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 spreadsheet for completeness in citation.
Last Update
2011-09-27
On 2011-09-26, the National Institute for Infectious Disease of Japan published 4 pH1N1 sequences at GISAID. These sequences were sampled from patients in Japan from January to April 2011 covering the second half of the Northern Hemisphere 2010-2011 season. No gender, age or clinical outcomes are specified. All HA sequences relate to Clade 2 (188T) and are HA fragments. Two of the four NA segments (50%) demonstrate genetic TamiFlu Resistance, one at NA 275 and the latest at NA 247.
A pattern is developing among Clade 1 (189T) and Clade 2 (188T) of genetic revision in the potential Immune Escape domains of HA aa122 to aa124 and aa163 to aa173. JapanAomori39_2011_04_09_TmX247 demonstrates revision in both areas with the rare HA 122M in a mixture with wild type and a rare HA 166T also in a mixture with wild type. JapanKawasaki122_2011_02_14_TmX275 falls onto a numerically significant Clade 2 (188T) background and adds the Vaccine Escape HA 158E in a mixture with wild type to a novel HA 169N. Three of the four sequences show at least one polymorphism in the HA aa154 to aa169 range totaling four polymorphisms (154I, 158E, 166T, 169N).
The advantage of a larger public database allows surfacing of cross-segment signals related to TamiFlu Resistance. HA 166T on JapanAomori39_2011_04_09_TmX247 becomes an investigational candidate. Only 7 sequences occur in the GISAID database bearing HA 166T. The United States West Coast (statistically significant Asian population) displays 2 of these sequences while Asia claims the remaining 5 of the rare HA 166T signals. Japan is represented on 3 of the Asian sequences. 100% of those 3 HA 166T-bearing sequences from Japan are genetically TamiFlu Resistant via NA 247N or 275Y. Those 3 HA gene segments are genetically distinct as well, demonstrating the ability of HA 166T to manifest across TamiFlu Resistant sequences with variant HA backgrounds.
The 4 Japanese HA fragments in this current deposit carry only 64% of a full HA, yet have generated an average of 8.5 polymorphisms (normed to ~13 for a full HA deposit). Data from Clade 2 (188T) continue to show significant genetic diversity and an ongoing ease of novel genetic acquisition.
. . . . JapanAomori39_2011_04_09_TmX247 (
. . . . . . . . GISAID HA EPI336876
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn23L (tTA) mix wt,
. . . . . . . . syn34N (AAt),
. . . . . . . . 122M mix wt [Rare to pH1N1],
. . . . . . . . syn131S (TCa),
. . . . . . . . 146G,
. . . . . . . . 166T mix wt [Rare to pH1N1],
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa348)
. . . . JapanAomori39_2011_04_09_TmX247 (
. . . . . . . . GISAID NA EPI336875
. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)
. . . . . . . . 44S,
. . . . . . . . syn140L (CTg),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 247N mix wt,
. . . . . . . . 284N mix wt,
. . . . . . . . syn304V (GTa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 466I)
. . . . JapanKawasaki122_2011_02_14_TmX275 (
. . . . . . . . GISAID HA EPI336870
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 158E mix wt,
. . . . . . . . 169N [Novel to pH1N1],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 330K,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa348)
. . . . JapanKawasaki122_2011_02_14_TmX275 (
. . . . . . . . GISAID NA EPI336869
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 275Y,
. . . . . . . . syn304V (GTa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 465S mix wt)
. . . . JapanFukuoka40_2011_02_02 (
. . . . . . . . GISAID HA EPI336874
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 143STOP mix wt,
. . . . . . . . 188T,
. . . . . . . . syn190D (GAt),
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . 324A,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa348)
. . . . JapanFukuoka40_2011_02_02 (
. . . . . . . . GISAID NA EPI336873
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . syn28N (AAt),
. . . . . . . . 44S,
. . . . . . . . 74L mix wt,
. . . . . . . . 178S mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)
. . . . JapanFukuoka35_2011_01_18 (
. . . . . . . . GISAID HA EPI336872
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 72T,
. . . . . . . . 154I,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 218E mix wt,
. . . . . . . . syn296Q (CAa),
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa348)
. . . . JapanFukuoka35_2011_01_18 (
. . . . . . . . GISAID NA EPI336871
. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)
. . . . . . . . syn28N (AAt),
. . . . . . . . 44S,
. . . . . . . . 94I mix wt,
. . . . . . . . 161Y mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 414E mix wt,
. . . . . . . . 415M)
2011-09-20
H5N1 Avian Markers, Side by Side, in 2011 Human pH1N1 Stockholm, Sweden Case
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 spreadsheet for completeness in citation.
Last Update
2011-09-20
On 2011-07-29, the UK National Institute for Medical Research published 29 pH1N1 sequences at GISAID. 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. The Swedish Institute for Infectious Disease Control originated 10 of the samples in this Mill Hill deposit including a highly zoonotic and potential H5N1 recombinant, Stockholm13_2011_03_28, with no specified gender, age or outcome.
Two contiguous H5N1 Avian markers, HA 415E and 416N, each novel to the human H1N1 pandemic, appear in this human case. The HA 416N is reported as a mixed peak trace, an output that is commonly interpreted as suggestive of multiple infecting strains. The single H5N1 potential donor HA segment on file is also unusual in that this Egyptian domestic poultry sequence carries numerous homologies to polymorphisms found on human pH1N1 Clade 1 (189T) and Clade 2 (188T) sequences. Several of those H5N1 to pH1N1 homologies are quite rare to H5N1, but are strongly emergent in pH1N1.
Stockholm13_2011_03_28 was sampled near the end of the traditional Northern Hemisphere influenza season and, as such, represents one probable foundation for ongoing Clade 2 transmission into the upcoming influenza season (2011-2012). As has been regularly discussed, Clade 2 (188T) is the most prevalent numerically of the 5 major pH1N1 divisions as reported in the public and private genetic databases. Being roughly par for the course, this Swedish sequence is hypermorphic, carrying 14 polymorphisms (9 Amino and 5 Silent).
Particular to the matter at hand, Clade 2 sequences have demonstrated a measurable propensity for accepting polymorphisms into pH1N1 and projecting those changes across pH1N1 (“Clade Jumping” / Clade Transfer). The method and means continue under investigation, whether due to the influence of Avian H1N1 common ancestry from the primary donors into the major human pH1N1 clades or due to some form of recombination / attractant magnetism occurring between and among the human pH1N1 clades.
GeneWurx has tracked development of the H1N1 pandemic from the publicly accepted Contact Zero in early 2009 (and potential prequels) up to the present emergent strains. As with prior H5N1 investigations, random variation remains far from the field of explanatory options in most cases. Malleability by random mallet has not been shown as an important means of genetic variation in this H1N1 human pandemic.
The back-to-back polymorphisms transferring HA 415E and 416N onto the human pH1N1 Stockholm13_2011_03_28 sequence are noted in the H5N1 database. That single H5N1 sequence is a human-adapted, avian case from Egypt. This dual signal transfer demonstrates one very concrete case of cross-species, cross-serotype genetic transfer from an animal to a human serotype.
H5N1 contiguous homology to the dominant clade in the dominant circulating human serotype (pH1N1) instructs the medical fraternity to the weight of emergent zoonoses and suggests that at least one avian flightpath may be worthy of investigation.
. . . . SwedenStockholm13_2011_03_28 (
. . . . . . . . PHz = 87%
. . . . . . . . PHzAv = 87%
. . . . . . . . GISAID HA EPI326240
. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)
. . . . . . . . syn41N (AAt) [H5N1 Human Emergent with TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2007],
. . . . . . . . . . . . . . . . . [H5N1 Avian with 166I],
. . . . . . . . 50I [WSN_1933, WSZ_1933],
. . . . . . . . . . [1918],
. . . . . . . . syn154L (tTA) [H3N2 Avian with 158E],
. . . . . . . . . . . . . . . . . . [H3N2 Canine, Feline wt]
. . . . . . . . . . . . . . . . . . [H3N2 Human wt (tTg)],
. . . . . . . . . . . . . . . . . . [H3N8 Avian (tTg)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian with 404G],
. . . . . . . . . . . . . . . . . . [H9N2 Avian (tTg)],
. . . . . . . . . . . . . . . . . . [H9N2 Human with syn40H (tTg)],
. . . . . . . . 158E mix wt [H3N8, H5N1],
. . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K
. . . . . . . . . . . . . . . . . . . . . . . 253A, 275I, syn346G],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with #1T, 8V, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . . . . . 72L, syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . . . . . . 144E, 189T, 193R, 237I,
. . . . . . . . . . . . . . . . . . . . . . . syn287G, syn346G, 523A],
. . . . . . . . . . . . . . . . . [sw1930],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . with 186P, 189T,
. . . . . . . . . . . . . . . . . . . and extensive pH1N1υ polymorphisms],
. . . . . . . . 259T [H9N2 Avian and Human (att)
. . . . . . . . . . . . . . . . with syn40H],
. . . . . . . . syn338G (GGc) [H3N2 Avian, Canine, Feline],
. . . . . . . . . . . . . . . . . . [H3N8, H4, H5N1 Avian 2010, H6, sw],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn346G],
. . . . . . . . 377K [H9N2],
. . . . . . . . syn388K (AAa) [Wisconsin08_30F_2010_08_10
. . . . . . . . . . . . . . . . . . . . . with 39R, 137T, 186P,
. . . . . . . . . . . . . . . . . . . . . . . . . 225N, syn346G, syn413K, 444K,
. . . . . . . . . . . . . . . . . . Utah20_C2_2_2009_07_25_VxX
. . . . . . . . . . . . . . . . . . . . . with #12E, 0I, 159D, 227G, 296H, 470I],
. . . . . . . . . . . . . . . . . . [H5N1 Avian, Equine, Human wt],
. . . . . . . . . . . . . . . . . . [H9N2 Avian and Human
. . . . . . . . . . . . . . . . . . . . . . with 39E, syn40H, syn42G, 296H],
. . . . . . . . . . . . . . . . . . [swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . . . with syn41N, 50I, 196H,
. . . . . . . . . . . . . . . . . . . . . . . . . 225N, 230I, 238D,
. . . . . . . . . . . . . . . . . . . . . . . . . syn346G, syn413K],
. . . . . . . . 415E [H5N1 Egypt wt],
. . . . . . . . 416N mix [H5N1 Avian Egypt
. . . . . . . . . . . . . . . . . . . with 100N, 196H, 415E],
. . . . . . . . 416Y mix,
. . . . . . . . 454N [H7N3, H7N7, H9N2],
. . . . . . . . syn527L (TTa) [BeijingHZ01_2011_01_14
. . . . . . . . . . . . . . . . . . . . . . . . with 188T, 242N],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt wt (cTa)]
Last Update
2011-09-20
On 2011-07-29, the UK National Institute for Medical Research published 29 pH1N1 sequences at GISAID. 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. The Swedish Institute for Infectious Disease Control originated 10 of the samples in this Mill Hill deposit including a highly zoonotic and potential H5N1 recombinant, Stockholm13_2011_03_28, with no specified gender, age or outcome.
Two contiguous H5N1 Avian markers, HA 415E and 416N, each novel to the human H1N1 pandemic, appear in this human case. The HA 416N is reported as a mixed peak trace, an output that is commonly interpreted as suggestive of multiple infecting strains. The single H5N1 potential donor HA segment on file is also unusual in that this Egyptian domestic poultry sequence carries numerous homologies to polymorphisms found on human pH1N1 Clade 1 (189T) and Clade 2 (188T) sequences. Several of those H5N1 to pH1N1 homologies are quite rare to H5N1, but are strongly emergent in pH1N1.
Stockholm13_2011_03_28 was sampled near the end of the traditional Northern Hemisphere influenza season and, as such, represents one probable foundation for ongoing Clade 2 transmission into the upcoming influenza season (2011-2012). As has been regularly discussed, Clade 2 (188T) is the most prevalent numerically of the 5 major pH1N1 divisions as reported in the public and private genetic databases. Being roughly par for the course, this Swedish sequence is hypermorphic, carrying 14 polymorphisms (9 Amino and 5 Silent).
Particular to the matter at hand, Clade 2 sequences have demonstrated a measurable propensity for accepting polymorphisms into pH1N1 and projecting those changes across pH1N1 (“Clade Jumping” / Clade Transfer). The method and means continue under investigation, whether due to the influence of Avian H1N1 common ancestry from the primary donors into the major human pH1N1 clades or due to some form of recombination / attractant magnetism occurring between and among the human pH1N1 clades.
GeneWurx has tracked development of the H1N1 pandemic from the publicly accepted Contact Zero in early 2009 (and potential prequels) up to the present emergent strains. As with prior H5N1 investigations, random variation remains far from the field of explanatory options in most cases. Malleability by random mallet has not been shown as an important means of genetic variation in this H1N1 human pandemic.
The back-to-back polymorphisms transferring HA 415E and 416N onto the human pH1N1 Stockholm13_2011_03_28 sequence are noted in the H5N1 database. That single H5N1 sequence is a human-adapted, avian case from Egypt. This dual signal transfer demonstrates one very concrete case of cross-species, cross-serotype genetic transfer from an animal to a human serotype.
H5N1 contiguous homology to the dominant clade in the dominant circulating human serotype (pH1N1) instructs the medical fraternity to the weight of emergent zoonoses and suggests that at least one avian flightpath may be worthy of investigation.
. . . . SwedenStockholm13_2011_03_28 (
. . . . . . . . PHz = 87%
. . . . . . . . PHzAv = 87%
. . . . . . . . GISAID HA EPI326240
. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)
. . . . . . . . syn41N (AAt) [H5N1 Human Emergent with TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2007],
. . . . . . . . . . . . . . . . . [H5N1 Avian with 166I],
. . . . . . . . 50I [WSN_1933, WSZ_1933],
. . . . . . . . . . [1918],
. . . . . . . . syn154L (tTA) [H3N2 Avian with 158E],
. . . . . . . . . . . . . . . . . . [H3N2 Canine, Feline wt]
. . . . . . . . . . . . . . . . . . [H3N2 Human wt (tTg)],
. . . . . . . . . . . . . . . . . . [H3N8 Avian (tTg)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian with 404G],
. . . . . . . . . . . . . . . . . . [H9N2 Avian (tTg)],
. . . . . . . . . . . . . . . . . . [H9N2 Human with syn40H (tTg)],
. . . . . . . . 158E mix wt [H3N8, H5N1],
. . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K
. . . . . . . . . . . . . . . . . . . . . . . 253A, 275I, syn346G],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with #1T, 8V, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . . . . . 72L, syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . . . . . . 144E, 189T, 193R, 237I,
. . . . . . . . . . . . . . . . . . . . . . . syn287G, syn346G, 523A],
. . . . . . . . . . . . . . . . . [sw1930],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . with 186P, 189T,
. . . . . . . . . . . . . . . . . . . and extensive pH1N1υ polymorphisms],
. . . . . . . . 259T [H9N2 Avian and Human (att)
. . . . . . . . . . . . . . . . with syn40H],
. . . . . . . . syn338G (GGc) [H3N2 Avian, Canine, Feline],
. . . . . . . . . . . . . . . . . . [H3N8, H4, H5N1 Avian 2010, H6, sw],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn346G],
. . . . . . . . 377K [H9N2],
. . . . . . . . syn388K (AAa) [Wisconsin08_30F_2010_08_10
. . . . . . . . . . . . . . . . . . . . . with 39R, 137T, 186P,
. . . . . . . . . . . . . . . . . . . . . . . . . 225N, syn346G, syn413K, 444K,
. . . . . . . . . . . . . . . . . . Utah20_C2_2_2009_07_25_VxX
. . . . . . . . . . . . . . . . . . . . . with #12E, 0I, 159D, 227G, 296H, 470I],
. . . . . . . . . . . . . . . . . . [H5N1 Avian, Equine, Human wt],
. . . . . . . . . . . . . . . . . . [H9N2 Avian and Human
. . . . . . . . . . . . . . . . . . . . . . with 39E, syn40H, syn42G, 296H],
. . . . . . . . . . . . . . . . . . [swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . . . with syn41N, 50I, 196H,
. . . . . . . . . . . . . . . . . . . . . . . . . 225N, 230I, 238D,
. . . . . . . . . . . . . . . . . . . . . . . . . syn346G, syn413K],
. . . . . . . . 415E [H5N1 Egypt wt],
. . . . . . . . 416N mix [H5N1 Avian Egypt
. . . . . . . . . . . . . . . . . . . with 100N, 196H, 415E],
. . . . . . . . 416Y mix,
. . . . . . . . 454N [H7N3, H7N7, H9N2],
. . . . . . . . syn527L (TTa) [BeijingHZ01_2011_01_14
. . . . . . . . . . . . . . . . . . . . . . . . with 188T, 242N],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt wt (cTa)]
2011-09-05
Upsilon Marker Jumps Clades, Adds Zoonoses, Escapes Vaccine, Hospitalises and Transmits Well
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 spreadsheet for completeness in citation.
Last Update
2011-09-06
On 2011-08-25, the WHO Collaborating Centre for Reference and Research on Influenza published 15 pH1N1 sequences at GISAID. These sequences were sampled from patients in Australia from April to July 2011. All are Clade 2 backgrounds (188T).
Although a recent GeneWurx analysis on Romanian sequences discussed a different defining Clade 1 marker (189T) jumping templates onto Clade 2, this Australian pattern maintains polymorphic throw for several generations. This deposit not only surfaces a novel face for Clade 2 (188T), but is a novelty that conducts reliable transmission though a defining marker downstream of the cleavage site is adopted from Clade 1.Upsilon (syn346G) in the same domain as the HA syn338G normally found on Clade 2.
The 5 very similar sequences each carry 17 to 20 HA polymorphisms. The superset of polymorphisms from this emergent mixed branch shows known Vaccine Escape changes at HA 156E and 158E. Hypermorphic behaviour is a hallmark of pH1N1 as are the Vaccine Breakthrough (AustraliaBrisbane500_32M_2011_06_22_VxX) and hospitalisation (AustraliaBrisbane190_25M_2011_06_14_s) instances also demonstrated by cases from this novel emergence.
These novel and rare HA polymorphisms to the Clade 2 background exhibit homological history at a very significant proportion in the H1N1 Avian genetics record, including several farm animal sequences. Those farm animal sequences, in turn, show a strong match rate to Clade 1.Upsilon (pH1N1υ) AND to these Clade 2 Human pH1N1 sequences. The superset of polymorphisms from the related Avian H1N1 farm animals exhibit strong homology to the superset of Clade 1.Upsilon HA polymorphisms.
The HA syn413K prevalent in fatal and severe cases from the early pandemic has mated with these Australian novelties as a further signal of zoonotic avian influence on the most widely reported pH1N1 Clade (Clade 2 – 188T). Cross-clade polymorphism jumping is only just beginning for the Pandemic reservoir of H1N1. Sporadic HA 230I on backgrounds similar to these 5 novel items is probable. Interaction between human pH1N1 and Avian Influenza strains (farm and wild) carrying both Clade 1 and Clade 2 immune escape markers on single strains will continue to drive human revision using the widely available avian delivery vector.
By GeneWurx calculations, clade elasticity will rise to become a primary method generating the 2011-2012 pH1N1 polymorphism bed.
. . . . AustraliaBrisbane190_25M_2011_06_14_s (
. . . . . . . . GISAID HA EPI333112
. . . . . . . . 19 Polymorphisms (7 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 156E mix wt [H2N3],
. . . . . . . . . . . . . . . . . [H3N8],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010
. . . . . . . . . . . . . . . . . . . . with 188E, 192I, 198S, 210T, 223I],
. . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with #1T, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . . . . . 72L, 87N, syn118E, 144K,
. . . . . . . . . . . . . . . . . . . . . . . 158E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . syn287G, syn346G,
. . . . . . . . . . . . . . . . . . . . . . . 453K, 502K],
. . . . . . . . . . . . . . . . . [H3N2 Avian
. . . . . . . . . . . . . . . . . . . . with 165N, 225G, 230I],
. . . . . . . . . . . . . . . . . [H1N1 swIowa44837_1_2009_11_08_xL with 225N, 230I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . syn513I (ATc) [H1N1 Avian (gTc)
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms & syn508L])
. . . . AustraliaBrisbane500_32M_2011_06_22_VxX (
. . . . . . . . GISAID HA EPI333109
. . . . . . . . 17 Polymorphisms (7 Amino and 10 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . 77R (AGa) [H9N2 Avian and Human wt
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 171G (GgT),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E])
. . . . SouthAustralia4_2011_06_24 (
. . . . . . . . GISAID HA EPI333105
. . . . . . . . 18 Polymorphisms (6 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn300P (CCt) [H5N1, H6N1, H7N3, H7N7],
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms & syn508L])
. . . . AustraliaBrisbane142_2011_04_12 (
. . . . . . . . GISAID HA EPI333005
. . . . . . . . 18 Polymorphisms (6 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn77S (AGt),
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms & syn508L])
. . . . AustraliaBrisbane70_IVR162_2011_07_25 (
. . . . . . . . GISAID HA EPI333107
. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 132T (AcC) [H1N1 Avian],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K
. . . . . . . . . . . . . . . . . . 253A, 275I, syn346G],
. . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . with #1T, 8V, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . 72L, syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . 144E, 189T, 193R, 237I,
. . . . . . . . . . . . . . . . . . syn287G, syn346G, 523A],
. . . . . . . . . . . . . . . . . [sw1930]
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 226R,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms & syn508L])
Last Update
2011-09-06
On 2011-08-25, the WHO Collaborating Centre for Reference and Research on Influenza published 15 pH1N1 sequences at GISAID. These sequences were sampled from patients in Australia from April to July 2011. All are Clade 2 backgrounds (188T).
Although a recent GeneWurx analysis on Romanian sequences discussed a different defining Clade 1 marker (189T) jumping templates onto Clade 2, this Australian pattern maintains polymorphic throw for several generations. This deposit not only surfaces a novel face for Clade 2 (188T), but is a novelty that conducts reliable transmission though a defining marker downstream of the cleavage site is adopted from Clade 1.Upsilon (syn346G) in the same domain as the HA syn338G normally found on Clade 2.
The 5 very similar sequences each carry 17 to 20 HA polymorphisms. The superset of polymorphisms from this emergent mixed branch shows known Vaccine Escape changes at HA 156E and 158E. Hypermorphic behaviour is a hallmark of pH1N1 as are the Vaccine Breakthrough (AustraliaBrisbane500_32M_2011_06_22_VxX) and hospitalisation (AustraliaBrisbane190_25M_2011_06_14_s) instances also demonstrated by cases from this novel emergence.
These novel and rare HA polymorphisms to the Clade 2 background exhibit homological history at a very significant proportion in the H1N1 Avian genetics record, including several farm animal sequences. Those farm animal sequences, in turn, show a strong match rate to Clade 1.Upsilon (pH1N1υ) AND to these Clade 2 Human pH1N1 sequences. The superset of polymorphisms from the related Avian H1N1 farm animals exhibit strong homology to the superset of Clade 1.Upsilon HA polymorphisms.
The HA syn413K prevalent in fatal and severe cases from the early pandemic has mated with these Australian novelties as a further signal of zoonotic avian influence on the most widely reported pH1N1 Clade (Clade 2 – 188T). Cross-clade polymorphism jumping is only just beginning for the Pandemic reservoir of H1N1. Sporadic HA 230I on backgrounds similar to these 5 novel items is probable. Interaction between human pH1N1 and Avian Influenza strains (farm and wild) carrying both Clade 1 and Clade 2 immune escape markers on single strains will continue to drive human revision using the widely available avian delivery vector.
By GeneWurx calculations, clade elasticity will rise to become a primary method generating the 2011-2012 pH1N1 polymorphism bed.
. . . . AustraliaBrisbane190_25M_2011_06_14_s (
. . . . . . . . GISAID HA EPI333112
. . . . . . . . 19 Polymorphisms (7 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 156E mix wt [H2N3],
. . . . . . . . . . . . . . . . . [H3N8],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010
. . . . . . . . . . . . . . . . . . . . with 188E, 192I, 198S, 210T, 223I],
. . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with #1T, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . . . . . 72L, 87N, syn118E, 144K,
. . . . . . . . . . . . . . . . . . . . . . . 158E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . syn287G, syn346G,
. . . . . . . . . . . . . . . . . . . . . . . 453K, 502K],
. . . . . . . . . . . . . . . . . [H3N2 Avian
. . . . . . . . . . . . . . . . . . . . with 165N, 225G, 230I],
. . . . . . . . . . . . . . . . . [H1N1 swIowa44837_1_2009_11_08_xL with 225N, 230I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . syn513I (ATc) [H1N1 Avian (gTc)
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms & syn508L])
. . . . AustraliaBrisbane500_32M_2011_06_22_VxX (
. . . . . . . . GISAID HA EPI333109
. . . . . . . . 17 Polymorphisms (7 Amino and 10 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . 77R (AGa) [H9N2 Avian and Human wt
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 171G (GgT),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E])
. . . . SouthAustralia4_2011_06_24 (
. . . . . . . . GISAID HA EPI333105
. . . . . . . . 18 Polymorphisms (6 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn300P (CCt) [H5N1, H6N1, H7N3, H7N7],
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms & syn508L])
. . . . AustraliaBrisbane142_2011_04_12 (
. . . . . . . . GISAID HA EPI333005
. . . . . . . . 18 Polymorphisms (6 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn77S (AGt),
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms & syn508L])
. . . . AustraliaBrisbane70_IVR162_2011_07_25 (
. . . . . . . . GISAID HA EPI333107
. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 132T (AcC) [H1N1 Avian],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K
. . . . . . . . . . . . . . . . . . 253A, 275I, syn346G],
. . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . with #1T, 8V, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . 72L, syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . 144E, 189T, 193R, 237I,
. . . . . . . . . . . . . . . . . . syn287G, syn346G, 523A],
. . . . . . . . . . . . . . . . . [sw1930]
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 226R,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms & syn508L])
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