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)]
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2011-07-20
Arizona 2011 on a Pandemic Background with an Observed 5% Case Fatality Rate
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
2011-07-20
On 2011-06-21, the lead public health agency from the United States released 50 sequences at GISAID containing a subset from a heavily zoonotic sub-clade that is circulating across a worldwide geography in Americans and in individuals of at least 11 other nationalities. Eight matched pairs (HA and NA segments) from the emergent sub-clade are found in this deposit.
This Pandemic H1N1 Upsilon Sub-Clade is termed as pH1N1υ for reference brevity and encompasses the 230I-Permissive, 189T-Bearing Hydra that has emerged from January 2010 to April 2011 across 62 HA and 53 NA sequences defining a clinical subset of 58 cases, including fatalities, vaccine escape situations and TamiFlu resistance. Across the HA segments (19 Fragments), 745 polymorphisms are found (93 distinct). The NA is less volatile, but does lead other sub-clades with 251 polymorphisms spread over 68 distinct codons.
Although complete clinical outcomes are not forthcoming, the Case Fatality Rate for pH1N1υ cases remains at or above 5% for a number of reasons, including very high Zoonotic Potential scores indicating rapid acquisition of genetic material from animal reservoirs. This sub-clade displays hypermorphic behaviour, carrying an average of 12 changes per HA and 4.7 per NA. At this analysis, GeneWurx investigates the potential donor reservoirs for the late season 2011 sequence that bears the highest count of pH1N1υ HA polymorphisms, Arizona02_43F_2011_03_08. The HA polymorphism count of 19 (7 Amino and 12 Silent) and 6 for the NA (0 Amino and 6 Silent) ranks this sequence within the ultimate decile of cladded pH1N1 sequences.
Four HA revisions novel to pH1N1υ demonstrate a continued genetic re-seeding though the base of this sub-clade is founded on a significant immune escape charge. A triad of novelties (210N, syn334G, syn337A) are found individually and grouped on various animal reservoirs closely related to the change pattern for pH1N1υ, H2N2 and H6N1. The fourth novelty, 516V, appears within H2N2. The 210N and syn337A have recently appeared on pH1N1 Clade 2: 188T.
Sequences
Clade 1.Upsilon:
34D, 165N, 189T, syn213F, syn305K
. . . . Arizona02_43F_2011_03_08 (
. . . . . . . . Zoonotic Potential: 100%
. . . . . . . . GISAID HA EPI319994
. . . . . . . . 19 Polymorphisms (7 Amino and 12 Silent)
. . . . . . . . syn31H (CAt) [H2N2 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H2N3 with syn40H],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2009],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2009],
. . . . . . . . . . . . . . . . . [H5N1 Europe Avian 1999-2009
. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],
. . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2002-2008
. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],
. . . . . . . . . . . . . . . . . [H5N1 Africa Avian 2004-2008],
. . . . . . . . . . . . . . . . . [H9N2 Avian and Human wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1988-1989
. . . . . . . . . . . . . . . . . . . . . with 219K, 225G, 230I, syn397G],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn42G, 72L,
. . . . . . . . . . . . . . . . . . . . . syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . . . . 156E, 158E, 200T, 218V,
. . . . . . . . . . . . . . . . . . . . . syn228G, 231S,
. . . . . . . . . . . . . . . . . . . . . syn287G, syn346G,
. . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K],
. . . . . . . . . . . . . . . . . [WSN_1933],
. . . . . . . . 34D [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . [H2N2 Human and Avian wt],
. . . . . . . . syn55L (TTa) [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . [H5N1 Azerbaijan Human 2006],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . . [H5N1 Feline with syn40H, syn469E],
. . . . . . . . . . . . . . . . . [H2N2 Avian with syn184H, 189T],
. . . . . . . . . . . . . . . . . [H2N2 Human and Avian (cTa)],
. . . . . . . . syn118E (GAa) [H3N8 Equine wt, Canine wt, Swine wt],
. . . . . . . . . . . . . . . . . . [H3N8 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010 (cAa):
. . . . . . . . . . . . . . . . . . . . . . ckEgypt1055_2010_02,
. . . . . . . . . . . . . . . . . . . . . . dkEgypt0972NLQP_2009_04],
. . . . . . . . . . . . . . . . . . [H4, H6N1],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn31H,
. . . . . . . . . . . . . . . . . . . . . . . . syn40H, syn42G, 72L,
. . . . . . . . . . . . . . . . . . . . . . . . syn80S, syn81Y, syn82I, 87N,
. . . . . . . . . . . . . . . . . . . . . . . . 144K, 156E, 158E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . 200T, 218S, 218V,
. . . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I, 231S,
. . . . . . . . . . . . . . . . . . . . . . . . 275I, syn287G, 313I, syn346G,
. . . . . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K, 523A, 523I],
. . . . . . . . . . . . . . . . . . [S8, 1918],
. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933],
. . . . . . . . . . . . . . . . . . [swBelgium1_1998],
. . . . . . . . syn140P (CCa) [H5N1 Egypt Human 2007-2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . 149N [H3N8 Equine, Canine, Avian, Swine (Agc)],
. . . . . . . . . . . . [H3N2 Avian (Agc)
. . . . . . . . . . . . . . . . with 165N, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 238K, 275I],
. . . . . . . . . . . . [H3N2 Avian (cgc)],
. . . . . . . . . . . . [H4 Avian],
. . . . . . . . 165N [H6N1 Avian
. . . . . . . . . . . . . . . . with 188T, 225G, 230I, 275I,
. . . . . . . . . . . . . . . . . . syn334G, syn346G, 377K, syn390N,
. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Avian Emergent
. . . . . . . . . . . . . . . . with 39E, syn40H, syn93C,
. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I,
. . . . . . . . . . . . . . . . . . . syn294P, 296H, syn404E],
. . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, syn177L,
. . . . . . . . . . . . . . . . . . . 188T, syn207S, syn213F, syn221P,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . [H3N2 Human with 225N, 230I],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline, Mink
. . . . . . . . . . . . . . . . with 225G, 230I],
. . . . . . . . . . . . [WSZ_1933],
. . . . . . . . 189T [H3N2 Human (aaa, aag, agg)]
. . . . . . . . . . . . [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2009],
. . . . . . . . . . . . [H6N1 Avian
. . . . . . . . . . . . . . . . with 165K, 188T, 225G, 230I,
. . . . . . . . . . . . . . . . . . 275I, syn334G, syn346G, syn390N,
. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Avian
. . . . . . . . . . . . . . . . with 39E, syn40H, syn42G, syn93C,
. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,
. . . . . . . . . . . . . . . . . . . syn399E, syn404E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Human
. . . . . . . . . . . . . . . . with 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,
. . . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H1N1 Avian Europe 2009
. . . . . . . . . . . . . . . . with #1T, syn42G, 72L, syn81Y, syn82I, 87N,
. . . . . . . . . . . . . . . . . . . 159T, 186P, 188T, syn346G],
. . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . with #1T, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . 72L, syn80S, syn81Y, 87N
. . . . . . . . . . . . . . . . . . . 144E, 158E, 186P,
. . . . . . . . . . . . . . . . . . . 230I, 237I, syn346G, 523A],
. . . . . . . . . . . . [H2N2 Human, Avian
. . . . . . . . . . . . . . . . with 200T, 208K, 225E,
. . . . . . . . . . . . . . . . . . 225G, 238D, 238K, 253A],
. . . . . . . . . . . . [1918 with 186P, 208K, 219A, 225G, 252I],
. . . . . . . . 210N mix wt [Novel to pH1N1υ],
. . . . . . . . . . . . . . . . . [pH1N1 Clade 2: 188T with 128D],
. . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H2N2 Human],
. . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn#1A, syn31H, 42E, syn147F,
. . . . . . . . . . . . . . . . . . . . . . . . . .188A, 189T, 190E, 200T,
. . . . . . . . . . . . . . . . . . . . . . . . . .210N, 225G, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 238K, 240N, syn346G],
. . . . . . . . . . . . . . . . . [H6N1 Avian wt],
. . . . . . . . . . . . . . . . . .[1918, WSN_1933, WSZ_1933],
. . . . . . . . syn213F (TTt) [H5N1, H7N3, H7N7, H9N2],
. . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 275I [H6N1 Avian wt],
. . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . . . . . [H3N2 Human 2011
. . . . . . . . . . . . . . . . with 165N, 225N, 230I, 238K],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K],
. . . . . . . . syn287G (GGg) [H3N2 Avian with 159S],
. . . . . . . . . . . . . . . . . . [H3N2 Canine & Feline],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2007-2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],
. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E, syn104L,
. . . . . . . . . . . . . . . . . . . . . . . . . 166R, syn184H,
. . . . . . . . . . . . . . . . . . . . . . . . . 189T, 225G, 238K, syn346G]
. . . . . . . . . . . . . . . . . . [H2N2 Human
. . . . . . . . . . . . . . . . . . . . . . with 42E, 189T, 225G, 238D, 253A],
. . . . . . . . . . . . . . . . . . [swBelgium1_1998],
. . . . . . . . syn305K (AAg) [H2N2 Avian & Human (gAg)],
. . . . . . . . . . . . . . . . . . [H2N3 Avian wt],
. . . . . . . . . . . . . . . . . . [H3N8 Avian (gcg)],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Gharbiyah/Qena Avian 2008 (AAa)],
. . . . . . . . . . . . . . . . . . [H5N1 Human VietJP4207_2005 (gAg)],
. . . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2001-2006 (gAg)],
. . . . . . . . . . . . . . . . . . [H7N3, H7N7],
. . . . . . . . . . . . . . . . . . [H1N1 Avian (gAg)],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt (gAg)
. . . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S,
. . . . . . . . . . . . . . . . . . . . . . . . . . 219K, 225G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn397G, syn494E],
. . . . . . . . . . . . . . . . . . [H1N1 swine
. . . . . . . . . . . . . . . . . . . . . . . with #1S, 219K, 225G, 230I, 491R],
. . . . . . . . . . . . . . . . . . [1918 (gAg)],
. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933 (gAg)],
. . . . . . . . syn334G (GGa) [Novel to pH1N1υ],
. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 189T, 200T, 208K, 210N,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 238K, syn287G, syn346G],
. . . . . . . . . . . . . . . . . . [H6N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H10N7 Avian wt
. . . . . . . . . . . . . . . . . . . . . . . with 156E, syn213F, syn346G, et al],
. . . . . . . . . . . . . . . . . . [1918, WSN_1933, WSZ_1933],
. . . . . . . . syn337A (GCa) [Novel to pH1N1υ],
. . . . . . . . . . . . . . . . . . [pH1N1 Clade 2: 188T with 158E],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . . with syn#1A, syn31H, syn147F, 166R
. . . . . . . . . . . . . . . . . . . . . . . . . . 188A, 190E, 200T,
. . . . . . . . . . . . . . . . . . . . . . . . . . 210N, 225G, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . . 238K, 240N, syn346G],
. . . . . . . . . . . . . . . . . . [H6N1 Avian wt],
. . . . . . . . syn346G (GGa) [H2N2 Human and Avian wt],
. . . . . . . . . . . . . . . . . . [H3N2 Human & Avian wt],
. . . . . . . . . . . . . . . . . . [H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Preschool 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . . . [H6N1, H6N2, H6N4 Avian],
. . . . . . . . . . . . . . . . . . [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],
. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],
. . . . . . . . syn391T (ACg) [H3N2 Human wt (gag)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine, Feline (gag)],
. . . . . . . . . . . . . . . . . . [H4 Avian wt (gag)],
. . . . . . . . . . . . . . . . . . [H7N3 Avian wt (cag)],
. . . . . . . . . . . . . . . . . . [H7N7 Avian, Equine, Marine Mammal (cag)],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 (Aag)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian 2011 (Aag)],
. . . . . . . . . . . . . . . . . . [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],
. . . . . . . . . . . . . . . . . . [H11 Avian extensive],
. . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn397G (GGc) [H6N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with 165N, syn181G, 188T, 190E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 210N, 225G, 230I, 275I,
. . . . . . . . . . . . . . . . . . . . . . . . . . 313K, syn334G, syn337A, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn399E, 453K, 502K],
. . . . . . . . . . . . . . . . . . [H7N3 Avian (Gac)],
. . . . . . . . . . . . . . . . . . [H7N7 Human & Avian (Gac)],
. . . . . . . . . . . . . . . . . . [H9N2 Human (Gac)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian Emergent (Gac)
. . . . . . . . . . . . . . . . . . . . . . . with 39E, syn40H, 296H, syn404E],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt
. . . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E,
. . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S,
. . . . . . . . . . . . . . . . . . . . . . . . . 219K, syn220R, 225G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . . . syn494E],
. . . . . . . . . . . . . . . . . . [H1N1 Avian 2009],
. . . . . . . . . . . . . . . . . . [S8], [swBelgium1_1998],
. . . . . . . . 516V [Novel to pH1N1υ],
. . . . . . . . . . . . [H2N2 Avian with 17N])
. . . . Arizona02_43F_2011_03_08 (
. . . . . . . . GISAID NA EPI319993
. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn139L (TTa),
. . . . . . . . syn300N (AAc),
. . . . . . . . syn327R (CGt),
. . . . . . . . syn330D (GAc),
. . . . . . . . syn453V (GTt))
Last Update
2011-07-20
On 2011-06-21, the lead public health agency from the United States released 50 sequences at GISAID containing a subset from a heavily zoonotic sub-clade that is circulating across a worldwide geography in Americans and in individuals of at least 11 other nationalities. Eight matched pairs (HA and NA segments) from the emergent sub-clade are found in this deposit.
This Pandemic H1N1 Upsilon Sub-Clade is termed as pH1N1υ for reference brevity and encompasses the 230I-Permissive, 189T-Bearing Hydra that has emerged from January 2010 to April 2011 across 62 HA and 53 NA sequences defining a clinical subset of 58 cases, including fatalities, vaccine escape situations and TamiFlu resistance. Across the HA segments (19 Fragments), 745 polymorphisms are found (93 distinct). The NA is less volatile, but does lead other sub-clades with 251 polymorphisms spread over 68 distinct codons.
Although complete clinical outcomes are not forthcoming, the Case Fatality Rate for pH1N1υ cases remains at or above 5% for a number of reasons, including very high Zoonotic Potential scores indicating rapid acquisition of genetic material from animal reservoirs. This sub-clade displays hypermorphic behaviour, carrying an average of 12 changes per HA and 4.7 per NA. At this analysis, GeneWurx investigates the potential donor reservoirs for the late season 2011 sequence that bears the highest count of pH1N1υ HA polymorphisms, Arizona02_43F_2011_03_08. The HA polymorphism count of 19 (7 Amino and 12 Silent) and 6 for the NA (0 Amino and 6 Silent) ranks this sequence within the ultimate decile of cladded pH1N1 sequences.
Four HA revisions novel to pH1N1υ demonstrate a continued genetic re-seeding though the base of this sub-clade is founded on a significant immune escape charge. A triad of novelties (210N, syn334G, syn337A) are found individually and grouped on various animal reservoirs closely related to the change pattern for pH1N1υ, H2N2 and H6N1. The fourth novelty, 516V, appears within H2N2. The 210N and syn337A have recently appeared on pH1N1 Clade 2: 188T.
Sequences
Clade 1.Upsilon:
34D, 165N, 189T, syn213F, syn305K
. . . . Arizona02_43F_2011_03_08 (
. . . . . . . . Zoonotic Potential: 100%
. . . . . . . . GISAID HA EPI319994
. . . . . . . . 19 Polymorphisms (7 Amino and 12 Silent)
. . . . . . . . syn31H (CAt) [H2N2 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H2N3 with syn40H],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2009],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2009],
. . . . . . . . . . . . . . . . . [H5N1 Europe Avian 1999-2009
. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],
. . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2002-2008
. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],
. . . . . . . . . . . . . . . . . [H5N1 Africa Avian 2004-2008],
. . . . . . . . . . . . . . . . . [H9N2 Avian and Human wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1988-1989
. . . . . . . . . . . . . . . . . . . . . with 219K, 225G, 230I, syn397G],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn42G, 72L,
. . . . . . . . . . . . . . . . . . . . . syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . . . . 156E, 158E, 200T, 218V,
. . . . . . . . . . . . . . . . . . . . . syn228G, 231S,
. . . . . . . . . . . . . . . . . . . . . syn287G, syn346G,
. . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K],
. . . . . . . . . . . . . . . . . [WSN_1933],
. . . . . . . . 34D [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . [H2N2 Human and Avian wt],
. . . . . . . . syn55L (TTa) [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . [H5N1 Azerbaijan Human 2006],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . . [H5N1 Feline with syn40H, syn469E],
. . . . . . . . . . . . . . . . . [H2N2 Avian with syn184H, 189T],
. . . . . . . . . . . . . . . . . [H2N2 Human and Avian (cTa)],
. . . . . . . . syn118E (GAa) [H3N8 Equine wt, Canine wt, Swine wt],
. . . . . . . . . . . . . . . . . . [H3N8 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010 (cAa):
. . . . . . . . . . . . . . . . . . . . . . ckEgypt1055_2010_02,
. . . . . . . . . . . . . . . . . . . . . . dkEgypt0972NLQP_2009_04],
. . . . . . . . . . . . . . . . . . [H4, H6N1],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn31H,
. . . . . . . . . . . . . . . . . . . . . . . . syn40H, syn42G, 72L,
. . . . . . . . . . . . . . . . . . . . . . . . syn80S, syn81Y, syn82I, 87N,
. . . . . . . . . . . . . . . . . . . . . . . . 144K, 156E, 158E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . 200T, 218S, 218V,
. . . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I, 231S,
. . . . . . . . . . . . . . . . . . . . . . . . 275I, syn287G, 313I, syn346G,
. . . . . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K, 523A, 523I],
. . . . . . . . . . . . . . . . . . [S8, 1918],
. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933],
. . . . . . . . . . . . . . . . . . [swBelgium1_1998],
. . . . . . . . syn140P (CCa) [H5N1 Egypt Human 2007-2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . 149N [H3N8 Equine, Canine, Avian, Swine (Agc)],
. . . . . . . . . . . . [H3N2 Avian (Agc)
. . . . . . . . . . . . . . . . with 165N, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 238K, 275I],
. . . . . . . . . . . . [H3N2 Avian (cgc)],
. . . . . . . . . . . . [H4 Avian],
. . . . . . . . 165N [H6N1 Avian
. . . . . . . . . . . . . . . . with 188T, 225G, 230I, 275I,
. . . . . . . . . . . . . . . . . . syn334G, syn346G, 377K, syn390N,
. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Avian Emergent
. . . . . . . . . . . . . . . . with 39E, syn40H, syn93C,
. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I,
. . . . . . . . . . . . . . . . . . . syn294P, 296H, syn404E],
. . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, syn177L,
. . . . . . . . . . . . . . . . . . . 188T, syn207S, syn213F, syn221P,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . [H3N2 Human with 225N, 230I],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline, Mink
. . . . . . . . . . . . . . . . with 225G, 230I],
. . . . . . . . . . . . [WSZ_1933],
. . . . . . . . 189T [H3N2 Human (aaa, aag, agg)]
. . . . . . . . . . . . [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2009],
. . . . . . . . . . . . [H6N1 Avian
. . . . . . . . . . . . . . . . with 165K, 188T, 225G, 230I,
. . . . . . . . . . . . . . . . . . 275I, syn334G, syn346G, syn390N,
. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Avian
. . . . . . . . . . . . . . . . with 39E, syn40H, syn42G, syn93C,
. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,
. . . . . . . . . . . . . . . . . . . syn399E, syn404E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Human
. . . . . . . . . . . . . . . . with 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,
. . . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H1N1 Avian Europe 2009
. . . . . . . . . . . . . . . . with #1T, syn42G, 72L, syn81Y, syn82I, 87N,
. . . . . . . . . . . . . . . . . . . 159T, 186P, 188T, syn346G],
. . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . with #1T, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . 72L, syn80S, syn81Y, 87N
. . . . . . . . . . . . . . . . . . . 144E, 158E, 186P,
. . . . . . . . . . . . . . . . . . . 230I, 237I, syn346G, 523A],
. . . . . . . . . . . . [H2N2 Human, Avian
. . . . . . . . . . . . . . . . with 200T, 208K, 225E,
. . . . . . . . . . . . . . . . . . 225G, 238D, 238K, 253A],
. . . . . . . . . . . . [1918 with 186P, 208K, 219A, 225G, 252I],
. . . . . . . . 210N mix wt [Novel to pH1N1υ],
. . . . . . . . . . . . . . . . . [pH1N1 Clade 2: 188T with 128D],
. . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H2N2 Human],
. . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn#1A, syn31H, 42E, syn147F,
. . . . . . . . . . . . . . . . . . . . . . . . . .188A, 189T, 190E, 200T,
. . . . . . . . . . . . . . . . . . . . . . . . . .210N, 225G, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 238K, 240N, syn346G],
. . . . . . . . . . . . . . . . . [H6N1 Avian wt],
. . . . . . . . . . . . . . . . . .[1918, WSN_1933, WSZ_1933],
. . . . . . . . syn213F (TTt) [H5N1, H7N3, H7N7, H9N2],
. . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 275I [H6N1 Avian wt],
. . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . . . . . [H3N2 Human 2011
. . . . . . . . . . . . . . . . with 165N, 225N, 230I, 238K],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K],
. . . . . . . . syn287G (GGg) [H3N2 Avian with 159S],
. . . . . . . . . . . . . . . . . . [H3N2 Canine & Feline],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2007-2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],
. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E, syn104L,
. . . . . . . . . . . . . . . . . . . . . . . . . 166R, syn184H,
. . . . . . . . . . . . . . . . . . . . . . . . . 189T, 225G, 238K, syn346G]
. . . . . . . . . . . . . . . . . . [H2N2 Human
. . . . . . . . . . . . . . . . . . . . . . with 42E, 189T, 225G, 238D, 253A],
. . . . . . . . . . . . . . . . . . [swBelgium1_1998],
. . . . . . . . syn305K (AAg) [H2N2 Avian & Human (gAg)],
. . . . . . . . . . . . . . . . . . [H2N3 Avian wt],
. . . . . . . . . . . . . . . . . . [H3N8 Avian (gcg)],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Gharbiyah/Qena Avian 2008 (AAa)],
. . . . . . . . . . . . . . . . . . [H5N1 Human VietJP4207_2005 (gAg)],
. . . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2001-2006 (gAg)],
. . . . . . . . . . . . . . . . . . [H7N3, H7N7],
. . . . . . . . . . . . . . . . . . [H1N1 Avian (gAg)],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt (gAg)
. . . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S,
. . . . . . . . . . . . . . . . . . . . . . . . . . 219K, 225G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn397G, syn494E],
. . . . . . . . . . . . . . . . . . [H1N1 swine
. . . . . . . . . . . . . . . . . . . . . . . with #1S, 219K, 225G, 230I, 491R],
. . . . . . . . . . . . . . . . . . [1918 (gAg)],
. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933 (gAg)],
. . . . . . . . syn334G (GGa) [Novel to pH1N1υ],
. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 189T, 200T, 208K, 210N,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 238K, syn287G, syn346G],
. . . . . . . . . . . . . . . . . . [H6N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H10N7 Avian wt
. . . . . . . . . . . . . . . . . . . . . . . with 156E, syn213F, syn346G, et al],
. . . . . . . . . . . . . . . . . . [1918, WSN_1933, WSZ_1933],
. . . . . . . . syn337A (GCa) [Novel to pH1N1υ],
. . . . . . . . . . . . . . . . . . [pH1N1 Clade 2: 188T with 158E],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . . with syn#1A, syn31H, syn147F, 166R
. . . . . . . . . . . . . . . . . . . . . . . . . . 188A, 190E, 200T,
. . . . . . . . . . . . . . . . . . . . . . . . . . 210N, 225G, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . . 238K, 240N, syn346G],
. . . . . . . . . . . . . . . . . . [H6N1 Avian wt],
. . . . . . . . syn346G (GGa) [H2N2 Human and Avian wt],
. . . . . . . . . . . . . . . . . . [H3N2 Human & Avian wt],
. . . . . . . . . . . . . . . . . . [H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Preschool 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . . . [H6N1, H6N2, H6N4 Avian],
. . . . . . . . . . . . . . . . . . [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],
. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],
. . . . . . . . syn391T (ACg) [H3N2 Human wt (gag)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine, Feline (gag)],
. . . . . . . . . . . . . . . . . . [H4 Avian wt (gag)],
. . . . . . . . . . . . . . . . . . [H7N3 Avian wt (cag)],
. . . . . . . . . . . . . . . . . . [H7N7 Avian, Equine, Marine Mammal (cag)],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 (Aag)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian 2011 (Aag)],
. . . . . . . . . . . . . . . . . . [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],
. . . . . . . . . . . . . . . . . . [H11 Avian extensive],
. . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn397G (GGc) [H6N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with 165N, syn181G, 188T, 190E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 210N, 225G, 230I, 275I,
. . . . . . . . . . . . . . . . . . . . . . . . . . 313K, syn334G, syn337A, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn399E, 453K, 502K],
. . . . . . . . . . . . . . . . . . [H7N3 Avian (Gac)],
. . . . . . . . . . . . . . . . . . [H7N7 Human & Avian (Gac)],
. . . . . . . . . . . . . . . . . . [H9N2 Human (Gac)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian Emergent (Gac)
. . . . . . . . . . . . . . . . . . . . . . . with 39E, syn40H, 296H, syn404E],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt
. . . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E,
. . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S,
. . . . . . . . . . . . . . . . . . . . . . . . . 219K, syn220R, 225G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . . . syn494E],
. . . . . . . . . . . . . . . . . . [H1N1 Avian 2009],
. . . . . . . . . . . . . . . . . . [S8], [swBelgium1_1998],
. . . . . . . . 516V [Novel to pH1N1υ],
. . . . . . . . . . . . [H2N2 Avian with 17N])
. . . . Arizona02_43F_2011_03_08 (
. . . . . . . . GISAID NA EPI319993
. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn139L (TTa),
. . . . . . . . syn300N (AAc),
. . . . . . . . syn327R (CGt),
. . . . . . . . syn330D (GAc),
. . . . . . . . syn453V (GTt))
2011-03-28
Scandinavia Accumulates Superset on Emergent 188T Background
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 Updated
2011-03-29
On 2011-03-20, the Statens Serum Institut of Copenhagen, Denmark published 6 pH1N1 sequences at GenBank sampled in a time period spanning approximately 3 weeks from late December 2010 until mid January 2011. Five of the six HA sequences demonstrate the 188T of the first pH1N1 emergent nucleotide coding having a second base revision (AcT) and two of those Denmark 188T sequences additionally carry HA 225G.
Denmark120_2010_12_20 and Denmark20_2011_01_04 with 188T and 225G demonstrate ongoing transmission of a template having 6 revisions (100N, syn179L, 188T, syn338G, syn448L, 454N) that congealed during November and December across published cases in at least nine American states and in severe and fatal UK cases. The backgrounds with 188T have exhibited experimentally and practically determined Vaccine Escape, as have backgrounds carrying 225G individually. The final silent revision at HA 448L on this particular 188T template appears to correlate with RBD revisions (190G, 221L, 224K) and to revisions at known Vaccine Escape amino acid positions (158E, 159D, 188T (AcT), 225G).
A potentially related, contemporary sequence from Sweden was sampled one day after Denmark120_2010_12_20. SwedenHalmstad1_23F_2010_12_21, from the adjacent European geography, is the first published on this 188T background to carry HA 230I. The Halmstad sequence also revised at a known Vaccine Escape position to 159K. As the 188T bearing sub-clades represent over 50% of all GISAID-published, human pH1N1 sequences between October 2010 and March 2011, the "swl" lineage appears to have widespread 188T seeding that is attractant to additional polymorphic accommodation from zoonotic sources.
Though Scandinavia is now the only published geography with the polymorphic superset of 159K, 188T, 225G and 230I on similar backgrounds, GeneWurx analysis suggests that a signal with 188T, 225G and 230I has reportable probability in Scandinavia and several other regions worldwide. Consideration must be given to this potential template (188T, 225G, 230I) also carrying a revision from aa156 to aa159. In a parallel, transmitting sub-clade, 189T, 225G and 230I show potential for convergence and / or expansion with 165N and / or 158E.
Polymorphism jumping appears to be occurring bi-directionally between the transmitting 189T sub-clade and the emergent 188T sub-clades.
. . . . Denmark120_2010_12_20 (
. . . . . . . . HA truncated before aa1,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T [SwedenHalmstad1_23F_2010_12_21
. . . . . . . . . . . . . . . . with 100N, 159K, 230I,
. . . . . . . . . . . . . . . . . . . . syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . 454N, syn537S],
. . . . . . . . 225G mix wt,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [UKEngland4940476_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4880378_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4920303_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland142_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland126_2010_11
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 221L, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4860049_2010_11
. . . . . . . . . . . . . . . . . . . . with 0A, 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn210S, syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . 454N, 528I,
. . . . . . . . . . . . . . . . Hawaii08_2010_04_12
. . . . . . . . . . . . . . . . . . . . with 159D, 269V,
. . . . . . . . . . . . . . . . . . . . . . . . 312R, 313K, 377K,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S],
. . . . . . . . 454N)
. . . . Denmark20_2011_01_04 (
. . . . . . . . HA truncated before aa1,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T [SwedenHalmstad1_23F_2010_12_21
. . . . . . . . . . . . . . . . with 100N, 159K, 230I,
. . . . . . . . . . . . . . . . . . . . syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . 454N, syn537S],
. . . . . . . . 225G mix wt,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [UKEngland4940476_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4880378_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4920303_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland142_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland126_2010_11
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 221L, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4860049_2010_11
. . . . . . . . . . . . . . . . . . . . with 0A, 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn210S, syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . 454N, 528I,
. . . . . . . . . . . . . . . . Hawaii08_2010_04_12
. . . . . . . . . . . . . . . . . . . . with 159D, 269V,
. . . . . . . . . . . . . . . . . . . . . . . . 312R, 313K, 377K,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S],
. . . . . . . . 454N,
. . . . . . . . syn541C)
Supporting Sequences
From GISAID database (GISAID Citation).
. . . . SwedenHalmstad1_23F_2010_12_21 (
. . . . . . . . 100N [Slovakia1625_56X_2010_03_30_xL
. . . . . . . . . . . . . . . . . . . . with 230I],
. . . . . . . . 159K [UKEngland4940476_2010_08
. . . . . . . . . . . . . . . . . . . . with 128D, 377K,
. . . . . . . . . . . . . NY3230_2010_01_25
. . . . . . . . . . . . . . . . . . . . with 100N, syn231N],
. . . . . . . . 188T,
. . . . . . . . 230I,
. . . . . . . . syn245F [RussiaBelgorod2_2010_03_15
. . . . . . . . . . . . . . . . . . . . with 158E, 225G, 230I & syn343G],
. . . . . . . . 280A [MXinDRE797_2010_TmX
. . . . . . . . . . . . . swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . with 156E, 225N, 230I & syn346G],
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S [UKEngland5040499_2010_12_f])
. . . . UKEngland142_2010_11_severe (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)
. . . . UKEngland126_2010_11 (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 221L,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)
. . . . UKEngland4860049_2010_11 (
. . . . . . . . 0A,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn210S,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N,
. . . . . . . . 528I)
. . . . Hawaii08_2010_04_12
. . . . . . . . 159D mix wt,
. . . . . . . . 269V,
. . . . . . . . syn288A,
. . . . . . . . 312R,
. . . . . . . . 313K,
. . . . . . . . 377K,
. . . . . . . . syn448L [England4940476_2010_12,
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . England4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S])
Last Updated
2011-03-29
On 2011-03-20, the Statens Serum Institut of Copenhagen, Denmark published 6 pH1N1 sequences at GenBank sampled in a time period spanning approximately 3 weeks from late December 2010 until mid January 2011. Five of the six HA sequences demonstrate the 188T of the first pH1N1 emergent nucleotide coding having a second base revision (AcT) and two of those Denmark 188T sequences additionally carry HA 225G.
Denmark120_2010_12_20 and Denmark20_2011_01_04 with 188T and 225G demonstrate ongoing transmission of a template having 6 revisions (100N, syn179L, 188T, syn338G, syn448L, 454N) that congealed during November and December across published cases in at least nine American states and in severe and fatal UK cases. The backgrounds with 188T have exhibited experimentally and practically determined Vaccine Escape, as have backgrounds carrying 225G individually. The final silent revision at HA 448L on this particular 188T template appears to correlate with RBD revisions (190G, 221L, 224K) and to revisions at known Vaccine Escape amino acid positions (158E, 159D, 188T (AcT), 225G).
A potentially related, contemporary sequence from Sweden was sampled one day after Denmark120_2010_12_20. SwedenHalmstad1_23F_2010_12_21, from the adjacent European geography, is the first published on this 188T background to carry HA 230I. The Halmstad sequence also revised at a known Vaccine Escape position to 159K. As the 188T bearing sub-clades represent over 50% of all GISAID-published, human pH1N1 sequences between October 2010 and March 2011, the "swl" lineage appears to have widespread 188T seeding that is attractant to additional polymorphic accommodation from zoonotic sources.
Though Scandinavia is now the only published geography with the polymorphic superset of 159K, 188T, 225G and 230I on similar backgrounds, GeneWurx analysis suggests that a signal with 188T, 225G and 230I has reportable probability in Scandinavia and several other regions worldwide. Consideration must be given to this potential template (188T, 225G, 230I) also carrying a revision from aa156 to aa159. In a parallel, transmitting sub-clade, 189T, 225G and 230I show potential for convergence and / or expansion with 165N and / or 158E.
Polymorphism jumping appears to be occurring bi-directionally between the transmitting 189T sub-clade and the emergent 188T sub-clades.
. . . . Denmark120_2010_12_20 (
. . . . . . . . HA truncated before aa1,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T [SwedenHalmstad1_23F_2010_12_21
. . . . . . . . . . . . . . . . with 100N, 159K, 230I,
. . . . . . . . . . . . . . . . . . . . syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . 454N, syn537S],
. . . . . . . . 225G mix wt,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [UKEngland4940476_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4880378_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4920303_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland142_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland126_2010_11
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 221L, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4860049_2010_11
. . . . . . . . . . . . . . . . . . . . with 0A, 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn210S, syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . 454N, 528I,
. . . . . . . . . . . . . . . . Hawaii08_2010_04_12
. . . . . . . . . . . . . . . . . . . . with 159D, 269V,
. . . . . . . . . . . . . . . . . . . . . . . . 312R, 313K, 377K,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S],
. . . . . . . . 454N)
. . . . Denmark20_2011_01_04 (
. . . . . . . . HA truncated before aa1,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T [SwedenHalmstad1_23F_2010_12_21
. . . . . . . . . . . . . . . . with 100N, 159K, 230I,
. . . . . . . . . . . . . . . . . . . . syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . 454N, syn537S],
. . . . . . . . 225G mix wt,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [UKEngland4940476_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4880378_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4920303_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland142_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland126_2010_11
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 221L, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4860049_2010_11
. . . . . . . . . . . . . . . . . . . . with 0A, 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn210S, syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . 454N, 528I,
. . . . . . . . . . . . . . . . Hawaii08_2010_04_12
. . . . . . . . . . . . . . . . . . . . with 159D, 269V,
. . . . . . . . . . . . . . . . . . . . . . . . 312R, 313K, 377K,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S],
. . . . . . . . 454N,
. . . . . . . . syn541C)
Supporting Sequences
From GISAID database (GISAID Citation).
. . . . SwedenHalmstad1_23F_2010_12_21 (
. . . . . . . . 100N [Slovakia1625_56X_2010_03_30_xL
. . . . . . . . . . . . . . . . . . . . with 230I],
. . . . . . . . 159K [UKEngland4940476_2010_08
. . . . . . . . . . . . . . . . . . . . with 128D, 377K,
. . . . . . . . . . . . . NY3230_2010_01_25
. . . . . . . . . . . . . . . . . . . . with 100N, syn231N],
. . . . . . . . 188T,
. . . . . . . . 230I,
. . . . . . . . syn245F [RussiaBelgorod2_2010_03_15
. . . . . . . . . . . . . . . . . . . . with 158E, 225G, 230I & syn343G],
. . . . . . . . 280A [MXinDRE797_2010_TmX
. . . . . . . . . . . . . swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . with 156E, 225N, 230I & syn346G],
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S [UKEngland5040499_2010_12_f])
. . . . UKEngland142_2010_11_severe (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)
. . . . UKEngland126_2010_11 (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 221L,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)
. . . . UKEngland4860049_2010_11 (
. . . . . . . . 0A,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn210S,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N,
. . . . . . . . 528I)
. . . . Hawaii08_2010_04_12
. . . . . . . . 159D mix wt,
. . . . . . . . 269V,
. . . . . . . . syn288A,
. . . . . . . . 312R,
. . . . . . . . 313K,
. . . . . . . . 377K,
. . . . . . . . syn448L [England4940476_2010_12,
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . England4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S])
2011-01-15
2011 Novel Jiangsu HA from Swine Signals Zoonotic Flux
Last Updated 2011-01-16
The WHO Chinese National Influenza Center in Beijing deposited a full set of gene segment sequences on 2011-01-14 from a 3M sample taken in Jiangsu Province during the first week of the year. The Hong Kong Ministry of Health issued a notification that the boy was on long-term steroid treatment for chronic kidney disease.
Preliminary review shows that ChinaJiangsu1_3M_2011_01_04 carries a novel Hemagglutinin most closely related to late decade swine from Asia. The captivating factor is that this swine-like HA also demonstrates homology at least 25 recent genetic acquisitions into the human pH1N1 reservoir related to the UK Severe Wave and associated sequences on the highly divergent and hyper-zoonotic emerging sub-clades.
GeneWurx has prepared a spreadsheet for collaboration detailing the preliminarily recognised pH1N1 homologies to this most recent sequence in the database, ChinaJiangsu1_3M_2011_01_04. Several additional matches are not yet vetted for the spreadsheet, including syn338G, syn343G, syn346G, syn353G and syn363G. Each must be investigated as variant silent codings to changes in pH1N1 at the same amino acid position.
GeneWurx_Novel_HA_Jiangsu1_3M_2011_01_04_v0.xls
The WHO Chinese National Influenza Center in Beijing deposited a full set of gene segment sequences on 2011-01-14 from a 3M sample taken in Jiangsu Province during the first week of the year. The Hong Kong Ministry of Health issued a notification that the boy was on long-term steroid treatment for chronic kidney disease.
Preliminary review shows that ChinaJiangsu1_3M_2011_01_04 carries a novel Hemagglutinin most closely related to late decade swine from Asia. The captivating factor is that this swine-like HA also demonstrates homology at least 25 recent genetic acquisitions into the human pH1N1 reservoir related to the UK Severe Wave and associated sequences on the highly divergent and hyper-zoonotic emerging sub-clades.
GeneWurx has prepared a spreadsheet for collaboration detailing the preliminarily recognised pH1N1 homologies to this most recent sequence in the database, ChinaJiangsu1_3M_2011_01_04. Several additional matches are not yet vetted for the spreadsheet, including syn338G, syn343G, syn346G, syn353G and syn363G. Each must be investigated as variant silent codings to changes in pH1N1 at the same amino acid position.
GeneWurx_Novel_HA_Jiangsu1_3M_2011_01_04_v0.xls
2010-08-14
Pune India Communicates Pandemic Genetic CrossTalk with England and United States
The practice of science exists to serve mankind by discovering answers.
Utilising advanced tools, accurate observations and absolute logic, the mysterious becomes discernable and the discernable, in turn, becomes actionable. Find a problem. Fix a problem.
Tonight, we ask science to take a cue from a bouncing red ball, a small red ball. Focus and faculty are requested. We will paint a blue 50V on one small, red bouncing ball and then see where it goes. If the results are plausible, we may try another.
Follow that springy, red ball from one continent to the next. And then back again.
The ΣPF11 influenza reservoir is not mysterious in the least when the data that has been collected is actually made available for evaluation. Even post-pandemic publications may be informative. We come to some such encounter today from a recent post-pandemic deposit of pandemic H1N1 sequences from England.
Watch the RnR * polymorphisms choose backgrounds and associate with other revisions as this Enhanced Acquisition virus becomes something new everyday in every city around the globe. Humans, swine and birds are vectors, but only humans and birds can fly. Swine store; humans and birds promote.
Let the following sequences describe the arc of two individual silent changes between and among India, the United Kingdom and the United States of America, including military personnel. Synonymous 50V and synonymous 348V are only two examples. These two representatives are certainly not comprehensive of this interchange behaviour.
. . . . England94840759_2009_11 (
. . . . . . . . syn50V [GDWujiang51_2010_03_18,
. . . . . . . . . . . . . . SouthCarolina02E3_2010_03_05
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . TexasJMS413_2010_02_03
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . TexasJMS391_2009_12_23
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . IndiaPune10604_2009_09],
. . . . . . . . 214R,
. . . . . . . . syn428L)
. . . . England734_2009_10 (
. . . . . . . . syn50V [GDWujiang51_2010_03_18,
. . . . . . . . . . . . . . SouthCarolina02E3_2010_03_05
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . TexasJMS413_2010_02_03
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . TexasJMS391_2009_12_23
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . IndiaPune10604_2009_09])
. . . . Eng662_2009_08 (
. . . . . . . . 25R [SouthCarolina02E3_2010_03_05
. . . . . . . . . . . . . . . .. . . . with syn50V,
. . . . . . . . . . . TexasJMS413_2010_02_03
. . . . . . . . . . . . . . . .. . . . with syn50V,
. . . . . . . . . . . TexasJMS391_2009_12_23
. . . . . . . . . . . . . . . .. . . . with syn50V,
. . . . . . . . . . . Texas extensive (10 more),
. . . . . . . . . . . Afghanistan (2),
. . . . . . . . . . . Russia149_2009_11_01_xL,
. . . . . . . . . . . Utah42_2009_07_24
. . . . . . . . . . . . . . . with 225G / 225N],
. . . . . . . . syn116R [NY6530_2010_02_21,
. . . . . . . . . . . . . . swOsaka1_2009_10,
. . . . . . . . . . . . . . Texas45071344_2009_09_07,
. . . . . . . . . . . . . . Portugal (2) 2009_08_19,
. . . . . . . . . . . . . . Military (30) 2009_08 to 2009_12,
. . . . . . . . . . . . . . Australia as early as 2009_07 (3),
. . . . . . . . . . . . . . SingTLL53_2009_06_14,
. . . . . . . . . . . . . . Columbia 2009_06 (2),
. . . . . . . . . . . . . . WiscD1606_2009_05_03],
. . . . . . . . syn348V [JapanAF2284_2009_11_27,
. . . . . . . . . . . . . . Frankfurt301_2009_11_23,
. . . . . . . . . . . . . . Ankara27_2009_11_11,
. . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . Thailand (24) as late as 2009_09_25,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . . IndiaPune807_2009_07,
. . . . . . . . . . . . . . PNG_PortMoresby2005_2009_07_08,
. . . . . . . . . . . . . . MoroccoRabat72_2009_07_02,
. . . . . . . . . . . . . . Slovenia2322_2009_07_01,
. . . . . . . . . . . . . . SingON442_2009_06_25,
. . . . . . . . . . . . . . ThailandCUB5_2009_06_13],
. . . . . . . . 494K [Indiana21_2009_12_10,
. . . . . . . . . . . . NewMexico07_2009_10_18,
. . . . . . . . . . . . NY5755_2009_10_01,
. . . . . . . . . . . . Ankara12_2009_09,
. . . . . . . . . . . . Ankara16_2009_09,
. . . . . . . . . . . . Ankara29_2009,
. . . . . . . . . . . . NY4568_2009_07_09,
. . . . . . . . . . . . NY4500_2009_07_01,
. . . . . . . . . . . . RhodeIsland04_2009_06_01])
Three American sequences are on file from December 2009 to March 2010 that accumulate both the 25R of Eng662_2009_08 and the syn50V of IndiaPune10604_2009_09. A pattern of attraction or permissiveness is suggested.
India is in the grip of a post-pandemic acceleration of death due to burgeoning caseloads and an apparent change in viral behaviour. They have experience, foresight, materials and initiative, but the disease is overcoming the system and killing the citizens. The health purveyors are doing everything by the book, but the chapters are out-dated apparently.
What will we find in those sequences? How may we adapt our methods and materials to assist the families in India? When will those viral changes be adopted in other countries?
Pondering is excellent, but action is better.
The sequences will tell the truth and provide a footing to act. Please publish the sequences from May to August 2010.
Supporting / Related Sequences
. . . . India3725_2010_04_03 (
. . . . . . . . 117T,
. . . . . . . . syn167S,
. . . . . . . . 186P,
. . . . . . . . syn474C,
. . . . . . . . syn526S [SwedenMalmoe2_2010_05_07])
. . . . IndiaPune10604_2009_09 (
. . . . . . . . syn2N [UkrSumy797_2009_11_13_f,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . .. . . . . SingON2416_2009_12_15],
. . . . . . . . syn50V [TexasJMS391_2009_12_23,
. . . . . . . . . . . . . . TexasJMS413_2009_02_03,
. . . . . . . . . . . . . . SouthCarolina02E3_2010_03_05],
. . . . . . . . syn178V (GTt) [NewHampshire02E3_2010_02_19 (GTa)],
. . . . . . . . 206S,
. . . . . . . . 296H,
. . . . . . . . syn348V [Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . syn485G [Nebraska 01_2010_01_28,
. . . . . . . . . . . . . . Orenburg2974_2009_11_16_xL,
. . . . . . . . . . . . . . NagasakiHA10_22_2010_03_01])
. . . . IndiaPune6196_2009_08 (
. . . . . . . . #12E,
. . . . . . . . syn2N [UkrSumy797_2009_11_13_f,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . .. . . . . SingON2416_2009_12_15],
. . . . . . . . syn152I [NY6939_2009_12_11,
. . . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07,
. . . . . . . . . . . . . . . CalifVRDL115_2009_12_04,
. . . . . . . . . . . . . . . England1051_2009_12,
. . . . . . . . . . . . . . . England1050_2009_12,
. . . . . . . . . . . . . . . Scotland103_2009_12,
. . . . . . . . . . . . . . . England94800096_2009_11,
. . . . . . . . . . . . . . . ItalyAncona451_2009_11_27_f,
. . . . . . . . . . . . . . . NY6607_2009_11_24,
. . . . . . . . . . . . . . . CalifVRDL107_2009_11_15,
. . . . . . . . . . . . . . . CalifVRDL101_2009_11_05,
. . . . . . . . . . . . . . . DC_114_2009_11_04,
. . . . . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . . . . NY5447_2009_10_23,
. . . . . . . . . . . . . . . CalifVRDL84_2009_10_09,
. . . . . . . . . . . . . . . CalifVRDL87_2009_10_09,
. . . . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . . . SantoDomingoWR1057N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1058N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1059N_2009_06_30],
. . . . . . . . 206S,
. . . . . . . . 296H,
. . . . . . . . syn300P (CCt) [H5N1, H6N1, H7N3, H7N7],
. . . . . . . . . . . . . . . . . [Virginia24_2009_06_03 (CCt),
. . . . . . . . . . . . . . . . . NY0352_2009_12_27 (CCt),
. . . . . . . . . . . . . . . . . IllinoisAF2223_2009_12_18 (CCt),
. . . . . . . . . . . . . . . . . SingON2416_2009_12_15 (CCa),
. . . . . . . . . . . . . . . . . Vietnam2043_2009_12_01_TmX (CCa),
. . . . . . . . . . . . . . . . . HunanFur129_2010_01_13 (CCa),
. . . . . . . . . . . . . . . . . Slovenia5613_2009_12 (CCa),
. . . . . . . . . . . . . . . . . Minnesota40_2009_11_19 (CCa) w syn252V],
. . . . . . . . 342R,
. . . . . . . . syn348V [Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . syn355H [H2, H5N1, H6N1],
. . . . . . . . . . . . . . [GDLiwan1170_2010_03_14,
. . . . . . . . . . . . . . NY2963_2010_01_22
. . . . . . . . . . . . . .. . . . . . . . with 50E, 100N,
. . . . . . . . . . . . . . ItalyAncona508_2009_12_31
. . . . . . . . . . . . . .. . . . . . . . with syn181G,
. . . . . . . . . . . . . . Yamagata803_2009_12_21,
. . . . . . . . . . . . . . Astrakhan_CHRM_2009_11_24_xL_f,
. . . . . . . . . . . . . . MoscowOb_ZNF_2009_11_24_xL_f,
. . . . . . . . . . . . . . Ivanovo_STV1_2009_11_21
. . . . . . . . . . . . . .. . . . . . . . with 225G,
. . . . . . . . . . . . . . FloridaPensacola107_2009_11_12,
. . . . . . . . . . . . . . MoscowOb_STV_2009_11_09_f
. . . . . . . . . . . . . .. . . . . . . . with 225N,
. . . . . . . . . . . . . . swTaiwanTD4119B2_2009_11_04,
. . . . . . . . . . . . . . ArgentinaHNRG44_2009_06_30
. . . . . . . . . . . . . .. . . . . . . . with 71G,
. . . . . . . . . . . . . . ArgentinaHNRG39_2009_06_23
. . . . . . . . . . . . . .. . . . . . . . with 259T,
. . . . . . . . . . . . . . WiscD0589_2009_06_03
. . . . . . . . . . . . . .. . . . . . . . with syn178V])
. . . . IndiaDhule9433_2009_08 (
. . . . . . . . #12E,
. . . . . . . . syn2N [UkrSumy797_2009_11_13_f,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . . . . . . . SingON2416_2009_12_15,
. . . . . . . . . . . . . IndiaPune10604_2009_09, et al],
. . . . . . . . syn152I [NY6939_2009_12_11,
. . . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07,
. . . . . . . . . . . . . . . CalifVRDL115_2009_12_04,
. . . . . . . . . . . . . . . England1051_2009_12,
. . . . . . . . . . . . . . . England1050_2009_12,
. . . . . . . . . . . . . . . Scotland103_2009_12,
. . . . . . . . . . . . . . . England94800096_2009_11,
. . . . . . . . . . . . . . . ItalyAncona451_2009_11_27_f,
. . . . . . . . . . . . . . . NY6607_2009_11_24,
. . . . . . . . . . . . . . . CalifVRDL107_2009_11_15,
. . . . . . . . . . . . . . . CalifVRDL101_2009_11_05,
. . . . . . . . . . . . . . . DC_114_2009_11_04,
. . . . . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . . . . NY5447_2009_10_23,
. . . . . . . . . . . . . . . CalifVRDL84_2009_10_09,
. . . . . . . . . . . . . . . CalifVRDL87_2009_10_09,
. . . . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . . . SantoDomingoWR1057N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1058N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1059N_2009_06_30],
. . . . . . . . 176I,
. . . . . . . . 205W,
. . . . . . . . 206S,
. . . . . . . . 252L (cTG) [Maryland03_2010_01_13 (tTG),
. . . . . . . . . . . . . . . Guangdong2361_2009_11_25 (tTG)],
. . . . . . . . 296H,
. . . . . . . . syn348V [Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . syn386I [1918, Unique to PF11])
. . . . IndiaPune807_2009_07 (
. . . . . . . . #12E,
. . . . . . . . syn2N [UkrSumy797_2009_11_13_f ,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . .. . . . . SingON2416_2009_12_15],
. . . . . . . . 100Q [Unique to PF11],
. . . . . . . . syn104L [CalifVRDL132_2009_12_30,
. . . . . . . . . . . . . . . Texas45122538_2009_09_12,
. . . . . . . . . . . . . . . WiscD0410_2009_09_24,
. . . . . . . . . . . . . . . WiscD1355_2009_09_21],
. . . . . . . . 206S,
. . . . . . . . 296H,
. . . . . . . . syn348V [Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . 461E [Unique to PF11]),
. . . . England1048_2009_12 (
. . . . . . . . 214R,
. . . . . . . . 225E,
. . . . . . . . 324I)
. . . . England1051_2009_12 (
. . . . . . . . syn10Y,
. . . . . . . . 35I,
. . . . . . . . syn152I [NY6939_2009_12_11,
. . . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07,
. . . . . . . . . . . . . . . CalifVRDL115_2009_12_04,
. . . . . . . . . . . . . . . England1050_2009_12,
. . . . . . . . . . . . . . . Scotland103_2009_12,
. . . . . . . . . . . . . . . England94800096_2009_11,
. . . . . . . . . . . . . . . ItalyAncona451_2009_11_27_f,
. . . . . . . . . . . . . . . NY6607_2009_11_24,
. . . . . . . . . . . . . . . CalifVRDL107_2009_11_15,
. . . . . . . . . . . . . . . CalifVRDL101_2009_11_05,
. . . . . . . . . . . . . . . DC_114_2009_11_04,
. . . . . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . . . . NY5447_2009_10_23,
. . . . . . . . . . . . . . . CalifVRDL84_2009_10_09,
. . . . . . . . . . . . . . . CalifVRDL87_2009_10_09,
. . . . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . . . SantoDomingoWR1057N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1058N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1059N_2009_06_30],
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn254P,
. . . . . . . . syn276H,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 502K [Ukraine],
. . . . . . . . 523A)
. . . . SouthCarolina02E3_2010_03_05 (
. . . . . . . . 25R [Utah42_2009_07_24 with 225G / 225N,
. . . . . . . . . . . Texas extensive (12),
. . . . . . . . . . . Afghanistan (2),
. . . . . . . . . . . Russia149_2009_11_01_xL],
. . . . . . . . syn50V [TexasJMS391_2009_12_23,
. . . . . . . . . . . . . TexasJMS413_2009_02_03,
. . . . . . . . . . . . . IndiaPune10604_2009_09],
. . . . . . . . 130E (GAa) [1918],
. . . . . . . . . . . . [Netherlands2243_2009_11_17_xL (GAg) mix
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . with 158E, 225G,
. . . . . . . . . . . . Iraq8531_2009_09_08_xL (GAa) with 131L,
. . . . . . . . . . . . Guangdong0872_2009_12_27 (GAa),
. . . . . . . . . . . . SingTLL52_2009_06_14 (GAa),
. . . . . . . . . . . . swAlbertaOTH_33_23_2009_05_03 (GAa)],
. . . . . . . . 206T)
. . . . TexasJMS413_2010_02_03 (
. . . . . . . . 25R,
. . . . . . . . syn50V,
. . . . . . . . syn84E)
. . . . TexasJMS391_2009_12_23 (
. . . . . . . . 25R,
. . . . . . . . syn50V,
. . . . . . . . syn84E,
. . . . . . . . syn374A)
. . . . NY2963_2010_01_22 (
. . . . . . . . 50E,
. . . . . . . . 100N,
. . . . . . . . syn270I,
. . . . . . . . syn291T,
. . . . . . . . syn355H,
. . . . . . . . 377K)
. . . . FloridaPensacola107_2009_11_12 (
. . . . . . . . 35I,
. . . . . . . . syn338G,
. . . . . . . . syn355H,
. . . . . . . . syn456L)
. . . . WiscD0589_2009_06_03 (
. . . . . . . . syn36L,
. . . . . . . . syn178V,
. . . . . . . . 193N,
. . . . . . . . syn355H)
. . . . Indiana21_2009_12_01 (
. . . . . . . . syn12A,
. . . . . . . . syn177L,
. . . . . . . . syn193S,
. . . . . . . . 212E mix,
. . . . . . . . 313K,
. . . . . . . . syn346G,
. . . . . . . . 359G,
. . . . . . . . 377K,
. . . . . . . . 494K)
. . . . IllinoisAF2223_2009_12_18 (
. . . . . . . . syn34N,
. . . . . . . . syn300P (CCt),
. . . . . . . . 377K,
. . . . . . . . HA truncated after aa386)
. . . . CalifVRDL107_2009_11_15 (
. . . . . . . . 35I,
. . . . . . . . 39N,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn276H,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . CalifVRDL115_2009_12_04 (
. . . . . . . . 35I,
. . . . . . . . 77N,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn276H,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . Malmoe2_2010_05_07 (
. . . . . . . . 89G,
. . . . . . . . syn108L [tn],
. . . . . . . . syn159N,
. . . . . . . . 206T,
. . . . . . . . 259T [ArgentinaHNRG39_2009_06_23
. . . . . . . . . . . . . . . . . . . . with syn355H],
. . . . . . . . syn280T [1918, WSN33],
. . . . . . . . syn526S [India3725_2010_04_03])
. . . . ItalyAncona508_2009_12_31 (
. . . . . . . . syn172K,
. . . . . . . . syn181G,
. . . . . . . . syn239P,
. . . . . . . . syn355H,
. . . . . . . . 373H)
. . . . GDLiwan1170_2010_03_14 (
. . . . . . . . 131P,
. . . . . . . . 202A,
. . . . . . . . 271T,
. . . . . . . . 298V,
. . . . . . . . syn355H,
. . . . . . . . 375F)
. . . . tkOntarioFAV117_1C_2009_12_07 (
. . . . . . . . 35I [H5N1],
. . . . . . . . syn55L,
. . . . . . . . syn152I,
. . . . . . . . 186P,
. . . . . . . . syn205G,
. . . . . . . . syn219I,
. . . . . . . . syn276H [1918, S5],
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . syn486T,
. . . . . . . . 523A)
Please refer to additional studies for further genetic analyses, including the survey on amino acid revisions potentially related to Vaccine Escape. A hyper-morphic, TamiFlu-resistant sequence from the state of Washington in Spring 2010 has recently been profiled with similar zoonotic influences.
This analysis was fueled by puneri amti and funded with contributions from concerned families, including HOD, BMS, MJV and CSB.
* Rare, not Random
Utilising advanced tools, accurate observations and absolute logic, the mysterious becomes discernable and the discernable, in turn, becomes actionable. Find a problem. Fix a problem.
Tonight, we ask science to take a cue from a bouncing red ball, a small red ball. Focus and faculty are requested. We will paint a blue 50V on one small, red bouncing ball and then see where it goes. If the results are plausible, we may try another.
Follow that springy, red ball from one continent to the next. And then back again.
The ΣPF11 influenza reservoir is not mysterious in the least when the data that has been collected is actually made available for evaluation. Even post-pandemic publications may be informative. We come to some such encounter today from a recent post-pandemic deposit of pandemic H1N1 sequences from England.
Watch the RnR * polymorphisms choose backgrounds and associate with other revisions as this Enhanced Acquisition virus becomes something new everyday in every city around the globe. Humans, swine and birds are vectors, but only humans and birds can fly. Swine store; humans and birds promote.
Let the following sequences describe the arc of two individual silent changes between and among India, the United Kingdom and the United States of America, including military personnel. Synonymous 50V and synonymous 348V are only two examples. These two representatives are certainly not comprehensive of this interchange behaviour.
. . . . England94840759_2009_11 (
. . . . . . . . syn50V [GDWujiang51_2010_03_18,
. . . . . . . . . . . . . . SouthCarolina02E3_2010_03_05
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . TexasJMS413_2010_02_03
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . TexasJMS391_2009_12_23
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . IndiaPune10604_2009_09],
. . . . . . . . 214R,
. . . . . . . . syn428L)
. . . . England734_2009_10 (
. . . . . . . . syn50V [GDWujiang51_2010_03_18,
. . . . . . . . . . . . . . SouthCarolina02E3_2010_03_05
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . TexasJMS413_2010_02_03
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . TexasJMS391_2009_12_23
. . . . . . . . . . . . . . . . . . . . . . with 25R,
. . . . . . . . . . . . . . IndiaPune10604_2009_09])
. . . . Eng662_2009_08 (
. . . . . . . . 25R [SouthCarolina02E3_2010_03_05
. . . . . . . . . . . . . . . .. . . . with syn50V,
. . . . . . . . . . . TexasJMS413_2010_02_03
. . . . . . . . . . . . . . . .. . . . with syn50V,
. . . . . . . . . . . TexasJMS391_2009_12_23
. . . . . . . . . . . . . . . .. . . . with syn50V,
. . . . . . . . . . . Texas extensive (10 more),
. . . . . . . . . . . Afghanistan (2),
. . . . . . . . . . . Russia149_2009_11_01_xL,
. . . . . . . . . . . Utah42_2009_07_24
. . . . . . . . . . . . . . . with 225G / 225N],
. . . . . . . . syn116R [NY6530_2010_02_21,
. . . . . . . . . . . . . . swOsaka1_2009_10,
. . . . . . . . . . . . . . Texas45071344_2009_09_07,
. . . . . . . . . . . . . . Portugal (2) 2009_08_19,
. . . . . . . . . . . . . . Military (30) 2009_08 to 2009_12,
. . . . . . . . . . . . . . Australia as early as 2009_07 (3),
. . . . . . . . . . . . . . SingTLL53_2009_06_14,
. . . . . . . . . . . . . . Columbia 2009_06 (2),
. . . . . . . . . . . . . . WiscD1606_2009_05_03],
. . . . . . . . syn348V [JapanAF2284_2009_11_27,
. . . . . . . . . . . . . . Frankfurt301_2009_11_23,
. . . . . . . . . . . . . . Ankara27_2009_11_11,
. . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . Thailand (24) as late as 2009_09_25,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . . IndiaPune807_2009_07,
. . . . . . . . . . . . . . PNG_PortMoresby2005_2009_07_08,
. . . . . . . . . . . . . . MoroccoRabat72_2009_07_02,
. . . . . . . . . . . . . . Slovenia2322_2009_07_01,
. . . . . . . . . . . . . . SingON442_2009_06_25,
. . . . . . . . . . . . . . ThailandCUB5_2009_06_13],
. . . . . . . . 494K [Indiana21_2009_12_10,
. . . . . . . . . . . . NewMexico07_2009_10_18,
. . . . . . . . . . . . NY5755_2009_10_01,
. . . . . . . . . . . . Ankara12_2009_09,
. . . . . . . . . . . . Ankara16_2009_09,
. . . . . . . . . . . . Ankara29_2009,
. . . . . . . . . . . . NY4568_2009_07_09,
. . . . . . . . . . . . NY4500_2009_07_01,
. . . . . . . . . . . . RhodeIsland04_2009_06_01])
Three American sequences are on file from December 2009 to March 2010 that accumulate both the 25R of Eng662_2009_08 and the syn50V of IndiaPune10604_2009_09. A pattern of attraction or permissiveness is suggested.
- SouthCarolina02E3_2010_03_05
- TexasJMS413_2010_02_03
- TexasJMS391_2009_12_23
India is in the grip of a post-pandemic acceleration of death due to burgeoning caseloads and an apparent change in viral behaviour. They have experience, foresight, materials and initiative, but the disease is overcoming the system and killing the citizens. The health purveyors are doing everything by the book, but the chapters are out-dated apparently.
What will we find in those sequences? How may we adapt our methods and materials to assist the families in India? When will those viral changes be adopted in other countries?
Pondering is excellent, but action is better.
The sequences will tell the truth and provide a footing to act. Please publish the sequences from May to August 2010.
Supporting / Related Sequences
. . . . India3725_2010_04_03 (
. . . . . . . . 117T,
. . . . . . . . syn167S,
. . . . . . . . 186P,
. . . . . . . . syn474C,
. . . . . . . . syn526S [SwedenMalmoe2_2010_05_07])
. . . . IndiaPune10604_2009_09 (
. . . . . . . . syn2N [UkrSumy797_2009_11_13_f,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . .. . . . . SingON2416_2009_12_15],
. . . . . . . . syn50V [TexasJMS391_2009_12_23,
. . . . . . . . . . . . . . TexasJMS413_2009_02_03,
. . . . . . . . . . . . . . SouthCarolina02E3_2010_03_05],
. . . . . . . . syn178V (GTt) [NewHampshire02E3_2010_02_19 (GTa)],
. . . . . . . . 206S,
. . . . . . . . 296H,
. . . . . . . . syn348V [Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . syn485G [Nebraska 01_2010_01_28,
. . . . . . . . . . . . . . Orenburg2974_2009_11_16_xL,
. . . . . . . . . . . . . . NagasakiHA10_22_2010_03_01])
. . . . IndiaPune6196_2009_08 (
. . . . . . . . #12E,
. . . . . . . . syn2N [UkrSumy797_2009_11_13_f,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . .. . . . . SingON2416_2009_12_15],
. . . . . . . . syn152I [NY6939_2009_12_11,
. . . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07,
. . . . . . . . . . . . . . . CalifVRDL115_2009_12_04,
. . . . . . . . . . . . . . . England1051_2009_12,
. . . . . . . . . . . . . . . England1050_2009_12,
. . . . . . . . . . . . . . . Scotland103_2009_12,
. . . . . . . . . . . . . . . England94800096_2009_11,
. . . . . . . . . . . . . . . ItalyAncona451_2009_11_27_f,
. . . . . . . . . . . . . . . NY6607_2009_11_24,
. . . . . . . . . . . . . . . CalifVRDL107_2009_11_15,
. . . . . . . . . . . . . . . CalifVRDL101_2009_11_05,
. . . . . . . . . . . . . . . DC_114_2009_11_04,
. . . . . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . . . . NY5447_2009_10_23,
. . . . . . . . . . . . . . . CalifVRDL84_2009_10_09,
. . . . . . . . . . . . . . . CalifVRDL87_2009_10_09,
. . . . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . . . SantoDomingoWR1057N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1058N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1059N_2009_06_30],
. . . . . . . . 206S,
. . . . . . . . 296H,
. . . . . . . . syn300P (CCt) [H5N1, H6N1, H7N3, H7N7],
. . . . . . . . . . . . . . . . . [Virginia24_2009_06_03 (CCt),
. . . . . . . . . . . . . . . . . NY0352_2009_12_27 (CCt),
. . . . . . . . . . . . . . . . . IllinoisAF2223_2009_12_18 (CCt),
. . . . . . . . . . . . . . . . . SingON2416_2009_12_15 (CCa),
. . . . . . . . . . . . . . . . . Vietnam2043_2009_12_01_TmX (CCa),
. . . . . . . . . . . . . . . . . HunanFur129_2010_01_13 (CCa),
. . . . . . . . . . . . . . . . . Slovenia5613_2009_12 (CCa),
. . . . . . . . . . . . . . . . . Minnesota40_2009_11_19 (CCa) w syn252V],
. . . . . . . . 342R,
. . . . . . . . syn348V [Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . syn355H [H2, H5N1, H6N1],
. . . . . . . . . . . . . . [GDLiwan1170_2010_03_14,
. . . . . . . . . . . . . . NY2963_2010_01_22
. . . . . . . . . . . . . .. . . . . . . . with 50E, 100N,
. . . . . . . . . . . . . . ItalyAncona508_2009_12_31
. . . . . . . . . . . . . .. . . . . . . . with syn181G,
. . . . . . . . . . . . . . Yamagata803_2009_12_21,
. . . . . . . . . . . . . . Astrakhan_CHRM_2009_11_24_xL_f,
. . . . . . . . . . . . . . MoscowOb_ZNF_2009_11_24_xL_f,
. . . . . . . . . . . . . . Ivanovo_STV1_2009_11_21
. . . . . . . . . . . . . .. . . . . . . . with 225G,
. . . . . . . . . . . . . . FloridaPensacola107_2009_11_12,
. . . . . . . . . . . . . . MoscowOb_STV_2009_11_09_f
. . . . . . . . . . . . . .. . . . . . . . with 225N,
. . . . . . . . . . . . . . swTaiwanTD4119B2_2009_11_04,
. . . . . . . . . . . . . . ArgentinaHNRG44_2009_06_30
. . . . . . . . . . . . . .. . . . . . . . with 71G,
. . . . . . . . . . . . . . ArgentinaHNRG39_2009_06_23
. . . . . . . . . . . . . .. . . . . . . . with 259T,
. . . . . . . . . . . . . . WiscD0589_2009_06_03
. . . . . . . . . . . . . .. . . . . . . . with syn178V])
. . . . IndiaDhule9433_2009_08 (
. . . . . . . . #12E,
. . . . . . . . syn2N [UkrSumy797_2009_11_13_f,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . . . . . . . SingON2416_2009_12_15,
. . . . . . . . . . . . . IndiaPune10604_2009_09, et al],
. . . . . . . . syn152I [NY6939_2009_12_11,
. . . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07,
. . . . . . . . . . . . . . . CalifVRDL115_2009_12_04,
. . . . . . . . . . . . . . . England1051_2009_12,
. . . . . . . . . . . . . . . England1050_2009_12,
. . . . . . . . . . . . . . . Scotland103_2009_12,
. . . . . . . . . . . . . . . England94800096_2009_11,
. . . . . . . . . . . . . . . ItalyAncona451_2009_11_27_f,
. . . . . . . . . . . . . . . NY6607_2009_11_24,
. . . . . . . . . . . . . . . CalifVRDL107_2009_11_15,
. . . . . . . . . . . . . . . CalifVRDL101_2009_11_05,
. . . . . . . . . . . . . . . DC_114_2009_11_04,
. . . . . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . . . . NY5447_2009_10_23,
. . . . . . . . . . . . . . . CalifVRDL84_2009_10_09,
. . . . . . . . . . . . . . . CalifVRDL87_2009_10_09,
. . . . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . . . SantoDomingoWR1057N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1058N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1059N_2009_06_30],
. . . . . . . . 176I,
. . . . . . . . 205W,
. . . . . . . . 206S,
. . . . . . . . 252L (cTG) [Maryland03_2010_01_13 (tTG),
. . . . . . . . . . . . . . . Guangdong2361_2009_11_25 (tTG)],
. . . . . . . . 296H,
. . . . . . . . syn348V [Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . syn386I [1918, Unique to PF11])
. . . . IndiaPune807_2009_07 (
. . . . . . . . #12E,
. . . . . . . . syn2N [UkrSumy797_2009_11_13_f ,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . .. . . . . SingON2416_2009_12_15],
. . . . . . . . 100Q [Unique to PF11],
. . . . . . . . syn104L [CalifVRDL132_2009_12_30,
. . . . . . . . . . . . . . . Texas45122538_2009_09_12,
. . . . . . . . . . . . . . . WiscD0410_2009_09_24,
. . . . . . . . . . . . . . . WiscD1355_2009_09_21],
. . . . . . . . 206S,
. . . . . . . . 296H,
. . . . . . . . syn348V [Yaroslavl_CHMV_2009_11_10_f with 225G,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . 461E [Unique to PF11]),
. . . . England1048_2009_12 (
. . . . . . . . 214R,
. . . . . . . . 225E,
. . . . . . . . 324I)
. . . . England1051_2009_12 (
. . . . . . . . syn10Y,
. . . . . . . . 35I,
. . . . . . . . syn152I [NY6939_2009_12_11,
. . . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07,
. . . . . . . . . . . . . . . CalifVRDL115_2009_12_04,
. . . . . . . . . . . . . . . England1050_2009_12,
. . . . . . . . . . . . . . . Scotland103_2009_12,
. . . . . . . . . . . . . . . England94800096_2009_11,
. . . . . . . . . . . . . . . ItalyAncona451_2009_11_27_f,
. . . . . . . . . . . . . . . NY6607_2009_11_24,
. . . . . . . . . . . . . . . CalifVRDL107_2009_11_15,
. . . . . . . . . . . . . . . CalifVRDL101_2009_11_05,
. . . . . . . . . . . . . . . DC_114_2009_11_04,
. . . . . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . . . . NY5447_2009_10_23,
. . . . . . . . . . . . . . . CalifVRDL84_2009_10_09,
. . . . . . . . . . . . . . . CalifVRDL87_2009_10_09,
. . . . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . . . SantoDomingoWR1057N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1058N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1059N_2009_06_30],
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn254P,
. . . . . . . . syn276H,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 502K [Ukraine],
. . . . . . . . 523A)
. . . . SouthCarolina02E3_2010_03_05 (
. . . . . . . . 25R [Utah42_2009_07_24 with 225G / 225N,
. . . . . . . . . . . Texas extensive (12),
. . . . . . . . . . . Afghanistan (2),
. . . . . . . . . . . Russia149_2009_11_01_xL],
. . . . . . . . syn50V [TexasJMS391_2009_12_23,
. . . . . . . . . . . . . TexasJMS413_2009_02_03,
. . . . . . . . . . . . . IndiaPune10604_2009_09],
. . . . . . . . 130E (GAa) [1918],
. . . . . . . . . . . . [Netherlands2243_2009_11_17_xL (GAg) mix
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . with 158E, 225G,
. . . . . . . . . . . . Iraq8531_2009_09_08_xL (GAa) with 131L,
. . . . . . . . . . . . Guangdong0872_2009_12_27 (GAa),
. . . . . . . . . . . . SingTLL52_2009_06_14 (GAa),
. . . . . . . . . . . . swAlbertaOTH_33_23_2009_05_03 (GAa)],
. . . . . . . . 206T)
. . . . TexasJMS413_2010_02_03 (
. . . . . . . . 25R,
. . . . . . . . syn50V,
. . . . . . . . syn84E)
. . . . TexasJMS391_2009_12_23 (
. . . . . . . . 25R,
. . . . . . . . syn50V,
. . . . . . . . syn84E,
. . . . . . . . syn374A)
. . . . NY2963_2010_01_22 (
. . . . . . . . 50E,
. . . . . . . . 100N,
. . . . . . . . syn270I,
. . . . . . . . syn291T,
. . . . . . . . syn355H,
. . . . . . . . 377K)
. . . . FloridaPensacola107_2009_11_12 (
. . . . . . . . 35I,
. . . . . . . . syn338G,
. . . . . . . . syn355H,
. . . . . . . . syn456L)
. . . . WiscD0589_2009_06_03 (
. . . . . . . . syn36L,
. . . . . . . . syn178V,
. . . . . . . . 193N,
. . . . . . . . syn355H)
. . . . Indiana21_2009_12_01 (
. . . . . . . . syn12A,
. . . . . . . . syn177L,
. . . . . . . . syn193S,
. . . . . . . . 212E mix,
. . . . . . . . 313K,
. . . . . . . . syn346G,
. . . . . . . . 359G,
. . . . . . . . 377K,
. . . . . . . . 494K)
. . . . IllinoisAF2223_2009_12_18 (
. . . . . . . . syn34N,
. . . . . . . . syn300P (CCt),
. . . . . . . . 377K,
. . . . . . . . HA truncated after aa386)
. . . . CalifVRDL107_2009_11_15 (
. . . . . . . . 35I,
. . . . . . . . 39N,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn276H,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . CalifVRDL115_2009_12_04 (
. . . . . . . . 35I,
. . . . . . . . 77N,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn276H,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . Malmoe2_2010_05_07 (
. . . . . . . . 89G,
. . . . . . . . syn108L [tn],
. . . . . . . . syn159N,
. . . . . . . . 206T,
. . . . . . . . 259T [ArgentinaHNRG39_2009_06_23
. . . . . . . . . . . . . . . . . . . . with syn355H],
. . . . . . . . syn280T [1918, WSN33],
. . . . . . . . syn526S [India3725_2010_04_03])
. . . . ItalyAncona508_2009_12_31 (
. . . . . . . . syn172K,
. . . . . . . . syn181G,
. . . . . . . . syn239P,
. . . . . . . . syn355H,
. . . . . . . . 373H)
. . . . GDLiwan1170_2010_03_14 (
. . . . . . . . 131P,
. . . . . . . . 202A,
. . . . . . . . 271T,
. . . . . . . . 298V,
. . . . . . . . syn355H,
. . . . . . . . 375F)
. . . . tkOntarioFAV117_1C_2009_12_07 (
. . . . . . . . 35I [H5N1],
. . . . . . . . syn55L,
. . . . . . . . syn152I,
. . . . . . . . 186P,
. . . . . . . . syn205G,
. . . . . . . . syn219I,
. . . . . . . . syn276H [1918, S5],
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . syn486T,
. . . . . . . . 523A)
Please refer to additional studies for further genetic analyses, including the survey on amino acid revisions potentially related to Vaccine Escape. A hyper-morphic, TamiFlu-resistant sequence from the state of Washington in Spring 2010 has recently been profiled with similar zoonotic influences.
This analysis was fueled by puneri amti and funded with contributions from concerned families, including HOD, BMS, MJV and CSB.
* Rare, not Random
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