Publish Date : 2011-12-21
Last Update : 2012-01-27
On 2011-12-20, the UK National Institute of Medical Research released a group of human pH1N1 sequences at GISAID including 46 full HA and 45 full NA segments. The sample dates cover 2010-12-15 to 2011-08-11 (44 during 2011). Fifteen originating labs provided the samples though no specification of clinical outcome is notated within the NIMR deposit. The cases produced 968 total polymorphisms on the Hemagglutinin and Neuraminidase gene segments (HA 638 / NA 330) averaging over 20 polymorphisms per full sequence (HA 13.9 / NA 7.3).
The superset of polymorphisms demonstrates notable non-swine, zoonotic homology according to the GeneWurx Zoonoses Listing (GZL) assessment with an 85% minimum of the 350 combined distinct HA and NA polymorphisms being found on non-swine, animal sequences (primarily avian). Trans-Zoonotic Serotype Analyses (TZSA), [HA] / [NA], provide the detail beneath the GZL. Additionally, GeneWurx LookAside analysis (Upstream & Downstream Distances of 1 Amino Acid each) demonstrates potential influencer relationships for pH1N1 HA polymorphisms that have not yet shown direct zoonotic homology.
The volume and span of the deposit demonstrates the ongoing significant rate of genetic acquisition onto 4 of the established clades, alongside several uncladed sequences. Four sequences carry clade-defining elements from multiple clades. Ambiguity in the traces is high with 44 mixed traces, 34 HA and 10 NA.
A certain population of geographically-dispersed sequences shows a combined HA and NA total of 25 or more revisions (10 sequences, 22% of the deposit). This deposit brings the first pH1N1 sequence with a combined 40 polymorphisms (HA and NA) on the highly avian-influenced, SenegalDakar14_1x_2011_04_14 (HA 29 / NA 11) [EPI346724]. On that Dakar HA, 23 of 29 polymorphisms (79%) are found within Avian H1N1, while at least 90% are identifiable in non-swine zoonotic reservoirs (26 of 29 HA). This single human sequence from a very young child carries 13 amino homologies to H5N1 (9 HA / 4 NA), 13 to H9N2 (9 HA / 4 NA) and 18 to H6N1 (10 HA / 8 NA). Dakar homology to TamiFlu Resistant strains due to NA 247N is significant with 14 matches (8 HA / 6 NA).
Enhanced acquisition of avian genetic data and convergence of polymorphisms found on High-CFR and highly-zoonotic pH1N1 strains are quantified. Variant clades appear to be gaining data from the same sources as the pH1N1 HA 230I strains (24 HA / 12 NA matches) and the Upsilon series (31 HA / 23 NA matches) of 84 sequences (5.33% CFR).
Five countries (Cameroon, France, England, Iceland and Hungary) produced a subset of 9 sequences bearing 12 total polymorphisms within the aa156-aa159 range, a domain documented to produce Vaccine Escape. Hungary7_xM_2011_01_31 (HA 11 / NA 06) [EPI346709] on Clade2: 188T with RBS 226R (Vaccine Match) applies polymorphic behaviour at 3 consecutive Vaccine Escape locations in this domain (HA 157E mix wt, 158E mix wt and 159D mix wt).
One sequence is TamiFlu Resistant with NA 275Y. More importantly a strong gravity is indicated in the polymorphic pattern suggestive that more TmX due to NA 247N will be seen in the future on these types of strains. Considering the HA and NA distinct polymorphic supersets on these human pandemic sequences, 96 (52 HA and 44 NA) changes (27%) appear on earlier pandemic sequences with TmX due to NA 247N and 85 (52 HA and 33 NA) changes (24%) appear on the subset of H5N1 sequences that carry the NA 247N marker.
Evaluating the 229 distinct HA changes derived from these 46 human pandemic sequences against fractional HA subsets of several animal serotypes, a minimum of 84% share homology. Avian H1N1 leads the match count at 140 polymorphic values (103 Farm Avian H1N1), while H6N1 continues to participate at a significant level (88 matches). Homology to Avian H9N2 (65), H13 (53) and the High-CFR H5N1 (104) demonstrates that this pandemic has ample opportunity for genetic input from the extant reservoirs to amplify clinical conditions. GeneWurx LookAside analysis shows that 109 of the 229 distinct pH1N1 HA polymorphisms demonstrate an amino acid homology within 1 position upstream or downstream in a zoonotic reservoir for a total of 311 HA LookAside influencers.
Of 121 distinct NA polymorphisms, 104 are non-swine, zoonotic (86%) and a minimum of 89 are found on Avian H1N1 (74%) with 74 (61%) of those found on a subset of a dozen Farm Avian H1N1 sequences that have consistently matched polymorphisms coming onto the human H1N1 pandemic background since 2009. NA homology with other non-swine, zoonotic reservoirs remains significant: Avian H6N1 (88 / 73%), Avian H9N2 (30) and the High-CFR H5N1 (54).
Though the zoonotic serotype backgrounds profiled against these human polymorphisms are entirely variant, these many codon-level homologies crossing multiple zoonotic reservoirs into the human pandemic illuminates the GeneWurx premise that the origin of the human H1N1 pandemic be reconsidered as avian.
Cladistics
Clade1: 189T - 07 Sequences
Clade2: 188T - 23 Sequences
Clade3: 186P - 05 Sequences
Clade5: 208K_219V - 06 Sequences
HA 638 Polymorphisms Averaging ~13.9 per Segment
NA 330 Polymorphisms Averaging ~ 7.3 per Segment
HA and NA 968 Total Polymorphisms Averaging ~20.0 across 45 w/ HA & NA
TamiFlu Resistance
One TamiFlu Resistant sequence (NA 275Y) features on a Clade2: 188T background and carries HA RBS 227G with the HA 158E (mixture with wild type) that has repeatedly been observed to promote Vaccine Escape. Avian H1N1 carries homology with 9 of the 11 HA and 100% of NA polymorphisms on the TamiFlu Resistant French case. One small population of Farm Avian H1N1 sequences matches on 7 of these 11 HA and 5 of 6 NA revisions. TamiFlu Resistance Confluence (multiple TmX markers) is correlated due to 8 of the 11 HA markers sharing homology to the superset of pH1N1 NA 247N TamiFlu Resistant sequences and 100% of the NA changes. Fourteen revisions (8 HA / 6 NA) pattern to the pH1N1 superset of HA 230I-bearing sequences. Eleven changes (8 HA / 3 NA) equate to the High-CFR human pandemic Upsilon sub-clade.
- [EPI346699] FranceLorraine1176_50x_2011_02_23_TmX
Sequences
. . . . Madagascar9274_7M_2011_08_11 (
. . . . . . . . GISAID HA EPI346721
. . . . . . . . Clade2: 188T
. . . . . . . . 22 Polymorphisms (12 Amino and 10 Silent)
. . . . . . . . #6M,
. . . . . . . . #4C,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn49G (GGa),
. . . . . . . . syn122K (AAa),
. . . . . . . . 141Q,
. . . . . . . . 146G,
. . . . . . . . 169S,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 216G,
. . . . . . . . 259P,
. . . . . . . . syn304G (GGg),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 388R,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn473K (AAg),
. . . . . . . . syn512R (AGa),
. . . . . . . . syn538F (TTt),
. . . . . . . . syn546L (tTA))
. . . . Madagascar9252_23F_2011_08_10 (
. . . . . . . . GISAID HA EPI346717
. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)
. . . . . . . . Clade2: 188T
. . . . . . . . #6M,
. . . . . . . . #4C,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn49G (GGa),
. . . . . . . . syn122K (AAa),
. . . . . . . . 141Q,
. . . . . . . . 146G,
. . . . . . . . 169S,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn301I (ATa),
. . . . . . . . syn338G (GGc),
. . . . . . . . 364S,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn473K (AAg),
. . . . . . . . syn496A (GCg),
. . . . . . . . syn538F (TTt))
. . . . Madagascar9252_23F_2011_08_10 (
. . . . . . . . GISAID NA EPI346718
. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)
. . . . . . . . 126S,
. . . . . . . . syn152R (AGa),
. . . . . . . . syn225R (AGg),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn295N (AAt),
. . . . . . . . syn313Q (CAa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 416N)
. . . . Madagascar8753_xF_2011_08_02 (
. . . . . . . . GISAID HA EPI346715
. . . . . . . . Clade2: 188T
. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)
. . . . . . . . #6M,
. . . . . . . . #4C,
. . . . . . . . syn1A (GCt),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn49G (GGa),
. . . . . . . . syn122K (AAa),
. . . . . . . . 141Q,
. . . . . . . . 146G,
. . . . . . . . 169S,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 400S,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn473K (AAg),
. . . . . . . . syn514Y (TAt),
. . . . . . . . syn538F (TTt))
. . . . Madagascar8753_xF_2011_08_02 (
. . . . . . . . GISAID NA EPI346716
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 56C,
. . . . . . . . 126S,
. . . . . . . . syn225R (AGg),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn295N (AAt),
. . . . . . . . syn307N (AAt),
. . . . . . . . syn313Q (CAa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))
. . . . SouthAfricaJohannesburg150_46F_2011_07_10 (
. . . . . . . . GISAID HA EPI346655
. . . . . . . . Clade5: 208K_219V
. . . . . . . . 16 Polymorphisms (8 Amino and 8 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc),
. . . . . . . . 100N,
. . . . . . . . syn131S (TCa),
. . . . . . . . 141Q,
. . . . . . . . 142D,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn307P (CCc),
. . . . . . . . 359A,
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa),
. . . . . . . . syn512R (AGa))
. . . . SouthAfricaJohannesburg150_46F_2011_07_10 (
. . . . . . . . GISAID NA EPI346656
. . . . . . . . 9 Polymorphisms (2 Amino and 7 Silent)
. . . . . . . . syn79S (TCg),
. . . . . . . . syn89S (TCt),
. . . . . . . . syn126P (CCt),
. . . . . . . . syn229S (TCc),
. . . . . . . . syn236G (GGc),
. . . . . . . . 269I mix wt,
. . . . . . . . 299A,
. . . . . . . . syn378N (AAt),
. . . . . . . . syn405S (AGc))
. . . . CameroonLEID07111870_24F_2011_07_07 (
. . . . . . . . GISAID HA EPI346647
. . . . . . . . Clade1: 189T
. . . . . . . . 13 Polymorphisms (8 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . syn168Y (TAt),
. . . . . . . . syn176V (GTt),
. . . . . . . . 189T,
. . . . . . . . 205E,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)
. . . . CameroonLEID07111870_24F_2011_07_07 (
. . . . . . . . GISAID NA EPI346648
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn135T (ACc),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa))
. . . . SenegalDakar18_4x_2011_07_07 (
. . . . . . . . GISAID HA EPI346685
. . . . . . . . 25 Polymorphisms (8 Amino and 17 Silent)
. . . . . . . . 10H mix wt,
. . . . . . . . 35I,
. . . . . . . . 51V,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T,
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K,
. . . . . . . . syn276H (CAt),
. . . . . . . . syn295F (TTc),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn331G (GGt),
. . . . . . . . syn337A (GCt),
. . . . . . . . syn379T (ACc),
. . . . . . . . syn433E (GAg),
. . . . . . . . syn451K (AAa),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V,
. . . . . . . . syn475D (GAc),
. . . . . . . . 523A)
. . . . SenegalDakar18_4x_2011_07_07 (
. . . . . . . . GISAID NA EPI346686
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . 74V,
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn160S (AGt),
. . . . . . . . 166I mix wt,
. . . . . . . . syn275H (CAt),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K,
. . . . . . . . syn433E (GAa))
. . . . SouthAfricaJohannesburg146_xM_2011_06_29 (
. . . . . . . . GISAID HA EPI346653
. . . . . . . . Clade5: 208K_219V
. . . . . . . . 16 Polymorphisms (9 Amino and 7 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . syn75T (ACc),
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc),
. . . . . . . . 100N,
. . . . . . . . 141Q,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 218V mix wt,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . 301V mix wt,
. . . . . . . . syn307P (CCc),
. . . . . . . . 359A,
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))
. . . . SouthAfricaJohannesburg146_xM_2011_06_29 (
. . . . . . . . GISAID NA EPI346654
. . . . . . . . 8 Polymorphisms (1 Amino and 7 Silent)
. . . . . . . . syn89S (TCt),
. . . . . . . . syn126P (CCt),
. . . . . . . . syn229S (TCc),
. . . . . . . . syn236G (GGc),
. . . . . . . . 299A,
. . . . . . . . syn355N (AAc),
. . . . . . . . syn405S (AGc),
. . . . . . . . syn427I (ATt))
. . . . Madagascar3520_52M_2011_06_17 (
. . . . . . . . GISAID HA EPI346719
. . . . . . . . Clade2: 188T
. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn44L (tTA),
. . . . . . . . syn122K (AAa),
. . . . . . . . 132D,
. . . . . . . . 145R,
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 237I,
. . . . . . . . syn265G (GGg),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 397S,
. . . . . . . . 452I,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn496A (GCc),
. . . . . . . . syn538F (TTt))
. . . . Madagascar3520_52M_2011_06_17 (
. . . . . . . . GISAID NA EPI346720
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . 44S,
. . . . . . . . 151N mix wt,
. . . . . . . . syn177V (GTt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 339P,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))
. . . . CameroonLEID06111809_33M_2011_06_16 (
. . . . . . . . GISAID HA EPI346645
. . . . . . . . Clade1: 189T
. . . . . . . . 15 Polymorphisms (10 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . 189T,
. . . . . . . . syn210S (AGt),
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 437I mix wt,
. . . . . . . . 439N,
. . . . . . . . syn465N (AAt),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A,
. . . . . . . . 531I)
. . . . CameroonLEID06111809_33M_2011_06_16 (
. . . . . . . . GISAID NA EPI346646
. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn161C (TGc),
. . . . . . . . 262R,
. . . . . . . . syn368R (AGg),
. . . . . . . . syn398E (GAa))
. . . . ThailandNonthaburi78_2011_06_08 (
. . . . . . . . GISAID HA EPI346707
. . . . . . . . Clade2: 188T
. . . . . . . . 14 Polymorphisms (8 Amino and 6 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . syn178V (GTa),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 218E mix wt,
. . . . . . . . 218V mix wt,
. . . . . . . . syn338G (GGc),
. . . . . . . . 375V,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))
. . . . ThailandNonthaburi78_2011_06_08 (
. . . . . . . . GISAID NA EPI346708
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn14C (TGc),
. . . . . . . . 26T,
. . . . . . . . syn41G (GGa),
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))
. . . . SouthAfricaJohannesburg128_1F_2011_06_07 (
. . . . . . . . GISAID HA EPI346651
. . . . . . . . Clade5: 208K_219V
. . . . . . . . 19 Polymorphisms (9 Amino and 10 Silent)
. . . . . . . . syn#6L (tTG),
. . . . . . . . syn47L (CTg),
. . . . . . . . 51T,
. . . . . . . . syn74S (TCt),
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc),
. . . . . . . . 100N,
. . . . . . . . 141Q,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn307P (CCc),
. . . . . . . . 359A,
. . . . . . . . syn366A (GCa),
. . . . . . . . 377K,
. . . . . . . . 404D,
. . . . . . . . syn446K (AAa),
. . . . . . . . syn477T (ACa))
. . . . SouthAfricaJohannesburg128_1F_2011_06_07 (
. . . . . . . . GISAID NA EPI346652
. . . . . . . . 10 Polymorphisms (2 Amino and 8 Silent)
. . . . . . . . syn89S (TCt),
. . . . . . . . syn126P (CCt),
. . . . . . . . 157A mix wt,
. . . . . . . . syn163I (ATc),
. . . . . . . . syn229S (TCc),
. . . . . . . . syn236G (GGc),
. . . . . . . . syn241V (GTg),
. . . . . . . . syn298G (GGa),
. . . . . . . . 299A,
. . . . . . . . syn342G (GGg))
. . . . HongKong3960_2M_2011_04_21 (
. . . . . . . . GISAID HA EPI346726
. . . . . . . . Clade1.Upsilon (5.33% CFR)
. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)
. . . . . . . . #12E [Novel to Upsilon],
. . . . . . . . #8I,
. . . . . . . . 34D,
. . . . . . . . syn118E (GAa),
. . . . . . . . 144E,
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 275I,
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . syn397G (GGc),
. . . . . . . . 453K,
. . . . . . . . 502K)
. . . . HongKong3960_2M_2011_04_21 (
. . . . . . . . GISAID NA EPI346727
. . . . . . . . 6 Polymorphisms (1 Amino and 5 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . 82P,
. . . . . . . . syn139L (TTa),
. . . . . . . . syn300N (AAc),
. . . . . . . . syn327R (CGt),
. . . . . . . . syn330D (GAc))
. . . . SenegalDakar14_1x_2011_04_14 (
. . . . . . . . GISAID HA EPI346724
. . . . . . . . 29 Polymorphisms (10 Amino and 19 Silent)
. . . . . . . . 16I,
. . . . . . . . 35I [H5N1 TmX247],
. . . . . . . . 89E [H1N1 Avian],
. . . . . . . . syn99I (ATt) [H1N1 Avian],
. . . . . . . . syn122K (AAa) [H5N1 Avian],
. . . . . . . . 131T [H5N1 Avian],
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg) [H9N2 Avian],
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa) [H9N2 Avian],
. . . . . . . . syn219I (ATt),
. . . . . . . . syn254P (CCa) [H9N2 Avian],
. . . . . . . . 262K [H5N1 Avian],
. . . . . . . . 266A,
. . . . . . . . syn276H (CAt) [H1N1 Avian],
. . . . . . . . syn295F (TTc) [H9N2 Avian],
. . . . . . . . syn301I (ATt),
. . . . . . . . syn331G (GGt) [H1N1 Avian],
. . . . . . . . syn337A (GCt) [H9N2 Avian],
. . . . . . . . syn338G (GGc) [H6N1 Avian],
. . . . . . . . 377K [H9N2 Avian],
. . . . . . . . syn379T (ACc) [H6N1 Avian],
. . . . . . . . syn433E (GAg) [H6N1 Avian],
. . . . . . . . syn451K (AAa) [H6N1 Avian],
. . . . . . . . syn456L (cTA) [H6N1 Avian],
. . . . . . . . 463V,
. . . . . . . . syn475D (GAc) [H6N1 Avian],
. . . . . . . . 523A [H1N1 Avian],
. . . . . . . . syn527L (TTa))
. . . . SenegalDakar14_1x_2011_04_14 (
. . . . . . . . GISAID NA EPI346725
. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)
. . . . . . . . syn20A (GCc) [H1N1 Avian],
. . . . . . . . 74V [H1N1 Avian],
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V [H1N1 Avian],
. . . . . . . . syn127L (cTG) [H1N1 Avian],
. . . . . . . . syn183A (GCc) [H1N1 Avian],
. . . . . . . . syn304V (GTt) [H1N1 Avian],
. . . . . . . . syn382G (GGa) [H1N1 Avian (Gaa)],
. . . . . . . . 385T,
. . . . . . . . 386K,
. . . . . . . . syn433E (GAa) [H1N1 Avian])
. . . . CameroonLEID04111671_1F_2011_04_12 (
. . . . . . . . GISAID HA EPI346691
. . . . . . . . Clade1: 189T
. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . syn97D (GAc),
. . . . . . . . syn130D (GAt),
. . . . . . . . 155I,
. . . . . . . . 189T,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 509D,
. . . . . . . . 523A)
. . . . CameroonLEID04111671_1F_2011_04_12 (
. . . . . . . . GISAID NA EPI346692
. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn170Y (TAt),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa),
. . . . . . . . syn421C (TGt))
. . . . SenegalDakar11_4x_2011_04_06 (
. . . . . . . . GISAID HA EPI346683
. . . . . . . . Clade3: 186P, novel sub-clade
. . . . . . . . 22 Polymorphisms (8 Amino and 14 Silent)
. . . . . . . . 12T,
. . . . . . . . 35I,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T,
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 186P,
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K,
. . . . . . . . syn276H (CAt),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn331G (GGt),
. . . . . . . . syn337A (GCt),
. . . . . . . . syn379T (ACc),
. . . . . . . . syn433E (GAg),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V,
. . . . . . . . 523A)
. . . . SenegalDakar11_4x_2011_04_06 (
. . . . . . . . GISAID NA EPI346684
. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn172S (TCt),
. . . . . . . . 259D,
. . . . . . . . syn304V (GTt),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K,
. . . . . . . . syn415L (tTG))
. . . . SenegalDakar09_3x_2011_03_25 (
. . . . . . . . GISAID HA EPI346703
. . . . . . . . 24 Polymorphisms (8 Amino and 16 Silent)
. . . . . . . . 35I,
. . . . . . . . 47I,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T,
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K,
. . . . . . . . syn276H (CAt),
. . . . . . . . syn288A (GCc),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn325P (CCt),
. . . . . . . . syn331G (GGt),
. . . . . . . . syn337A (GCt),
. . . . . . . . syn379T (ACc),
. . . . . . . . syn433E (GAg),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V,
. . . . . . . . 481N,
. . . . . . . . 523A)
. . . . SenegalDakar09_3x_2011_03_25 (
. . . . . . . . GISAID NA EPI346704
. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn281C (TGc),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn370G (GGc),
. . . . . . . . syn371F (TTc),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K)
. . . . Iceland59_xF_2011_03_24 (
. . . . . . . . GISAID HA EPI346697
. . . . . . . . Clade3: 186P
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 137T mix wt,
. . . . . . . . 144S,
. . . . . . . . syn163K (AAa),
. . . . . . . . 186P,
. . . . . . . . syn251L (CTg),
. . . . . . . . syn287G (GGg),
. . . . . . . . syn293L (CTt),
. . . . . . . . 298V,
. . . . . . . . syn363G (GGg),
. . . . . . . . 377K,
. . . . . . . . syn455Q (CAa),
. . . . . . . . syn474C (TGt),
. . . . . . . . 482I)
. . . . Iceland59_xF_2011_03_24 (
. . . . . . . . GISAID NA EPI346698
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 46T,
. . . . . . . . syn187G (GGt),
. . . . . . . . 313R,
. . . . . . . . 321V,
. . . . . . . . 394I,
. . . . . . . . syn412L (tTA),
. . . . . . . . syn430R (CGg),
. . . . . . . . 467V)
. . . . CameroonLEID03111616_xM_2011_03_22 (
. . . . . . . . GISAID HA EPI346689
. . . . . . . . Clade1: 189T
. . . . . . . . 12 Polymorphisms (8 Amino and 4 Silent)
. . . . . . . . 1T,
. . . . . . . . 167F,
. . . . . . . . 189T,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A,
. . . . . . . . syn538F (TTt))
. . . . CameroonLEID03111616_xM_2011_03_22 (
. . . . . . . . GISAID NA EPI346690
. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn118R (AGa),
. . . . . . . . syn262K (AAa),
. . . . . . . . 386D,
. . . . . . . . syn398E (GAa))
. . . . FrancePaysdeLoire1347_12x_2011_03_22 (
. . . . . . . . GISAID HA EPI346701
. . . . . . . . Clade2: 188T
. . . . . . . . 12 Polymorphisms (4 Amino and 8 Silent)
. . . . . . . . 100N,
. . . . . . . . syn135V (GTg),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn321L (cTG),
. . . . . . . . syn336I (ATc),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn400F (TTt),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn482V (GTt))
. . . . FrancePaysdeLoire1347_12x_2011_03_22 (
. . . . . . . . GISAID NA EPI346702
. . . . . . . . 8 Polymorphisms (2 Amino and 6 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn313Q (CAa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn401G (GGg),
. . . . . . . . syn416D (GAc))
. . . . Iceland52_xM_2011_03_18 (
. . . . . . . . GISAID HA EPI346643
. . . . . . . . Clade2: 188T
. . . . . . . . 12 Polymorphisms (9 Amino and 3 Silent)
. . . . . . . . 87I,
. . . . . . . . 100N,
. . . . . . . . 158E mix wt,
. . . . . . . . 188T,
. . . . . . . . 212N mix wt,
. . . . . . . . syn304G (GGg),
. . . . . . . . syn319T (ACg),
. . . . . . . . 324I,
. . . . . . . . 377K,
. . . . . . . . 440H mix wt,
. . . . . . . . syn441H (CAt),
. . . . . . . . 454N)
. . . . Iceland52_xM_2011_03_18 (
. . . . . . . . GISAID NA EPI346644
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . UkraineDnipropetrovsk4929_21F_2011_03_10 (
. . . . . . . . GISAID HA EPI346637
. . . . . . . . Clade2: 188T
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
. . . . UkraineDnipropetrovsk4929_21F_2011_03_10 (
. . . . . . . . GISAID NA EPI346638
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . UkraineZaporizhzhya5200_31F_2011_03_09 (
. . . . . . . . GISAID HA EPI346663
. . . . . . . . Clade2: 188T
. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 326F,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 415E,
. . . . . . . . syn441H (CAt),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
. . . . UkraineZaporizhzhya5200_31F_2011_03_09 (
. . . . . . . . GISAID NA EPI346664
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 96R mix wt,
. . . . . . . . 127F,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . UkraineLuhansk5192_xF_2011_03_07 (
. . . . . . . . GISAID HA EPI346639
. . . . . . . . Clade2: 188T
. . . . . . . . . . . . crossing Clade3: 186P
. . . . . . . . 16 Polymorphisms (6 Amino and 10 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn118E (GAa),
. . . . . . . . syn130D (GAt),
. . . . . . . . 146G,
. . . . . . . . 186P mix wt,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . syn358N (Aac) mix,
. . . . . . . . syn358T mix,
. . . . . . . . 377K,
. . . . . . . . syn412K (AAg),
. . . . . . . . syn418F (TTt),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))
. . . . UkraineLuhansk5192_xF_2011_03_07 (
. . . . . . . . GISAID NA EPI346640
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 83G,
. . . . . . . . syn206L (cTA),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))
. . . . CameroonLEID03111573_xM_2011_03_01 (
. . . . . . . . GISAID HA EPI346687
. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . syn157K (AAg),
. . . . . . . . 158E mix wt,
. . . . . . . . syn173G (GGa),
. . . . . . . . 190G,
. . . . . . . . 205E mix wt,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . syn334G (GGa),
. . . . . . . . 377K,
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)
. . . . CameroonLEID03111573_xM_2011_03_01 (
. . . . . . . . GISAID NA EPI346688
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn6K (AAa),
. . . . . . . . syn22L (cTA),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa))
. . . . UkraineOdessa5197_24F_2011_03_01 (
. . . . . . . . GISAID HA EPI346641
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . syn391T (ACc),
. . . . . . . . syn413K (AAg),
. . . . . . . . 415E mix wt)
. . . . UkraineOdessa5197_24F_2011_03_01 (
. . . . . . . . GISAID NA EPI346642
. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)
. . . . . . . . syn330D (GAc),
. . . . . . . . syn407V (GTc))
. . . . FranceLorraine1176_50x_2011_02_23_TmX (
. . . . . . . . GISAID HA EPI346699
. . . . . . . . Clade2: 188T
. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)
. . . . . . . . 100N,
. . . . . . . . 158E mix wt,
. . . . . . . . 188T,
. . . . . . . . 227G,
. . . . . . . . syn245F (TTt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn461K (AAa),
. . . . . . . . syn470F (TTc),
. . . . . . . . syn537S (AGc))
. . . . FranceLorraine1176_50x_2011_02_23_TmX (
. . . . . . . . GISAID NA EPI346700
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 275Y,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . LithuaniaKlaipeda1067_xF_2011_02_22 (
. . . . . . . . GISAID HA EPI346673
. . . . . . . . Clade3: 186P
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . syn279N (AAc),
. . . . . . . . syn288A (GCc),
. . . . . . . . syn352Y (TAt),
. . . . . . . . 377G,
. . . . . . . . syn408E (GAa),
. . . . . . . . syn474C (TGt),
. . . . . . . . syn475D (GAc),
. . . . . . . . 512M,
. . . . . . . . 530I)
. . . . LithuaniaKlaipeda1067_xF_2011_02_22 (
. . . . . . . . GISAID NA EPI346674
. . . . . . . . 14 Polymorphisms (3 Amino and 11 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn66Y (TAc),
. . . . . . . . syn124C (TGt),
. . . . . . . . syn130R (AGg),
. . . . . . . . syn157T (ACt),
. . . . . . . . syn175E (GAa),
. . . . . . . . 232V,
. . . . . . . . syn302P (CCa),
. . . . . . . . syn382G (GGa),
. . . . . . . . 389V,
. . . . . . . . 394I,
. . . . . . . . syn425E (GAg),
. . . . . . . . syn428R (AGg),
. . . . . . . . syn430R (CGg))
. . . . LithuaniaTelsiai1038_xM_2011_02_19 (
. . . . . . . . GISAID HA EPI346671
. . . . . . . . Clade2: 188T
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn#6L (CTa),
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . syn245F (TTt),
. . . . . . . . syn321L (cTG),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))
. . . . LithuaniaTelsiai1038_xM_2011_02_19 (
. . . . . . . . GISAID NA EPI346672
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . syn436I (ATa))
. . . . LithuaniaTelsiai1037_xM_2011_02_19 (
. . . . . . . . GISAID HA EPI346669
. . . . . . . . Clade2: 188T
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn#6L (CTa),
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . syn245F (TTt),
. . . . . . . . syn321L (cTG),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))
. . . . LithuaniaTelsiai1037_xM_2011_02_19 (
. . . . . . . . GISAID NA EPI346670
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . syn436I (ATa))
. . . . LithuaniaKaunas146s_xM_2011_02_17 (
. . . . . . . . GISAID HA EPI346675
. . . . . . . . Clade2: 188T
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . 152M,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
. . . . LithuaniaKaunas146s_xM_2011_02_17 (
. . . . . . . . GISAID NA EPI346676
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . 453M)
. . . . LithuaniaKaunas988_xM_2011_02_15 (
. . . . . . . . GISAID HA EPI346667
. . . . . . . . Clade2: 188T
. . . . . . . . . . . . crossed with Clade4:128D
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa) [Upsilon?],
. . . . . . . . 100N,
. . . . . . . . 128D,
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))
. . . . LithuaniaKaunas988_xM_2011_02_15 (
. . . . . . . . GISAID NA EPI346668
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . FranceParis940_16x_2011_02_11 (
. . . . . . . . GISAID HA EPI346722
. . . . . . . . Clade2: 188T
. . . . . . . . 15 Polymorphisms (8 Amino and 7 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 76T,
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 205E mix wt,
. . . . . . . . 277N,
. . . . . . . . syn338G (GGc),
. . . . . . . . syn358N (AAc),
. . . . . . . . 377K,
. . . . . . . . syn418F (TTt),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))
. . . . FranceParis940_16x_2011_02_11 (
. . . . . . . . GISAID NA EPI346723
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))
. . . . FranceCentre869_60x_2011_02_08 (
. . . . . . . . GISAID HA EPI346681
. . . . . . . . Clade2: 188T
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . syn31H (CAt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 205E,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
. . . . FranceCentre869_60x_2011_02_08 (
. . . . . . . . GISAID NA EPI346682
. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn316Y (TAt),
. . . . . . . . 344K,
. . . . . . . . syn365I (ATc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn390K (AAa),
. . . . . . . . syn416D (GAc))
. . . . FranceHauteNormandie774_3x_2011_02_01 (
. . . . . . . . GISAID HA EPI346679
. . . . . . . . Clade5: 208K_219V
. . . . . . . . 14 Polymorphisms (7 Amino and 7 Silent)
. . . . . . . . syn41N (AAt),
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . 133E,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . syn319T (ACg),
. . . . . . . . 352F,
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))
. . . . FranceHauteNormandie774_3x_2011_02_01 (
. . . . . . . . GISAID NA EPI346680
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . syn60T (ACc),
. . . . . . . . 81A,
. . . . . . . . syn138A (GCt),
. . . . . . . . 151N mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))
. . . . Hungary13_xM_2011_01_31 (
. . . . . . . . GISAID HA EPI346711
. . . . . . . . Clade2: 188T
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . 157E,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 226R,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
. . . . Hungary13_xM_2011_01_31 (
. . . . . . . . GISAID NA EPI346712
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn191L (tTA),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . Hungary7_xM_2011_01_31 (
. . . . . . . . GISAID HA EPI346709
. . . . . . . . Clade2: 188T
. . . . . . . . 11 Polymorphisms (8 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . 157E mix wt,
. . . . . . . . 158E mix wt,
. . . . . . . . 159D mix wt,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 226R,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
. . . . Hungary7_xM_2011_01_31 (
. . . . . . . . GISAID NA EPI346710
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . TurkeyMalatyaTR_29_28M_2011_01_28 (
. . . . . . . . GISAID HA EPI346659
. . . . . . . . Clade3: 186P
. . . . . . . . 11 Polymorphisms (8 Amino and 3 Silent)
. . . . . . . . syn16T (ACg),
. . . . . . . . 137T,
. . . . . . . . 167F,
. . . . . . . . 186P,
. . . . . . . . 263K,
. . . . . . . . 377G,
. . . . . . . . syn408E (GAa),
. . . . . . . . 413R mix wt,
. . . . . . . . syn474C (TGt),
. . . . . . . . 512M,
. . . . . . . . 530I)
. . . . TurkeyMalatyaTR_29_28M_2011_01_28 (
. . . . . . . . GISAID NA EPI346660
. . . . . . . . 13 Polymorphisms (4 Amino and 9 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn66Y (TAc),
. . . . . . . . syn124C (TGt),
. . . . . . . . syn130R (AGg),
. . . . . . . . syn157T (ACt),
. . . . . . . . syn175E (GAa),
. . . . . . . . 232V,
. . . . . . . . 267I,
. . . . . . . . syn382G (GGa),
. . . . . . . . 389V,
. . . . . . . . 394I,
. . . . . . . . syn425E (GAg),
. . . . . . . . syn430R (CGg))
. . . . CameroonLEID01111467_28F_2011_01_27 (
. . . . . . . . GISAID HA EPI346705
. . . . . . . . Clade1: 189T
. . . . . . . . 11 Polymorphisms (7 Amino and 4 Silent)
. . . . . . . . 1T,
. . . . . . . . 189T,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . syn340I (ATc),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)
. . . . CameroonLEID01111467_28F_2011_01_27 (
. . . . . . . . GISAID NA EPI346706
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn271A (GCt),
. . . . . . . . syn398E (GAa))
. . . . Kazakhstan2081_xF_2011_01_23 (
. . . . . . . . GISAID HA EPI346713
. . . . . . . . Clade3: 186P
. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . syn297N (AAc),
. . . . . . . . syn316R (AGg),
. . . . . . . . syn326S (TCc),
. . . . . . . . syn383N (AAc),
. . . . . . . . syn388K (AAa),
. . . . . . . . 433K,
. . . . . . . . 444K,
. . . . . . . . syn474C (TGt))
. . . . Kazakhstan2081_xF_2011_01_23 (
. . . . . . . . GISAID NA EPI346714
. . . . . . . . 7 Polymorphisms (1 Amino and 6 Silent)
. . . . . . . . syn6K (AAa),
. . . . . . . . syn139L (cTG),
. . . . . . . . syn202A (GCt),
. . . . . . . . syn274Y (TAc),
. . . . . . . . syn275H (CAt),
. . . . . . . . syn372E (GAa),
. . . . . . . . 394I)
. . . . CameroonLEID01111450_3F_2011_01_19 (
. . . . . . . . GISAID HA EPI346649
. . . . . . . . Clade1: 189T
. . . . . . . . 12 Polymorphisms (9 Amino and 3 Silent)
. . . . . . . . 1T,
. . . . . . . . 159S,
. . . . . . . . 189T,
. . . . . . . . 205E,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)
. . . . CameroonLEID01111450_3F_2011_01_19 (
. . . . . . . . GISAID NA EPI346650
. . . . . . . . 4 Polymorphisms (1 Amino and 3 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . 59R,
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa))
. . . . Iceland9_xF_2011_01_19 (
. . . . . . . . GISAID HA EPI346695
. . . . . . . . Clade2: 188T
. . . . . . . . 15 Polymorphisms (10 Amino and 5 Silent)
. . . . . . . . 100N,
. . . . . . . . 159D,
. . . . . . . . syn179L (tTA),
. . . . . . . . 188T,
. . . . . . . . 225N,
. . . . . . . . syn245F (TTt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 437I (Atc) mix wt,
. . . . . . . . 437I (Att) mix wt,
. . . . . . . . 437N (Aac) mix wt,
. . . . . . . . 437N (Aat) mix wt,
. . . . . . . . syn437T (Acc) mix wt,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))
. . . . Iceland9_xF_2011_01_19 (
. . . . . . . . GISAID NA EPI346696
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . TurkeyTokatTR_26_26M_2011_01_19 (
. . . . . . . . GISAID HA EPI346657
. . . . . . . . Clade5: 208K_219V
. . . . . . . . . . . . crossing Clade4: 128D
. . . . . . . . 14 Polymorphisms (8 Amino and 6 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . 128D,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 210I mix wt,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . syn319T (ACg),
. . . . . . . . 377K,
. . . . . . . . 431Q mix wt,
. . . . . . . . syn446K (AAa))
. . . . TurkeyTokatTR_26_26M_2011_01_19 (
. . . . . . . . GISAID NA EPI346658
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . syn60T (ACc),
. . . . . . . . 81A,
. . . . . . . . syn138A (GCt),
. . . . . . . . 211T mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))
. . . . Iceland7_xM_2011_01_16 (
. . . . . . . . GISAID HA EPI346661
. . . . . . . . Clade2: 188T
. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)
. . . . . . . . #7I,
. . . . . . . . 100N,
. . . . . . . . 157N mix wt,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 449C mix wt,
. . . . . . . . 454N)
. . . . Iceland7_xM_2011_01_16 (
. . . . . . . . GISAID NA EPI346662
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . 117M,
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))
. . . . Iceland3_xM_2011_01_10 (
. . . . . . . . GISAID HA EPI346677
. . . . . . . . Clade2: 188T
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn379T (ACc),
. . . . . . . . 440H,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))
. . . . Iceland3_xM_2011_01_10 (
. . . . . . . . GISAID NA EPI346678
. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)
. . . . . . . . syn38I (ATc),
. . . . . . . . 44S,
. . . . . . . . 151E mix wt,
. . . . . . . . 151K mix wt,
. . . . . . . . 151N mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn274Y (TAc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))
. . . . TurkeyAnkaraTR_23_20M_2010_12_30 (
. . . . . . . . GISAID HA EPI346693
. . . . . . . . Clade5: 208K_219V
. . . . . . . . . . . . crossing Clade3: 186P
. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . 159D mix wt,
. . . . . . . . syn170N (AAc),
. . . . . . . . 186P mix wt,
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn346G (GGa),
. . . . . . . . 377K,
. . . . . . . . 426V,
. . . . . . . . syn446K (AAa),
. . . . . . . . syn507K (AAa),
. . . . . . . . 530I)
. . . . TurkeyAnkaraTR_23_20M_2010_12_30 (
. . . . . . . . GISAID NA EPI346694
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn238C (TGt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))
. . . . UKEngland687_2010_12_15 (
. . . . . . . . GISAID HA EPI346665
. . . . . . . . Clade2: 188T
. . . . . . . . 11 Polymorphisms (7 Amino and 4 Silent)
. . . . . . . . syn#7V (GTc),
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa),
. . . . . . . . 100N,
. . . . . . . . 158E mix wt,
. . . . . . . . 179I,
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))
. . . . UKEngland687_2010_12_15 (
. . . . . . . . GISAID NA EPI346666
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . syn161C (TGc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn398E (GAa),
. . . . . . . . syn416D (GAc))
This analysis catalysed with ingenuity from 2 lead Professors of Group10 at Ion203. We never cease to find inspiration in your halls of instruction.
