The Mahidol University in Bangkok deposited a group of 6 pH1N1 HA sequences at GenBank on 2010-11-22. The samples were all taken last month, October 2010, and produced partial sequences.
ThaiSN_0116_2010_10 deploys a rare polymorphism at aa163 that may be related to our discussion of change at that position in April of this year. Only New Zealand reports another instance of 163T. Each 163T-bearing sequence is recent indicating potential emergent behaviour at this key amino acid position. A second Thai sequence, ThaiSN_0112_2010_10, corroborates another novel amino acid revision (found only in Cuba). 232H, just downstream of the recent critical RBD revisions to 230I, increases the genetic diversity of the ΣPF11 reservoir. The post-pandemic H1N1 virus appears to be as unstable as during the early pandemic.
Previously, we have detailed this genetic diversity and Vaccine Escape tendencies within this viral reservoir. 100% of the Hemagglutinin positions between 186 and 248, including antigenic areas of the Receptor Binding Domain (RBD/RBS), are on record as polymorphic. No position in that range is stable. Many positions rate multiple changes. Protein revision is documented at 58 of the 63 positions (92%), engaging a wide potential for antibody resistance (natural Immune Escape and Vaccine Escape).
The related 232H-bearing Cuban sequence is from 2010 and mirrors directly and via domaining the emerging post-pandemic sub-clade recently profiled.
. . . . ThaiSN_0116_2010_10 (
. . . . . . . . HA truncated before aa119,
. . . . . . . . 163T [NZChristchurch16_2010_07_12],
. . . . . . . . syn177L,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . HA truncated after aa237)
. . . . ThaiSN_0112_2010_10 (
. . . . . . . . HA truncated before aa103,
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . 232H [CubaHabana7374_2010_01],
. . . . . . . . HA truncated after aa239)
Supporting Sequences
. . . . NZChristchurch16_2010_07_12 (
. . . . . . . . #4H,
. . . . . . . . syn44L,
. . . . . . . . 97N,
. . . . . . . . syn106E,
. . . . . . . . 128D,
. . . . . . . . 163T,
. . . . . . . . 225N,
. . . . . . . . 253A,
. . . . . . . . syn362S,
. . . . . . . . 377K)
. . . . CubaHabana7374_2010_01 (
. . . . . . . . HA truncated before aa05,
. . . . . . . . 28P,
. . . . . . . . syn32S,
. . . . . . . . 33G,
. . . . . . . . 165N,
. . . . . . . . 232H,
. . . . . . . . 275I,
. . . . . . . . syn287G,
. . . . . . . . syn305K,
. . . . . . . . syn346G,
. . . . . . . . 421M,
. . . . . . . . 432W,
. . . . . . . . 444Y,
. . . . . . . . HA truncated after aa535)
2010-11-22
HA 230I Demonstrated in Ukraine Cross-Linkage and in Russia with 225G
Last Updated
2011-02-09
The National Institute for Medical Research in the UK published a group of sequences on 2010-08-20 that included two instances of HA 230I from 2010 samples. As predicted using GeneWurx RnR heuristics against the ΣPF11 reservoir (pH1N1), the Ukrainian reservoir and the Russian reservoir each now demonstrates support of the M230I polymorphism. At this moment, this allegedly unpredictable disease has now been predicted in detail 3 times as to specific time, location and genetic change in addition to the original prediction of 230I emergence.
Previously, one military sequence from Texas, TexasAF2579_2009_10_04, was documented as the first 230I to meet the GeneWurx geographic prediction. A dual RBD change (230I & 225E) is carried on the Texas sequence. The Russian sequence detailed in this analysis is the first 230I with 225G, demonstrating multiple supports for dual RBD changes on these related backgrounds.
As early as November 2009 when less than 30 sequences with 225G had been published, our team discussed the high potential and variant mechanisms, including avian lateral transfer, for this pandemic to produce a recombinant with both 225G and 230I. The change to 225G in pH1N1 has been associated with higher severity of disease and fatality potentially due to an increased ability to infect the ciliated cells of the respiratory system. In effect, the 225G variants of Pandemic Influenza 2009 have a wider affinity for α2-3-linked sialic acid binding variety than the 1918 225G sample from New York.
The GeneWurx RnR model is now validated with predicted 230I data points within three geographic regions. The original emergence of 230I in the Pandemic H1N1 reservoir was accurately predicted using a model predating the RnR. Furthermore, the M230I polymorphism count in this reservoir (H1N1pdm, pH1N1, PF11), increases to 8 at the same time that the H3N2 reservoir is building toward immune escape with an emerging sub-clade by revising at the same amino acid position (I230V). Meanwhile, the Pandemic H1N1 reservoir is actively establishing an emergent sub-clade now crossing 9 distinct geographic regions, including the United States, Germany, South Africa and the Ukraine. This emergent H1N1 sub-clade is permissive to 230I and 225G RBD changes. One instance of this new pandemic H1N1 sub-clade is documented in Pennsylvania, a location where the H3N2 reservoir has begun the I230V revision.
A cursory contemporary analysis shows additional instances of H1N1 v. H3N2 reversals at similar positions or similar domains within particular geographic regions. Will we find that the two serotypes (H1N1, H3N2) are in communication and are richly interactive? Science has an unparalleled and unprecedented opportunity today to surveil, in real-time, a post-pandemic period. Will deep surveillance and analysis be conducted or will the status quo be maintained, continuing with the same outdated models limited to the same inputs?
Age Factor and Mechanism Hypothesis
The 230I genetic modification appears to have a higher potential among children and young adults (0-24 years old). The mechanism remains only in postulation due to sparsity of patient meta-data, treatment modality and clinical outcomes. The pattern of revision on the known 230I sequences and on an emerging permissive background is suggestive that 230I is a tertiary immune escape polymorphism, whether developed in situ via a stepwise escape program or acquired via recombination from zoonotic sources. Among individuals who have formed a wide, but only partially competent, series of antibodies, the longer viral infectious period due to incomplete clearance establishes the ideal incubation frame for a stepwise, hyper-morphic and/or novel viral revision.
Very generalised assays from various countries have reported pandemic virus exposure in their younger citizens at rates between 60% and 70%, seemingly a profound rate of protection or so-called herd immunity. However, the re-infection rates clarify that exposure does not equate to protection, though frequently the numbers are reported as protective due to assay titers results that have been deemed as “protective”. As the present evidence has demonstrated, the course of a pandemic viral disease is unaffected by the resulting outdated measures from these overly generalised assays that assume protection.
The younger group’s multiplicity of exposure to a wider variation of influenza strains may factor into the host response/viral revision equation. Viral exertion against a complex host response challenges the reservoir subset to revise toward an optimal solution. In short, for a virus to successfully replicate within a younger person today, increasing novelty may be required. And this viral reservoir has demonstrated a very high capacity for continual novelty.
Additionally, studies have shown that anti-viral usage, specifically the neuraminidase inhibitors in wide usage, through the artificial mechanism of stalling the virus inside infected cells, may be involved in reducing the secondary immune response due to antigen sparsity and limiting the host ability to develop fully competent and protective antibodies. Given the Pandemic H1N1 reservoir’s demonstrated ability to hobble the early innate response (Natural Killer cells, Plasmocytoid Dendritic cells, et al) in combination with the NI anti-viral’s handicapping of the secondary (adaptive) response and the clinical outcomes are more explainable.
Ergo, take the wider exposure of the young population (antibody complexity/variety) and the TamiFlu blanketing used in schools and other institutions around the world (partial antibody competence) as synergistic factors toward a mechanism moulding the environment for 230I emergence as a tertiary immune escape revision. Take the concern another step and consider the prospect of host latency due to viral-induced immune handicap . . . a simmering virus is a variable virus. Furthermore, additional markers from fatalities and vaccine escape strains appear to be accumulating onto these 230I sequences and the sub-clades that are permissive to 230I.
Recall that a mature H5N1 strain in Gharbiyah, Egypt adapted to this same RBD revision under discussion here (230I) and increased the fatality rate substantially above worldwide baseline. Single genetic changes (SNP) are well-represented as fatality markers in this pandemic reservoir and in other zoonotic emergences.
230I Additions
The Institute of Epidemiology and Infectious Diseases AMS of Ukraine originated Ukraine123_2010_02_14_xL and the Russian Academy of Medical Sciences originated RussiaBelgorod2_2010_03_15. Age and gender information remain undisclosed on each sequence of interest.
The hyper-morphic Ukraine123_2010_02_14_xL sequence carries 12 changes on the HA gene segment alone (6 silent). This Ukrainian sample is the first instance of a cross-linked sequence with 230I and the first instantiation of a 230I-bearing strain carrying the 289V signature from India. The synonymous 0T on the Ukrainian sequence is quite rare, but is found in two geographic locations that also demonstrate within their geographic pool the synonymous 238E found on the Ukrainian sequence: Thailand and Hvidovre.
. . . . Ukraine123_2010_02_14_xL (
. . . . . . . . syn0T [BangkokINS427_27M_2010_03_04
. . . . . . . . . . . . . . . . . with syn209Y, syn232Y, syn490P & syn506V,
. . . . . . . . . . . . . DenmarkHvidovreINS290_20F_2009_11_27
. . . . . . . . . . . . . . . . . with 35I, syn490P, 502K & 526T,
. . . . . . . . . . . . . LaReunion3479_2009
. . . . . . . . . . . . . . . . . with syn97D, syn139C & 225E]
. . . . . . . . 186P,
. . . . . . . . 208K,
. . . . . . . . 230I (ATa),
. . . . . . . . syn238E [Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . . . WiscD2424_2009_12_15
. . . . . . . . . . . . . . . . . . . with 225E, 300S & 463T,
. . . . . . . . . . . . . . . Netherlands2629_2009_12_04_xL
. . . . . . . . . . . . . . . . . . . with 225N, syn233Y, 324I, syn413K & 507E,
. . . . . . . . . . . . . . . RussiaAnadyrIIV177_2009_12_04_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . JapanNagasakiHA64_2009_11_27
. . . . . . . . . . . . . . . . . . . with syn35L, syn92T, 200T, 324I & 513V,
. . . . . . . . . . . . . . . Arkhangelsk_GNY_2009_11_25_xL_f
. . . . . . . . . . . . . . . . . . . with 324I, syn413K, 437N & syn484N,
. . . . . . . . . . . . . . . MoscowCHSN_2009_11_23_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I & syn413K & syn484N,
. . . . . . . . . . . . . . . DenmarkHvidovreINS141_2009_11_20_xL
. . . . . . . . . . . . . . . . . . . with syn23L, 324I, syn413K, syn484N & syn549R,
. . . . . . . . . . . . . . . Lipetsk_BVV_2009_11_10_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Orel_KAI1_2009_11_05
. . . . . . . . . . . . . . . . . . . with 280A, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia4_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia14_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia191_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with syn103E, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Belarus220_2009_11,
. . . . . . . . . . . . . . . Belarus360_2009_11,
. . . . . . . . . . . . . . . EgyptN14648_2009_11
. . . . . . . . . . . . . . . . . . . with 225N, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Belarus131_2009_10,
. . . . . . . . . . . . . . . GuamNHRC0032_2009_09_14
. . . . . . . . . . . . . . . . . . . with 89G,
. . . . . . . . . . . . . . . Managua5295_02_2009_07_23,
. . . . . . . . . . . . . . . ThailandTHA0364_2009_07_22
. . . . . . . . . . . . . . . . . . . with #12E, 37N, 296H & syn348V,
. . . . . . . . . . . . . . . Missouri02_2009_05_01
. . . . . . . . . . . . . . . . . . . with syn215P, syn377E, syn456L & syn523V,
. . . . . . . . . . . . . . . Bayern62_2009_04_29_VxX
. . . . . . . . . . . . . . . . . . . with 158E & syn456L,
. . . . . . . . . . . . . . . GermanyRegensburg01_2009_04_27
. . . . . . . . . . . . . . . . . . . with syn456L,
. . . . . . . . . . . . . . . GermanyRegensburgD6_2009
. . . . . . . . . . . . . . . . . . . with syn456L],
. . . . . . . . 252M [Fixed in 2010 Illinois swine with 119M,
. . . . . . . . . . . . . Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . Seoul2883_2009_12_02,
. . . . . . . . . . . . . Seoul1829_2009_11_26,
. . . . . . . . . . . . . LagosWRAIR1982N_2009_11_23,
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . LagosWRAIR1984N_2009_11_18,
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . LagosWRAIR1984T_2009_11_18
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f
. . . . . . . . . . . . . . . . . . . with 186P, 225G, syn238E, 324I,
. . . . . . . . . . . . . . . . . . . . . . . syn413K, syn431L, syn484N,
. . . . . . . . . . . . . Texas45132202_2009_09_13,
. . . . . . . . . . . . . Ancona86_2009_08_31
. . . . . . . . . . . . . . . . . . . with 225E & 300S,
. . . . . . . . . . . . . TurkeyAnkara17_2009_08,
. . . . . . . . . . . . . BZ_SaoPaulo43812_2009_07_03_f],
. . . . . . . . 289V [HK1881_2010_04_18,
. . . . . . . . . . . . . EstoniaTallinnINS431_2010_02_05,
. . . . . . . . . . . . . Luxembourg184_2010_01_25,
. . . . . . . . . . . . . Saarland21_2009_12_11,
. . . . . . . . . . . . . IndiaPune21115_2009_12 with 233H,
. . . . . . . . . . . . . Hiroshima457 _2009_11_02,
. . . . . . . . . . . . . JiangsuNanjinggulouSWL11146_2009_09_17,
. . . . . . . . . . . . . Kobe91993_2009_08_18,
. . . . . . . . . . . . . Kobe91992_2009_08_17,
. . . . . . . . . . . . . UK_Glascow_SC10_2009_06 with 225G,
. . . . . . . . . . . . . UK_Glascow_SC19_2009_06,
. . . . . . . . . . . . . UK_Glascow_SC20_2009_06],
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn431L [Emergent],
. . . . . . . . . . . . . . . [OZ_Grafton2_20F_2010_08_05
. . . . . . . . . . . . . . . . . . . . . . . with 128D, syn173G & syn273T,
. . . . . . . . . . . . . . . OZ_Perth504_5M_2010_07_07
. . . . . . . . . . . . . . . . . . . . . . . with 128D, syn173G & syn273T,
. . . . . . . . . . . . . . . swIllinois03037_2010_06_24
. . . . . . . . . . . . . . . . . . . . . . . with 77G,
. . . . . . . . . . . . . . . swIowa03032_2010_06_04
. . . . . . . . . . . . . . . . . . . . . . . with 77G,
. . . . . . . . . . . . . . . PNG_Goroka16_1F__2010_04_07
. . . . . . . . . . . . . . . . . . . . . . . with 77G & 252L,
. . . . . . . . . . . . . . . PNG_Goroka16E3_1F_2010_04_07
. . . . . . . . . . . . . . . . . . . . . . . with 77G, 186P, 204M, syn205G & 252L,
. . . . . . . . . . . . . . . PNG_Goroka15_2010_02_24
. . . . . . . . . . . . . . . . . . . . . . . with 77G & 252L,
. . . . . . . . . . . . . . . Ukraine122_2010_01_15_xL,
. . . . . . . . . . . . . . . HainanDinganSWL123_2010_01_08,
. . . . . . . . . . . . . . . swOregon10_004060_2009_12_31
. . . . . . . . . . . . . . . . . . . . . . . with syn189A,
. . . . . . . . . . . . . . . AthensINS359_2009_12_26
. . . . . . . . . . . . . . . . . . . . . . . with syn189A,
. . . . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f,
. . . . . . . . . . . . . . . SpainCatS1632_2009_10_28,
. . . . . . . . . . . . . . . swHongKong2314_2009_10_22,
. . . . . . . . . . . . . . . ItalyAncona05_2009_07-12
. . . . . . . . . . . . . . . . . . . . . . . with 225E,
. . . . . . . . . . . . . . . England673_2009_07
. . . . . . . . . . . . . . . . . . . . . . . with 225E],
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11]),
. . . . . . . . . . . . . . . [NY04_2010_02_25
. . . . . . . . . . . . . . . . . . . with 3T, 50E, syn53L, 100N, syn232Y,
. . . . . . . . . . . . . . . . . . . . . . . syn270I, 377K, 437N,
. . . . . . . . . . . . . . . RussiaStPeter204E2E2_2010_02_08_VxX,
. . . . . . . . . . . . . . . RussiaStPeter204E2E1_2010_02_08_VxX,
. . . . . . . . . . . . . . . RussiaStPeter204E2_2010_02_08_VxX,
. . . . . . . . . . . . . . . Saratov07E2E1_2010_02_01_VxX,
. . . . . . . . . . . . . . . Saratov07E2_2010_02_01_VxX,
. . . . . . . . . . . . . . . Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . . . RussiaAnadyrIIV177_2009_12_04_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, syn238E, 324I & syn413K,
. . . . . . . . . . . . . . . Arkhangelsk_GNY_2009_11_25_xL_f
. . . . . . . . . . . . . . . . . . . with 324I, syn413K, 437N & syn484N,
. . . . . . . . . . . . . . . MoscowCHSN_2009_11_23_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I & syn413K,
. . . . . . . . . . . . . . . DenmarkHvidovreINS141_2009_11_20_xL
. . . . . . . . . . . . . . . . . . . with syn23L, 324I, syn413K, syn484N & syn549R,
. . . . . . . . . . . . . . . RussiaStPeterVMN_2009_11_19_f,
. . . . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f
. . . . . . . . . . . . . . . . . . . with 186P, 225G, syn238E, 252M,
. . . . . . . . . . . . . . . . . . . . . . . 324I, syn413K, syn431L,
. . . . . . . . . . . . . . . UkrChernihiv855L_2009_11_11_xL_f,
. . . . . . . . . . . . . . . Lipetsk_BVV_2009_11_10_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . OrelKAI1_2009_11_05,
. . . . . . . . . . . . . . . Russia4_2009_11_01_xL,
. . . . . . . . . . . . . . . Russia14_2009_11_01_xL,
. . . . . . . . . . . . . . . Russia191_2009_11_01_xL,
. . . . . . . . . . . . . . . EgyptN14648_2009_11
. . . . . . . . . . . . . . . . . . . with 225N, syn238E, 324I & syn413K,
. . . . . . . . . . . . . . . RussiaStPeterRII96_2009_10_29
. . . . . . . . . . . . . . . . . . . with 187N,
. . . . . . . . . . . . . . . NizhniNovgorodMEV_2009_07_30,
. . . . . . . . . . . . . . . ItalyAncona15_2009_07_17,
. . . . . . . . . . . . . . . Fixed in Thai Swine including
. . . . . . . . . . . . . . . . . . . swThaiCU_RA75_2010_01 with 188T],
. . . . . . . . syn500R [Unique to GenBank/GISAID])
. . . . RussiaBelgorod2_2010_03_15 (
. . . . . . . . syn13N [WiscD0459_2009_12_18_xL
. . . . . . . . . . . . . . . . . . with 189T, 324I & 499K,
. . . . . . . . . . . . . . LouisianaAF2435_2009_11_30
. . . . . . . . . . . . . . . . . . with syn338G],
. . . . . . . . 77N [tn, swine, S5]
. . . . . . . . . . . [JapanOsaka60_2010_07_02
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . Maryland04_2010_02_08
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . ShandongShizhongSWL24_2010_01_24,
. . . . . . . . . . . NY7020_2009_12_14
. . . . . . . . . . . . . . . . with syn166K & 189T,
. . . . . . . . . . . CalifVRDL115_2009_12_04
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . JapanAF2267_2009_11_09
. . . . . . . . . . . . . . . . with 286E,
. . . . . . . . . . . NevadaAF2490_2009_11_02
. . . . . . . . . . . . . . . . with 100N & syn270I,
. . . . . . . . . . . AlaskaAF2093_2009_11_02
. . . . . . . . . . . . . . . . with 286E,
. . . . . . . . . . . Russia74_2009_11_01_xL,
. . . . . . . . . . . ThailandTHB0441_2009_07_28,
. . . . . . . . . . . Lisboa40_2009_06_23,
. . . . . . . . . . . AnhuiSWL1_2009_06_18
. . . . . . . . . . . . . . . . with 275I,
. . . . . . . . . . . Lithuania1942_2009,
. . . . . . . . . . . swKoreaSCJ10_2009_12,
. . . . . . . . . . . swKoreaSCJ09_2009_12]
. . . . . . . . 158E mix,
. . . . . . . . 225G (Gga) stepwise from 225E,
. . . . . . . . 230I (ATa),
. . . . . . . . 238D [H2N3, H7N3, H7N7, tn, swine],
. . . . . . . . . . . . [PNG_Goroka17_2010_04_14,
. . . . . . . . . . . . AthensINS398_2010_01_24,
. . . . . . . . . . . . AthensINS339_2009_12_30,
. . . . . . . . . . . . Kaliningrad01_11M_2009_11_02
. . . . . . . . . . . . . . . . . . with 225E & 226R,
. . . . . . . . . . . . KaliningradCRIE_DA_2009_09_26,
. . . . . . . . . . . . KaliningradCRIE_KG_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_SHD_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_MA_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_ZD_2009_09_25],
. . . . . . . . syn245F [H2N3, H5N1, H7N7, H10N7, H11]
. . . . . . . . . . . . . . [SingON2416_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with syn166K & 300P,
. . . . . . . . . . . . . . . EgyptAswan2288_2009_11_02
. . . . . . . . . . . . . . . . . . . . . with 189T],
. . . . . . . . 300S [H7N3, H7N7 (tCt)],
. . . . . . . . 305N (AAc) [ThaiChiangRai226_2M_2010_03_04
. . . . . . . . . . . . . . . . . . . . . . . with 270T,
. . . . . . . . . . . . . . . . . . Brunei5_52M_2010,
. . . . . . . . . . . . . . . . . . SouthCarolinaAF2562_2009_11_15 (AAt),
. . . . . . . . . . . . . . . . . . DenmarkAalborgINS133_2009_12_02 (AAt)],
. . . . . . . . syn343G [H3N8, H5N1, H6N1, H7N3, H7N7, H10N7, H11, 1918],
. . . . . . . . . . . . . . . [Thuringen189_2009_11_24_xL,
. . . . . . . . . . . . . . . Thuringen227_11_17_xL])
Prediction
Supporting Sequences
. . . . Fukuoka_C34_2010_04_09 (
. . . . . . . . syn#12K,
. . . . . . . . 22I,
. . . . . . . . syn103E,
. . . . . . . . 115K,
. . . . . . . . 165N,
. . . . . . . . 230I (ATa),
. . . . . . . . 274S [Iowa14_2009_12_07
. . . . . . . . . . . . . . . . with 119M],
. . . . . . . . HA truncated after aa329)
. . . . Minnesota04_18M_2010_03_22 (
. . . . . . . . 34D,
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F,
. . . . . . . . 218V,
. . . . . . . . 230I (ATa),
. . . . . . . . syn305K,
. . . . . . . . 313I [Orenburg2974_2009_11_16_xL
. . . . . . . . . . . . . . . . with 225N],
. . . . . . . . syn346G)
. . . . Wisc0337_09M_2009_12_15 (
. . . . . . . . 230I (ATa),
. . . . . . . . 275A,
. . . . . . . . 377K [H9N2])
. . . . TexasAF2579_18M_2009_10_04 (
. . . . . . . . syn20D,
. . . . . . . . 225E,
. . . . . . . . 230I (ATa),
. . . . . . . . syn246E,
. . . . . . . . 264D,
. . . . . . . . 300S,
. . . . . . . . HA truncated after aa386)
. . . . Guangdong2282_20M_2009_11_23 (
. . . . . . . . 131P,
. . . . . . . . 202A,
. . . . . . . . 230I (ATt),
. . . . . . . . 244I,
. . . . . . . . 275A)
. . . . LiaoningShuncheng1148_17F _2009_10_14 (
. . . . . . . . 131P,
. . . . . . . . 202A,
. . . . . . . . 230I (ATt),
. . . . . . . . 244I,
. . . . . . . . 275A)
Related Sequences
. . . . RussiaAnadyrIIV177_2009_12_04_xL_f (
. . . . . . . . 212T [H3N8],
. . . . . . . . 225G,
. . . . . . . . syn238E [H2, H4],
. . . . . . . . 324I,
. . . . . . . . syn413K [H9N2],
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])
. . . . Moscow_CHSN_2009_11_23_xL_f (
. . . . . . . . syn177L [H3N8, H6, H7N7],
. . . . . . . . 225G,
. . . . . . . . 324I,
. . . . . . . . syn376D [H2, H3N8, H4, H5, H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn484N [H3N8, H4, H5N1 (E/A/H), H6, H7N7, H9N2, H11]),
. . . . . . . . syn542S [H2, H5N1, H9N2])
. . . . Lipetsk_BVV_2009_11_10_xL_f (
. . . . . . . . syn177L [H3N8, H6, H7N7],
. . . . . . . . 225G mix,
. . . . . . . . syn238E [H2, H4],
. . . . . . . . syn240G [H3N8, H6, H9N2, H11],
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn542S [H2, H5N1, H9N2])
. . . . Arkhangelsk_GNY_2009_11_25_xL_f (
. . . . . . . . syn134G [H2, H3N8, H4, H5N1 (E/A/H), H6, H9N2, H11],
. . . . . . . . syn177L [H3N8, H6, H7N7],
. . . . . . . . syn238E [H2, H4],
. . . . . . . . syn240G [H3N8, H6, H9N2, H11],
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . 437N,
. . . . . . . . syn484N [H3N8, H4, H5N1 (E/A/H), H6, H7N7, H9N2, H11])
. . . . Orel_KAI1_2009_11_05 (
. . . . . . . . syn238E,
. . . . . . . . 280A,
. . . . . . . . 324I,
. . . . . . . . syn406R,
. . . . . . . . syn413K,
. . . . . . . . syn484N,
. . . . . . . . syn542S)
. . . . Saratov07E2E1_2010_02_01_ xL_VxX (
. . . . . . . . 46I mix,
. . . . . . . . 157E,
. . . . . . . . 158E mix,
. . . . . . . . 225G,
. . . . . . . . syn235T,
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn419L (CTt),
. . . . . . . . syn484N),
. . . . StPeter_VMN_2009_11_19_f (
. . . . . . . . syn202V,
. . . . . . . . syn238E,
. . . . . . . . syn240G,
. . . . . . . . 275F,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn484N,
. . . . . . . . syn542S [H2, H5, H9N2])
. . . . RussiaStPeter204E2_2010_02_08_ xL_VxX (
. . . . . . . . 157E,
. . . . . . . . 225G,
. . . . . . . . syn238E,
. . . . . . . . syn240G
. . . . . . . . 324I,
. . . . . . . . 275F,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn484N),
. . . . Netherlands2629_2009_12_04_xL (
. . . . . . . . syn58C [H2N3, H3N8, H4, H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . 225N,
. . . . . . . . syn233Y,
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . 377K [H9N2],
. . . . . . . . syn413K [H9N2],
. . . . . . . . 507E),
. . . . EgyptN14648_2009_11 (
. . . . . . . . 225N,
. . . . . . . . syn238E,
. . . . . . . . 285S,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])
. . . . RussiaStPeterRII96_2009_10_29 (
. . . . . . . . syn23L,
. . . . . . . . syn91G,
. . . . . . . . syn166K,
. . . . . . . . 187N,
. . . . . . . . syn305K,
. . . . . . . . syn484N)
. . . . UkrChernihiv857_2009_11_14_xL_f (
. . . . . . . . 186P,
. . . . . . . . 225G mix wt,
. . . . . . . . syn238E,
. . . . . . . . 252M,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn431L,
. . . . . . . . syn484N)
. . . . Ukraine122_2010_01_15_xL (
. . . . . . . . 20Y,
. . . . . . . . 186P,
. . . . . . . . syn238E,
. . . . . . . . 252M,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn431L,
. . . . . . . . syn484N)
. . . . Ukraine221_2009_11_02_xL (
. . . . . . . . syn213F,
. . . . . . . . 324I,
. . . . . . . . syn413K)
. . . . Ukraine229_2009_12_25 (
. . . . . . . . syn19V,
. . . . . . . . syn213F,
. . . . . . . . syn346G,
. . . . . . . . 377K)
. . . . DenmarkHvidovreINS141_2009_11_20_xL (
. . . . . . . . syn23L,
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn484N,
. . . . . . . . syn549R)
. . . . DenmarkAalborgINS133_2009_12_02 (
. . . . . . . . 305N (AAt) [SouthCarolinaAF2562_2009_11_15
. . . . . . . . . . . . . . . . . . RussiaBelgorod2_2010_03_15 (AAc)],
. . . . . . . . 377K,
. . . . . . . . syn472H,
. . . . . . . . 530I)
. . . . LouisianaAF2435_2009_11_30 (
. . . . . . . . syn13N,
. . . . . . . . syn256Y,
. . . . . . . . syn283Q,
. . . . . . . . syn338G,
. . . . . . . . syn339F,
. . . . . . . . 377K,
. . . . . . . . HA truncated after aa386)
. . . . WiscD0459_2009_12_18_xL (
. . . . . . . . syn13N,
. . . . . . . . syn32S,
. . . . . . . . 189T,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn474C,
. . . . . . . . 499K)
. . . . WiscD2424_2009_12_15 (
. . . . . . . . syn119I,
. . . . . . . . syn121P,
. . . . . . . . syn132N,
. . . . . . . . 225E,
. . . . . . . . syn238E,
. . . . . . . . 300S,
. . . . . . . . 463T)
. . . . SouthCarolinaAF2562_2009_11_15 (
. . . . . . . . syn177L (CTt),
. . . . . . . . 305N (AAt) [DenmarkAalborgINS133_2009_12_02,
. . . . . . . . . . . . . . . . . . RussiaBelgorod2_2010_03_15 (AAc)],
. . . . . . . . HA truncated after aa386)
. . . . Georgia4032_2009_12_09 (
. . . . . . . . syn27V,
. . . . . . . . syn71E [Moscow, Ivanovo graphic],
. . . . . . . . syn158G,
. . . . . . . . syn213F,
. . . . . . . . 214R,
. . . . . . . . 225E,
. . . . . . . . syn276H,
. . . . . . . . syn321L [MXinDRE797 2010 TmX,
. . . . . . . . . . . . . . . UkrSumy795_2009_11_13_f ,
. . . . . . . . . . . . . . . UkrRivne596_2009_11_12_f],
. . . . . . . . 377K)
. . . . NevadaAF2490_2009_11_02 (
. . . . . . . . 77N,
. . . . . . . . 100N,
. . . . . . . . syn270I,
. . . . . . . . 377K,
. . . . . . . . HA truncated after aa386)
. . . . Maryland04_2010_02_08
. . . . . . . . 35I,
. . . . . . . . 77N,
. . . . . . . . 88T,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn276H,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . NY7020_2009_12_14 (
. . . . . . . . 77N,
. . . . . . . . syn166K,
. . . . . . . . 189T,
. . . . . . . . 377K)
. . . . FL_PenINS213_2009_11_17 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . 273A,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A)
. . . . CalifVRDL107_2009_11_15 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . 39N,
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A)
. . . . CalifVRDL115_2009_12_04 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . 77N [NY7020_2009_12_14 with 189T],
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A),
. . . . HongKong1881_2010_04_18 (
. . . . ~ FL_PenINS213_2009_11_17 with Ukraine and India additions
. . . . . . . . syn2N [SingON2416_2009_12_15,
. . . . . . . . . . . . . UkrSumy797_2009_11_13_f,
. . . . . . . . . . . . . UkrLviv673_2009_11_09_xL,
. . . . . . . . . . . . . UkrLviv673S2_2009_11_09,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . . . . . . . UkrLvivN2_2009_10_28_xL_f,
. . . . . . . . . . . . . IndiaPune10604_2009_09,
. . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . IndiaPune807_2009_07],
. . . . . . . . 35I,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn254P,
. . . . . . . . syn276H,
. . . . . . . . 289V,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . GhanaFS1940_2009_11_13 (
. . . . . . . . syn139C,
. . . . . . . . syn213F,
. . . . . . . . syn228G,
. . . . . . . . 261K,
. . . . . . . . 296H,
. . . . . . . . syn346G,
. . . . . . . . syn404E)
. . . . GhanaFS09_1181_2009_08_07 (
. . . . . . . . syn213F,
. . . . . . . . 380D mix wt [Unique to GISAID])
. . . . EgyptAswan2288_2009_11_02 (
. . . . . . . . 189T,
. . . . . . . . syn245F,
. . . . . . . . 377K [H9N2]),
. . . . JapanOsaka60_2010_07_02 (
. . . . . . . . 35I,
. . . . . . . . 77N,
. . . . . . . . 115K,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn214K,
. . . . . . . . syn219I,
. . . . . . . . syn254P,
. . . . . . . . syn276H,
. . . . . . . . HA truncated after aa330)
. . . . JapanNagasakiHA64_2009_11_27 (
. . . . . . . . syn35L,
. . . . . . . . syn92T,
. . . . . . . . syn136T,
. . . . . . . . 200T,
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . 513V),
. . . . ShandongShizhongSWL24_2010_01_24 (
. . . . . . . . HA truncated until aa23,
. . . . . . . . 24A,
. . . . . . . . 25M,
. . . . . . . . 77N,
. . . . . . . . 131P,
. . . . . . . . syn439D,
. . . . . . . . HA truncated after aa526)
. . . . AnhuiSWL1_2009_06_18 (
. . . . . . . . 77N,
. . . . . . . . 206S,
. . . . . . . . 275I,
. . . . . . . . syn397G)
2011-02-09
The National Institute for Medical Research in the UK published a group of sequences on 2010-08-20 that included two instances of HA 230I from 2010 samples. As predicted using GeneWurx RnR heuristics against the ΣPF11 reservoir (pH1N1), the Ukrainian reservoir and the Russian reservoir each now demonstrates support of the M230I polymorphism. At this moment, this allegedly unpredictable disease has now been predicted in detail 3 times as to specific time, location and genetic change in addition to the original prediction of 230I emergence.
Previously, one military sequence from Texas, TexasAF2579_2009_10_04, was documented as the first 230I to meet the GeneWurx geographic prediction. A dual RBD change (230I & 225E) is carried on the Texas sequence. The Russian sequence detailed in this analysis is the first 230I with 225G, demonstrating multiple supports for dual RBD changes on these related backgrounds.
As early as November 2009 when less than 30 sequences with 225G had been published, our team discussed the high potential and variant mechanisms, including avian lateral transfer, for this pandemic to produce a recombinant with both 225G and 230I. The change to 225G in pH1N1 has been associated with higher severity of disease and fatality potentially due to an increased ability to infect the ciliated cells of the respiratory system. In effect, the 225G variants of Pandemic Influenza 2009 have a wider affinity for α2-3-linked sialic acid binding variety than the 1918 225G sample from New York.
The GeneWurx RnR model is now validated with predicted 230I data points within three geographic regions. The original emergence of 230I in the Pandemic H1N1 reservoir was accurately predicted using a model predating the RnR. Furthermore, the M230I polymorphism count in this reservoir (H1N1pdm, pH1N1, PF11), increases to 8 at the same time that the H3N2 reservoir is building toward immune escape with an emerging sub-clade by revising at the same amino acid position (I230V). Meanwhile, the Pandemic H1N1 reservoir is actively establishing an emergent sub-clade now crossing 9 distinct geographic regions, including the United States, Germany, South Africa and the Ukraine. This emergent H1N1 sub-clade is permissive to 230I and 225G RBD changes. One instance of this new pandemic H1N1 sub-clade is documented in Pennsylvania, a location where the H3N2 reservoir has begun the I230V revision.
A cursory contemporary analysis shows additional instances of H1N1 v. H3N2 reversals at similar positions or similar domains within particular geographic regions. Will we find that the two serotypes (H1N1, H3N2) are in communication and are richly interactive? Science has an unparalleled and unprecedented opportunity today to surveil, in real-time, a post-pandemic period. Will deep surveillance and analysis be conducted or will the status quo be maintained, continuing with the same outdated models limited to the same inputs?
Age Factor and Mechanism Hypothesis
The 230I genetic modification appears to have a higher potential among children and young adults (0-24 years old). The mechanism remains only in postulation due to sparsity of patient meta-data, treatment modality and clinical outcomes. The pattern of revision on the known 230I sequences and on an emerging permissive background is suggestive that 230I is a tertiary immune escape polymorphism, whether developed in situ via a stepwise escape program or acquired via recombination from zoonotic sources. Among individuals who have formed a wide, but only partially competent, series of antibodies, the longer viral infectious period due to incomplete clearance establishes the ideal incubation frame for a stepwise, hyper-morphic and/or novel viral revision.
Very generalised assays from various countries have reported pandemic virus exposure in their younger citizens at rates between 60% and 70%, seemingly a profound rate of protection or so-called herd immunity. However, the re-infection rates clarify that exposure does not equate to protection, though frequently the numbers are reported as protective due to assay titers results that have been deemed as “protective”. As the present evidence has demonstrated, the course of a pandemic viral disease is unaffected by the resulting outdated measures from these overly generalised assays that assume protection.
The younger group’s multiplicity of exposure to a wider variation of influenza strains may factor into the host response/viral revision equation. Viral exertion against a complex host response challenges the reservoir subset to revise toward an optimal solution. In short, for a virus to successfully replicate within a younger person today, increasing novelty may be required. And this viral reservoir has demonstrated a very high capacity for continual novelty.
Additionally, studies have shown that anti-viral usage, specifically the neuraminidase inhibitors in wide usage, through the artificial mechanism of stalling the virus inside infected cells, may be involved in reducing the secondary immune response due to antigen sparsity and limiting the host ability to develop fully competent and protective antibodies. Given the Pandemic H1N1 reservoir’s demonstrated ability to hobble the early innate response (Natural Killer cells, Plasmocytoid Dendritic cells, et al) in combination with the NI anti-viral’s handicapping of the secondary (adaptive) response and the clinical outcomes are more explainable.
Ergo, take the wider exposure of the young population (antibody complexity/variety) and the TamiFlu blanketing used in schools and other institutions around the world (partial antibody competence) as synergistic factors toward a mechanism moulding the environment for 230I emergence as a tertiary immune escape revision. Take the concern another step and consider the prospect of host latency due to viral-induced immune handicap . . . a simmering virus is a variable virus. Furthermore, additional markers from fatalities and vaccine escape strains appear to be accumulating onto these 230I sequences and the sub-clades that are permissive to 230I.
Recall that a mature H5N1 strain in Gharbiyah, Egypt adapted to this same RBD revision under discussion here (230I) and increased the fatality rate substantially above worldwide baseline. Single genetic changes (SNP) are well-represented as fatality markers in this pandemic reservoir and in other zoonotic emergences.
230I Additions
The Institute of Epidemiology and Infectious Diseases AMS of Ukraine originated Ukraine123_2010_02_14_xL and the Russian Academy of Medical Sciences originated RussiaBelgorod2_2010_03_15. Age and gender information remain undisclosed on each sequence of interest.
The hyper-morphic Ukraine123_2010_02_14_xL sequence carries 12 changes on the HA gene segment alone (6 silent). This Ukrainian sample is the first instance of a cross-linked sequence with 230I and the first instantiation of a 230I-bearing strain carrying the 289V signature from India. The synonymous 0T on the Ukrainian sequence is quite rare, but is found in two geographic locations that also demonstrate within their geographic pool the synonymous 238E found on the Ukrainian sequence: Thailand and Hvidovre.
. . . . Ukraine123_2010_02_14_xL (
. . . . . . . . syn0T [BangkokINS427_27M_2010_03_04
. . . . . . . . . . . . . . . . . with syn209Y, syn232Y, syn490P & syn506V,
. . . . . . . . . . . . . DenmarkHvidovreINS290_20F_2009_11_27
. . . . . . . . . . . . . . . . . with 35I, syn490P, 502K & 526T,
. . . . . . . . . . . . . LaReunion3479_2009
. . . . . . . . . . . . . . . . . with syn97D, syn139C & 225E]
. . . . . . . . 186P,
. . . . . . . . 208K,
. . . . . . . . 230I (ATa),
. . . . . . . . syn238E [Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . . . WiscD2424_2009_12_15
. . . . . . . . . . . . . . . . . . . with 225E, 300S & 463T,
. . . . . . . . . . . . . . . Netherlands2629_2009_12_04_xL
. . . . . . . . . . . . . . . . . . . with 225N, syn233Y, 324I, syn413K & 507E,
. . . . . . . . . . . . . . . RussiaAnadyrIIV177_2009_12_04_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . JapanNagasakiHA64_2009_11_27
. . . . . . . . . . . . . . . . . . . with syn35L, syn92T, 200T, 324I & 513V,
. . . . . . . . . . . . . . . Arkhangelsk_GNY_2009_11_25_xL_f
. . . . . . . . . . . . . . . . . . . with 324I, syn413K, 437N & syn484N,
. . . . . . . . . . . . . . . MoscowCHSN_2009_11_23_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I & syn413K & syn484N,
. . . . . . . . . . . . . . . DenmarkHvidovreINS141_2009_11_20_xL
. . . . . . . . . . . . . . . . . . . with syn23L, 324I, syn413K, syn484N & syn549R,
. . . . . . . . . . . . . . . Lipetsk_BVV_2009_11_10_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Orel_KAI1_2009_11_05
. . . . . . . . . . . . . . . . . . . with 280A, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia4_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia14_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia191_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with syn103E, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Belarus220_2009_11,
. . . . . . . . . . . . . . . Belarus360_2009_11,
. . . . . . . . . . . . . . . EgyptN14648_2009_11
. . . . . . . . . . . . . . . . . . . with 225N, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Belarus131_2009_10,
. . . . . . . . . . . . . . . GuamNHRC0032_2009_09_14
. . . . . . . . . . . . . . . . . . . with 89G,
. . . . . . . . . . . . . . . Managua5295_02_2009_07_23,
. . . . . . . . . . . . . . . ThailandTHA0364_2009_07_22
. . . . . . . . . . . . . . . . . . . with #12E, 37N, 296H & syn348V,
. . . . . . . . . . . . . . . Missouri02_2009_05_01
. . . . . . . . . . . . . . . . . . . with syn215P, syn377E, syn456L & syn523V,
. . . . . . . . . . . . . . . Bayern62_2009_04_29_VxX
. . . . . . . . . . . . . . . . . . . with 158E & syn456L,
. . . . . . . . . . . . . . . GermanyRegensburg01_2009_04_27
. . . . . . . . . . . . . . . . . . . with syn456L,
. . . . . . . . . . . . . . . GermanyRegensburgD6_2009
. . . . . . . . . . . . . . . . . . . with syn456L],
. . . . . . . . 252M [Fixed in 2010 Illinois swine with 119M,
. . . . . . . . . . . . . Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . Seoul2883_2009_12_02,
. . . . . . . . . . . . . Seoul1829_2009_11_26,
. . . . . . . . . . . . . LagosWRAIR1982N_2009_11_23,
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . LagosWRAIR1984N_2009_11_18,
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . LagosWRAIR1984T_2009_11_18
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f
. . . . . . . . . . . . . . . . . . . with 186P, 225G, syn238E, 324I,
. . . . . . . . . . . . . . . . . . . . . . . syn413K, syn431L, syn484N,
. . . . . . . . . . . . . Texas45132202_2009_09_13,
. . . . . . . . . . . . . Ancona86_2009_08_31
. . . . . . . . . . . . . . . . . . . with 225E & 300S,
. . . . . . . . . . . . . TurkeyAnkara17_2009_08,
. . . . . . . . . . . . . BZ_SaoPaulo43812_2009_07_03_f],
. . . . . . . . 289V [HK1881_2010_04_18,
. . . . . . . . . . . . . EstoniaTallinnINS431_2010_02_05,
. . . . . . . . . . . . . Luxembourg184_2010_01_25,
. . . . . . . . . . . . . Saarland21_2009_12_11,
. . . . . . . . . . . . . IndiaPune21115_2009_12 with 233H,
. . . . . . . . . . . . . Hiroshima457 _2009_11_02,
. . . . . . . . . . . . . JiangsuNanjinggulouSWL11146_2009_09_17,
. . . . . . . . . . . . . Kobe91993_2009_08_18,
. . . . . . . . . . . . . Kobe91992_2009_08_17,
. . . . . . . . . . . . . UK_Glascow_SC10_2009_06 with 225G,
. . . . . . . . . . . . . UK_Glascow_SC19_2009_06,
. . . . . . . . . . . . . UK_Glascow_SC20_2009_06],
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn431L [Emergent],
. . . . . . . . . . . . . . . [OZ_Grafton2_20F_2010_08_05
. . . . . . . . . . . . . . . . . . . . . . . with 128D, syn173G & syn273T,
. . . . . . . . . . . . . . . OZ_Perth504_5M_2010_07_07
. . . . . . . . . . . . . . . . . . . . . . . with 128D, syn173G & syn273T,
. . . . . . . . . . . . . . . swIllinois03037_2010_06_24
. . . . . . . . . . . . . . . . . . . . . . . with 77G,
. . . . . . . . . . . . . . . swIowa03032_2010_06_04
. . . . . . . . . . . . . . . . . . . . . . . with 77G,
. . . . . . . . . . . . . . . PNG_Goroka16_1F__2010_04_07
. . . . . . . . . . . . . . . . . . . . . . . with 77G & 252L,
. . . . . . . . . . . . . . . PNG_Goroka16E3_1F_2010_04_07
. . . . . . . . . . . . . . . . . . . . . . . with 77G, 186P, 204M, syn205G & 252L,
. . . . . . . . . . . . . . . PNG_Goroka15_2010_02_24
. . . . . . . . . . . . . . . . . . . . . . . with 77G & 252L,
. . . . . . . . . . . . . . . Ukraine122_2010_01_15_xL,
. . . . . . . . . . . . . . . HainanDinganSWL123_2010_01_08,
. . . . . . . . . . . . . . . swOregon10_004060_2009_12_31
. . . . . . . . . . . . . . . . . . . . . . . with syn189A,
. . . . . . . . . . . . . . . AthensINS359_2009_12_26
. . . . . . . . . . . . . . . . . . . . . . . with syn189A,
. . . . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f,
. . . . . . . . . . . . . . . SpainCatS1632_2009_10_28,
. . . . . . . . . . . . . . . swHongKong2314_2009_10_22,
. . . . . . . . . . . . . . . ItalyAncona05_2009_07-12
. . . . . . . . . . . . . . . . . . . . . . . with 225E,
. . . . . . . . . . . . . . . England673_2009_07
. . . . . . . . . . . . . . . . . . . . . . . with 225E],
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11]),
. . . . . . . . . . . . . . . [NY04_2010_02_25
. . . . . . . . . . . . . . . . . . . with 3T, 50E, syn53L, 100N, syn232Y,
. . . . . . . . . . . . . . . . . . . . . . . syn270I, 377K, 437N,
. . . . . . . . . . . . . . . RussiaStPeter204E2E2_2010_02_08_VxX,
. . . . . . . . . . . . . . . RussiaStPeter204E2E1_2010_02_08_VxX,
. . . . . . . . . . . . . . . RussiaStPeter204E2_2010_02_08_VxX,
. . . . . . . . . . . . . . . Saratov07E2E1_2010_02_01_VxX,
. . . . . . . . . . . . . . . Saratov07E2_2010_02_01_VxX,
. . . . . . . . . . . . . . . Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . . . RussiaAnadyrIIV177_2009_12_04_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, syn238E, 324I & syn413K,
. . . . . . . . . . . . . . . Arkhangelsk_GNY_2009_11_25_xL_f
. . . . . . . . . . . . . . . . . . . with 324I, syn413K, 437N & syn484N,
. . . . . . . . . . . . . . . MoscowCHSN_2009_11_23_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I & syn413K,
. . . . . . . . . . . . . . . DenmarkHvidovreINS141_2009_11_20_xL
. . . . . . . . . . . . . . . . . . . with syn23L, 324I, syn413K, syn484N & syn549R,
. . . . . . . . . . . . . . . RussiaStPeterVMN_2009_11_19_f,
. . . . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f
. . . . . . . . . . . . . . . . . . . with 186P, 225G, syn238E, 252M,
. . . . . . . . . . . . . . . . . . . . . . . 324I, syn413K, syn431L,
. . . . . . . . . . . . . . . UkrChernihiv855L_2009_11_11_xL_f,
. . . . . . . . . . . . . . . Lipetsk_BVV_2009_11_10_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . OrelKAI1_2009_11_05,
. . . . . . . . . . . . . . . Russia4_2009_11_01_xL,
. . . . . . . . . . . . . . . Russia14_2009_11_01_xL,
. . . . . . . . . . . . . . . Russia191_2009_11_01_xL,
. . . . . . . . . . . . . . . EgyptN14648_2009_11
. . . . . . . . . . . . . . . . . . . with 225N, syn238E, 324I & syn413K,
. . . . . . . . . . . . . . . RussiaStPeterRII96_2009_10_29
. . . . . . . . . . . . . . . . . . . with 187N,
. . . . . . . . . . . . . . . NizhniNovgorodMEV_2009_07_30,
. . . . . . . . . . . . . . . ItalyAncona15_2009_07_17,
. . . . . . . . . . . . . . . Fixed in Thai Swine including
. . . . . . . . . . . . . . . . . . . swThaiCU_RA75_2010_01 with 188T],
. . . . . . . . syn500R [Unique to GenBank/GISAID])
. . . . RussiaBelgorod2_2010_03_15 (
. . . . . . . . syn13N [WiscD0459_2009_12_18_xL
. . . . . . . . . . . . . . . . . . with 189T, 324I & 499K,
. . . . . . . . . . . . . . LouisianaAF2435_2009_11_30
. . . . . . . . . . . . . . . . . . with syn338G],
. . . . . . . . 77N [tn, swine, S5]
. . . . . . . . . . . [JapanOsaka60_2010_07_02
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . Maryland04_2010_02_08
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . ShandongShizhongSWL24_2010_01_24,
. . . . . . . . . . . NY7020_2009_12_14
. . . . . . . . . . . . . . . . with syn166K & 189T,
. . . . . . . . . . . CalifVRDL115_2009_12_04
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . JapanAF2267_2009_11_09
. . . . . . . . . . . . . . . . with 286E,
. . . . . . . . . . . NevadaAF2490_2009_11_02
. . . . . . . . . . . . . . . . with 100N & syn270I,
. . . . . . . . . . . AlaskaAF2093_2009_11_02
. . . . . . . . . . . . . . . . with 286E,
. . . . . . . . . . . Russia74_2009_11_01_xL,
. . . . . . . . . . . ThailandTHB0441_2009_07_28,
. . . . . . . . . . . Lisboa40_2009_06_23,
. . . . . . . . . . . AnhuiSWL1_2009_06_18
. . . . . . . . . . . . . . . . with 275I,
. . . . . . . . . . . Lithuania1942_2009,
. . . . . . . . . . . swKoreaSCJ10_2009_12,
. . . . . . . . . . . swKoreaSCJ09_2009_12]
. . . . . . . . 158E mix,
. . . . . . . . 225G (Gga) stepwise from 225E,
. . . . . . . . 230I (ATa),
. . . . . . . . 238D [H2N3, H7N3, H7N7, tn, swine],
. . . . . . . . . . . . [PNG_Goroka17_2010_04_14,
. . . . . . . . . . . . AthensINS398_2010_01_24,
. . . . . . . . . . . . AthensINS339_2009_12_30,
. . . . . . . . . . . . Kaliningrad01_11M_2009_11_02
. . . . . . . . . . . . . . . . . . with 225E & 226R,
. . . . . . . . . . . . KaliningradCRIE_DA_2009_09_26,
. . . . . . . . . . . . KaliningradCRIE_KG_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_SHD_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_MA_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_ZD_2009_09_25],
. . . . . . . . syn245F [H2N3, H5N1, H7N7, H10N7, H11]
. . . . . . . . . . . . . . [SingON2416_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with syn166K & 300P,
. . . . . . . . . . . . . . . EgyptAswan2288_2009_11_02
. . . . . . . . . . . . . . . . . . . . . with 189T],
. . . . . . . . 300S [H7N3, H7N7 (tCt)],
. . . . . . . . 305N (AAc) [ThaiChiangRai226_2M_2010_03_04
. . . . . . . . . . . . . . . . . . . . . . . with 270T,
. . . . . . . . . . . . . . . . . . Brunei5_52M_2010,
. . . . . . . . . . . . . . . . . . SouthCarolinaAF2562_2009_11_15 (AAt),
. . . . . . . . . . . . . . . . . . DenmarkAalborgINS133_2009_12_02 (AAt)],
. . . . . . . . syn343G [H3N8, H5N1, H6N1, H7N3, H7N7, H10N7, H11, 1918],
. . . . . . . . . . . . . . . [Thuringen189_2009_11_24_xL,
. . . . . . . . . . . . . . . Thuringen227_11_17_xL])
Prediction
- 2010-09-26 HA 230I RBS Polymorphism Potential for Pennsylvania
- 2010-08-31 HA 230I RBS Polymorphism Potential for Europe
- 2010-08-09 HA 230I Receptor Binding Domain Polymorphism Potential for Spread
- 2010-02-25 HA 230I Receptor Binding Domain Polymorphism Probable for PF11
- 2009-11-20 225G New to Norway and Ukraine; Worldwide Evaluation Concerning Range and Co-Circulation with 225E
- 2010-08-27 HA 230I Documented in Texas with 225E RBD Revision
- 2010-05-10 pH1N1 Surpasses 95% Instability In Critical Genetics Range with Extensive Bird Flu Inclusions
- 2010-05-05 90% Change Rate on Unstable HA Antigen Range with H9N2 and H5N1 Bird Flu Matches
- 2010-03-31 Zoonotic H9N2 Avian Influenza Further Destabilises H1N1 Pandemic Genetics
Supporting Sequences
. . . . Fukuoka_C34_2010_04_09 (
. . . . . . . . syn#12K,
. . . . . . . . 22I,
. . . . . . . . syn103E,
. . . . . . . . 115K,
. . . . . . . . 165N,
. . . . . . . . 230I (ATa),
. . . . . . . . 274S [Iowa14_2009_12_07
. . . . . . . . . . . . . . . . with 119M],
. . . . . . . . HA truncated after aa329)
. . . . Minnesota04_18M_2010_03_22 (
. . . . . . . . 34D,
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F,
. . . . . . . . 218V,
. . . . . . . . 230I (ATa),
. . . . . . . . syn305K,
. . . . . . . . 313I [Orenburg2974_2009_11_16_xL
. . . . . . . . . . . . . . . . with 225N],
. . . . . . . . syn346G)
. . . . Wisc0337_09M_2009_12_15 (
. . . . . . . . 230I (ATa),
. . . . . . . . 275A,
. . . . . . . . 377K [H9N2])
. . . . TexasAF2579_18M_2009_10_04 (
. . . . . . . . syn20D,
. . . . . . . . 225E,
. . . . . . . . 230I (ATa),
. . . . . . . . syn246E,
. . . . . . . . 264D,
. . . . . . . . 300S,
. . . . . . . . HA truncated after aa386)
. . . . Guangdong2282_20M_2009_11_23 (
. . . . . . . . 131P,
. . . . . . . . 202A,
. . . . . . . . 230I (ATt),
. . . . . . . . 244I,
. . . . . . . . 275A)
. . . . LiaoningShuncheng1148_17F _2009_10_14 (
. . . . . . . . 131P,
. . . . . . . . 202A,
. . . . . . . . 230I (ATt),
. . . . . . . . 244I,
. . . . . . . . 275A)
Related Sequences
. . . . RussiaAnadyrIIV177_2009_12_04_xL_f (
. . . . . . . . 212T [H3N8],
. . . . . . . . 225G,
. . . . . . . . syn238E [H2, H4],
. . . . . . . . 324I,
. . . . . . . . syn413K [H9N2],
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])
. . . . Moscow_CHSN_2009_11_23_xL_f (
. . . . . . . . syn177L [H3N8, H6, H7N7],
. . . . . . . . 225G,
. . . . . . . . 324I,
. . . . . . . . syn376D [H2, H3N8, H4, H5, H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn484N [H3N8, H4, H5N1 (E/A/H), H6, H7N7, H9N2, H11]),
. . . . . . . . syn542S [H2, H5N1, H9N2])
. . . . Lipetsk_BVV_2009_11_10_xL_f (
. . . . . . . . syn177L [H3N8, H6, H7N7],
. . . . . . . . 225G mix,
. . . . . . . . syn238E [H2, H4],
. . . . . . . . syn240G [H3N8, H6, H9N2, H11],
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn542S [H2, H5N1, H9N2])
. . . . Arkhangelsk_GNY_2009_11_25_xL_f (
. . . . . . . . syn134G [H2, H3N8, H4, H5N1 (E/A/H), H6, H9N2, H11],
. . . . . . . . syn177L [H3N8, H6, H7N7],
. . . . . . . . syn238E [H2, H4],
. . . . . . . . syn240G [H3N8, H6, H9N2, H11],
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . 437N,
. . . . . . . . syn484N [H3N8, H4, H5N1 (E/A/H), H6, H7N7, H9N2, H11])
. . . . Orel_KAI1_2009_11_05 (
. . . . . . . . syn238E,
. . . . . . . . 280A,
. . . . . . . . 324I,
. . . . . . . . syn406R,
. . . . . . . . syn413K,
. . . . . . . . syn484N,
. . . . . . . . syn542S)
. . . . Saratov07E2E1_2010_02_01_ xL_VxX (
. . . . . . . . 46I mix,
. . . . . . . . 157E,
. . . . . . . . 158E mix,
. . . . . . . . 225G,
. . . . . . . . syn235T,
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn419L (CTt),
. . . . . . . . syn484N),
. . . . StPeter_VMN_2009_11_19_f (
. . . . . . . . syn202V,
. . . . . . . . syn238E,
. . . . . . . . syn240G,
. . . . . . . . 275F,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn484N,
. . . . . . . . syn542S [H2, H5, H9N2])
. . . . RussiaStPeter204E2_2010_02_08_ xL_VxX (
. . . . . . . . 157E,
. . . . . . . . 225G,
. . . . . . . . syn238E,
. . . . . . . . syn240G
. . . . . . . . 324I,
. . . . . . . . 275F,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn484N),
. . . . Netherlands2629_2009_12_04_xL (
. . . . . . . . syn58C [H2N3, H3N8, H4, H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . 225N,
. . . . . . . . syn233Y,
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . 377K [H9N2],
. . . . . . . . syn413K [H9N2],
. . . . . . . . 507E),
. . . . EgyptN14648_2009_11 (
. . . . . . . . 225N,
. . . . . . . . syn238E,
. . . . . . . . 285S,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])
. . . . RussiaStPeterRII96_2009_10_29 (
. . . . . . . . syn23L,
. . . . . . . . syn91G,
. . . . . . . . syn166K,
. . . . . . . . 187N,
. . . . . . . . syn305K,
. . . . . . . . syn484N)
. . . . UkrChernihiv857_2009_11_14_xL_f (
. . . . . . . . 186P,
. . . . . . . . 225G mix wt,
. . . . . . . . syn238E,
. . . . . . . . 252M,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn431L,
. . . . . . . . syn484N)
. . . . Ukraine122_2010_01_15_xL (
. . . . . . . . 20Y,
. . . . . . . . 186P,
. . . . . . . . syn238E,
. . . . . . . . 252M,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn431L,
. . . . . . . . syn484N)
. . . . Ukraine221_2009_11_02_xL (
. . . . . . . . syn213F,
. . . . . . . . 324I,
. . . . . . . . syn413K)
. . . . Ukraine229_2009_12_25 (
. . . . . . . . syn19V,
. . . . . . . . syn213F,
. . . . . . . . syn346G,
. . . . . . . . 377K)
. . . . DenmarkHvidovreINS141_2009_11_20_xL (
. . . . . . . . syn23L,
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn484N,
. . . . . . . . syn549R)
. . . . DenmarkAalborgINS133_2009_12_02 (
. . . . . . . . 305N (AAt) [SouthCarolinaAF2562_2009_11_15
. . . . . . . . . . . . . . . . . . RussiaBelgorod2_2010_03_15 (AAc)],
. . . . . . . . 377K,
. . . . . . . . syn472H,
. . . . . . . . 530I)
. . . . LouisianaAF2435_2009_11_30 (
. . . . . . . . syn13N,
. . . . . . . . syn256Y,
. . . . . . . . syn283Q,
. . . . . . . . syn338G,
. . . . . . . . syn339F,
. . . . . . . . 377K,
. . . . . . . . HA truncated after aa386)
. . . . WiscD0459_2009_12_18_xL (
. . . . . . . . syn13N,
. . . . . . . . syn32S,
. . . . . . . . 189T,
. . . . . . . . 324I,
. . . . . . . . syn413K,
. . . . . . . . syn474C,
. . . . . . . . 499K)
. . . . WiscD2424_2009_12_15 (
. . . . . . . . syn119I,
. . . . . . . . syn121P,
. . . . . . . . syn132N,
. . . . . . . . 225E,
. . . . . . . . syn238E,
. . . . . . . . 300S,
. . . . . . . . 463T)
. . . . SouthCarolinaAF2562_2009_11_15 (
. . . . . . . . syn177L (CTt),
. . . . . . . . 305N (AAt) [DenmarkAalborgINS133_2009_12_02,
. . . . . . . . . . . . . . . . . . RussiaBelgorod2_2010_03_15 (AAc)],
. . . . . . . . HA truncated after aa386)
. . . . Georgia4032_2009_12_09 (
. . . . . . . . syn27V,
. . . . . . . . syn71E [Moscow, Ivanovo graphic],
. . . . . . . . syn158G,
. . . . . . . . syn213F,
. . . . . . . . 214R,
. . . . . . . . 225E,
. . . . . . . . syn276H,
. . . . . . . . syn321L [MXinDRE797 2010 TmX,
. . . . . . . . . . . . . . . UkrSumy795_2009_11_13_f ,
. . . . . . . . . . . . . . . UkrRivne596_2009_11_12_f],
. . . . . . . . 377K)
. . . . NevadaAF2490_2009_11_02 (
. . . . . . . . 77N,
. . . . . . . . 100N,
. . . . . . . . syn270I,
. . . . . . . . 377K,
. . . . . . . . HA truncated after aa386)
. . . . Maryland04_2010_02_08
. . . . . . . . 35I,
. . . . . . . . 77N,
. . . . . . . . 88T,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn276H,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . NY7020_2009_12_14 (
. . . . . . . . 77N,
. . . . . . . . syn166K,
. . . . . . . . 189T,
. . . . . . . . 377K)
. . . . FL_PenINS213_2009_11_17 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . 273A,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A)
. . . . CalifVRDL107_2009_11_15 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . 39N,
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A)
. . . . CalifVRDL115_2009_12_04 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . 77N [NY7020_2009_12_14 with 189T],
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A),
. . . . HongKong1881_2010_04_18 (
. . . . ~ FL_PenINS213_2009_11_17 with Ukraine and India additions
. . . . . . . . syn2N [SingON2416_2009_12_15,
. . . . . . . . . . . . . UkrSumy797_2009_11_13_f,
. . . . . . . . . . . . . UkrLviv673_2009_11_09_xL,
. . . . . . . . . . . . . UkrLviv673S2_2009_11_09,
. . . . . . . . . . . . . MongoliaJP5756_2009_10_15,
. . . . . . . . . . . . . UkrLvivN2_2009_10_28_xL_f,
. . . . . . . . . . . . . IndiaPune10604_2009_09,
. . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . IndiaPune807_2009_07],
. . . . . . . . 35I,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn219I,
. . . . . . . . syn254P,
. . . . . . . . syn276H,
. . . . . . . . 289V,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . GhanaFS1940_2009_11_13 (
. . . . . . . . syn139C,
. . . . . . . . syn213F,
. . . . . . . . syn228G,
. . . . . . . . 261K,
. . . . . . . . 296H,
. . . . . . . . syn346G,
. . . . . . . . syn404E)
. . . . GhanaFS09_1181_2009_08_07 (
. . . . . . . . syn213F,
. . . . . . . . 380D mix wt [Unique to GISAID])
. . . . EgyptAswan2288_2009_11_02 (
. . . . . . . . 189T,
. . . . . . . . syn245F,
. . . . . . . . 377K [H9N2]),
. . . . JapanOsaka60_2010_07_02 (
. . . . . . . . 35I,
. . . . . . . . 77N,
. . . . . . . . 115K,
. . . . . . . . syn152I,
. . . . . . . . 206S,
. . . . . . . . syn214K,
. . . . . . . . syn219I,
. . . . . . . . syn254P,
. . . . . . . . syn276H,
. . . . . . . . HA truncated after aa330)
. . . . JapanNagasakiHA64_2009_11_27 (
. . . . . . . . syn35L,
. . . . . . . . syn92T,
. . . . . . . . syn136T,
. . . . . . . . 200T,
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . 513V),
. . . . ShandongShizhongSWL24_2010_01_24 (
. . . . . . . . HA truncated until aa23,
. . . . . . . . 24A,
. . . . . . . . 25M,
. . . . . . . . 77N,
. . . . . . . . 131P,
. . . . . . . . syn439D,
. . . . . . . . HA truncated after aa526)
. . . . AnhuiSWL1_2009_06_18 (
. . . . . . . . 77N,
. . . . . . . . 206S,
. . . . . . . . 275I,
. . . . . . . . syn397G)
2010-11-16
225Y from Finland Increases Depth of Genetic Diversity within Critical Receptor Binding Site
Last Updated 2010-12-11
The National Institute for Health and Welfare of Finland deposited a group of 133 HA sequences at GenBank on 2010-11-13. The amino acid range of position 225 is extended by the mixed peaks found on an unidentified age / gender sampled on 2009-11-28, Finland649_2009_11_28. Though 225E is the most common change at the position within this geography, this particular infection attempted immune escape by revising to a Tyrosine at 225. This inflection point sample was taken at a peak of the pandemic practically one year ago and was not published until November 2010.
. . . . Finland649_2009_11_28 (
. . . . . . . . syn49G [MyanmarJPS020_2010_07_07
. . . . . . . . . . . . . . . . . . . . plus 8 in 2010,
. . . . . . . . . . . . . . India8910_2010-05-08
. . . . . . . . . . . . . . . . . . . . with 188T,
. . . . . . . . . . . . . . SingaporeKK081_2010_02_12,
. . . . . . . . . . . . . . TexasJMS411_2010_01_25
. . . . . . . . . . . . . . . . . . . . plus 2 in late 2009,
. . . . . . . . . . . . . . Virginia01_2010_01-21,
. . . . . . . . . . . . . . Hawaii01_2010_01-03,
. . . . . . . . . . . . . . Hawaii02_2010_01-02,
. . . . . . . . . . . . . . England935_2009_12,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . with 225N, 230I,
. . . . . . . . . . . . . . CaliforniaVRDL71_2009_08_28,
. . . . . . . . . . . . . . WiscS0435_2009,
. . . . . . . . . . . . . . HK01_2009_04_30, et al],
. . . . . . . . syn216E,
. . . . . . . . 225Y mix wt (kAT),
. . . . . . . . 324I,
. . . . . . . . syn413K)
Another trace supporting this Finnish deposit showed a mix at 225 equating to 225G and wild type. Note the consecutive numbering of the 225Y sample to the 225G sample and the similarity of the two sequences. Of the 5 morphic positions, they share 4 and have matching revision values at 3 of those 5.
. . . . Finland648_2009_11_19 (
. . . . . . . . 129Q,
. . . . . . . . syn216E,
. . . . . . . . 225G mix wt,
. . . . . . . . 324I,
. . . . . . . . syn413K)
Previously, we have detailed the genetic diversity and Vaccine Escape tendencies within this viral reservoir. 100% of the Hemagglutinin positions between 186 and 248, including antigenic areas of the Receptor Binding Domain (RBD/RBS), are on record as polymorphic. No position in that range is stable.
Many positions rate multiple changes with position 225 increasing by the novel Tyrosine with the Finnish deposit. Protein revision is documented at 58 of the 63 positions (92%), engaging a wide potential for antibody resistance (natural Immune Escape and Vaccine Escape). Specifically, the range from 220 to 226 shows deep diversity, driving sequences that are laboratory confirmed as Low Reactors (Vaccine Escape). With the critical position 225 depth chart now moving into double digits at 10 values within this reservoir, ample consideration must be given to the rapid acquisition feature on display.
Amino Acid Position 225 Variation in ΣPF11
Supporting Sequences
. . . . Yakutsk_EAV_2009_11_18 (
. . . . . . . . syn49G,
. . . . . . . . syn164L [1918],
. . . . . . . . 206S [Yaro_CHMV_2009_11_10_f (224K & 225G)],
. . . . . . . . 286N [H3N8],
. . . . . . . . . . . [Yaro_CHMV],
. . . . . . . . 296H [Yaro_CHMV],
. . . . . . . . syn348V [Yaro_CHMV,
. . . . . . . . . . . . . . . IndiaPune10604_2009_09,
. . . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . syn429L (TTa) [H3N8 Avian, 1918, WSN33, S5, M7],
. . . . . . . . syn448L [S9],
. . . . . . . . . . . . . [Yaro_CHMV],
. . . . . . . . syn490P [S5, tn],
. . . . . . . . . . . . . [Yaro_CHMV],
. . . . . . . . syn511T [Yaro_CHMV],
. . . . . . . . syn542S [H2, H5, H9N2],
. . . . . . . . . . . . . [Yaro_CHMV])
The National Institute for Health and Welfare of Finland deposited a group of 133 HA sequences at GenBank on 2010-11-13. The amino acid range of position 225 is extended by the mixed peaks found on an unidentified age / gender sampled on 2009-11-28, Finland649_2009_11_28. Though 225E is the most common change at the position within this geography, this particular infection attempted immune escape by revising to a Tyrosine at 225. This inflection point sample was taken at a peak of the pandemic practically one year ago and was not published until November 2010.
. . . . Finland649_2009_11_28 (
. . . . . . . . syn49G [MyanmarJPS020_2010_07_07
. . . . . . . . . . . . . . . . . . . . plus 8 in 2010,
. . . . . . . . . . . . . . India8910_2010-05-08
. . . . . . . . . . . . . . . . . . . . with 188T,
. . . . . . . . . . . . . . SingaporeKK081_2010_02_12,
. . . . . . . . . . . . . . TexasJMS411_2010_01_25
. . . . . . . . . . . . . . . . . . . . plus 2 in late 2009,
. . . . . . . . . . . . . . Virginia01_2010_01-21,
. . . . . . . . . . . . . . Hawaii01_2010_01-03,
. . . . . . . . . . . . . . Hawaii02_2010_01-02,
. . . . . . . . . . . . . . England935_2009_12,
. . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . with 225N, 230I,
. . . . . . . . . . . . . . CaliforniaVRDL71_2009_08_28,
. . . . . . . . . . . . . . WiscS0435_2009,
. . . . . . . . . . . . . . HK01_2009_04_30, et al],
. . . . . . . . syn216E,
. . . . . . . . 225Y mix wt (kAT),
. . . . . . . . 324I,
. . . . . . . . syn413K)
Another trace supporting this Finnish deposit showed a mix at 225 equating to 225G and wild type. Note the consecutive numbering of the 225Y sample to the 225G sample and the similarity of the two sequences. Of the 5 morphic positions, they share 4 and have matching revision values at 3 of those 5.
. . . . Finland648_2009_11_19 (
. . . . . . . . 129Q,
. . . . . . . . syn216E,
. . . . . . . . 225G mix wt,
. . . . . . . . 324I,
. . . . . . . . syn413K)
Previously, we have detailed the genetic diversity and Vaccine Escape tendencies within this viral reservoir. 100% of the Hemagglutinin positions between 186 and 248, including antigenic areas of the Receptor Binding Domain (RBD/RBS), are on record as polymorphic. No position in that range is stable.
Many positions rate multiple changes with position 225 increasing by the novel Tyrosine with the Finnish deposit. Protein revision is documented at 58 of the 63 positions (92%), engaging a wide potential for antibody resistance (natural Immune Escape and Vaccine Escape). Specifically, the range from 220 to 226 shows deep diversity, driving sequences that are laboratory confirmed as Low Reactors (Vaccine Escape). With the critical position 225 depth chart now moving into double digits at 10 values within this reservoir, ample consideration must be given to the rapid acquisition feature on display.
Amino Acid Position 225 Variation in ΣPF11
- 225D (GAt) wt
- 225D synonymous (GAc)
- 225A
- 225E (GAa)
- 225E (GAg)
- 225E (GAa) plus 226R
- 225G (Gga) from 225E
- 225G (GgT)
- 225N
- 225V
- 225Y
Supporting Sequences
. . . . Yakutsk_EAV_2009_11_18 (
. . . . . . . . syn49G,
. . . . . . . . syn164L [1918],
. . . . . . . . 206S [Yaro_CHMV_2009_11_10_f (224K & 225G)],
. . . . . . . . 286N [H3N8],
. . . . . . . . . . . [Yaro_CHMV],
. . . . . . . . 296H [Yaro_CHMV],
. . . . . . . . syn348V [Yaro_CHMV,
. . . . . . . . . . . . . . . IndiaPune10604_2009_09,
. . . . . . . . . . . . . . . BZ_SaoPaulo53823_2009_08_01_f,
. . . . . . . . . . . . . . . Eng662_2009_08],
. . . . . . . . syn429L (TTa) [H3N8 Avian, 1918, WSN33, S5, M7],
. . . . . . . . syn448L [S9],
. . . . . . . . . . . . . [Yaro_CHMV],
. . . . . . . . syn490P [S5, tn],
. . . . . . . . . . . . . [Yaro_CHMV],
. . . . . . . . syn511T [Yaro_CHMV],
. . . . . . . . syn542S [H2, H5, H9N2],
. . . . . . . . . . . . . [Yaro_CHMV])
2010-11-02
HA 230I with 225N Demonstrated in Iowa Swine during November 2009
Last Updated 2010-11-08
On 2010-11-01, a collaboration of researchers based in Ames, Iowa deposited a swine sequence at GenBank. November 2009 is the sample month, approximately one year prior to publication. The first instance of the dual RBD change 225N and 230I is found in this swine data.
Though the HA is hyper-morphic, the cross-linked Iowa swine has only one NA change (syn414G) other than the cross-linkage syn407V for a total of 2 silent changes. Those two changes on the NA appear only in a single pandemic sequence, Liaoning_HepingSWL1606_13M_2009_12_23. The two changes (syn407V with syn414G) also appear in 16 recent H5N1 (2006-2009) sequences: 2 human, 10 birds and 4 environmental.
The potential HA recombinant appears to be on a pandemic H1N1 background with multiple donation bases from S7 H1N1 and S7 & S5 H1N2 including several blocks coding for contiguous amino acid revision. The swine HA sequence has 92% homology to the nearest HA. More than 100 changes are demonstrated on the swine HA, the bulk of which appear on Seasonal H1N1 2007.
swIowa44837_1_2009_11_08_xL carries a universe of changes suggestive as a progenitor of / donor to the recently discussed emergence of a 230I-permissive sub-clade. The swine matches and domaining are evident around several of the six markers for the new sub-clade as well as around several non-marker polymorphisms from the emerging sub-clade sequences.
Furthermore, this single swine sequence also carries markers implicated in the cross-linked Russian fatality analysis. An annotated chart was developed to investigate the various paths to fatality in Russia, determining that high genetic lability existed for fatal outcomes and that changes at amino acid 225 were not required to produce fatal outcomes. The group of fatal sequences from Moscow and Ivanovo in the bottom right of the annotated phylogenetic tree carries a large number of changes including the syn355H found on the swine sequence under review in this analysis. The opposed group of fatal sequences from Ulyanovsk in the top left of the chart carries the smallest count of changes from the larger deposit and includes the syn372Q found on swIowa44837_1_2009_11_08_xL.
Similar sequences to this Iowa swine recombinant have been recorded circulating throughout the United States in Minnesota, North Carolina, Illinois and Indiana during late 2009 and early 2010 including:
swMinnesota02979_2010_02_17
swMinnesota02976_2010_01_12
swIllinois3910_2010_01_11
swIllinois02957_2010
swIllinois02960_2010
swIllinois02938_2009-12-29
swIllinois02935_2009_12_20
swIllinois02936_2009_12_20
swIllinois02919_2009_11_12
swIllinois32975_2009_11_11
swNorthCarolina02926_2009_11_24
swIndiana27007_2009
. . . . swIowa44837_1_2009_11_08_xL (
. . . . . . . . Hyper-morphic HA recombinant on PF11 background
. . . . . . . . with multiple donation bases from S7 H1N1 and S7 & S5 H1N2:
. . . . . . . . ~ 92% Homology to nearest HA
. . . . . . . . with more than 100 changes including, but not limited to:
. . . . . . . . syn36L,
. . . . . . . . syn38E,
. . . . . . . . syn40H,
. . . . . . . . syn41N,
. . . . . . . . syn42G,
. . . . . . . . 48K [S7],
. . . . . . . . syn49G,
. . . . . . . . 50I [S7],
. . . . . . . . syn56G, syn58C, syn70C, syn86S, 92M,
. . . . . . . . 131S,
. . . . . . . . 132T [S7],
. . . . . . . . 156E [swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn169I, syn170N, 171E,
. . . . . . . . 182V [S7],
. . . . . . . . . . . . . [NY7480_2010_03_01 with 253A],
. . . . . . . . 188R,
. . . . . . . . 189G [S7],
. . . . . . . . 193G,
. . . . . . . . 196H [S7],
. . . . . . . . 197H,
. . . . . . . . 198E [S7],
. . . . . . . . 199N [S7],
. . . . . . . . 214T [S7],
. . . . . . . . syn222K [S7],
. . . . . . . . syn224R [S7],
. . . . . . . . 225N [swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn226Q [S7],
. . . . . . . . syn228G [S7],
. . . . . . . . 230I [S7],
. . . . . . . . syn232Y [S7],
. . . . . . . . syn235T [S7],
. . . . . . . . 238D [H2N3, H7N3, H7N7, tn, swine],
. . . . . . . . . . . . . [RussiaBelgorod2_2010_03_15
. . . . . . . . . . . . . . . . . . with 158E, 225G, 230I],
. . . . . . . . 241Y,
. . . . . . . . 244I [S7],
. . . . . . . . syn246E [S7],
. . . . . . . . . . . . . . . [TexasAF2579_2009_10_04 with 230I],
. . . . . . . . 248N,
. . . . . . . . syn251L,
. . . . . . . . 253A [NY7480_2010_03_01 with 182V],
. . . . . . . . 260L [S7],
. . . . . . . . 263G,
. . . . . . . . 264F [S7],
. . . . . . . . 272N [S7],
. . . . . . . . 273A [S7],
. . . . . . . . 275M [S7],
. . . . . . . . 276G,
. . . . . . . . 277E [S7],
. . . . . . . . 280A [MI09_2007_H1N2],
. . . . . . . . 281N,
. . . . . . . . 298V [S7],
. . . . . . . . 305E [swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn329S [S7],
. . . . . . . . syn346G [S7],
. . . . . . . . . . . . . . . [H3N2, H3N8, H5N1, H6N2, H6N4, H10N7],
. . . . . . . . . . . . . . [Fixed in non-PF11 Emergent swine lineages,
. . . . . . . . . . . . . . swNC19646_2010_04_20 with 158E,
. . . . . . . . . . . . . . Minnesota04_2010_03_22 with 230I,
. . . . . . . . . . . . . . Nevada01_2010_01_02,
. . . . . . . . . . . . . . Nevada20_2009_12_03,
. . . . . . . . . . . . . . Sachsen180_2009_12_02,
. . . . . . . . . . . . . . Lisboa108_2009_11_30 with 225E, syn228G,
. . . . . . . . . . . . . . GhanaFS2206_2009_11_25 with syn228G,
. . . . . . . . . . . . . . GhanaFS1982_2009_11_16 with syn228G,
. . . . . . . . . . . . . . NewMexico16MXC1_2009_11_07,
. . . . . . . . . . . . . . BZ_RioJaneiro7131_2009_08_01_f],
. . . . . . . . syn355H [MI09_2007_H1N2,
. . . . . . . . . . . . . . . . swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn361G [S7],
. . . . . . . . syn372Q [S7],
. . . . . . . . 376N [MI09_2007_H1N2,
. . . . . . . . . . . . swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn379T [S7],
. . . . . . . . . . . . . . . [Wisconsin06_2010_04_28],
. . . . . . . . syn381K [S7],
. . . . . . . . syn382V [S7],
. . . . . . . . syn385V [S7],
. . . . . . . . syn388K [S7],
. . . . . . . . syn390N [S7],
. . . . . . . . . . . . . . . [H2, H3N8, H5, H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . . . . . . . . [Calif09_2010_05_11],
. . . . . . . . syn391T [S7],
. . . . . . . . syn392Q [S7],
. . . . . . . . syn395A [S7],
. . . . . . . . syn396V [S7],
. . . . . . . . syn397G [S7],
. . . . . . . . syn399E [S7],
. . . . . . . . . . . . . . . [Arizona06_2010_05_29 with 158E],
. . . . . . . . syn403L [S7],
. . . . . . . . 405R [S7],
. . . . . . . . 407M [S7],
. . . . . . . . syn413K [S7],
. . . . . . . . syn419L [S7],
. . . . . . . . syn428L [S7],
. . . . . . . . syn443S [S7],
. . . . . . . . syn495E [MI09_2007_H1N2],
. . . . . . . . 508R,
. . . . . . . . syn515Q)
On 2010-11-01, a collaboration of researchers based in Ames, Iowa deposited a swine sequence at GenBank. November 2009 is the sample month, approximately one year prior to publication. The first instance of the dual RBD change 225N and 230I is found in this swine data.
Though the HA is hyper-morphic, the cross-linked Iowa swine has only one NA change (syn414G) other than the cross-linkage syn407V for a total of 2 silent changes. Those two changes on the NA appear only in a single pandemic sequence, Liaoning_HepingSWL1606_13M_2009_12_23. The two changes (syn407V with syn414G) also appear in 16 recent H5N1 (2006-2009) sequences: 2 human, 10 birds and 4 environmental.
The potential HA recombinant appears to be on a pandemic H1N1 background with multiple donation bases from S7 H1N1 and S7 & S5 H1N2 including several blocks coding for contiguous amino acid revision. The swine HA sequence has 92% homology to the nearest HA. More than 100 changes are demonstrated on the swine HA, the bulk of which appear on Seasonal H1N1 2007.
swIowa44837_1_2009_11_08_xL carries a universe of changes suggestive as a progenitor of / donor to the recently discussed emergence of a 230I-permissive sub-clade. The swine matches and domaining are evident around several of the six markers for the new sub-clade as well as around several non-marker polymorphisms from the emerging sub-clade sequences.
Furthermore, this single swine sequence also carries markers implicated in the cross-linked Russian fatality analysis. An annotated chart was developed to investigate the various paths to fatality in Russia, determining that high genetic lability existed for fatal outcomes and that changes at amino acid 225 were not required to produce fatal outcomes. The group of fatal sequences from Moscow and Ivanovo in the bottom right of the annotated phylogenetic tree carries a large number of changes including the syn355H found on the swine sequence under review in this analysis. The opposed group of fatal sequences from Ulyanovsk in the top left of the chart carries the smallest count of changes from the larger deposit and includes the syn372Q found on swIowa44837_1_2009_11_08_xL.
Similar sequences to this Iowa swine recombinant have been recorded circulating throughout the United States in Minnesota, North Carolina, Illinois and Indiana during late 2009 and early 2010 including:
swMinnesota02979_2010_02_17
swMinnesota02976_2010_01_12
swIllinois3910_2010_01_11
swIllinois02957_2010
swIllinois02960_2010
swIllinois02938_2009-12-29
swIllinois02935_2009_12_20
swIllinois02936_2009_12_20
swIllinois02919_2009_11_12
swIllinois32975_2009_11_11
swNorthCarolina02926_2009_11_24
swIndiana27007_2009
. . . . swIowa44837_1_2009_11_08_xL (
. . . . . . . . Hyper-morphic HA recombinant on PF11 background
. . . . . . . . with multiple donation bases from S7 H1N1 and S7 & S5 H1N2:
. . . . . . . . ~ 92% Homology to nearest HA
. . . . . . . . with more than 100 changes including, but not limited to:
. . . . . . . . syn36L,
. . . . . . . . syn38E,
. . . . . . . . syn40H,
. . . . . . . . syn41N,
. . . . . . . . syn42G,
. . . . . . . . 48K [S7],
. . . . . . . . syn49G,
. . . . . . . . 50I [S7],
. . . . . . . . syn56G, syn58C, syn70C, syn86S, 92M,
. . . . . . . . 131S,
. . . . . . . . 132T [S7],
. . . . . . . . 156E [swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn169I, syn170N, 171E,
. . . . . . . . 182V [S7],
. . . . . . . . . . . . . [NY7480_2010_03_01 with 253A],
. . . . . . . . 188R,
. . . . . . . . 189G [S7],
. . . . . . . . 193G,
. . . . . . . . 196H [S7],
. . . . . . . . 197H,
. . . . . . . . 198E [S7],
. . . . . . . . 199N [S7],
. . . . . . . . 214T [S7],
. . . . . . . . syn222K [S7],
. . . . . . . . syn224R [S7],
. . . . . . . . 225N [swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn226Q [S7],
. . . . . . . . syn228G [S7],
. . . . . . . . 230I [S7],
. . . . . . . . syn232Y [S7],
. . . . . . . . syn235T [S7],
. . . . . . . . 238D [H2N3, H7N3, H7N7, tn, swine],
. . . . . . . . . . . . . [RussiaBelgorod2_2010_03_15
. . . . . . . . . . . . . . . . . . with 158E, 225G, 230I],
. . . . . . . . 241Y,
. . . . . . . . 244I [S7],
. . . . . . . . syn246E [S7],
. . . . . . . . . . . . . . . [TexasAF2579_2009_10_04 with 230I],
. . . . . . . . 248N,
. . . . . . . . syn251L,
. . . . . . . . 253A [NY7480_2010_03_01 with 182V],
. . . . . . . . 260L [S7],
. . . . . . . . 263G,
. . . . . . . . 264F [S7],
. . . . . . . . 272N [S7],
. . . . . . . . 273A [S7],
. . . . . . . . 275M [S7],
. . . . . . . . 276G,
. . . . . . . . 277E [S7],
. . . . . . . . 280A [MI09_2007_H1N2],
. . . . . . . . 281N,
. . . . . . . . 298V [S7],
. . . . . . . . 305E [swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn329S [S7],
. . . . . . . . syn346G [S7],
. . . . . . . . . . . . . . . [H3N2, H3N8, H5N1, H6N2, H6N4, H10N7],
. . . . . . . . . . . . . . [Fixed in non-PF11 Emergent swine lineages,
. . . . . . . . . . . . . . swNC19646_2010_04_20 with 158E,
. . . . . . . . . . . . . . Minnesota04_2010_03_22 with 230I,
. . . . . . . . . . . . . . Nevada01_2010_01_02,
. . . . . . . . . . . . . . Nevada20_2009_12_03,
. . . . . . . . . . . . . . Sachsen180_2009_12_02,
. . . . . . . . . . . . . . Lisboa108_2009_11_30 with 225E, syn228G,
. . . . . . . . . . . . . . GhanaFS2206_2009_11_25 with syn228G,
. . . . . . . . . . . . . . GhanaFS1982_2009_11_16 with syn228G,
. . . . . . . . . . . . . . NewMexico16MXC1_2009_11_07,
. . . . . . . . . . . . . . BZ_RioJaneiro7131_2009_08_01_f],
. . . . . . . . syn355H [MI09_2007_H1N2,
. . . . . . . . . . . . . . . . swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn361G [S7],
. . . . . . . . syn372Q [S7],
. . . . . . . . 376N [MI09_2007_H1N2,
. . . . . . . . . . . . swCloppenIDT4777_S5_H1N2,
. . . . . . . . . . . . swDoetIDT4735_S5_H1N2],
. . . . . . . . syn379T [S7],
. . . . . . . . . . . . . . . [Wisconsin06_2010_04_28],
. . . . . . . . syn381K [S7],
. . . . . . . . syn382V [S7],
. . . . . . . . syn385V [S7],
. . . . . . . . syn388K [S7],
. . . . . . . . syn390N [S7],
. . . . . . . . . . . . . . . [H2, H3N8, H5, H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . . . . . . . . [Calif09_2010_05_11],
. . . . . . . . syn391T [S7],
. . . . . . . . syn392Q [S7],
. . . . . . . . syn395A [S7],
. . . . . . . . syn396V [S7],
. . . . . . . . syn397G [S7],
. . . . . . . . syn399E [S7],
. . . . . . . . . . . . . . . [Arizona06_2010_05_29 with 158E],
. . . . . . . . syn403L [S7],
. . . . . . . . 405R [S7],
. . . . . . . . 407M [S7],
. . . . . . . . syn413K [S7],
. . . . . . . . syn419L [S7],
. . . . . . . . syn428L [S7],
. . . . . . . . syn443S [S7],
. . . . . . . . syn495E [MI09_2007_H1N2],
. . . . . . . . 508R,
. . . . . . . . syn515Q)
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