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaArchangelskCRIE_PE_2011_02_01 (<br />. . . . . . . . GISAID NA EPI339346<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn38I (ATc),<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 264I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . RussiaMoscowOblastCRIE_HDV_2011_01_28 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339355<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_HDV_2011_01_28 (<br />. . . . . . . . GISAID NA EPI339356<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 353H mix wt,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaMoscowOblastCRIE_LNR_2011_01_28 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339371<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_LNR_2011_01_28 (<br />. . . . . . . . GISAID NA EPI339372<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaMoscowOblastCRIE_VFE_2011_01_28 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339373<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_VFE_2011_01_28 (<br />. . . . . . . . GISAID NA EPI339374<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaMoscowOblastCRIE_7_2011_01_27 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339377<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_7_2011_01_27 (<br />. . . . . . . . GISAID NA EPI339378<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaMoscowOblastCRIE_6_2011_01_27 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339375<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_6_2011_01_27 (<br />. . . . . . . . GISAID NA EPI339376<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_BLM_L_2011_01_26<strong><span style="color: #660000;">_TmX_f</span></strong> (<br />. . . . . . . . Clade2: 188T with 142V &amp; 230I<br />. . . . . . . . GISAID HA EPI339320<br />. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)<br />. . . . . . . . <strong><span style="color: blue;">77N</span></strong> [Recently Novel to Clade1.Upsilon],<br />. . . . . . . . . . . . [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 124N, 233H, 275A],<br />. . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . with syn42G, 159T, <br />. . . . . . . . . . . . . . . . . . . . 188T, 189T, syn346G, 453K],<br />. . . . . . . . . . . . [Rare to H1N1 US Swine with 124N (6)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V (GtT)</span></strong> [H5N1 Avian (atg, ctt, ctg, ttg)], <br />. . . . . . . . 188T,<br />. . . . . . . . <strong><span style="color: blue;">230I (ATt)</span></strong> [H9N2 Avian &amp; Human wt],<br />. . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt) [H2 2009], <br />. . . . . . . . . . . . . . . . . . [H3N8 Canine 2007, Equine 2009, Swine],<br />. . . . . . . . . . . . . . . . . . [H5N1 wt],<br />. . . . . . . . . . . . . . . . . . [H5N2 Avian],<br />. . . . . . . . . . . . . . . . . . [H9N2 2009], <br />. . . . . . . . . . . . . . . . . . [H1N1 Avian 2010],<br />. . . . . . . . . . . . . . . . . . [H1N1 swine 2010],<br />. . . . . . . . syn542S (TCc) [H2, H5, H9N2],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms])<br /><br />. . . . RussiaNizhniiNovgorodCRIE_BLM_L_2011_01_26<strong><span style="color: #660000;">_TmX_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339322<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . syn51Q (CAg) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . 76S [H1N1 Avian <br />. . . . . . . . . . . . . . with syn240T, 241I],<br />. . . . . . . . syn111K (AAa) [H1N1 Avian Farm],<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc) [H1N1 Avian Farm],<br />. . . . . . . . 241I [H1N1 Avian Farm],<br />. . . . . . . . 275Y mix wt,<br />. . . . . . . . 369K [H1N1 Avian <br />. . . . . . . . . . . . . . . . with syn111K, syn240T, 241I],<br />. . . . . . . . syn377P (CCa) [H5N1 Avian], <br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with 241I],<br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . exclusive of syn240T (ACc)],<br />. . . . . . . . syn416D (GAc) [H5N1 Avian Emergent 2011],<br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with syn51Q, syn240T, 241I],<br />. . . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with syn111K, syn377P])<br /><br />. . . . RussiaMoscowOblastCRIE_135_2011_01_25 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339365<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_135_2011_01_25 (<br />. . . . . . . . GISAID NA EPI339366<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaMoscowOblastCRIE_134_2011_01_25 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339363<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_134_2011_01_25 (<br />. . . . . . . . GISAID NA EPI339364<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaMoscowOblastCRIE_132_2011_01_25 (<br />. . . . . . . . GISAID HA EPI339369<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_131_2011_01_25 (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339367<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 73F (tTC) [H1N1 Avian (tTa, tTg)],<br />. . . . . . . . . . . . . . . [H9N2 Avian Emergent (tTg)],<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">124N</span></strong> [Emergent on pH1N1 Clade 1 (189T)<br />. . . . . . . . . . . . . . . . with 77N, 233H, 275A],<br />. . . . . . . . . . . [H5N1 Avian, Human and Equine],<br />. . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . with syn42G, 189T, syn346G, 453K],<br />. . . . . . . . . . . [H3N2 Human Emergent],<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaMoscowOblastCRIE_131_2011_01_25 (<br />. . . . . . . . GISAID NA EPI339368<br />. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_KDA_L_2011_01_24<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339353<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . <strong><span style="color: blue;">225N mix wt</span></strong>,<br />. . . . . . . . 280A,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_KDA_L_2011_01_24<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339354<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . 59K,<br />. . . . . . . . syn177V (GTa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_BOU_L_2011_01_21<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339359<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_BOU_L_2011_01_21<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339360<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn177V (GTa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_CEN_L_2011_01_19<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339357<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_CEN_L_2011_01_19<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339358<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn177V (GTa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_PAV_L_2011_01_10<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T with 142V<br />. . . . . . . . GISAID HA EPI339341<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V (GtT)</span></strong> [H5N1 Avian (atg, ctt, ctg, ttg)], <br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_PAV_L_2011_01_10<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339342<br />. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)<br />. . . . . . . . syn51Q (CAg),<br />. . . . . . . . 76S,<br />. . . . . . . . 115L,<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 322L [H1N1 Avian with syn240T, 241I],<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_ZCA_L_2011_01_02<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T<br />. . . . . . . . GISAID HA EPI339361<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . <strong><span style="color: blue;">225N</span></strong>,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N,<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_ZCA_L_2011_01_02<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . GISAID NA EPI339362<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn177V (GTa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_NGV_L_2010_12_31<strong><span style="color: #660000;">_f</span></strong> (<br />. . . . . . . . Clade2: 188T with 142V<br />. . . . . . . . GISAID HA EPI339312<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . <strong><span style="color: blue;">142V (GtT)</span></strong> [H5N1 Avian (atg, ctt, ctg, ttg)], <br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn542S (TCc))<br /><br />. . . . RussiaNizhniiNovgorodCRIE_NGV_L_2010_12_31_f (<br />. . . . . . . . GISAID NA EPI339314<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn51Q (CAg),<br />. . . . . . . . 76S,<br />. . . . . . . . 115L,<br />. . . . . . . . <strong><span style="color: blue;">syn204A (GCa),</span></strong><br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-6037625794881920230?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-30313833259703734922011-10-18T22:35:00.003-05:002011-10-18T22:47:59.852-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_08_30_SPBZ_Avian_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br />Last Update<br />2011-10-18<br /><br />On 2011-08-30,&nbsp;a&nbsp;group of researchers from <strong><span style="color: #783f04;">Instituto Adolfo Lutz Sao Paulo</span></strong> in Brasil, including <strong><span style="color: #783f04;">Santos,C.L.S.; Oliveira,M.I.; Borborema,S.E.T.; Ferreira,J.L.P. and Paiva,T.M.</span></strong>, deposited a large group of early <strong><span style="color: #4c1130;">Pandemic H1N1</span></strong> sequences at <strong>GenBank</strong>&nbsp;and <strong>GISAID</strong>.&nbsp; For this analysis, 7 <strong><span style="color: #274e13;">HA</span></strong> sequences were selected for review due to&nbsp;their <strong><span style="color: #783f04;">high affinity</span></strong> for polymorphisms homologous to <strong><span style="color: #660000;">Avian</span></strong> sequences. <br /><br />The set of <strong><span style="color: #274e13;">HA</span></strong> polymorphisms spans the gene segment.&nbsp; <strong><span style="color: #783f04;">23 distinct</span></strong> values are demonstrated.&nbsp; Of the 35 total&nbsp;<strong><span style="color: #274e13;">HA</span></strong> polymorphisms found across the 7 selected sequences, <strong><span style="color: #660000;">33 trace to Avian Influenza</span></strong> A serotypes (H1N1, <strong><span style="color: #660000;">H3N8, H5N1</span></strong> &amp; <strong><span style="color: #660000;">H9N2</span></strong>).&nbsp; The remaining 2 changes (<strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">225N</span></strong>)&nbsp;are from <strong><span style="color: #783f04;">mixed traces</span></strong> that resulted in <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">225G</span></strong> &amp; <strong><span style="color: blue;">225N</span></strong>.&nbsp; These non-Avian, <strong><span style="color: #783f04;">Receptor Binding Site</span></strong> <strong><span style="color: blue;">225N</span></strong> values are wild-type, <strong><span style="color: #783f04;">Human H3N2</span></strong> homologies.&nbsp; This early, large scale acquisition (<strong><span style="color: #783f04;">94%</span></strong>) of <strong><span style="color: #783f04;">disparate Avian polymorphisms</span></strong> across multiple backgrounds is suggestive that the basic <strong><span style="color: #4c1130;">Pandemic H1N1</span></strong> background is <strong><span style="color: #660000;">related to Avian progenitors</span></strong> or is <strong><span style="color: #783f04;">highly attractant to Avian</span></strong> genetic data upon co-infection.<br /><br />Co-infection is known to produce <strong><span style="color: #783f04;">mixed peaks</span></strong> on sequencing traces.&nbsp; The mixed trace sequences in this selection carry <strong><span style="color: #660000;">H5N1</span></strong> homology.&nbsp; 100% of the polymorphisms on <strong><span style="color: #783f04;">BrasilSaoPaulo64519_2009_08_18</span></strong> are <strong><span style="color: #783f04;">mixed</span></strong>, as are the early changes on <strong><span style="color: #783f04;">BrasilMatoGrossoDoSul64045_2009_08_13</span></strong>.&nbsp; Each sequence carries recognised <strong><span style="color: #783f04;">fatality markers</span></strong>.&nbsp; Evidence supports the probability of <strong><span style="color: #783f04;">H5N1 influence</span></strong> on the human carriers of the mixed trace sequences or on a progenitor animal that <strong><span style="color: #783f04;">subsequently transported the H5N1</span></strong> genetic material into <strong><span style="color: #783f04;">proximity with the human</span></strong> subjects from Brasil.<br /><br />. . . . BrasilSaoPaulo2227_2010_01_13 (<br />. . . . . . . . GISAID HA EPI335469<br />. . . . . . . . 6 Polymorphisms (1 Amino and 5 Silent)<br />. . . . . . . . HA Truncated before aa92,<br />. . . . . . . . syn301I (ATt) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn338G (GGc) [H3N2 Avian, Canine, Feline],<br />. . . . . . . . . . . . . . . . . . [H3N8, H4, H5N1 Avian 2010, H6, sw],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn346G],<br />. . . . . . . . syn346G (GGa) [H3N2 Human &amp; Avian wt],<br />. . . . . . . . . . . . . . . . . . [H3N8],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Preschool 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009], <br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H6N2, H6N4],<br />. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],<br />. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],<br />. . . . . . . . syn366A (GCt) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . 377K [H9N2 Avian and Human],<br />. . . . . . . . syn548C (TGc) [H1N1 Avian wt])<br /><br />. . . . BrasilSaoPaulo91656_2009_10_23 (<br />. . . . . . . . GISAID HA EPI335471<br />. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)<br />. . . . . . . . syn354Y (TAc) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],<br />. . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . syn486T (ACc) [H3N8 Avian])<br /><br />. . . . BrasilSaoPaulo89876_2009_10_19 (<br />. . . . . . . . GISAID HA EPI335473<br />. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)<br />. . . . . . . . syn68P (CCg) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn202V (GTc) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],<br />. . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . syn446K (AAa) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms])<br /><br />. . . . BrasilSaoPaulo83218_2009_09_27 (<br />. . . . . . . . GISAID HA EPI335474<br />. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)<br />. . . . . . . . syn41N (AAt) [H5N1 Egypt Human 2007],<br />. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2008],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn140P (CCc) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn356H (CAc) [H5N1 Human Egypt 2009],<br />. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn375I (ATc) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . syn461K (AAa) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms])<br /><br />. . . . BrasilSaoPaulo64519_2009_08_18 (<br />. . . . . . . . GISAID HA EPI335504<br />. . . . . . . . GenBank HA HQ595254<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 34D mix wt [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . syn53L (TTa) mix wt [H5N1 Human, Avian, Civet],<br />. . . . . . . . . . . . . . . . . . . . . . [H6N1 Avian],<br />. . . . . . . . . . . . . . . . . . . . . .&nbsp;[H2 Avian]<br />. . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . <strong><span style="color: blue;">225G</span></strong> mix wt [pH1N1 Fatality Marker],<br />. . . . . . . . . . . . . . . . . [H5N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [1918],<br />. . . . . . . . <strong><span style="color: blue;">225N</span></strong> mix wt [pH1N1 Fatality Marker],<br />. . . . . . . . syn413K (AAg) mix wt [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . syn419L (CTa) mix wt [H5N1 Human, Equine, Avian],<br />. . . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . 523A mix wt [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . with extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms])<br /><br />. . . . BrasilMatoGrossoDoSul64045_2009_08_13 (<br />. . . . . . . . GISAID HA EPI335505<br />. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)<br />. . . . . . . . 34D mix wt [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . <strong><span style="color: blue;">225G</span></strong> mix wt [pH1N1 Fatality Marker],<br />. . . . . . . . . . . . . . . . . [H5N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [1918],<br />. . . . . . . . <strong><span style="color: blue;">225N</span></strong> mix wt [pH1N1 Fatality Marker],<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian])<br /><br />. . . . BrasilSaoPaulo52142_2009_07_30 (<br />. . . . . . . . GISAID HA EPI335518<br />. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian])<br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-3031383325970373492?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-18659439733184840702011-09-27T23:56:00.002-05:002011-09-27T23:57:57.192-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_09_26_Japan_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br />Last Update<br />2011-09-27<br /><br />On 2011-09-26, the <strong><span style="color: #783f04;">National Institute for Infectious Disease of Japan</span></strong> published 4 <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences at <strong>GISAID</strong>.&nbsp; These sequences were sampled from patients in Japan from January to&nbsp;April 2011 covering the second half of the Northern Hemisphere 2010-2011 season.&nbsp; No gender, age or clinical outcomes are specified.&nbsp; All <strong><span style="color: #274e13;">HA</span></strong> sequences relate to Clade 2 (<strong><span style="color: blue;">188T</span></strong>) and are <strong><span style="color: #274e13;">HA</span></strong> fragments.&nbsp; Two of the four <strong><span style="color: #274e13;">NA</span></strong> segments (50%) demonstrate <strong><span style="color: #660000;">genetic TamiFlu Resistance</span></strong>, one at <strong><span style="color: #274e13;">NA</span></strong> 275 and the latest at <strong><span style="color: #274e13;">NA</span></strong> 247.<br /><br />A pattern is developing among Clade 1 (<strong><span style="color: blue;">189T</span></strong>) and Clade 2 (<strong><span style="color: blue;">188T</span></strong>) of genetic revision in the potential <strong><span style="color: #783f04;">Immune Escape</span></strong> domains of <strong><span style="color: #274e13;">HA</span></strong> aa122 to aa124 and aa163 to aa173. <strong><span style="color: #783f04;">JapanAomori39_2011_04_09</span><span style="color: #660000;">_TmX247</span></strong> demonstrates revision in <strong><span style="color: #783f04;">both areas</span></strong> with the <strong><span style="color: #783f04;">rare</span></strong> <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">122M</span></strong> in a mixture with wild type and a <strong><span style="color: #783f04;">rare</span></strong> <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">166T</span></strong> also in a mixture with wild type. <strong><span style="color: #783f04;">JapanKawasaki122_2011_02_14</span><span style="color: #660000;">_TmX275</span></strong> falls onto a numerically significant Clade 2 (<strong><span style="color: blue;">188T</span></strong>) background and adds the <strong><span style="color: #660000;">Vaccine Escape</span></strong> <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">158E</span></strong> in a mixture with wild type to a <strong><span style="color: #783f04;">novel</span></strong> <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">169N</span></strong>.&nbsp; Three of the four sequences show at least one polymorphism in the <strong><span style="color: #274e13;">HA</span></strong> aa154 to aa169 range totaling four polymorphisms (<strong><span style="color: blue;">154I, 158E, 166T, 169N</span></strong>).<br /><br />The advantage of a larger public database allows surfacing of <strong><span style="color: #783f04;">cross-segment signals</span></strong> related to <strong><span style="color: #660000;">TamiFlu Resistance</span></strong>.&nbsp; <strong><span style="color: #274e13;">HA </span><span style="color: blue;">166T</span></strong> on <strong><span style="color: #783f04;">JapanAomori39_2011_04_09</span><span style="color: #660000;">_TmX247</span></strong> becomes an investigational candidate. &nbsp;Only 7 sequences occur in the <strong>GISAID</strong> database bearing <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">166T</span></strong>.&nbsp; The United States West Coast (statistically significant Asian population) displays 2 of these sequences while Asia claims the remaining 5 of the <strong><span style="color: #783f04;">rare </span><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">166T</span></strong> signals.&nbsp; Japan is represented on 3 of the Asian sequences.&nbsp; <strong><span style="color: #783f04;">100%</span></strong> of those 3 <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">166T</span></strong>-bearing sequences from Japan are <strong><span style="color: #660000;">genetically TamiFlu Resistant</span></strong> via <strong><span style="color: #274e13;">NA</span></strong> <strong><span style="color: blue;">247N</span></strong> or <strong><span style="color: blue;">275Y</span></strong>.&nbsp; Those 3 <strong><span style="color: #274e13;">HA</span></strong> gene segments are <strong><span style="color: #783f04;">genetically distinct</span></strong> as well, demonstrating the ability of <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">166T</span></strong> to manifest across <strong><span style="color: #660000;">TamiFlu Resistant</span></strong> sequences with <strong><span style="color: #783f04;">variant </span><span style="color: #274e13;">HA</span></strong> backgrounds. <br /><br />The 4 Japanese <strong><span style="color: #274e13;">HA</span></strong> fragments in this current deposit carry <strong><span style="color: #783f04;">only 64%</span></strong> of a full <strong><span style="color: #274e13;">HA</span></strong>, yet have generated an average of <strong><span style="color: #783f04;">8.5 polymorphisms</span></strong> (normed to ~13 for a full HA deposit).&nbsp; Data from Clade 2 (<strong><span style="color: blue;">188T</span></strong>) continue to show significant genetic diversity and an ongoing <strong><span style="color: #783f04;">ease of novel</span></strong> genetic acquisition. <br /><br />. . . . JapanAomori39_2011_04_09<strong><span style="color: #660000;">_TmX247</span></strong> (<br />. . . . . . . . GISAID HA EPI336876<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn23L (tTA) mix wt,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . <strong><span style="color: blue;">122M</span></strong> mix wt [<strong><span style="color: #783f04;">Rare to</span></strong> <strong><span style="color: #4c1130;">pH1N1</span></strong>],<br />. . . . . . . . syn131S (TCa),<br />. . . . . . . . 146G,<br />. . . . . . . . <strong><span style="color: blue;">166T</span></strong> mix wt [<strong><span style="color: #783f04;">Rare to</span></strong> <strong><span style="color: #4c1130;">pH1N1</span></strong>],<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanAomori39_2011_04_09<strong><span style="color: #660000;">_TmX247</span></strong> (<br />. . . . . . . . GISAID NA EPI336875<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn140L (CTg),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . <strong><span style="color: blue;">247N</span></strong> mix wt,<br />. . . . . . . . 284N mix wt,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 466I)<br /><br />. . . . JapanKawasaki122_2011_02_14<strong><span style="color: #660000;">_TmX275</span></strong> (<br />. . . . . . . . GISAID HA EPI336870<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . <strong><span style="color: blue;">158E</span></strong> mix wt,<br />. . . . . . . . <strong><span style="color: blue;">169N </span></strong>[<strong><span style="color: #783f04;">Novel to</span></strong> <strong><span style="color: #4c1130;">pH1N1</span></strong>],<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 330K,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanKawasaki122_2011_02_14<strong><span style="color: #660000;">_TmX275</span></strong> (<br />. . . . . . . . GISAID NA EPI336869<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . <strong><span style="color: blue;">275Y</span></strong>,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 465S mix wt)<br /><br />. . . . JapanFukuoka40_2011_02_02 (<br />. . . . . . . . GISAID HA EPI336874<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 143<strong><span style="color: #660000;">STOP</span></strong> mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . syn190D (GAt),<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . 324A,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanFukuoka40_2011_02_02 (<br />. . . . . . . . GISAID NA EPI336873<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . syn28N (AAt),<br />. . . . . . . . 44S,<br />. . . . . . . . 74L mix wt,<br />. . . . . . . . 178S mix wt,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanFukuoka35_2011_01_18 (<br />. . . . . . . . GISAID HA EPI336872<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 72T,<br />. . . . . . . . <strong><span style="color: blue;">154I</span></strong>,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . <strong><span style="color: blue;">218E</span></strong> mix wt,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanFukuoka35_2011_01_18 (<br />. . . . . . . . GISAID NA EPI336871<br />. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)<br />. . . . . . . . syn28N (AAt),<br />. . . . . . . . 44S,<br />. . . . . . . . 94I mix wt,<br />. . . . . . . . 161Y mix wt,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 414E mix wt,<br />. . . . . . . . 415M)<br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-1865943973318484070?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-8155379318516968422011-09-20T20:09:00.005-05:002011-09-20T22:03:04.994-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_07_29_NIMR_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br />Last Update<br />2011-09-20<br /><br />On 2011-07-29, the <strong><span style="color: #783f04;">UK National Institute for Medical Research</span></strong> published 29 <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences at <strong>GISAID</strong>.&nbsp; These sequences were sampled from patients in Scandinavia, Eastern Europe, the Balkans and Hong Kong from January to May 2011 covering the second half of the Northern Hemisphere 2010-2011 season.&nbsp; The <strong><span style="color: #783f04;">Swedish Institute for Infectious Disease Control</span></strong> originated 10 of the samples in this Mill Hill deposit including a <strong><span style="color: #660000;">highly zoonotic</span></strong> and <strong><span style="color: #660000;">potential H5N1 recombinant</span></strong>, <strong><span style="color: #783f04;">Stockholm13_2011_03_28</span></strong>, with no specified gender, age or outcome. <br /><br />Two contiguous <strong><span style="color: #660000;">H5N1 Avian</span></strong> markers, <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">415E</span></strong> and <strong><span style="color: blue;">416N</span></strong>, each <strong><span style="color: #783f04;">novel</span></strong> to the human H1N1 pandemic, appear in this human case.&nbsp; The <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">416N</span></strong> is reported as a <strong><span style="color: #783f04;">mixed peak trace</span></strong>, an output that is commonly interpreted as suggestive of <strong><span style="color: #783f04;">multiple infecting strains</span></strong>.&nbsp;&nbsp;The single <strong><span style="color: #660000;">H5N1</span></strong> potential donor <strong><span style="color: #274e13;">HA</span></strong> segment on file is also unusual in that this <strong><span style="color: #783f04;">Egyptian domestic poultry</span></strong> sequence carries <strong><span style="color: #783f04;">numerous homologies</span></strong> to polymorphisms found on human <strong><span style="color: #4c1130;">pH1N1</span></strong> Clade 1 (<strong><span style="color: blue;">189T</span></strong>) and Clade 2 (<strong><span style="color: blue;">188T</span></strong>) sequences.&nbsp; Several of those <strong><span style="color: #660000;">H5N1</span></strong> to <strong><span style="color: #4c1130;">pH1N1</span></strong> <strong><span style="color: #783f04;">homologies</span></strong> are <strong><span style="color: #783f04;">quite rare</span></strong> to <strong><span style="color: #660000;">H5N1</span></strong>, but are <strong><span style="color: #783f04;">strongly emergent</span></strong> in <strong><span style="color: #4c1130;">pH1N1</span></strong>.<br /><br /><strong><span style="color: #783f04;">Stockholm13_2011_03_28</span></strong> was sampled near the end of the traditional Northern Hemisphere influenza season and, as such, represents one probable <strong><span style="color: #783f04;">foundation for ongoing </span></strong>Clade 2 transmission into the upcoming influenza season (2011-2012).&nbsp; As has been regularly discussed, Clade 2 (<strong><span style="color: blue;">188T</span></strong>) is the most prevalent numerically of the 5 major <strong><span style="color: #4c1130;">pH1N1</span></strong> divisions as reported in the public and private genetic databases.&nbsp; Being roughly par for the course, this Swedish sequence is <strong><span style="color: #783f04;">hypermorphic</span></strong>, carrying <strong><span style="color: #783f04;">14 polymorphisms</span></strong> (9 Amino and 5 Silent).<br /><br />Particular to the matter at hand, Clade 2 sequences have demonstrated a measurable propensity for <strong><span style="color: #783f04;">accepting polymorphisms</span></strong> into <strong><span style="color: #4c1130;">pH1N1</span></strong> and <a href="http://pf11.blogspot.com/2011/06/189t-upsilon-in-czech-republic-ha.html" target="_blank">projecting</a> those changes across <strong><span style="color: #4c1130;">pH1N1</span></strong> (“<strong><span style="color: #783f04;">Clade Jumping</span></strong>” / <strong><span style="color: #783f04;">Clade Transfer</span></strong>).&nbsp; The method and means continue under investigation, whether due to the influence of Avian H1N1 <a href="http://pf11.blogspot.com/2011/06/sweden-signals-rapid-zoonosis-from.html" target="_blank">common ancestry</a> from the primary donors into the major human <strong><span style="color: #4c1130;">pH1N1</span></strong> clades or due to <strong><span style="color: #783f04;">some form</span></strong> of recombination / attractant magnetism occurring <strong><span style="color: #783f04;">between and among</span></strong> the human <strong><span style="color: #4c1130;">pH1N1</span></strong> clades. <br /><br /><strong><span style="color: #783f04;">GeneWurx</span></strong> has tracked development of the <strong><span style="color: #4c1130;">H1N1</span></strong> pandemic from the publicly accepted Contact Zero in early 2009 (and&nbsp;potential prequels) up&nbsp;to the present emergent strains.&nbsp; As with prior <strong><span style="color: #660000;">H5N1</span></strong> investigations, random variation remains far from the field of explanatory options in most cases.&nbsp; <strong><span style="color: #783f04;">Malleability by random mallet </span></strong>has not been shown as an important means of genetic variation in this <strong><span style="color: #4c1130;">H1N1</span></strong> human pandemic. <br /><br />The <strong><span style="color: #783f04;">back-to-back</span></strong> polymorphisms transferring <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">415E</span></strong> and <strong><span style="color: blue;">416N</span></strong> onto the human <strong><span style="color: #4c1130;">pH1N1</span></strong> <strong><span style="color: #783f04;">Stockholm13_2011_03_28</span></strong> sequence are noted in the <strong><span style="color: #660000;">H5N1</span></strong> database.&nbsp; That single <strong><span style="color: #660000;">H5N1</span></strong> sequence is a <strong><span style="color: #660000;">human-adapted, avian case</span></strong> from Egypt.&nbsp; This <strong><span style="color: #783f04;">dual signal</span></strong> transfer demonstrates one very concrete case of <strong><span style="color: #783f04;">cross-species, cross-serotype</span></strong> genetic transfer from an <strong><span style="color: #783f04;">animal to a human</span></strong> serotype.&nbsp; <br /><br /><strong><span style="color: #660000;">H5N1 </span><span style="color: #783f04;">contiguous homology</span></strong> to the <strong><span style="color: #783f04;">dominant clade</span></strong> in the <strong><span style="color: #783f04;">dominant circulating human serotype</span></strong> (<strong><span style="color: #4c1130;">pH1N1</span></strong>) instructs the medical fraternity to the <strong><span style="color: #783f04;">weight of emergent zoonoses</span></strong> and suggests that at least one avian <strong><span style="color: #783f04;">flightpath</span></strong> may be worthy of investigation. <br /><br />. . . . SwedenStockholm13_2011_03_28 (<br />. . . . . . . . PHz = <a href="http://pf11.blogspot.com/2009/08/introduction-to-pf11.html#glossary" target="_blank">87%</a><br />. . . . . . . . PHzAv = <a href="http://pf11.blogspot.com/2009/08/introduction-to-pf11.html#glossary" target="_blank">87%</a><br />. . . . . . . . GISAID HA EPI326240<br />. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)<br />. . . . . . . . syn41N (AAt) [<strong><span style="color: #660000;">H5N1</span></strong> Human Emergent with <strong><span style="color: #660000;">TamiFlu Resistance</span></strong>],<br />. . . . . . . . . . . . . . . . .&nbsp; [<strong><span style="color: #660000;">H5N1</span></strong> Egypt Human 2007], <br />. . . . . . . . . . . . . . . . .&nbsp; [<strong><span style="color: #660000;">H5N1 Avian</span></strong> with <strong><span style="color: blue;">166I</span></strong>],<br />. . . . . . . . 50I [WSN_1933, WSZ_1933], <br />. . . . . . . . . .&nbsp; [1918],<br />. . . . . . . . syn154L (tTA) [H3N2 Avian with <strong><span style="color: blue;">158E</span></strong>],<br />. . . . . . . . . . . . . . . . . . [H3N2 Canine, Feline wt]<br />. . . . . . . . . . . . . . . . . . [H3N2 Human wt (tTg)],<br />. . . . . . . . . . . . . . . . . . [H3N8 Avian (tTg)],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian with 404G],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian (tTg)],<br />. . . . . . . . . . . . . . . . . . [H9N2 Human with syn40H (tTg)],<br />. . . . . . . . <strong><span style="color: blue;">158E</span></strong> <strong><span style="color: #783f04;">mix wt</span></strong> [H3N8, <strong><span style="color: #660000;">H5N1</span></strong>],<br />. . . . . . . . . . . . . . . . . [H3N2 Avian],<br />. . . . . . . . . . . . . . . . . . . . with <strong><span style="color: blue;">165N</span></strong>, 190E, <strong><span style="color: blue;">225G, 230I</span></strong>, 238K<br />. . . . . . . . . . . . . . . . . . . . . . . 253A, 275I, syn346G],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . . . . . with #1T, 8V, syn31H, syn40H, syn42G,<br />. . . . . . . . . . . . . . . . . . . . . . . 72L, syn80S, syn82I, 87N, syn118E,<br />. . . . . . . . . . . . . . . . . . . . . . . 144E, <strong><span style="color: blue;">189T</span></strong>, 193R, 237I,<br />. . . . . . . . . . . . . . . . . . . . . . . syn287G, syn346G, 523A],<br />. . . . . . . . . . . . . . . . . [sw1930],<br />. . . . . . . . 188T [H6N1, H7N7],<br />. . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . <strong><span style="color: blue;">156E</span></strong>, 157E, 163T, <strong><span style="color: blue;">165N</span></strong>, <br />. . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . <strong><span style="color: blue;">225G, 230I</span></strong>, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . with <strong><span style="color: blue;">186P, 189T</span></strong>, <br />. . . . . . . . . . . . . . . . . . . and extensive <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . 259T [H9N2 Avian and Human (att) <br />. . . . . . . . . . . . . . . . with syn40H],<br />. . . . . . . . syn338G (GGc) [H3N2 Avian, Canine, Feline],<br />. . . . . . . . . . . . . . . . . . [H3N8, H4, <strong><span style="color: #660000;">H5N1 Avian 2010</span></strong>, H6, sw],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn346G],<br />. . . . . . . . 377K [H9N2],<br />. . . . . . . . syn388K (AAa) [<a href="http://genewurx.com/data/GeneWurx_US_Diversity_2011_02_02_GIS_v1.jpg" target="_blank">Wisconsin08</a>_30F_2010_08_10<br />. . . . . . . . . . . . . . . . . . . . . with 39R, 137T, <strong><span style="color: blue;">186P</span></strong>, <br />. . . . . . . . . . . . . . . . . . . . . . . . . <strong><span style="color: blue;">225N</span></strong>, syn346G, <strong><span style="color: blue;">syn413K</span></strong>, 444K,<br />. . . . . . . . . . . . . . . . . . Utah20_C2_2_2009_07_25<strong><span style="color: #660000;">_VxX</span></strong><br />. . . . . . . . . . . . . . . . . . . . . with #12E, 0I, <strong><span style="color: blue;">159D</span></strong>, 227G, 296H, 470I],<br />. . . . . . . . . . . . . . . . . . [<strong><span style="color: #660000;">H5N1</span></strong> Avian, Equine, Human wt],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian and Human<br />. . . . . . . . . . . . . . . . . . . . . . with 39E, syn40H, syn42G, 296H],<br />. . . . . . . . . . . . . . . . . . [swIowa44837_1_2009_11_08_xL<br />. . . . . . . . . . . . . . . . . . . . . . with syn41N, 50I, <strong><span style="color: blue;">196H</span></strong>, <br />. . . . . . . . . . . . . . . . . . . . . . . . . <strong><span style="color: blue;">225N, 230I</span></strong>, 238D, <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn346G, <strong><span style="color: blue;">syn413K</span></strong>],<br />. . . . . . . . <strong><span style="color: #660000;">415E</span></strong> [<strong><span style="color: #660000;">H5N1</span></strong> Egypt wt],<br />. . . . . . . . <strong><span style="color: #660000;">416N mix</span></strong> [<strong><span style="color: #660000;">H5N1</span></strong> Avian Egypt<br />. . . . . . . . . . . . . . . . . . . with 100N, <strong><span style="color: #660000;">196H</span></strong>, 415E],<br />. . . . . . . . 416Y mix,<br />. . . . . . . . 454N [H7N3, H7N7, H9N2],<br />. . . . . . . . syn527L (TTa) [BeijingHZ01_2011_01_14 <br />. . . . . . . . . . . . . . . . . . . . . . . . with 188T, 242N],<br />. . . . . . . . . . . . . . . . . . [<strong><span style="color: #660000;">H5N1</span></strong> Egypt wt (cTa)]<br /><br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-815537931851696842?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-34457749897964061452011-09-05T23:50:00.018-05:002011-09-06T18:10:06.085-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_08_25_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br />Last Update<br />2011-09-06<br /><br />On 2011-08-25, the <strong><span style="color: #783f04;">WHO Collaborating Centre for Reference and Research on Influenza</span></strong> published 15 pH1N1 sequences at <strong>GISAID</strong>.&nbsp; These sequences were sampled from patients in Australia from April to July 2011.&nbsp; All are Clade 2 backgrounds (<strong><span style="color: blue;">188T</span></strong>).<br /><br />Although a recent <strong><span style="color: #783f04;">GeneWurx</span></strong> analysis on <a href="http://pf11.blogspot.com/2011/07/romania-demonstrates-zoonotic-potential.html" target="_blank">Romanian sequences</a> discussed a different&nbsp;defining Clade 1&nbsp;marker (<strong><span style="color: blue;">189T</span></strong>)&nbsp;jumping templates onto Clade 2, this Australian&nbsp;pattern <strong><span style="color: #783f04;">maintains&nbsp;polymorphic throw</span></strong> for several generations.&nbsp;This deposit not only surfaces a <strong><span style="color: #783f04;">novel</span></strong> face for Clade 2 (<strong><span style="color: blue;">188T</span></strong>), but is a novelty that conducts <strong><span style="color: #783f04;">reliable transmission</span></strong> though a defining marker downstream of the cleavage site is adopted from <span style="color: #741b47;">Clade 1.Upsilon</span> (<strong><span style="color: blue;">syn346G</span></strong>) in the same domain as the <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">syn338G</span></strong> normally found on Clade 2.&nbsp; <br /><br />The 5 very similar sequences each carry 17 to 20 <strong><span style="color: #274e13;">HA</span></strong> polymorphisms.&nbsp; The superset of polymorphisms from this emergent mixed branch shows known <strong><span style="color: #660000;">Vaccine Escape</span></strong> changes at <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">156E</span></strong> and <strong><span style="color: blue;">158E</span></strong>.&nbsp; <strong><span style="color: #783f04;">Hypermorphic</span></strong> behaviour is a hallmark of <strong><span style="color: #4c1130;">pH1N1</span></strong> as are the <strong><span style="color: #783f04;">Vaccine Breakthrough</span></strong> (<strong><span style="color: #783f04;">AustraliaBrisbane500_32M_2011_06_22_</span><span style="color: #660000;">VxX</span></strong>) and hospitalisation (<strong><span style="color: #783f04;">AustraliaBrisbane190_25M_2011_06_14_s</span></strong>) instances also demonstrated by cases from this novel emergence.<br /><br />These <strong><span style="color: #783f04;">novel and rare</span></strong> <strong><span style="color: #274e13;">HA</span></strong> polymorphisms to the Clade 2 background <strong><span style="color: #783f04;">exhibit homological history</span></strong> at a very significant proportion in the <strong><span style="color: #660000;">H1N1 Avian</span></strong> genetics record, including several farm animal sequences.&nbsp; Those farm animal sequences, in turn, show a strong match rate to <strong><span style="color: #741b47;">Clade 1.Upsilon</span></strong> (<strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong>) <strong><span style="color: #660000;">AND</span></strong> to these Clade 2 Human <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences.&nbsp; The superset of polymorphisms from the related <strong><span style="color: #660000;">Avian H1N1</span></strong> farm animals exhibit strong homology to the superset of <strong><span style="color: #741b47;">Clade 1.Upsilon</span></strong> <strong><span style="color: #274e13;">HA</span></strong> polymorphisms.<br /><br />The <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">syn413K</span></strong> prevalent in fatal and severe cases from the early pandemic has mated with these Australian novelties as a further signal of <strong><span style="color: #660000;">zoonotic avian influence</span></strong> on the most widely reported <strong><span style="color: #4c1130;">pH1N1</span></strong> Clade (Clade 2 – <strong><span style="color: blue;">188T</span></strong>).&nbsp; Cross-clade <strong><span style="color: #783f04;">polymorphism jumping</span></strong> is only just beginning for the Pandemic reservoir of H1N1.&nbsp; Sporadic <strong><span style="color: #274e13;">HA</span></strong> <strong><span style="color: blue;">230I</span></strong> on backgrounds similar to these 5 <strong><span style="color: #660000;">novel</span></strong> items is probable.&nbsp; Interaction between human <strong><span style="color: #4c1130;">pH1N1</span></strong> and <strong><span style="color: #660000;">Avian Influenza strains (farm and wild)</span></strong> carrying both Clade 1 and Clade 2 <strong><span style="color: #783f04;">immune escape markers </span></strong>on <strong><span style="color: #783f04;">single</span></strong> strains will continue to drive human revision using the widely available <strong><span style="color: #783f04;">avian delivery vector</span></strong>.&nbsp; <br /><br />By <strong><span style="color: #783f04;">GeneWurx</span></strong> calculations, <strong><span style="color: #783f04;">clade elasticity</span></strong> <a href="http://pf11.blogspot.com/2011/06/189t-upsilon-in-czech-republic-ha.html" target="_blank">will rise</a> to become a primary method generating the 2011-2012 <strong><span style="color: #4c1130;">pH1N1</span></strong> polymorphism bed.<br /><br /><br />. . . . AustraliaBrisbane190_25M_2011_06_14<strong><span style="color: #660000;">_s</span></strong> (<br />. . . . . . . . GISAID HA EPI333112<br />. . . . . . . . 19 Polymorphisms (7 Amino and 12 Silent)<br />. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H5N1 wt],<br />. . . . . . . . syn33V (GTc) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .&nbsp; with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I &amp; syn346G],<br />. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15 <br />. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,<br />. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f<br />. . . . . . . . . . . . . . . . . . . . . with 225G,<br />. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09 <br />. . . . . . . . . . . . . . . . . . . . . with 225G],<br />. . . . . . . . syn34N (AAt) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],<br />. . . . . . . . syn99I (ATt) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],<br />. . . . . . . . syn115E (GAg) [H1N1 Avian<br />&nbsp;. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;502K, 504G, syn538F],<br />. . . . . . . . 146G [H3N8 Avian],<br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline <br />. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],<br />. . . . . . . . 156E mix wt [H2N3], <br />. . . . . . . . . . . . . . . . . [H3N8],<br />. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010 <br />. . . . . . . . . . . . . . . . . . . . with 188E, 192I, 198S, 210T, 223I],<br />. . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . with #1T, syn31H, syn40H, syn42G,<br />. . . . . . . . . . . . . . . . . . . . . . . 72L, 87N, syn118E, 144K, <br />. . . . . . . . . . . . . . . . . . . . . . . 158E, 158N, 159G,<br />. . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I, <br />. . . . . . . . . . . . . . . . . . . . . . . syn287G, syn346G, <br />. . . . . . . . . . . . . . . . . . . . . . . 453K, 502K],<br />. . . . . . . . . . . . . . . . . [H3N2 Avian <br />. . . . . . . . . . . . . . . . . . . . with 165N, 225G, 230I],<br />. . . . . . . . . . . . . . . . . [H1N1 swIowa44837_1_2009_11_08_xL with 225N, 230I],<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],<br />. . . . . . . . syn346G (GGa) [<strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> defining marker],<br />. . . . . . . . . . . . . . . . . .&nbsp; [H1N1 Avian Farm with syn338G],<br />. . . . . . . . 377K,<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2], <br />. . . . . . . . 454N,<br />. . . . . . . . syn465N,<br />. . . . . . . . syn508L (tTG) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],<br />. . . . . . . . syn513I (ATc) [H1N1 Avian (gTc)<br />. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I &amp; syn346G],<br />. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],<br />. . . . . . . . syn538F (TTt) [H1N1 Avian<br />. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms &amp; syn508L])<br /><br />. . . . AustraliaBrisbane500_32M_2011_06_22<strong><span style="color: #660000;">_VxX</span></strong> (<br />. . . . . . . . GISAID HA EPI333109<br />. . . . . . . . 17 Polymorphisms (7 Amino and 10 Silent)<br />. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H5N1 wt],<br />. . . . . . . . syn33V (GTc) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .&nbsp;with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I &amp; syn346G],<br />. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15 <br />. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,<br />. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f<br />. . . . . . . . . . . . . . . . . . . . . with 225G,<br />. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09 <br />. . . . . . . . . . . . . . . . . . . . . with 225G],<br />. . . . . . . . syn34N (AAt) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],<br />. . . . . . . . 77R (AGa) [H9N2 Avian and Human wt<br />. . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms],<br />. . . . . . . . syn99I (ATt) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],<br />. . . . . . . . syn115E (GAg) [H1N1 Avian<br />&nbsp;. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;502K, 504G, syn538F],<br />. . . . . . . . 146G [H3N8 Avian],<br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline <br />. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],<br />. . . . . . . . 171G (GgT), <br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],<br />. . . . . . . . syn346G (GGa) [<strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> defining marker],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N,<br />. . . . . . . . syn508L (tTG) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],<br />. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E])<br /><br />. . . . SouthAustralia4_2011_06_24 (<br />. . . . . . . . GISAID HA EPI333105<br />. . . . . . . . 18 Polymorphisms (6 Amino and 12 Silent)<br />. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H5N1 wt],<br />. . . . . . . . syn33V (GTc) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .&nbsp;with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I &amp; syn346G],<br />. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15 <br />. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,<br />. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f<br />. . . . . . . . . . . . . . . . . . . . . with 225G,<br />. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09 <br />. . . . . . . . . . . . . . . . . . . . . with 225G],<br />. . . . . . . . syn34N (AAt) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],<br />. . . . . . . . syn99I (ATt) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],<br />. . . . . . . . syn115E (GAg) [H1N1 Avian<br />&nbsp;. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;502K, 504G, syn538F],<br />. . . . . . . . 146G [H3N8 Avian],<br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline <br />. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn300P (CCt) [H5N1, H6N1, H7N3, H7N7],<br />. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],<br />. . . . . . . . syn346G (GGa) [<strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> defining marker],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],<br />. . . . . . . . 377K,<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N,<br />. . . . . . . . syn508L (tTG) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],<br />. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],<br />. . . . . . . . syn538F (TTt) [H1N1 Avian<br />. . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms &amp; syn508L])<br /><br />. . . . AustraliaBrisbane142_2011_04_12 (<br />. . . . . . . . GISAID HA EPI333005<br />. . . . . . . . 18 Polymorphisms (6 Amino and 12 Silent)<br />. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H5N1 wt],<br />. . . . . . . . syn33V (GTc) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .&nbsp;with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I &amp; syn346G],<br />. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15 <br />. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,<br />. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f<br />. . . . . . . . . . . . . . . . . . . . . with 225G,<br />. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09 <br />. . . . . . . . . . . . . . . . . . . . . with 225G],<br />. . . . . . . . syn34N (AAt) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],<br />. . . . . . . . syn77S (AGt),<br />. . . . . . . . syn99I (ATt) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],<br />. . . . . . . . syn115E (GAg) [H1N1 Avian<br />&nbsp;. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;502K, 504G, syn538F],<br />. . . . . . . . 146G [H3N8 Avian],<br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline <br />. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],<br />. . . . . . . . syn346G (GGa) [<strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> defining marker],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],<br />. . . . . . . . 377K,<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N,<br />. . . . . . . . syn508L (tTG) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],<br />. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],<br />. . . . . . . . syn538F (TTt) [H1N1 Avian<br />. . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms &amp; syn508L])<br /><br />. . . . AustraliaBrisbane70_IVR162_2011_07_25 (<br />. . . . . . . . GISAID HA EPI333107<br />. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)<br />. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H5N1 wt],<br />. . . . . . . . syn33V (GTc) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .&nbsp;with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I &amp; syn346G],<br />. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15 <br />. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,<br />. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f<br />. . . . . . . . . . . . . . . . . . . . . with 225G,<br />. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09 <br />. . . . . . . . . . . . . . . . . . . . . with 225G],<br />. . . . . . . . syn34N (AAt) [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],<br />. . . . . . . . syn99I (ATt) [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],<br />. . . . . . . . syn115E (GAg) [H1N1 Avian<br />&nbsp;. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;502K, 504G, syn538F],<br />. . . . . . . . 132T (AcC) [H1N1 Avian],<br />. . . . . . . . 146G [H3N8 Avian],<br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline <br />. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],<br />. . . . . . . . 158E [H3N8, H5N1],<br />. . . . . . . . . . . . [H3N2 Avian],<br />. . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K<br />. . . . . . . . . . . . . . . . . . 253A, 275I, syn346G],<br />. . . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . with #1T, 8V, syn31H, syn40H, syn42G,<br />. . . . . . . . . . . . . . . . . . 72L, syn80S, syn82I, 87N, syn118E,<br />. . . . . . . . . . . . . . . . . . 144E, 189T, 193R, 237I,<br />. . . . . . . . . . . . . . . . . . syn287G, syn346G, 523A],<br />. . . . . . . . . . . . . . . . . [sw1930]<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 226R,<br />. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],<br />. . . . . . . . syn346G (GGa) [<strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> defining marker],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],<br />. . . . . . . . 377K,<br />. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N,<br />. . . . . . . . syn508L (tTG) [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms and <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],<br />. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],<br />. . . . . . . . syn538F (TTt) [H1N1 Avian<br />. . . . . . . . . . . . . . . . . . . . with <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> polymorphisms &amp; syn508L])<br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-3445774989796406145?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-73804098430293872792011-07-23T00:06:00.001-05:002011-07-23T00:09:14.563-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_07_14_CDC_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br />Last Update<br />2011-07-23<br /><br />On 2011-07-14, the <strong><span style="color: #783f04;">lead public health agency</span></strong> from the United States released&nbsp;14 matched pairs of <strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong>&nbsp;sequences at <strong>GISAID</strong> sampled between January and May of 2011 and covering a worldwide geography.<span style="mso-spacerun: yes;">&nbsp; </span>Nine fall into Clade 2: 188T and five are Clade 5: 208K, 219V. <span style="mso-spacerun: yes;">&nbsp;</span>Multi-clade augmentation is noted with Clade 3: 186P appearing on one Clade 5 background.<br /><br /><strong>189</strong> <strong><span style="color: #274e13;">HA</span></strong> Polymorphisms across&nbsp;86 codons with an <strong><span style="color: #783f04;">average of 13.5</span></strong> changes per HA.<br /><strong>108</strong> <strong><span style="color: #274e13;">NA</span></strong> Polymorphisms across&nbsp;47 codons&nbsp;with an <strong><span style="color: #783f04;">average of 7.7</span></strong> changes per NA.<br />----<br /><strong>297</strong>&nbsp;Total Polymorphisms with an <strong><span style="color: #783f04;">average of 21.2</span></strong> changes per matched pair (HA/NA).<br /><br /><span style="font-size: x-large;"><strong>Receptor Binding Site</strong></span><br /><br />193R: Clade 5 NewYork07_19F_2011_03_14<br />194I:&nbsp; Clade 5 Chile293_E3_8M_2011_05_13 (Egg passaged)<br /><br /><span style="font-size: x-large;"><strong>Sequences</strong></span><br /><br />SortKeys: <br />SequenceDate Desc,<br />SequenceID Asc,<br />SegmentID Asc<br /><br />. . . . India4947_39F_2011_05_22 (<br />. . . . . . . . Clade 2: 188T<br />. . . . . . . . GISAID HA EPI325579<br />. . . . . . . . 14 Polymorphisms (7 Amino and 7 Silent)<br />. . . . . . . . syn19V (GTg),<br />. . . . . . . . syn53L (cTG),<br />. . . . . . . . 100N,<br />. . . . . . . . syn103E (GAa),<br />. . . . . . . . 123A,<br />. . . . . . . . 166N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . syn262R (AGg),<br />. . . . . . . . 324I,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn445V (GTa),<br />. . . . . . . . 454N)<br /><br />. . . . India4947_39F_2011_05_22 (<br />. . . . . . . . GISAID NA EPI325578<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn230E (GAg),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn346V (GTt),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 394A,<br />. . . . . . . . syn416D (GAc),<br />. . . . . . . . 469N)<br /><br />. . . . Chile293_C1_8M_2011_05_13 (<br />. . . . . . . . Clade 5: 208K219V<br />. . . . . . . . GISAID HA EPI325557<br />. . . . . . . . 15 Polymorphisms (6 Amino and 9 Silent)<br />. . . . . . . . 39R,<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . syn221P (CCt),<br />. . . . . . . . 252L,<br />. . . . . . . . syn277D (GAc),<br />. . . . . . . . syn281T (ACc),<br />. . . . . . . . syn319T (ACg),<br />. . . . . . . . syn329S (TCc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa))<br /><br />. . . . Chile293_C1_8M_2011_05_13 (<br />. . . . . . . . GISAID NA EPI325556<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn60T (ACc),<br />. . . . . . . . 81A,<br />. . . . . . . . syn138A (GCt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . Chile293_E3_8M_2011_05_13 (<br />. . . . . . . . Clade 5: 208K219V<br />. . . . . . . . GISAID HA EPI325567<br />. . . . . . . . 16 Polymorphisms (7 Amino and 9 Silent)<br />. . . . . . . . 39R,<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 194I,<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . syn221P (CCt),<br />. . . . . . . . 252L,<br />. . . . . . . . syn277D (GAc),<br />. . . . . . . . syn281T (ACc),<br />. . . . . . . . syn319T (ACg),<br />. . . . . . . . syn329S (TCc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa))<br /><br />. . . . Chile293_E3_8M_2011_05_13 (<br />. . . . . . . . GISAID NA EPI325566<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn60T (ACc),<br />. . . . . . . . 81A,<br />. . . . . . . . syn138A (GCt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . Micronesia6119_13F_2011_05_08 (<br />. . . . . . . . Clade 2: 188T<br />. . . . . . . . GISAID HA EPI325588<br />. . . . . . . . 14 Polymorphisms (6 Amino and 8 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn15S (TCt),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn258F (TTt),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn442D (GAc),<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . Micronesia6119_13F_2011_05_08 (<br />. . . . . . . . GISAID NA EPI325587<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 189S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt))<br /><br />. . . . CanadaOntarioRV1255_69F_2011_05_06 (<br />. . . . . . . . Clade 5: 208K219V Crossing with Clade 3: 186P<br />. . . . . . . . GISAID HA EPI325560<br />. . . . . . . . 16 Polymorphisms (9 Amino and 7 Silent)<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . syn82I (ATc),<br />. . . . . . . . syn93C (TGc),<br />. . . . . . . . 100N,<br />. . . . . . . . 141Q,<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 186P,<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . 252L,<br />. . . . . . . . 289V,<br />. . . . . . . . syn307P (CCc),<br />. . . . . . . . 359A,<br />. . . . . . . . syn361G (GGa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa))<br /><br />. . . . CanadaOntarioRV1255_69F_2011_05_06 (<br />. . . . . . . . GISAID NA EPI325559<br />. . . . . . . . 8 Polymorphisms (2 Amino and 6 Silent)<br />. . . . . . . . 74S,<br />. . . . . . . . syn89S (TCt),<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . syn229S (TCc),<br />. . . . . . . . syn236G (GGc),<br />. . . . . . . . syn241V (GTg),<br />. . . . . . . . 299A,<br />. . . . . . . . syn304V (GTa))<br /><br />. . . . Minnesota11_52F_2011_04_19 (<br />. . . . . . . . Clade 2: 188T<br />. . . . . . . . GISAID HA EPI325545<br />. . . . . . . . 11 Polymorphisms (7 Amino and 4 Silent)<br />. . . . . . . . 59S,<br />. . . . . . . . syn69E (GAa),<br />. . . . . . . . 100N,<br />. . . . . . . . 132T mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 218T [Upsilon],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn477T (ACa),<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . Minnesota11_52F_2011_04_19 (<br />. . . . . . . . GISAID NA EPI325544<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn161C (TGc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K mix wt,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . ChileSantiago7774_xM_2011_04_14 (<br />. . . . . . . . Clade 2.Tau: <br />. . . . . . . . 100N, syn179L, 188T, syn338G, syn448L, 454N<br />. . . . . . . . GISAID HA EPI325573<br />. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)<br />. . . . . . . . syn#7V (GTc),<br />. . . . . . . . 100N,<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 226R,<br />. . . . . . . . syn255R (AGg),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N)<br /><br />. . . . ChileSantiago7774_xM_2011_04_14 (<br />. . . . . . . . GISAID NA EPI325572<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . syn162P (CCc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn298G (GGt) mix wt,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . Connecticut08_34M_2011_04_02 (<br />. . . . . . . . Clade 2.Tau: <br />. . . . . . . . 100N, syn179L, 188T, syn338G, syn448L, 454N<br />. . . . . . . . GISAID HA EPI325585<br />. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)<br />. . . . . . . . 100N,<br />. . . . . . . . syn130D (GAt),<br />. . . . . . . . syn179L (CTg),<br />. . . . . . . . 188T,<br />. . . . . . . . 205E mix wt,<br />. . . . . . . . 244R,<br />. . . . . . . . syn301I (ATt),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn431L (tTA),<br />. . . . . . . . syn448L (TTg),<br />. . . . . . . . 454N)<br /><br />. . . . Connecticut08_34M_2011_04_02 (<br />. . . . . . . . GISAID NA EPI325584<br />. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)<br />. . . . . . . . syn46I (ATc),<br />. . . . . . . . syn82S (TCt),<br />. . . . . . . . syn202A (GCg),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 343S,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . NewMexico10_40M_2011_03_29 (<br />. . . . . . . . Clade 2: 188T<br />. . . . . . . . GISAID HA EPI325563<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . 59S,<br />. . . . . . . . syn69E (GAa),<br />. . . . . . . . syn96G (GGg),<br />. . . . . . . . 100N,<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn477T (ACa),<br />. . . . . . . . syn537S (AGc))<br /><br />. . . . NewMexico10_40M_2011_03_29 (<br />. . . . . . . . GISAID NA EPI325562<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . 153N,<br />. . . . . . . . syn161C (TGc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . Venezuela80_30M_2011_03_24 (<br />. . . . . . . . Clade 5: 208K219V<br />. . . . . . . . GISAID HA EPI325554<br />. . . . . . . . 15 Polymorphisms (7 Amino and 8 Silent)<br />. . . . . . . . syn11H (CAc),<br />. . . . . . . . 17N,<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 87N,<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . 252L,<br />. . . . . . . . syn309Y (TAc),<br />. . . . . . . . syn360Q (CAa),<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa),<br />. . . . . . . . syn505G (GGa))<br /><br />. . . . Venezuela80_30M_2011_03_24 (<br />. . . . . . . . GISAID NA EPI325553<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . 19V,<br />. . . . . . . . syn35S (AGt),<br />. . . . . . . . syn139L (cTG),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn312Y (TAc),<br />. . . . . . . . 364N,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . AmericanSamoa4520_52M_2011_03_18 (<br />. . . . . . . . Clade 2: 188T<br />. . . . . . . . GISAID HA EPI325551<br />. . . . . . . . 15 Polymorphisms (7 Amino and 8 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 262K,<br />. . . . . . . . 263D,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . syn367D (GAt),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn474C (TGt),<br />. . . . . . . . syn478C (TGt),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . AmericanSamoa4520_52M_2011_03_18 (<br />. . . . . . . . GISAID NA EPI325550<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 41R,<br />. . . . . . . . 44S,<br />. . . . . . . . syn135T (ACc),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . NewYork07_19F_2011_03_14 (<br />. . . . . . . . Clade 5: 208K219V<br />. . . . . . . . GISAID HA EPI325548<br />. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)<br />. . . . . . . . syn36L (CTt),<br />. . . . . . . . syn47L (CTg),<br />. . . . . . . . 100N,<br />. . . . . . . . syn102E (GAa),<br />. . . . . . . . syn170N (AAc),<br />. . . . . . . . 193R mix wt,<br />. . . . . . . . 208K,<br />. . . . . . . . 219V,<br />. . . . . . . . syn221P (CCt),<br />. . . . . . . . 252L,<br />. . . . . . . . 377K,<br />. . . . . . . . syn446K (AAa),<br />. . . . . . . . syn475D (GAc))<br /><br />. . . . NewYork07_19F_2011_03_14 (<br />. . . . . . . . GISAID NA EPI325547<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 81A,<br />. . . . . . . . 84R,<br />. . . . . . . . syn138A (GCt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 416E)<br /><br />. . . . Kenya6758_6F_2011_03_08 (<br />. . . . . . . . Clade 2: 188T<br />. . . . . . . . GISAID HA EPI325582<br />. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)<br />. . . . . . . . 8T,<br />. . . . . . . . syn32S (TCc),<br />. . . . . . . . 100N,<br />. . . . . . . . syn138A (GCt),<br />. . . . . . . . 188T,<br />. . . . . . . . syn222K (AAg),<br />. . . . . . . . syn275V (GTt),<br />. . . . . . . . syn277D (GAc),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . syn379T (ACc),<br />. . . . . . . . 454N,<br />. . . . . . . . 513V)<br /><br />. . . . Kenya6758_6F_2011_03_08 (<br />. . . . . . . . GISAID NA EPI325581<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . syn78Q (CAa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . syn338V (GTg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn416D (GAc))<br /><br />. . . . ChinaHeilongjiang_Xiangfang191_2011_01_08 (<br />. . . . . . . . Clade 2: 188T<br />. . . . . . . . GISAID HA EPI325576<br />. . . . . . . . 14 Polymorphisms (7 Amino and 7 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn21T (ACc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn47L (tTA),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 226R,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . 377K,<br />. . . . . . . . 454N,<br />. . . . . . . . syn465N (AAt),<br />. . . . . . . . syn538F (TTt))<br /><br />. . . . ChinaHeilongjiang_Xiangfang191_2011_01_08 (<br />. . . . . . . . GISAID NA EPI325575<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn171N (AAt),<br />. . . . . . . . syn237S (TCc) mix wt,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt),<br />. . . . . . . . 412Q mix wt)<br /><br /><br /><br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-7380409843029387279?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-91384546555666926932011-07-20T07:32:00.001-05:002011-07-20T07:33:49.980-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_06_21_Arizona02_2011_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br />Last Update<br />2011-07-20<br /><br />On 2011-06-21, the <strong><span style="color: #783f04;">lead public health agency</span></strong> from the United States released 50 sequences at <strong>GISAID</strong> containing a subset from a <strong><span style="color: #660000;">heavily zoonotic sub-clade</span></strong> that is circulating across a worldwide geography in Americans and in individuals of at least <strong><span style="color: #783f04;">11 other nationalities</span></strong>.&nbsp; Eight matched pairs (<strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #274e13;">NA</span></strong> segments) from the <strong><span style="color: #783f04;">emergent sub-clade</span></strong> are found in this deposit.<br /><br />This <strong><span style="color: #4c1130;">Pandemic H1N1</span></strong> <strong><span style="color: #4c1130;">Upsilon </span></strong>Sub-Clade is termed as <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> for reference brevity and encompasses the <strong><span style="color: blue;">230I</span></strong>-Permissive, <strong><span style="color: blue;">189T</span></strong>-Bearing Hydra that has emerged from January 2010 to April 2011 across 62 <strong><span style="color: #274e13;">HA</span></strong> and 53 <strong><span style="color: #274e13;">NA</span></strong> sequences defining a <strong><span style="color: #783f04;">clinical subset of 58 cases</span></strong>, including <strong><span style="color: #660000;">fatalities</span></strong>, <strong><span style="color: #660000;">vaccine escape</span></strong> situations and <strong><span style="color: #660000;">TamiFlu resistance</span></strong>.&nbsp; Across the <strong><span style="color: #274e13;">HA</span></strong> segments (19 Fragments), <strong>745</strong> polymorphisms are found (93 distinct).&nbsp; The <strong><span style="color: #274e13;">NA</span></strong> is less volatile, but does lead other sub-clades with <strong>251</strong> polymorphisms spread over 68 distinct codons.&nbsp; <br /><br />Although complete clinical outcomes are not forthcoming, the <strong><span style="color: #660000;">Case Fatality Rate</span></strong> for <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> cases remains <strong><span style="color: #660000;">at or above 5%</span></strong> for a number of reasons, including very high <strong><span style="color: #660000;">Zoonotic Potential</span></strong> scores indicating rapid acquisition of genetic material from animal reservoirs.&nbsp; This sub-clade displays hypermorphic behaviour, carrying an average of <strong><span style="color: #783f04;">12 changes</span></strong> per <strong><span style="color: #274e13;">HA</span></strong> and <strong><span style="color: #783f04;">4.7</span></strong> per <strong><span style="color: #274e13;">NA</span></strong>.&nbsp; At this analysis, <strong><span style="color: #783f04;">GeneWurx</span></strong> investigates the potential donor reservoirs for the late season 2011 sequence that bears the highest count of <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong> <strong><span style="color: #274e13;">HA </span></strong>polymorphisms, <strong><span style="color: #783f04;">Arizona02_43F_2011_03_08</span></strong>.&nbsp; The <strong><span style="color: #274e13;">HA</span></strong> polymorphism count of <strong>19 (7 Amino and 12 Silent)</strong> and <strong>6</strong> for the <strong><span style="color: #274e13;">NA</span></strong> <strong>(0 Amino and 6 Silent)</strong> ranks this sequence within the ultimate decile of cladded <strong><span style="color: #4c1130;">pH1N1</span></strong> sequences. <br /><br />Four <strong><span style="color: #274e13;">HA</span></strong> revisions novel to <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong>&nbsp;demonstrate a continued genetic re-seeding though the&nbsp;base of this sub-clade&nbsp;is founded on&nbsp;a significant <strong><span style="color: #783f04;">immune escape charge</span></strong>.&nbsp; A triad of novelties (<strong><span style="color: blue;">210N, syn334G, syn337A</span></strong>) are found individually and grouped on various animal reservoirs closely related to the change pattern for <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong>, <strong>H2N2</strong> and <strong>H6N1</strong>.&nbsp; The fourth novelty, <strong><span style="color: blue;">516V</span></strong>, appears within <strong>H2N2</strong>. The <strong><span style="color: blue;">210N</span></strong> and <strong><span style="color: blue;">syn337A</span></strong> have recently appeared on <strong><span style="color: #4c1130;">pH1N1</span></strong> <strong>Clade 2: 188T</strong>.<br /><br /><span style="font-size: x-large;">Sequences</span><br /><br /><span style="font-size: large;">Clade 1.Upsilon:</span><br /><span style="font-size: large;">34D, 165N, 189T, syn213F, syn305K</span><br /><br />. . . . Arizona02_43F_2011_03_08 (<br />. . . . . . . . <strong><span style="color: #660000;">Zoonotic Potential: 100%</span></strong><br />. . . . . . . . GISAID HA EPI319994<br />. . . . . . . . 19 Polymorphisms (7 Amino and 12 Silent)<br />. . . . . . . . syn31H (CAt) [H2N2 Human and Avian wt],<br />. . . . . . . . . . . . . . . . . [H2N3 with syn40H],<br />. . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2009],<br />. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2009],<br />. . . . . . . . . . . . . . . . . [H5N1 Europe Avian 1999-2009<br />. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],<br />. . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2002-2008<br />. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],<br />. . . . . . . . . . . . . . . . . [H5N1 Africa Avian 2004-2008],<br />. . . . . . . . . . . . . . . . . [H9N2 Avian and Human wt],<br />. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1988-1989<br />. . . . . . . . . . . . . . . . . . . . . with 219K, 225G, 230I, syn397G],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn42G, 72L,<br />. . . . . . . . . . . . . . . . . . . . . syn80S, syn82I, 87N, syn118E,<br />. . . . . . . . . . . . . . . . . . . . . 156E, 158E, 200T, 218V,<br />. . . . . . . . . . . . . . . . . . . . . syn228G, 231S, <br />. . . . . . . . . . . . . . . . . . . . . syn287G, syn346G, <br />. . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K],<br />. . . . . . . . . . . . . . . . . [WSN_1933],<br />. . . . . . . . 34D [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . .&nbsp; [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . .&nbsp; [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . .&nbsp; [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . .&nbsp; [H2N2 Human and Avian wt],<br />. . . . . . . . syn55L (TTa) [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . . . . . . . .&nbsp; [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . .&nbsp; [H5N1 Azerbaijan Human 2006],<br />. . . . . . . . . . . . . . . . .&nbsp; [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . .&nbsp; [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . . . . . . . .&nbsp; [H5N1 Feline with syn40H, syn469E],<br />. . . . . . . . . . . . . . . . .&nbsp; [H2N2 Avian with syn184H, 189T],<br />. . . . . . . . . . . . . . . . .&nbsp; [H2N2 Human and Avian (cTa)],<br />. . . . . . . . syn118E (GAa) [H3N8 Equine wt, Canine wt, Swine wt],<br />. . . . . . . . . . . . . . . . . . [H3N8 Avian],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010 (cAa): <br />. . . . . . . . . . . . . . . . . . . . . . ckEgypt1055_2010_02,<br />. . . . . . . . . . . . . . . . . . . . . . dkEgypt0972NLQP_2009_04],<br />. . . . . . . . . . . . . . . . . . [H4, H6N1],<br />. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn31H, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn40H, syn42G, 72L,<br />. . . . . . . . . . . . . . . . . . . . . . . . syn80S, syn81Y, syn82I, 87N, <br />. . . . . . . . . . . . . . . . . . . . . . . . 144K, 156E, 158E, 158N, 159G,<br />. . . . . . . . . . . . . . . . . . . . . . . . 200T, 218S, 218V, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I, 231S, <br />. . . . . . . . . . . . . . . . . . . . . . . . 275I, syn287G, 313I, syn346G, <br />. . . . . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K, 523A, 523I],<br />. . . . . . . . . . . . . . . . . . [S8, 1918], <br />. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933],<br />. . . . . . . . . . . . . . . . . . [swBelgium1_1998],<br />. . . . . . . . syn140P (CCa) [H5N1 Egypt Human 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . 149N [H3N8 Equine, Canine, Avian, Swine (Agc)],<br />. . . . . . . . . . . . [H3N2 Avian (Agc)<br />. . . . . . . . . . . . . . . . with 165N, 190E, <br />. . . . . . . . . . . . . . . . . . . 225G, 230I, 238K, 275I],<br />. . . . . . . . . . . . [H3N2 Avian (cgc)],<br />. . . . . . . . . . . . [H4 Avian],<br />. . . . . . . . 165N [H6N1 Avian <br />. . . . . . . . . . . . . . . . with 188T, 225G, 230I, 275I, <br />. . . . . . . . . . . . . . . . . . syn334G, syn346G, 377K, syn390N, <br />. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],<br />. . . . . . . . . . . . [H9N2 Avian Emergent<br />. . . . . . . . . . . . . . . . with 39E, syn40H, syn93C, <br />. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I,<br />. . . . . . . . . . . . . . . . . . . syn294P, 296H, syn404E],<br />. . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, syn177L,<br />. . . . . . . . . . . . . . . . . . . 188T, syn207S, syn213F, syn221P,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . [H3N2 Human with 225N, 230I], <br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline, Mink <br />. . . . . . . . . . . . . . . . with 225G, 230I],<br />. . . . . . . . . . . . [WSZ_1933],<br />. . . . . . . . 189T [H3N2 Human (aaa, aag, agg)]<br />. . . . . . . . . . . . [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . . . [H5N1 Egypt Equine 2009], <br />. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2009], <br />. . . . . . . . . . . . [H6N1 Avian <br />. . . . . . . . . . . . . . . . with 165K, 188T, 225G, 230I, <br />. . . . . . . . . . . . . . . . . . 275I, syn334G, syn346G, syn390N, <br />. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],<br />. . . . . . . . . . . . [H9N2 Avian<br />. . . . . . . . . . . . . . . . with 39E, syn40H, syn42G, syn93C, <br />. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,<br />. . . . . . . . . . . . . . . . . . . syn399E, syn404E, 453K, 502K],<br />. . . . . . . . . . . . [H9N2 Human<br />. . . . . . . . . . . . . . . . with 189T, 190E,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,<br />. . . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],<br />. . . . . . . . . . . . [H1N1 Avian Europe 2009<br />. . . . . . . . . . . . . . . . with #1T, syn42G, 72L, syn81Y, syn82I, 87N,<br />. . . . . . . . . . . . . . . . . . . 159T, 186P, 188T, syn346G],<br />. . . . . . . . . . . . [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . with #1T, syn40H, syn42G,<br />. . . . . . . . . . . . . . . . . . . 72L, syn80S, syn81Y, 87N<br />. . . . . . . . . . . . . . . . . . . 144E, 158E, 186P, <br />. . . . . . . . . . . . . . . . . . . 230I, 237I, syn346G, 523A],<br />. . . . . . . . . . . . [H2N2 Human, Avian<br />. . . . . . . . . . . . . . . . with 200T, 208K, 225E, <br />. . . . . . . . . . . . . . . . . . 225G, 238D, 238K, 253A], <br />. . . . . . . . . . . . [1918 with 186P, 208K, 219A, 225G, 252I],<br />. . . . . . . . 210N mix wt [Novel to <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong>],<br />. . . . . . . . . . . . . . . . .&nbsp; [<strong><span style="color: #4c1130;">pH1N1</span></strong> Clade 2: <strong><span style="color: blue;">188T</span></strong>&nbsp;with <strong><span style="color: blue;">128D</span></strong>],<br />. . . . . . . . . . . . . . . . .&nbsp; [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . .&nbsp; [H2N2 Human],<br />. . . . . . . . . . . . . . . . .&nbsp; [H2N2 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with syn#1A, syn31H, 42E, syn147F, <br />. . . . . . . . . . . . . . . . . . . . . . . . . .188A, 189T, 190E, 200T, <br />. . . . . . . . . . . . . . . . . . . . . . . . . .210N, 225G, syn228G, <br />. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp; 238K, 240N, syn346G],<br />. . . . . . . . . . . . . . . . .&nbsp; [H6N1 Avian wt],<br />. . . . . . . . . . . . . . . . . .[1918, WSN_1933, WSZ_1933],<br />. . . . . . . . syn213F (TTt) [H5N1, H7N3, H7N7, H9N2],<br />. . . . . . . . . . . . . . . . .&nbsp; [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . .&nbsp; [H1N1 Avian],<br />. . . . . . . . 275I [H6N1 Avian wt],<br />. . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . . . . . [H3N2 Human 2011<br />. . . . . . . . . . . . . . . . with 165N, 225N, 230I, 238K],<br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline<br />. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K],<br />. . . . . . . . syn287G (GGg) [H3N2 Avian with 159S],<br />. . . . . . . . . . . . . . . . . . [H3N2 Canine &amp; Feline],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . . [H2N2 Avian<br />. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E, syn104L, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 166R, syn184H,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 189T, 225G, 238K, syn346G]<br />. . . . . . . . . . . . . . . . . . [H2N2 Human<br />. . . . . . . . . . . . . . . . . . . . . . with 42E, 189T, 225G, 238D, 253A],<br />. . . . . . . . . . . . . . . . . . [swBelgium1_1998],<br />. . . . . . . . syn305K (AAg) [H2N2 Avian &amp; Human (gAg)], <br />. . . . . . . . . . . . . . . . . . [H2N3 Avian wt],<br />. . . . . . . . . . . . . . . . . . [H3N8 Avian (gcg)],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Gharbiyah/Qena Avian 2008 (AAa)],<br />. . . . . . . . . . . . . . . . . . [H5N1 Human VietJP4207_2005 (gAg)],<br />. . . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2001-2006 (gAg)],<br />. . . . . . . . . . . . . . . . . . [H7N3, H7N7],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian (gAg)],<br />. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt (gAg) <br />. . . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . 219K, 225G, 230I,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn397G, syn494E], <br />. . . . . . . . . . . . . . . . . . [H1N1 swine <br />. . . . . . . . . . . . . . . . . . . . . . . with #1S, 219K, 225G, 230I, 491R],<br />. . . . . . . . . . . . . . . . . . [1918 (gAg)], <br />. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933 (gAg)],<br />. . . . . . . . syn334G (GGa) [Novel to <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong>],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . . [H2N2 Avian<br />. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . 189T, 200T, 208K, 210N,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 238K, syn287G, syn346G],<br />. . . . . . . . . . . . . . . . . . [H6N1 Avian wt],<br />. . . . . . . . . . . . . . . . . . [H10N7 Avian wt <br />. . . . . . . . . . . . . . . . . . . . . . . with 156E, syn213F, syn346G, et al],<br />. . . . . . . . . . . . . . . . . . [1918, WSN_1933, WSZ_1933],<br />. . . . . . . . syn337A (GCa) [Novel to <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong>],<br />. . . . . . . . . . . . . . . . . . [<strong><span style="color: #4c1130;">pH1N1</span></strong> Clade 2: <strong><span style="color: blue;">188T&nbsp;</span></strong>with <strong><span style="color: blue;">158E</span></strong>],<br />. . . . . . . . . . . . . . . . . .&nbsp;[H2N2 Avian <br />. . . . . . . . . . . . . . . . . . . . . . . with syn#1A, syn31H, syn147F, 166R<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 188A, 190E, 200T, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . 210N, 225G, syn228G, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . 238K, 240N, syn346G],<br />. . . . . . . . . . . . . . . . . .&nbsp; [H6N1 Avian wt],<br />. . . . . . . . syn346G (GGa) [H2N2 Human and Avian wt],<br />. . . . . . . . . . . . . . . . . . [H3N2 Human &amp; Avian wt],<br />. . . . . . . . . . . . . . . . . . [H3N8],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Preschool 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009], <br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H6N1, H6N2, H6N4 Avian],<br />. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],<br />. . . . . . . . syn391T (ACg) [H3N2 Human wt (gag)],<br />. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine, Feline (gag)],<br />. . . . . . . . . . . . . . . . . . [H4 Avian wt (gag)],<br />. . . . . . . . . . . . . . . . . . [H7N3 Avian wt (cag)],<br />. . . . . . . . . . . . . . . . . . [H7N7 Avian, Equine, Marine Mammal (cag)],<br />. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 (Aag)],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian 2011 (Aag)],<br />. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . [H11 Avian extensive],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . syn397G (GGc) [H6N1 Avian <br />. . . . . . . . . . . . . . . . . . . . . . with 165N, syn181G, 188T, 190E,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 210N, 225G, 230I, 275I,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 313K, syn334G, syn337A, 377K,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn399E, 453K, 502K],<br />. . . . . . . . . . . . . . . . . . [H7N3 Avian (Gac)],<br />. . . . . . . . . . . . . . . . . . [H7N7 Human &amp; Avian (Gac)],<br />. . . . . . . . . . . . . . . . . . [H9N2 Human (Gac)],<br />. . . . . . . . . . . . . . . . . . [H9N2 Avian Emergent (Gac)<br />. . . . . . . . . . . . . . . . . . . . . . . with 39E, syn40H, 296H, syn404E],<br />. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt<br />. . . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E, <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 219K, syn220R, 225G, 230I,<br />. . . . . . . . . . . . . . . . . . . . . . . . . syn494E], <br />. . . . . . . . . . . . . . . . . . [H1N1 Avian 2009],<br />. . . . . . . . . . . . . . . . . . [S8], [swBelgium1_1998],<br />. . . . . . . . 516V [Novel to <strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong>],<br />. . . . . . . . . . . . [H2N2 Avian with <strong><span style="color: blue;">17N</span></strong>])<br /><br />. . . . Arizona02_43F_2011_03_08 (<br />. . . . . . . . GISAID NA EPI319993<br />. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)<br />. . . . . . . . syn20A (GCc),<br />. . . . . . . . syn139L (TTa),<br />. . . . . . . . syn300N (AAc),<br />. . . . . . . . syn327R (CGt),<br />. . . . . . . . syn330D (GAc),<br />. . . . . . . . syn453V (GTt))<br /><br /><br /><br /><br /><div align="center"><span style="font-size: x-small;">Please visit </span><a href="http://genewurx.com/" target="_blank"><span style="font-size: x-small;">GeneWurx.com</span></a><span style="font-size: x-small;"> for insight into the latest published studies.</span> <a href="http://genewurx.com/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img alt="GeneWurx.com" border="0" src="http://2.bp.blogspot.com/_jI7cXeWx09Q/SwoIyoL7KRI/AAAAAAAAAIA/sJBrdX6nzq8/s320/Logo_GeneWurx_corner_bk_1in.jpg" yr="true" /></a> </div><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/4506613821928567934-9138454655566692693?l=pf11.blogspot.com' alt='' /></div>NS1http://www.blogger.com/profile/02690880554918462424noreply@blogger.comtag:blogger.com,1999:blog-4506613821928567934.post-48107820674638468982011-07-20T06:14:00.003-05:002011-07-20T06:35:46.562-05:00<span style="font-size: x-small;"><em>Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked </em></span><a href="http://genewurx.com/data/citation/GISAID_2011_07_01_Japan_Citation.xls" target="_blank"><span style="font-size: x-small;"><em>spreadsheet</em></span></a><span style="font-size: x-small;"><em> for completeness in citation.</em></span><br /><br />Last Update<br />2011-07-20<br /><br />On 2011-07-01, the <strong><span style="color: #783f04;">National Institute of Infectious Diseases (NIID) of Japan</span></strong> published sequences of 74 <strong><span style="color: #4c1130;">pH1N1</span></strong> segments (40 HA and&nbsp;34 NA) at <strong>GISAID</strong> with no clinical outcome noted, but with&nbsp;manifestations of drug resistance markers related to <strong><span style="color: #660000;">TamiFlu Resistance</span></strong> spread across multiple geographies.&nbsp; All HA segments are fragments.&nbsp; Multi-clade augmentation, sometimes termed “clade-jumping”, is noted.&nbsp;&nbsp;The <strong><span style="color: #660000;">high CFR</span></strong> <strong><span style="color: #4c1130;">Upsilon</span></strong> sub-clade (<strong><span style="color: #4c1130;">pH1N1</span><span style="color: #660000;">_υ</span></strong>) presents in Japan with one entry.<br /><br /><strong>340</strong> <strong><span style="color: #274e13;">HA</span></strong> Polymorphisms across 100 codons for an <strong><span style="color: #783f04;">average of 8.5</span></strong> changes per HA.<br /><strong>262</strong> <strong><span style="color: #274e13;">NA</span></strong> Polymorphisms across 64 codons for an <strong><span style="color: #783f04;">average of 7.7</span></strong> changes per NA.<br />----<br /><strong>602</strong>&nbsp;Total Polymorphisms.<br /><br /><br /><span style="font-size: x-large;"><strong>Vaccine Escape Modulators: 19</strong></span><br /><br />HA 156E (2)<br />HA 156E mix wt (3)<br />HA 156Q (1, Investigational)<br />HA 157E mix wt (1)<br />HA 158E mix wt (9)<br />HA 159D mix wt (2)<br />HA 194I mix wt (1, Investigational)<br /><br /><span style="font-size: x-large;"><strong>TamiFlu Resistance (Genetic): 22 sequences</strong></span><br /><br />JapanNara59_2011_03_02_TmX<br />JapanIshikawa70_2011_03_01_TmX<br />JapanHokkaido93_2011_02_28_TmX<br />JapanTochigi64_2011_02_23_TmX<br />JapanNara56_2011_02_21_TmX<br />JapanNara54_2011_02_21_TmX<br />JapanMiyazaki40_2011_02_18_TmX247<br />JapanIbaraki107_2011_02_16_TmX<br />JapanIbaraki106_2011_02_16_TmX<br />JapanIbaraki108_2011_02_16_TmX<br />JapanIbaraki104_2011_02_10_TmX<br />JapanOita77_2011_02_10_TmX<br />JapanIbaraki103_2011_02_10_TmX<br />JapanOita72_2011_02_08_TmX<br />JapanAkita5_2011_02_03_TmX<br />JapanKagawa1_2011_01_31_TmX<br />JapanGifu21_2011_01_19_TmX<br />JapanWakayama_C6_2011_01_16_TmX<br />JapanChiba1027_2011_01_11_TmX<br />JapanShiga28_M1M1_2011_01_04_TmX<br />JapanShiga28_2011_01_04_TmX<br />JapanNagasaki_C58_2009_10_26_TmX<br /><br /><span style="font-size: x-large;">Sequences</span><br /><br /><span style="font-size: large;">Clade 1.Upsilon:</span><br /><span style="font-size: large;">34D, 165N, 189T, syn213F, syn305K</span><br /><br />. . . . JapanFukui67_2011_03_01 (<br />. . . . . . . . GISAID HA EPI321458<br />. . . . . . . . 14 Polymorphisms (5 Amino and 9 Silent)<br />. . . . . . . . syn31H (CAt) [H2N2 Human and Avian wt],<br />. . . . . . . . . . . . . . . . . [H2N3 with syn40H],<br />. . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2009],<br />. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2009],<br />. . . . . . . . . . . . . . . . . [H5N1 Europe Avian 1999-2009<br />. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],<br />. . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2002-2008<br />. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],<br />. . . . . . . . . . . . . . . . . [H5N1 Africa Avian 2004-2008],<br />. . . . . . . . . . . . . . . . . [H9N2 Avian and Human wt],<br />. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1988-1989<br />. . . . . . . . . . . . . . . . . . . . . with 219K, 225G, 230I, syn397G],<br />. . . . . . . . . . . . . . . . . [H1N1 Avian <br />. . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn42G, 72L,<br />. . . . . . . . . . . . . . . . . . . . . syn80S, syn82I, 87N, syn118E,<br />. . . . . . . . . . . . . . . . . . . . . 156E, 158E, 200T, 218V,<br />. . . . . . . . . . . . . . . . . . . . . syn228G, 231S, <br />. . . . . . . . . . . . . . . . . . . . . syn287G, syn346G, <br />. . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K],<br />. . . . . . . . . . . . . . . . . [WSN_1933],<br />. . . . . . . . 34D [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . .&nbsp;. [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . . [H2N2 Human and Avian wt],<br />. . . . . . . . syn55L (TTa) [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . . . . . . . .&nbsp; [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . .[H5N1 Azerbaijan Human 2006],<br />. . . . . . . . . . . . . . . . . .[H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . .&nbsp; [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . . . . . . . . .[H5N1 Feline with syn40H, syn469E],<br />. . . . . . . . . . . . . . . . .&nbsp; [H2N2 Avian with syn184H, 189T],<br />. . . . . . . . . . . . . . . . . .[H2N2 Human and Avian (cTa)],<br />. . . . . . . . syn118E (GAa) [H3N8 Equine wt, Canine wt, Swine wt],<br />. . . . . . . . . . . . . . . . . . [H3N8 Avian],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010 (cAa): <br />. . . . . . . . . . . . . . . . . . . . . . ckEgypt1055_2010_02,<br />. . . . . . . . . . . . . . . . . . . . . . dkEgypt0972NLQP_2009_04],<br />. . . . . . . . . . . . . . . . . . [H4, H6N1],<br />. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian<br />. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn31H, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn40H, syn42G, 72L,<br />. . . . . . . . . . . . . . . . . . . . . . . . syn80S, syn81Y, syn82I, 87N, <br />. . . . . . . . . . . . . . . . . . . . . . . . 144K, 156E, 158E, 158N, 159G,<br />. . . . . . . . . . . . . . . . . . . . . . . . 200T, 218S, 218V, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I, 231S, <br />. . . . . . . . . . . . . . . . . . . . . . . . 275I, syn287G, 313I, syn346G, <br />. . . . . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K, 523A, 523I],<br />. . . . . . . . . . . . . . . . . . [S8, 1918], <br />. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933],<br />. . . . . . . . . . . . . . . . . . [swBelgium1_1998],<br />. . . . . . . . syn140P (CCa) [H5N1 Egypt Human 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . 149N [H3N8 Equine, Canine, Avian, Swine (Agc)],<br />. . . . . . . . . . . . [H3N2 Avian (Agc)<br />. . . . . . . . . . . . . . . . with 165N, 190E, <br />. . . . . . . . . . . . . . . . . . . 225G, 230I, 238K, 275I],<br />. . . . . . . . . . . . [H3N2 Avian (cgc)],<br />. . . . . . . . . . . . [H4 Avian],<br />. . . . . . . . 165N [H6N1 Avian <br />. . . . . . . . . . . . . . . . with 188T, 225G, 230I, 275I, <br />. . . . . . . . . . . . . . . . . . syn346G, 377K, syn390N, <br />. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],<br />. . . . . . . . . . . . [H9N2 Avian Emergent<br />. . . . . . . . . . . . . . . . with 39E, syn40H, syn93C, <br />. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I,<br />. . . . . . . . . . . . . . . . . . . syn294P, 296H, syn404E],<br />. . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, syn177L,<br />. . . . . . . . . . . . . . . . . . . 188T, syn207S, syn213F, syn221P,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . [H3N2 Human with 225N, 230I], <br />. . . . . . . . . . . . [H3N2 Avian, Canine, Feline, Mink <br />. . . . . . . . . . . . . . . . with 225G, 230I],<br />. . . . . . . . . . . . [WSZ_1933],<br />. . . . . . . . syn184H (CAc) [H5N1 Human Fatality 2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Equine, Avian emergent],<br />. . . . . . . . . . . . . . . . . . [H2N2 Human and Avian]<br />. . . . . . . . . . . . . . . . . . [H2N3, H3N8],<br />. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11]<br />. . . . . . . . 189T [H3N2 Human (aaa, aag, agg)]<br />. . . . . . . . . . . . [H5N1 Egypt Human 2009-2010],<br />. . . . . . . . . . . . [H5N1 Egypt Equine 2009], <br />. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2009], <br />. . . . . . . . . . . . [H6N1 Avian <br />. . . . . . . . . . . . . . . . with 165K, 188T, 225G, 230I, <br />. . . . . . . . . . . . . . . . . . 275I, syn346G, syn390N, <br />. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],<br />. . . . . . . . . . . . [H9N2 Avian<br />. . . . . . . . . . . . . . . . with 39E, syn40H, syn42G, syn93C, <br />. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,<br />. . . . . . . . . . . . . . . . . . . syn399E, syn404E, 453K, 502K],<br />. . . . . . . . . . . . [H9N2 Human<br />. . . . . . . . . . . . . . . . with 189T, 190E,<br />. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,<br />. . . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],<br />. . . . . . . . . . . . [H1N1 Avian Europe 2009<br />. . . . . . . . . . . . . . . . with #1T, syn42G, 72L, syn81Y, syn82I, 87N,<br />. . . . . . . . . . . . . . . . . . . 159T, 186P, 188T, syn346G],<br />. . . . . . . . . . . . [H1N1 Avian Farm<br />. . . . . . . . . . . . . . . . with #1T, syn40H, syn42G,<br />. . . . . . . . . . . . . . . . . . . 72L, syn80S, syn81Y, 87N<br />. . . . . . . . . . . . . . . . . . . 144E, 158E, 186P, <br />. . . . . . . . . . . . . . . . . . . 230I, 237I, syn346G, 523A],<br />. . . . . . . . . . . . [H2N2 Human, Avian<br />. . . . . . . . . . . . . . . . with 200T, 208K, 225E, <br />. . . . . . . . . . . . . . . . . . 225G, 238D, 238K, 253A], <br />. . . . . . . . . . . . [1918 with 186P, 208K, 219A, 225G, 252I],<br />. . . . . . . . syn213F (TTt) [H5N1, H7N3, H7N7, H9N2],<br />. . . . . . . . . . . . . . . . .&nbsp; [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . .&nbsp; [H1N1 Avian],<br />. . . . . . . . 275I [H6N1 Avian wt],<br />. . . . . . . . . . . [H1N1 Avian],<br />. . . . . . . . . . . [H3N2 Human 2011<br />. . . . . . . . . . . . . . . with 165N, 225N, 230I, 238K],<br />. . . . . . . . . . . [H3N2 Avian, Canine, Feline<br />. . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K],<br />. . . . . . . . syn287G (GGg) [H3N2 Avian with 159S],<br />. . . . . . . . . . . . . . . . . . [H3N2 Canine &amp; Feline],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],<br />. . . . . . . . . . . . . . . . . . [H2N2 Avian<br />. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E, syn104L, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 166R, syn184H,<br />. . . . . . . . . . . . . . . . . . . . . . . . . 189T, 225G, 238K, syn346G]<br />. . . . . . . . . . . . . . . . . . [H2N2 Human<br />. . . . . . . . . . . . . . . . . . . . . . with 42E, 189T, 225G, 238D, 253A],<br />. . . . . . . . . . . . . . . . . . [swBelgium1_1998],<br />. . . . . . . . syn305K (AAg) [H2N2 Avian &amp; Human (gAg)], <br />. . . . . . . . . . . . . . . . . . [H2N3 Avian wt],<br />. . . . . . . . . . . . . . . . . . [H3N8 Avian (gcg)],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Gharbiyah/Qena Avian 2008 (AAa)],<br />. . . . . . . . . . . . . . . . . . [H5N1 Human VietJP4207_2005 (gAg)],<br />. . . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2001-2006 (gAg)],<br />. . . . . . . . . . . . . . . . . . [H7N3, H7N7],<br />. . . . . . . . . . . . . . . . . . [H1N1 Avian (gAg)],<br />. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt (gAg) <br />. . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E, <br />. . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S, <br />. . . . . . . . . . . . . . . . . . . . . . . . . 219K, 225G, 230I,<br />. . . . . . . . . . . . . . . . . . . . . . . . . syn397G, syn494E], <br />. . . . . . . . . . . . . . . . . . [H1N1 swine <br />. . . . . . . . . . . . . . . . . . . . . . with #1S, 219K, 225G, 230I, 491R],<br />. . . . . . . . . . . . . . . . . . [1918 (gAg)], <br />. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933 (gAg)],<br />. . . . . . . . syn346G (GGa) [H2N2 Human and Avian wt],<br />. . . . . . . . . . . . . . . . . . [H3N2 Human &amp; Avian wt],<br />. . . . . . . . . . . . . . . . . . [H3N8],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Preschool 2009],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],<br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009], <br />. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],<br />. . . . . . . . . . . . . . . . . . [H6N1, H6N2, H6N4 Avian],<br />. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008 <br />. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,<br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H, <br />. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],<br />. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanFukui67_2011_03_01 (<br />. . . . . . . . GISAID NA EPI321457<br />. . . . . . . . 7 Polymorphisms (0 Amino and 7 Silent)<br />. . . . . . . . syn20A (GCc),<br />. . . . . . . . syn139L (TTa),<br />. . . . . . . . syn209N (AAt),<br />. . . . . . . . syn300N (AAc),<br />. . . . . . . . syn327R (CGt),<br />. . . . . . . . syn330D (GAc),<br />. . . . . . . . syn453V (GTt))<br /><br /><span style="font-size: large;">Clade 2:</span><br /><span style="font-size: large;">188T</span><br /><br />. . . . JapanKochi40_2011_03_14 (<br />. . . . . . . . GISAID HA EPI321478<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . syn#8V (GTg) mix wt,<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn121P (CCa) mix wt,<br />. . . . . . . . syn130D (GAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 210N mix wt [Upsilon],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanKochi40_2011_03_14 (<br />. . . . . . . . GISAID NA EPI321477<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 127S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 263T mix wt,<br />. . . . . . . . syn315G (GGg) mix wt,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 397D mix wt,<br />. . . . . . . . syn436I (ATt) mix wt)<br /><br />. . . . JapanHokkaido93_2011_02_28_TmX (<br />. . . . . . . . GISAID HA EPI321482<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 77N,<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn258F (TTt),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanHokkaido93_2011_02_28_TmX (<br />. . . . . . . . GISAID NA EPI321481<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y mix wt,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn378N (AAt))<br /><br />. . . . JapanTochigi64_2011_02_23_TmX (<br />. . . . . . . . GISAID HA EPI321476<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 194I mix wt [Upsilon],<br />. . . . . . . . 200T,<br />. . . . . . . . 205E mix wt,<br />. . . . . . . . 218E mix wt,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanTochigi64_2011_02_23_TmX (<br />. . . . . . . . GISAID NA EPI321475<br />. . . . . . . . Crossing with Upsilon<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanGifu_C31_2011_02_22 (<br />. . . . . . . . GISAID HA EPI321419<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn130D (GAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanMiyazaki40_2011_02_18_TmX247 (<br />. . . . . . . . GISAID HA EPI321462<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 156E mix wt,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn325P (CCa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanMiyazaki40_2011_02_18_TmX247 (<br />. . . . . . . . GISAID NA EPI321461<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . syn28N (AAt),<br />. . . . . . . . 44S,<br />. . . . . . . . syn202A (GCt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 247N,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanShimane140_2011_02_17 (<br />. . . . . . . . GISAID HA EPI321428<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . #6M,<br />. . . . . . . . syn15S (TCt),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . syn196Q (CAa),<br />. . . . . . . . 200T,<br />. . . . . . . . syn258F (TTt),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanIbaraki108_2011_02_16_TmX (<br />. . . . . . . . GISAID HA EPI321472<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 122N mix wt,<br />. . . . . . . . 146G,<br />. . . . . . . . 156E mix wt,<br />. . . . . . . . 166E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn222K (AAg),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanIbaraki108_2011_02_16_TmX (<br />. . . . . . . . GISAID NA EPI321471<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn291V (GTa),<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanIbaraki107_2011_02_16_TmX (<br />. . . . . . . . GISAID HA EPI321470<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 128D mix wt,<br />. . . . . . . . 146G,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 159D mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn222K (AAg),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanIbaraki107_2011_02_16_TmX (<br />. . . . . . . . GISAID NA EPI321469<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn291V (GTa),<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanIbaraki106_2011_02_16_TmX (<br />. . . . . . . . GISAID HA EPI321468<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 159D mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn222K (AAg),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanIbaraki106_2011_02_16_TmX (<br />. . . . . . . . GISAID NA EPI321467<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn291V (GTa),<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanIshikawa58_2011_02_12 (<br />. . . . . . . . GISAID HA EPI321454<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn221P (CCa),<br />. . . . . . . . syn259A (GCg),<br />. . . . . . . . 275A [Potentially New to 188T, not found up to 2011-05-17]<br />. . . . . . . . . . . . [Assoc TmX], <br />. . . . . . . . . . . . [Assoc pH1N1 RBS 159S, 186P, 188N, 189T, <br />. . . . . . . . . . . . . . . . . 208K, 218E, 219V, 226R, 230I],<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanIbaraki104_2011_02_10_TmX (<br />. . . . . . . . GISAID HA EPI321466<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 114I mix wt,<br />. . . . . . . . 146G,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn222K (AAg),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanIbaraki104_2011_02_10_TmX (<br />. . . . . . . . GISAID NA EPI321465<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanIbaraki103_2011_02_10_TmX (<br />. . . . . . . . GISAID HA EPI321464<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 122E mix wt,<br />. . . . . . . . 146G,<br />. . . . . . . . 157E mix wt,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn222K (AAg),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanIbaraki103_2011_02_10_TmX (<br />. . . . . . . . GISAID NA EPI321463<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn291V (GTa),<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanOita78_2011_02_10 (<br />. . . . . . . . GISAID HA EPI321436<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn98F (TTt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 150S,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanOita78_2011_02_10 (<br />. . . . . . . . GISAID NA EPI321435<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn104N (AAt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 451N)<br /><br />. . . . JapanOita77_2011_02_10_TmX (<br />. . . . . . . . GISAID HA EPI321434<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn98F (TTt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 150S,<br />. . . . . . . . syn176V (GTt) mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanOita77_2011_02_10_TmX (<br />. . . . . . . . GISAID NA EPI321433<br />. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn104N (AAt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 451H mix,<br />. . . . . . . . 451N mix)<br /><br />. . . . JapanOita76_2011_02_08 (<br />. . . . . . . . GISAID HA EPI321432<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn98F (TTt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 150S,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanOita76_2011_02_08 (<br />. . . . . . . . GISAID NA EPI321431<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn104N (AAt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 451N)<br /><br />. . . . JapanOita72_2011_02_08_TmX (<br />. . . . . . . . GISAID HA EPI321430<br />. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn98F (TTt),<br />. . . . . . . . syn122K (AAa),<br />. . . . . . . . 146G,<br />. . . . . . . . 150S,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanOita72_2011_02_08_TmX (<br />. . . . . . . . GISAID NA EPI321429<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn104N (AAt),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 451N,<br />. . . . . . . . syn453V (GTa) mix wt)<br /><br />. . . . JapanYamanashi222_2011_02_03 (<br />. . . . . . . . GISAID HA EPI321460<br />. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanYamanashi222_2011_02_03 (<br />. . . . . . . . GISAID NA EPI321459<br />. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 249E mix wt,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanAkita5_2011_02_03_TmX (<br />. . . . . . . . GISAID HA EPI321418<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . 1V,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 128D mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanAkita5_2011_02_03_TmX (<br />. . . . . . . . GISAID NA EPI321417<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn45Q (CAa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanKagawa1_2011_01_31_TmX (<br />. . . . . . . . GISAID HA EPI321441<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 132D mix wt,<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 212Q mix wt,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanKagawa1_2011_01_31_TmX (<br />. . . . . . . . GISAID NA EPI321440<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn127L (TTa),<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa))<br /><br />. . . . JapanGifu21_2011_01_19_TmX (<br />. . . . . . . . GISAID HA EPI321474<br />. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 128S,<br />. . . . . . . . 131T mix wt,<br />. . . . . . . . 146G,<br />. . . . . . . . 156E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn322R (AGa) mix wt,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanGifu21_2011_01_19_TmX (<br />. . . . . . . . GISAID NA EPI321473<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn140L (CTg),<br />. . . . . . . . syn207K (AAa) mix wt,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn304V (GTa),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . syn444S (TCt))<br /><br />. . . . JapanWakayama_C6_2011_01_16_TmX (<br />. . . . . . . . GISAID HA EPI321425<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa),<br />. . . . . . . . 87N,<br />. . . . . . . . 156Q,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanWakayama_C6_2011_01_16_TmX (<br />. . . . . . . . GISAID NA EPI321424<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn338V (GTg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanHamamatu_C7_2011_01_11 (<br />. . . . . . . . GISAID HA EPI321452<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn10Y (TAc),<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 146G,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 214N mix wt,<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanChiba1027_2011_01_11_TmX (<br />. . . . . . . . GISAID HA EPI321438<br />. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa),<br />. . . . . . . . 87N,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanChiba1027_2011_01_11_TmX (<br />. . . . . . . . GISAID NA EPI321437<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn338V (GTg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanTottori8_2011_01_08 (<br />. . . . . . . . GISAID HA EPI321447<br />. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)<br />. . . . . . . . 31Y mix wt,<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa),<br />. . . . . . . . 156E,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn238E (GAa),<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanTottori8_2011_01_08 (<br />. . . . . . . . GISAID NA EPI321446<br />. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 119K mix wt,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanTottori8_M1M2_2011_01_08 (<br />. . . . . . . . GISAID HA EPI321445<br />. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa) [Upsilon],<br />. . . . . . . . 156E,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn238E (GAa) [Upsilon],<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanTottori8_M1M2_2011_01_08 (<br />. . . . . . . . GISAID NA EPI321444<br />. . . . . . . . 8 Polymorphisms (6 Amino and 2 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . 119K mix wt,<br />. . . . . . . . 134F [Domaining with Upsilon 132F, 133F],<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanKumamoto7_2011_01_07 (<br />. . . . . . . . GISAID HA EPI321426<br />. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . 122N mix wt,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanShiga28_M1M1_2011_01_04_TmX (<br />. . . . . . . . GISAID HA EPI321451<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa),<br />. . . . . . . . 87N,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 206A,<br />. . . . . . . . 239S,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanShiga28_M1M1_2011_01_04_TmX (<br />. . . . . . . . GISAID NA EPI321450<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn338V (GTg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br />. . . . JapanShiga28_2011_01_04_TmX (<br />. . . . . . . . GISAID HA EPI321449<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . syn34N (AAt),<br />. . . . . . . . syn42G (GGa),<br />. . . . . . . . 87N,<br />. . . . . . . . 188T,<br />. . . . . . . . 200T,<br />. . . . . . . . 206A,<br />. . . . . . . . 239S,<br />. . . . . . . . syn296Q (CAa),<br />. . . . . . . . syn338G (GGc),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanShiga28_2011_01_04_TmX (<br />. . . . . . . . GISAID NA EPI321448<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 44S,<br />. . . . . . . . syn240T (ACc),<br />. . . . . . . . 241I,<br />. . . . . . . . 275Y,<br />. . . . . . . . syn338V (GTg),<br />. . . . . . . . 369K,<br />. . . . . . . . syn377P (CCa),<br />. . . . . . . . 415M)<br /><br /><span style="font-size: large;">Clade 3:</span><br /><span style="font-size: large;">186P</span><br /><br />. . . . JapanYamagata203_2011_02_14 (<br />. . . . . . . . GISAID HA EPI321427<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . 50I,<br />. . . . . . . . 137T,<br />. . . . . . . . 144S,<br />. . . . . . . . syn163K (AAa),<br />. . . . . . . . 186P,<br />. . . . . . . . syn251L (CTg),<br />. . . . . . . . syn287G (GGg),<br />. . . . . . . . syn293L (CTt),<br />. . . . . . . . 298V,<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanAichi172_2011_03_07 (<br />. . . . . . . . GISAID HA EPI321480<br />. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)<br />. . . . . . . . syn#12K (AAa),<br />. . . . . . . . syn#5L (tTA),<br />. . . . . . . . 137T,<br />. . . . . . . . 144S,<br />. . . . . . . . syn163K (AAa),<br />. . . . . . . . 186P,<br />. . . . . . . . syn251L (CTg),<br />. . . . . . . . syn287G (GGg),<br />. . . . . . . . syn293L (CTt),<br />. . . . . . . . 296H,<br />. . . . . . . . 298V,<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanAichi172_2011_03_07 (<br />. . . . . . . . GISAID NA EPI321479<br />. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)<br />. . . . . . . . syn45Q (CAa),<br />. . . . . . . . 46T,<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . syn187G (GGt),<br />. . . . . . . . 313R,<br />. . . . . . . . 389V,<br />. . . . . . . . 394I,<br />. . . . . . . . syn430R (CGg),<br />. . . . . . . . 467V)<br /><br />. . . . JapanIshikawa70_2011_03_01_TmX (<br />. . . . . . . . GISAID HA EPI321456<br />. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)<br />. . . . . . . . syn#12K (AAa),<br />. . . . . . . . 137T,<br />. . . . . . . . 144S,<br />. . . . . . . . 158E mix wt,<br />. . . . . . . . syn163K (AAa),<br />. . . . . . . . 186P,<br />. . . . . . . . 212E mix wt,<br />. . . . . . . . syn251L (CTg),<br />. . . . . . . . syn287G (GGg),<br />. . . . . . . . syn293L (CTt),<br />. . . . . . . . 298V,<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanIshikawa70_2011_03_01_TmX (<br />. . . . . . . . GISAID NA EPI321455<br />. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)<br />. . . . . . . . 46T,<br />. . . . . . . . syn126P (CCt),<br />. . . . . . . . syn187G (GGt),<br />. . . . . . . . 275Y,<br />. . . . . . . . 313R,<br />. . . . . . . . 394I,<br />. . . . . . . . syn430R (CGg),<br />. . . . . . . . 467V)<br /><br /><span style="font-size: large;">Clade 4:</span><br /><span style="font-size: large;">128D</span><br /><br />. . . . JapanNara59_2011_03_02_TmX (<br />. . . . . . . . GISAID HA EPI321490<br />. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)<br />. . . . . . . . 12V mix wt,<br />. . . . . . . . syn44L (tTA),<br />. . . . . . . . syn106E (GAa),<br />. . . . . . . . 128D,<br />. . . . . . . . syn177L (CTa),<br />. . . . . . . . 259T,<br />. . . . . . . . syn272D (GAc),<br />. . . . . . . . syn276H (CAt),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanNara59_2011_03_02_TmX (<br />. . . . . . . . GISAID NA EPI321489<br />. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)<br />. . . . . . . . 15I,<br />. . . . . . . . 83A,<br />. . . . . . . . syn142D (GAt) mix wt,<br />. . . . . . . . syn169P (CCt),<br />. . . . . . . . 189S,<br />. . . . . . . . syn238C (TGt),<br />. . . . . . . . syn264V (GTt),<br />. . . . . . . . 275Y,<br />. . . . . . . . syn381T (ACc) mix wt,<br />. . . . . . . . syn451D (GAt))<br /><br />. . . . JapanNara56_2011_02_21_TmX (<br />. . . . . . . . GISAID HA EPI321488<br />. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)<br />. . . . . . . . syn44L (tTA),<br />. . . . . . . . syn106E (GAa),<br />. . . . . . . . 128D,<br />. . . . . . . . 259T,<br />. . . . . . . . syn272D (GAc),<br />. . . . . . . . syn276H (CAt),<br />. . . . . . . . HA Truncated after aa348)<br /><br />. . . . JapanNara56_2011_02_21_TmX (<br />. . . . . . . . GISAID NA EPI321487<br />. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)<br />. . . . . . . . 15I,<br />. . . . . . . . 83A,<br />. . . . . . . . syn169P (CCt),<br />. . . . . . . . 189S,<br />. . . . . . . . syn238C (TGt),<br />. . . . . . . . syn264V (GTt),<br />. . . . . . . . 275Y,<br />. . . . . . . . syn451D (GAt))<br /><br />. . . . JapanNara48_2011_02_08 (<br />. . . . . . . . GISAID HA EPI321486<br />. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)<br />. . . . . . . . syn44L (tTA),<br />. . . . . . . . syn106E (GAa),<br />. . . . . . . . 128D,<br />.