Brasil Shows 94% Avian Zoonotic Potential on Diverse Early Pandemic Sequences

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
2011-10-18

On 2011-08-30, a group of researchers from Instituto Adolfo Lutz Sao Paulo in Brasil, including Santos,C.L.S.; Oliveira,M.I.; Borborema,S.E.T.; Ferreira,J.L.P. and Paiva,T.M., deposited a large group of early Pandemic H1N1 sequences at GenBank and GISAID.  For this analysis, 7 HA sequences were selected for review due to their high affinity for polymorphisms homologous to Avian sequences.

The set of HA polymorphisms spans the gene segment.  23 distinct values are demonstrated.  Of the 35 total HA polymorphisms found across the 7 selected sequences, 33 trace to Avian Influenza A serotypes (H1N1, H3N8, H5N1 & H9N2).  The remaining 2 changes (HA 225N) are from mixed traces that resulted in HA 225G & 225N.  These non-Avian, Receptor Binding Site 225N values are wild-type, Human H3N2 homologies.  This early, large scale acquisition (94%) of disparate Avian polymorphisms across multiple backgrounds is suggestive that the basic Pandemic H1N1 background is related to Avian progenitors or is highly attractant to Avian genetic data upon co-infection.

Co-infection is known to produce mixed peaks on sequencing traces.  The mixed trace sequences in this selection carry H5N1 homology.  100% of the polymorphisms on BrasilSaoPaulo64519_2009_08_18 are mixed, as are the early changes on BrasilMatoGrossoDoSul64045_2009_08_13.  Each sequence carries recognised fatality markers.  Evidence supports the probability of H5N1 influence on the human carriers of the mixed trace sequences or on a progenitor animal that subsequently transported the H5N1 genetic material into proximity with the human subjects from Brasil.

. . . . BrasilSaoPaulo2227_2010_01_13 (
. . . . . . . . GISAID HA EPI335469
. . . . . . . . 6 Polymorphisms (1 Amino and 5 Silent)
. . . . . . . . HA Truncated before aa92,
. . . . . . . . syn301I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn338G (GGc) [H3N2 Avian, Canine, Feline],
. . . . . . . . . . . . . . . . . . [H3N8, H4, H5N1 Avian 2010, H6, sw],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [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],
. . . . . . . . . . . . . . . . . . [H6N2, H6N4],
. . . . . . . . . . . . . . . . . . [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 Farm with syn338G],
. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],
. . . . . . . . syn366A (GCt) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 377K [H9N2 Avian and Human],
. . . . . . . . syn548C (TGc) [H1N1 Avian wt])

. . . . BrasilSaoPaulo91656_2009_10_23 (
. . . . . . . . GISAID HA EPI335471
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn354Y (TAc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn486T (ACc) [H3N8 Avian])

. . . . BrasilSaoPaulo89876_2009_10_19 (
. . . . . . . . GISAID HA EPI335473
. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)
. . . . . . . . syn68P (CCg) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn202V (GTc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn446K (AAa) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilSaoPaulo83218_2009_09_27 (
. . . . . . . . GISAID HA EPI335474
. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)
. . . . . . . . syn41N (AAt) [H5N1 Egypt Human 2007],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2008],
. . . . . . . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn140P (CCc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn356H (CAc) [H5N1 Human Egypt 2009],
. . . . . . . . . . . . . . . . . . [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 extensive pH1N1_υ polymorphisms],
. . . . . . . . syn375I (ATc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn461K (AAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilSaoPaulo64519_2009_08_18 (
. . . . . . . . GISAID HA EPI335504
. . . . . . . . GenBank HA HQ595254
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 34D mix wt [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . syn53L (TTa) mix wt [H5N1 Human, Avian, Civet],
. . . . . . . . . . . . . . . . . . . . . . [H6N1 Avian],
. . . . . . . . . . . . . . . . . . . . . . [H2 Avian]
. . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 225G mix wt [pH1N1 Fatality Marker],
. . . . . . . . . . . . . . . . . [H5N1 Avian wt],
. . . . . . . . . . . . . . . . . [1918],
. . . . . . . . 225N mix wt [pH1N1 Fatality Marker],
. . . . . . . . syn413K (AAg) mix wt [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) mix wt [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 523A mix wt [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilMatoGrossoDoSul64045_2009_08_13 (
. . . . . . . . GISAID HA EPI335505
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 34D mix wt [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . 225G mix wt [pH1N1 Fatality Marker],
. . . . . . . . . . . . . . . . . [H5N1 Avian wt],
. . . . . . . . . . . . . . . . . [1918],
. . . . . . . . 225N mix wt [pH1N1 Fatality Marker],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . [H1N1 Avian])

. . . . BrasilSaoPaulo52142_2009_07_30 (
. . . . . . . . GISAID HA EPI335518
. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . [H1N1 Avian])

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H5N1 Avian Markers, Side by Side, in 2011 Human pH1N1 Stockholm, Sweden Case

Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked spreadsheet for completeness in citation.

Last Update
2011-09-20

On 2011-07-29, the UK National Institute for Medical Research published 29 pH1N1 sequences at GISAID.  These sequences were sampled from patients in Scandinavia, Eastern Europe, the Balkans and Hong Kong from January to May 2011 covering the second half of the Northern Hemisphere 2010-2011 season.  The Swedish Institute for Infectious Disease Control originated 10 of the samples in this Mill Hill deposit including a highly zoonotic and potential H5N1 recombinant, Stockholm13_2011_03_28, with no specified gender, age or outcome.

Two contiguous H5N1 Avian markers, HA 415E and 416N, each novel to the human H1N1 pandemic, appear in this human case.  The HA 416N is reported as a mixed peak trace, an output that is commonly interpreted as suggestive of multiple infecting strains.  The single H5N1 potential donor HA segment on file is also unusual in that this Egyptian domestic poultry sequence carries numerous homologies to polymorphisms found on human pH1N1 Clade 1 (189T) and Clade 2 (188T) sequences.  Several of those H5N1 to pH1N1 homologies are quite rare to H5N1, but are strongly emergent in pH1N1.

Stockholm13_2011_03_28 was sampled near the end of the traditional Northern Hemisphere influenza season and, as such, represents one probable foundation for ongoing Clade 2 transmission into the upcoming influenza season (2011-2012).  As has been regularly discussed, Clade 2 (188T) is the most prevalent numerically of the 5 major pH1N1 divisions as reported in the public and private genetic databases.  Being roughly par for the course, this Swedish sequence is hypermorphic, carrying 14 polymorphisms (9 Amino and 5 Silent).

Particular to the matter at hand, Clade 2 sequences have demonstrated a measurable propensity for accepting polymorphisms into pH1N1 and projecting those changes across pH1N1 (“Clade Jumping” / Clade Transfer).  The method and means continue under investigation, whether due to the influence of Avian H1N1 common ancestry from the primary donors into the major human pH1N1 clades or due to some form of recombination / attractant magnetism occurring between and among the human pH1N1 clades.

GeneWurx has tracked development of the H1N1 pandemic from the publicly accepted Contact Zero in early 2009 (and potential prequels) up to the present emergent strains.  As with prior H5N1 investigations, random variation remains far from the field of explanatory options in most cases.  Malleability by random mallet has not been shown as an important means of genetic variation in this H1N1 human pandemic.

The back-to-back polymorphisms transferring HA 415E and 416N onto the human pH1N1 Stockholm13_2011_03_28 sequence are noted in the H5N1 database.  That single H5N1 sequence is a human-adapted, avian case from Egypt.  This dual signal transfer demonstrates one very concrete case of cross-species, cross-serotype genetic transfer from an animal to a human serotype. 

H5N1 contiguous homology to the dominant clade in the dominant circulating human serotype (pH1N1) instructs the medical fraternity to the weight of emergent zoonoses and suggests that at least one avian flightpath may be worthy of investigation.

. . . . SwedenStockholm13_2011_03_28 (
. . . . . . . . PHz = 87%
. . . . . . . . PHzAv = 87%
. . . . . . . . GISAID HA EPI326240
. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)
. . . . . . . . syn41N (AAt) [H5N1 Human Emergent with TamiFlu Resistance],
. . . . . . . . . . . . . . . . .  [H5N1 Egypt Human 2007],
. . . . . . . . . . . . . . . . .  [H5N1 Avian with 166I],
. . . . . . . . 50I [WSN_1933, WSZ_1933],
. . . . . . . . . .  [1918],
. . . . . . . . syn154L (tTA) [H3N2 Avian with 158E],
. . . . . . . . . . . . . . . . . . [H3N2 Canine, Feline wt]
. . . . . . . . . . . . . . . . . . [H3N2 Human wt (tTg)],
. . . . . . . . . . . . . . . . . . [H3N8 Avian (tTg)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian with 404G],
. . . . . . . . . . . . . . . . . . [H9N2 Avian (tTg)],
. . . . . . . . . . . . . . . . . . [H9N2 Human with syn40H (tTg)],
. . . . . . . . 158E mix wt [H3N8, H5N1],
. . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K
. . . . . . . . . . . . . . . . . . . . . . . 253A, 275I, syn346G],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with #1T, 8V, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . . . . . 72L, syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . . . . . . 144E, 189T, 193R, 237I,
. . . . . . . . . . . . . . . . . . . . . . . syn287G, syn346G, 523A],
. . . . . . . . . . . . . . . . . [sw1930],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . with 186P, 189T,
. . . . . . . . . . . . . . . . . . . and extensive pH1N1_υ 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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Upsilon Marker Jumps Clades, Adds Zoonoses, Escapes Vaccine, Hospitalises and Transmits Well

Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked spreadsheet for completeness in citation.

Last Update
2011-09-06

On 2011-08-25, the WHO Collaborating Centre for Reference and Research on Influenza published 15 pH1N1 sequences at GISAID.  These sequences were sampled from patients in Australia from April to July 2011.  All are Clade 2 backgrounds (188T).

Although a recent GeneWurx analysis on Romanian sequences discussed a different defining Clade 1 marker (189T) jumping templates onto Clade 2, this Australian pattern maintains polymorphic throw for several generations. This deposit not only surfaces a novel face for Clade 2 (188T), but is a novelty that conducts reliable transmission though a defining marker downstream of the cleavage site is adopted from Clade 1.Upsilon (syn346G) in the same domain as the HA syn338G normally found on Clade 2. 

The 5 very similar sequences each carry 17 to 20 HA polymorphisms.  The superset of polymorphisms from this emergent mixed branch shows known Vaccine Escape changes at HA 156E and 158E.  Hypermorphic behaviour is a hallmark of pH1N1 as are the Vaccine Breakthrough (AustraliaBrisbane500_32M_2011_06_22_VxX) and hospitalisation (AustraliaBrisbane190_25M_2011_06_14_s) instances also demonstrated by cases from this novel emergence.

These novel and rare HA polymorphisms to the Clade 2 background exhibit homological history at a very significant proportion in the H1N1 Avian genetics record, including several farm animal sequences.  Those farm animal sequences, in turn, show a strong match rate to Clade 1.Upsilon (pH1N1_υ) AND to these Clade 2 Human pH1N1 sequences.  The superset of polymorphisms from the related Avian H1N1 farm animals exhibit strong homology to the superset of Clade 1.Upsilon HA polymorphisms.

The HA syn413K prevalent in fatal and severe cases from the early pandemic has mated with these Australian novelties as a further signal of zoonotic avian influence on the most widely reported pH1N1 Clade (Clade 2 – 188T).  Cross-clade polymorphism jumping is only just beginning for the Pandemic reservoir of H1N1.  Sporadic HA 230I on backgrounds similar to these 5 novel items is probable.  Interaction between human pH1N1 and Avian Influenza strains (farm and wild) carrying both Clade 1 and Clade 2 immune escape markers on single strains will continue to drive human revision using the widely available avian delivery vector. 

By GeneWurx calculations, clade elasticity will rise to become a primary method generating the 2011-2012 pH1N1 polymorphism bed.


. . . . AustraliaBrisbane190_25M_2011_06_14_s (
. . . . . . . . GISAID HA EPI333112
. . . . . . . . 19 Polymorphisms (7 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .  with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
 . . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 156E mix wt [H2N3],
. . . . . . . . . . . . . . . . . [H3N8],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010
. . . . . . . . . . . . . . . . . . . . with 188E, 192I, 198S, 210T, 223I],
. . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with #1T, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . . . . . 72L, 87N, syn118E, 144K,
. . . . . . . . . . . . . . . . . . . . . . . 158E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . syn287G, syn346G,
. . . . . . . . . . . . . . . . . . . . . . . 453K, 502K],
. . . . . . . . . . . . . . . . . [H3N2 Avian
. . . . . . . . . . . . . . . . . . . . with 165N, 225G, 230I],
. . . . . . . . . . . . . . . . . [H1N1 swIowa44837_1_2009_11_08_xL with 225N, 230I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1_υ defining marker],
. . . . . . . . . . . . . . . . . .  [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . syn513I (ATc) [H1N1 Avian (gTc)
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms & syn508L])

. . . . AustraliaBrisbane500_32M_2011_06_22_VxX (
. . . . . . . . GISAID HA EPI333109
. . . . . . . . 17 Polymorphisms (7 Amino and 10 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . 77R (AGa) [H9N2 Avian and Human wt
. . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
 . . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 171G (GgT),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1_υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E])

. . . . SouthAustralia4_2011_06_24 (
. . . . . . . . GISAID HA EPI333105
. . . . . . . . 18 Polymorphisms (6 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
 . . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn300P (CCt) [H5N1, H6N1, H7N3, H7N7],
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1_υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms & syn508L])

. . . . AustraliaBrisbane142_2011_04_12 (
. . . . . . . . GISAID HA EPI333005
. . . . . . . . 18 Polymorphisms (6 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn77S (AGt),
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
 . . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1_υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms & syn508L])

. . . . AustraliaBrisbane70_IVR162_2011_07_25 (
. . . . . . . . GISAID HA EPI333107
. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . syn33V (GTc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, 59S, 156E, 230I & syn346G],
. . . . . . . . . . . . . . . . . [Arizona17_2009_10_15
. . . . . . . . . . . . . . . . . . . . . with 158E, 233H,
. . . . . . . . . . . . . . . . . BZ_Bahia15525_42M_2009_09_05_f
. . . . . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . . . . . . . . IndiaNsk10348_2009_09
. . . . . . . . . . . . . . . . . . . . . with 225G],
. . . . . . . . syn34N (AAt) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1995],
. . . . . . . . syn99I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . .with syn42G, 156E, syn346G],
. . . . . . . . syn115E (GAg) [H1N1 Avian
 . . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, syn538F],
. . . . . . . . 132T (AcC) [H1N1 Avian],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K
. . . . . . . . . . . . . . . . . . 253A, 275I, syn346G],
. . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . with #1T, 8V, syn31H, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . 72L, syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . 144E, 189T, 193R, 237I,
. . . . . . . . . . . . . . . . . . syn287G, syn346G, 523A],
. . . . . . . . . . . . . . . . . [sw1930]
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 226R,
. . . . . . . . syn338G (GGc) [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [pH1N1_υ defining marker],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . 454N,
. . . . . . . . syn465N,
. . . . . . . . syn508L (tTG) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms and
. . . . . . . . . . . . . . . . . . . . . . . . . syn10Y, syn33V, 59S, syn77S, 128D,
. . . . . . . . . . . . . . . . . . . . . . . . . 156E, 158E, 159G, 159N, 159T,
. . . . . . . . . . . . . . . . . . . . . . . . . 188T, 189T, 200T, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . 230I, syn295F, syn346G, syn418F,
. . . . . . . . . . . . . . . . . . . . . . . . . 502K, 504G, 512M, syn538F],
. . . . . . . . 523A [Cameroon10v_1090_2010_04_08 with 158E],
. . . . . . . . syn538F (TTt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . with pH1N1_υ polymorphisms & syn508L])

Please visit GeneWurx.com for insight into the latest published studies.

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 pH1N1_υ 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 pH1N1_υ 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 pH1N1_υ 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 pH1N1_υ 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 pH1N1_υ, 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 pH1N1_υ],
. . . . . . . . . . . . . . . . .  [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 pH1N1_υ],
. . . . . . . . . . . . . . . . . . [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 pH1N1_υ],
. . . . . . . . . . . . . . . . . . [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 pH1N1_υ],
. . . . . . . . . . . . [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))

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Romania Demonstrates Zoonotic Potential Scores of 100% on HA Fragments

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
2011-07-18

The Cantacuzino Insttitute of Bucharest, Romania released sequences from 50 HA Segments and 2 unmatched NA segments at GenBank and GISAID on 2011-05-19.  The sample dates span 452 days from 2009-11-12 to 2011-02-07.  All 52 segment sequences are fragments and show extensive variation, including several with high Zoonotic Potential scores.  Template crossing is documented in this deposit.

Diverse geography is represented across this batch and an overall heavy zoonotic homology is found.  Animal reservoirs are represented including H9N2, H7N7, H5N1, H3N8 and H3N2.  With the Romanian HA polymorphisms, homology is found to H9N2 Human & Avian, to H7N7 Human, Avian and Equine, to H5N1 Emergent Human, to H3N8 Avian and to H3N2 Emergent Human from H3N2 Avian, Feline & Canine.  This group of sequences may, in time, be found to demonstrate significant zoonotic genetic re-seeding from the animal reservoirs at the 5’ ends of the fragments as well as the 3’ ends.

Zoonotic Potential

At least two sequences in this deposit demonstrate a 100% Zoonotic Potential score.  H5N1 homology is found on RomaniaConstanta330_2010_01_05, a 201 amino HA fragment from Winter 2010.  All 5 polymorphisms (2 Amino and 2 Silent) on this pH1N1 Romanian sequence are found in the H5N1 reservoir on various samples and the combination appears novel to pH1N1 and novel to H5N1.  The superset of changes on RomaniaCluj14972_2009_12_23 (205aa frag) may also be accommodated by the influence of zoonotic reservoirs.

Receptor Binding Site - HA aa225

HA aa225 polymorphisms are found in 6 instances, 225N (3) & 225G (3).

RomaniaConstanta50378_2011_01_21 (296aa frag) affixes HA 225N on an 188T (Clade 2) background with 100N and syn#8V, a position significant to the emergent Upsilon pH1N1 Sub-Clade (Clade 1: 189T).  RomaniaCarasSeverin663_2010_01_07 (173aa frag) carries 225N with 100N.  A singlet HA 225N appears on RomaniaPrahova2704_2010_01_18 (175aa frag) approximately one year earlier.

Another winter 2010 sequence, RomaniaSuceava406_2010_01_05 (196aa span), carries 225G with 2 zoonotic polymorphisms having homology to H3N2, H3N8, H7N7 Human and H9N2 Human.  On RomaniaBuzau14584_2009_12_21 (196aa frag), 225G is found with syn181G, a homology to H5N1 Human, H5N1 Emergent Avian and H9N2 Avian.  HA syn168Y, a regional pH1N1 marker from Russian and Ukrainian fatalities, appears 4 times, including a pairing with 225G on RomaniaPrahova564_2010_01_06 (172aa frag) and a pairing with 100N on RomaniaMaramures13812_2009_12_15 (198aa frag).

HA Template Jumping

In addition, clade-defining elements are observed appearing on different clade backgrounds, including RomaniaBihor51551_54F_2011_01_31 on a Clade 2 (188T Tau) background with the addition of 189T (Clade 1).  A Clade 5 (208K, 219V) background in 2011, RomaniaArad50090_2011_01_20 (287aa frag), received 188T (Clade 2).

Nine HA segment sequences spanning 2009_11_12 to 2010_01_26 measure zero polymorphisms.

Sequences

SortKeys:
SequenceDate Desc,
SequenceID Asc,
SegmentID Asc

. . . . RomaniaNeamt51999_2011_02_07 (
. . . . . . . . Clade 2: 188T
. . . . . . . . GISAID HA EPI317512
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa287)

. . . . RomaniaBucuresti52010_2011_02_04 (
. . . . . . . . Clade 5: 208K, 219V
. . . . . . . . GISAID HA EPI317528
. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . syn66G (GGg) [H5N1 wt, H6, H9N2],
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 Avian Domestic & Wild],
. . . . . . . . . . . . . . . . . [H9N2 Avian Emergent 2009],
. . . . . . . . 100N,
. . . . . . . . 141Q,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaBihor51551_54F_2011_01_31 (
. . . . . . . . Clade 2: 188T crossing with Clade 1: 189T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317529
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . syn215P (CCa),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaBrasov49666_2011_01_30 (
. . . . . . . . Clade 3: 186P
. . . . . . . . GISAID HA EPI317530
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . syn212K (AAa),
. . . . . . . . syn214K (AAa),
. . . . . . . . syn272D (GAc) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian Emergent 2010],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaBucuresti50820_2011_01_30 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317532
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn31H (CAt),
. . . . . . . . 73F,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn283Q (CAa),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaArad51247_2011_01_29 (
. . . . . . . . Clade 5: 208K, 219V
. . . . . . . . GISAID HA EPI317518
. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)
. . . . . . . . syn36L (tTA),
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . . . [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],
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn292S (AGt),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaArad51034_2011_01_29 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317531
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaSalaj51422_2011_01_28 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317505
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . 174R,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa295)

. . . . RomaniaCluj51505_2011_01_27 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317504
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaMures51180_2011_01_27 (
. . . . . . . . Clade 5: 208K, 219V
. . . . . . . . GISAID HA EPI317506
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn36L (tTA),
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . . . [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],
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn276H (CAt),
. . . . . . . . HA Truncated after aa295)

. . . . RomaniaBucuresti51194_2011_01_26 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317507
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn107Q (CAg),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa295)

. . . . RomaniaPrahova50643_2011_01_26 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317510
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa287)

. . . . RomaniaBucuresti50823_2011_01_26 (
. . . . . . . . Clade 4: 128D
. . . . . . . . GISAID HA EPI317533
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . syn60I (ATc),
. . . . . . . . 107L,
. . . . . . . . 128D,
. . . . . . . . HA Truncated after aa295)

. . . . RomaniaCalarasi2225_2011_01_21 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317508
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn107Q (CAg),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa295)

. . . . RomaniaConstanta50378_2011_01_21 (
. . . . . . . . Clade 2: 188T
. . . . . . . . GISAID HA EPI317525
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . syn#8V (GTg),
. . . . . . . . syn32S (TCc),
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . 210G,
. . . . . . . . 225N,
. . . . . . . . syn232Y (TAc),
. . . . . . . . syn277D (GAc),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaArad50090_2011_01_20 (
. . . . . . . . Clade 5: 208K, 219V crossing with Clade 2: 188T
. . . . . . . . GISAID HA EPI317509
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . syn36L (tTA),
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . . . [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],
. . . . . . . . 188T,
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . HA Truncated after aa287)

. . . . RomaniaTimis49900_2011_01_19 (
. . . . . . . . GISAID HA EPI317501
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . syn60I (ATc),
. . . . . . . . syn273T (ACg),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaMaramures49545_2011_01_15 (
. . . . . . . . Clade 2: 188T
. . . . . . . . GISAID HA EPI317502
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaIasi48801_2011_01_11 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317511
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 38G,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn292S (AGt),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaBucuresti48333_2011_01_09 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317503
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaBihor48551_2011_01_09 (
. . . . . . . . GISAID NA EPI317527
. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa253,
. . . . . . . . syn307N (AAt),
. . . . . . . . syn312Y (TAc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . NA Truncated after aa435)

. . . . RomaniaIasi47959_2010_12_31 (
. . . . . . . . GISAID NA EPI317526
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . NA Truncated before aa253,
. . . . . . . . syn330D (GAc),
. . . . . . . . 386S,
. . . . . . . . NA Truncated after aa435)

. . . . RomaniaPrahova3261_2010_01_26 (
. . . . . . . . GISAID HA EPI317487
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . HA Truncated after aa280)

. . . . RomaniaIasi2807_2010_01_19 (
. . . . . . . . GISAID HA EPI317486
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . syn279N (AAc),
. . . . . . . . HA Truncated after aa280)

. . . . RomaniaPrahova2704_2010_01_18 (
. . . . . . . . GISAID HA EPI317485
. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . 225N,
. . . . . . . . HA Truncated after aa280)

. . . . RomaniaNeamt2058_2010_01_13 (
. . . . . . . . GISAID HA EPI317484
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . syn140P (CCc),
. . . . . . . . HA Truncated after aa280)

. . . . RomaniaCarasSeverin663_2010_01_07 (
. . . . . . . . GISAID HA EPI317491
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . 100N,
. . . . . . . . 225N,
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa273)

. . . . RomaniaBistritaNasaud677_2010_01_07 (
. . . . . . . . GISAID HA EPI317492
. . . . . . . . 4 Polymorphisms (1 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa93,
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . 100N,
. . . . . . . . syn220R (AGg) [H1N1 Avian with extensive pH1N1 polymorphisms],
. . . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human],
. . . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . . . . . . . . . . . [WSN_1933],
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa273)

. . . . RomaniaIlfov481_2010_01_06 (
. . . . . . . . GISAID HA EPI317488
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa137,
. . . . . . . . syn167S (TCt),
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . 297S,
. . . . . . . . HA Truncated after aa297)

. . . . RomaniaPrahova564_2010_01_06 (
. . . . . . . . GISAID HA EPI317489
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . syn168Y (TAt),
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa272)

. . . . RomaniaGalati591_2010_01_06 (
. . . . . . . . GISAID HA EPI317490
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa110,
. . . . . . . . HA Truncated after aa276)

. . . . RomaniaConstanta330_2010_01_05 (
. . . . . . . . Zoonotic Potential: 100%
. . . . . . . . GISAID HA EPI317480
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa92,
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . 127S [H5N1 Egypt wt],
. . . . . . . . 166E [H5N1 Egypt Emergent Human 2010],
. . . . . . . . syn181G (GGa) [H5N1 Egypt Human 2007, 2009],
. . . . . . . . . . . . . . . . . . . . . . [H5N1 Avian Emergent 2010],
. . . . . . . . . . . . . . . . . . . . . . [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . . with 39E, syn42G, 296R mix wt],
. . . . . . . . syn258F (TTt) [pH1N1 rare GISAID (under 30)],
. . . . . . . . . . . . . . . . . . [pH1N1 GISAID Low Homology to this Sequence],
. . . . . . . . . . . . . . . . . . [pH1N1 GISAID 4 with VxX Markers],
. . . . . . . . . . . . . . . . . . [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2009 (Tat)],
. . . . . . . . HA Truncated after aa293)

. . . . RomaniaSuceava406_2010_01_05 (
. . . . . . . . GISAID HA EPI317481
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa101,
. . . . . . . . 225G,
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . 297S,
. . . . . . . . HA Truncated after aa297)

. . . . RomaniaBotosani169_2010_01_03 (
. . . . . . . . GISAID HA EPI317479
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa91,
. . . . . . . . 91S [H3N2 Asia Avian],
. . . . . . . . . . . [H3N2 Human wt (aGc)],
. . . . . . . . 93F,
. . . . . . . . syn95P (CCc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H3N2 Human and Avian wt (agc)],
. . . . . . . . . . . . . . . . . [H9N2 Early Human],
. . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . 99L,
. . . . . . . . 100V,
. . . . . . . . HA Truncated after aa289)

. . . . RomaniaOlt114_2010_01_02 (
. . . . . . . . GISAID HA EPI317465
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa280)

. . . . RomaniaOlt119_2010_01_02 (
. . . . . . . . GISAID HA EPI317466
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa280)

. . . . RomaniaBotosani15520_2009_12_30 (
. . . . . . . . GISAID HA EPI317476
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . HA Truncated after aa280)

. . . . RomaniaCluj15569_2009_12_30 (
. . . . . . . . GISAID HA EPI317477
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . 100N,
. . . . . . . . 111L [H3N2 Human and Avian wt (cTa)],
. . . . . . . . . . . . . [H9N2 Avian Emergent with pH1N1 polymorphisms (tct)],
. . . . . . . . syn251L (tTA),
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa280)

. . . . RomaniaBraila15575_2009_12_30 (
. . . . . . . . GISAID HA EPI317478
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa97,
. . . . . . . . 99M (ATg) [H1N1 Avian with pH1N1 polymorphisms],
. . . . . . . . . . . . . . . [H9N2 Human 2000],
. . . . . . . . . . . . . . . [H9N2 Asia and Europe Avian (gag)],
. . . . . . . . syn135V (GTg),
. . . . . . . . syn168Y (TAt),
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaBotosani15033_2009_12_26 (
. . . . . . . . GISAID HA EPI317474
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . HA Truncated after aa291)

. . . . RomaniaDambovita15050_2009_12_26 (
. . . . . . . . GISAID HA EPI317475
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa91,
. . . . . . . . 91S [H3N2 Asia Avian],
. . . . . . . . . . . [H3N2 Human wt (aGc)],
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . HA Truncated after aa288)

. . . . RomaniaCluj14972_2009_12_23 (
. . . . . . . . Zoonotic Potential: 100%
. . . . . . . . GISAID HA EPI317473
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa91,
. . . . . . . . 91S [H3N2 Asia Avian],
. . . . . . . . . . . [H3N2 Human wt (aGc)],
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . 99M (ATg) [H1N1 Avian with pH1N1 polymorphisms],
. . . . . . . . . . . . . . . [H9N2 Human 2000],
. . . . . . . . . . . . . . . [H9N2 Asia and Europe Avian (gag)],
. . . . . . . . syn272D (GAc) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian Emergent 2010],
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaIasi14805_2009_12_22 (
. . . . . . . . GISAID HA EPI317471
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa96,
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . HA Truncated after aa291)

. . . . RomaniaIlfov14852_2009_12_22 (
. . . . . . . . GISAID HA EPI317472
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa98,
. . . . . . . . 99M (ATg) [H1N1 Avian with pH1N1 polymorphisms],
. . . . . . . . . . . . . . . [H9N2 Human 2000],
. . . . . . . . . . . . . . . [H9N2 Asia and Europe Avian (gag)],
. . . . . . . . syn168Y (TAt),
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)

. . . . RomaniaBuzau14584_2009_12_21 (
. . . . . . . . GISAID HA EPI317470
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa97,
. . . . . . . . syn181G (GGa) [H5N1 Egypt Human 2007, 2009],
. . . . . . . . . . . . . . . . . . . . . . [H5N1 Avian Emergent 2010],
. . . . . . . . . . . . . . . . . . . . . . [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . . with 39E, syn42G, 296R mix wt],
. . . . . . . . 182V,
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa293)

. . . . RomaniaMures14446_2009_12_20 (
. . . . . . . . GISAID HA EPI317469
. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa124,
. . . . . . . . 255K,
. . . . . . . . HA Truncated after aa268)

. . . . RomaniaMaramures13812_2009_12_15 (
. . . . . . . . GISAID HA EPI317468
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa99,
. . . . . . . . 99R,
. . . . . . . . 100N,
. . . . . . . . syn168Y (TAt),
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . 297S,
. . . . . . . . HA Truncated after aa297)

. . . . RomaniaHarghita12170_2009_12_08 (
. . . . . . . . GISAID HA EPI317467
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa114,
. . . . . . . . HA Truncated after aa273)

. . . . RomaniaIasi11140_2009_12_02 (
. . . . . . . . GISAID HA EPI317464
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa107,
. . . . . . . . HA Truncated after aa246)

. . . . RomaniaBotosani10121_2009_11_26 (
. . . . . . . . GISAID HA EPI317463
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa135,
. . . . . . . . HA Truncated after aa281)

. . . . RomaniaIasi9422_2009_11_22 (
. . . . . . . . GISAID HA EPI317483
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . HA Truncated after aa272)

. . . . RomaniaBotosani8204_2009_11_12 (
. . . . . . . . GISAID HA EPI317482
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa107,
. . . . . . . . HA Truncated after aa280)

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