Greece Deposits pH1N1 Clade5 from 2011 Hospitalisation with Novel Diversity

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

Last Update
2011-11-05

On 2011-10-31, the Institut Pasteur Hellenique deposited one human pH1N1 HA fragment sequence at GISAID of 216 amino acids (aa35 to aa220), documenting roughly 38% of a full pH1N1 Hemagglutinin segment.  GreeceAthens7033_75M_2011_02_22_s was sampled from a 75 year old male, hospital inpatient.  This hypermorphic fragment patterns onto Clade5: 208K_219V, a highly zoonotic, recently emergent series with a sequence count that has quickly accumulated to triple digits.

Two dispersed polymorphisms, each novel to pH1N1.Clade5, appear on this Greek sequence.  HA 77R, a novel Clade5 revision, is rare to the human pandemic and is emergent on Clade2 (3 instances).  Those 3 Clade2, HA 77R-bearing HA segment sequences are hypermorphic (accounting for 48 total HA changes); however, no HA cross-over onto this Greek sequence occurs from the full superset of polymorphisms with HA 77R.  HA 169T, also novel to Clade5, is rare to the human pandemic and is found once on Clade2, the numerically dominant series for human pH1N1.

Avian H13 serotypes share significant homology with pH1N1.Clade5 and this Greek sequence.  Given the serology background of the more recently discovered Hemagglutinin forms above H12 (~30 years for H13 to ~6 years for H16), question arise concerning cross-serotype compatibility.  Returning to the archives after these recent discoveries, investigators repeatedly found that H16 samples from the past had been mis-typed on first inspection to various Hemagglutinin forms (H1, H7, H13) due to cross-reactive serology on various inhibition panels.  Serotypes known to infect humans, including H1 and H7, featured in those earlier mistaken categorisations. 

Precise discernment of the exact relationship between the current human pandemic H1N1 and the more recently discovered Hemagglutinin forms (H13 to H16) merits evaluation due to the significant H13 homology with the heavily zoonotic and rapidly emergent pH1N1.Clade5 and the High CFR pH1N1.Clade1.Upsilon.

Sequence

. . . . GreeceAthens7033_75M_2011_02_22_s (
. . . . . . . . Clade5: 208K_219V
. . . . . . . . GISAID HA EPI340964
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . HA Truncated before aa35,
. . . . . . . . syn47L (CTg) [H1N1 Avian],
. . . . . . . . 77R (AGa) [Rare to Human pH1N1 (11 Total / 5 Asia)],
. . . . . . . . . . . . . . . [Novel to pH1N1.Clade5],
. . . . . . . . . . . . . . . [Emergent pH1N1.Clade2 (3)],
. . . . . . . . . . . . . . . [H9N2 Avian and Human wt
. . . . . . . . . . . . . . . . . . . . with pH1N1υ polymorphisms],
. . . . . . . . . . . . . . . [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . . . . [WSN_1933, WSZ_1933],
. . . . . . . . 100N [H5N1 Egypt Avian 2009-2010
. . . . . . . . . . . . . . . . . with syn40H, syn55L, 192I, 196K],
. . . . . . . . . . . . [H5N1 Egypt Avian 2008 with syn40H, syn55L],
. . . . . . . . . . . . [H5N2 Italy Avian 2005-2007],
. . . . . . . . . . . . [H7N3, H7N7, H9N2],
. . . . . . . . . . . . [H13N2 Mammal],
. . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn102E (GAa) [H5N1 wt],
. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . 169T [Rare to Human pH1N1 (6 Total / 3 Asia)],
. . . . . . . . . . . [Novel to pH1N1.Clade5],
. . . . . . . . . . . [Singular to pH1N1.Clade2],
. . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . [H1N1 swine],
. . . . . . . . syn170N (AAc) [H5N1 Egypt Human 2009],
. . . . . . . . . . . . . . . . . . [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . . . . [H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . . . with 225G & 252L],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . 208K (AaA) [pH1N1 Canine 2009],
. . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . [H3N2 Avian 2006, 2009],
. . . . . . . . 219V (gTA) [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . . [H13N2, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . syn221P (CCt) [H3N2 Avian
. . . . . . . . . . . . . . . . . . . . . with 157S, 159S, syn287G],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human and Avian (tCt)],
. . . . . . . . . . . . . . . . . . [H5N1 Nigeria Avian (tCt)],
. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . [H13N2 Mammal],
. . . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . HA Truncated after aa250)

Supporting Sequences

HA 169T

. . . . Montana03_2011_02_02 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI310031
. . . . . . . . 8 Polymorphisms (6 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . 169T,
. . . . . . . . 188T,
. . . . . . . . 213S,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . Lebanon09L_29_2009_11_05 (
. . . . . . . . GISAID HA EPI320624
. . . . . . . . 4 Polymorphisms (4 Amino and 0 Silent)
. . . . . . . . #1T,
. . . . . . . . 169T,
. . . . . . . . 225E,
. . . . . . . . 300S,
. . . . . . . . HA Truncated after aa355)

. . . . ShanxiChengquSWL547_2009_10_19 (
. . . . . . . . GISAID HA EPI256314
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 57N,
. . . . . . . . 131P,
. . . . . . . . 169T,
. . . . . . . . syn238E (GAa))

. . . . TianjinTangguSWL1110_2009_10_13 (
. . . . . . . . GISAID HA EPI256126
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 169T,
. . . . . . . . 206S,
. . . . . . . . 447K,
. . . . . . . . syn455Q (CAa))

. . . . BeijingHuairouSWL1805_2009_10_01 (
. . . . . . . . GISAID HA EPI256274
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 169T,
. . . . . . . . 206S,
. . . . . . . . 447K,
. . . . . . . . syn455Q (CAa))

. . . . Russia01_MA_2009 (
. . . . . . . . GISAID HA EPI297205
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . 169T,
. . . . . . . . 208K,
. . . . . . . . syn359E (GAa))

HA 77R on Clade2

. . . . OzBrisbane500_2011_06_22 (
. . . . . . . . GISAID HA EPI333109
. . . . . . . . 18 Polymorphisms (8 Amino and 10 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn33V (GTc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 77R,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn115E (GAg),
. . . . . . . . 146G,
. . . . . . . . 171G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . syn346G (GGa),
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn508L (tTG),
. . . . . . . . 523A,
. . . . . . . . HA Truncated after aa552)

. . . . OzNewcastle1_2011_04_11 (
. . . . . . . . GISAID HA EPI331558
. . . . . . . . 21 Polymorphisms (9 Amino and 12 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn33V (GTc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 77R,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn115E (GAg),
. . . . . . . . 146G,
. . . . . . . . 157Q mix wt,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . syn346G (GGa),
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn508L (tTG),
. . . . . . . . 523A,
. . . . . . . . syn538F (TTt),
. . . . . . . . syn549R (AGg),
. . . . . . . . 550S,
. . . . . . . . HA Truncated after aa550)

. . . . JapanHiroshimaC2_2011_01_05 (
. . . . . . . . GISAID HA EPI305466
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 71D,
. . . . . . . . 77R,
. . . . . . . . 102G mix wt,
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa348)

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Mexico Evaluates Upper Respiratory Swabs from Fatal and Severe Cases with 225A, 225G, 225N & 225V

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

Last Update
2011-11-03

On 2011-10-27, the Instituto Nacional de Enfermedades Respiratorias from the Centro de Investigacion en Enfermedades Infecciosas of Mexico deposited a group of human pH1N1 sequences at GenBank and GISAID.  The deposit is composed of HA segments, 14 sequence fragments of 232 amino acids (aa38 to aa269), each documenting roughly 41% of a full pH1N1 Hemagglutinin segment.  Various homology to Clade1.Upsilon exists on 5 of the sequences.

This Mexican genetic data supports an investigation entitled, H1N1pdm HA D222 variants associated with severity and mortality in patients during a second wave in Mexico and their pathogenicity in mouse model.  Mexico City, Mexico is the geography indicated on the sequence names.  Each sequence is annotated with gender and isolation source (nasopharyngeal swab), while 12 of the 14 also indicate the subject age.  Subject ages range from 23 to 54 years old, all outside the general severity range for seasonal influenza (under 2 years old or over 60 years old).  The sample dates span 2009-10-01 to 2010-04-05 with no case-level specification of treatment protocol, clinical progression or clinical outcome.

The severity and fatality correlation in cases with polymorphisms at amino acid position 222 (aa225 in H3 numbering) was established very early in the pandemic.  The issue of sample location has been repeatedly posed, with ongoing discussion that samples taken from the lower respiratory tract are more probable to produce valid evidence of aa225 revisions.  This INER deposit, relying entirely on upper respiratory swabs, documents cases where aa225 revisions are found in the upper airway.  The individual details of clinical progression and outcome (severe v. fatal) will establish measurable correlation to the upper respiratory sample location.

Four of the samples show multi-nucleotide ambiguity at amino acid position 225 (contiguous mixed traces, residues 715 and 716) producing a codon of rrT.  That sequencing outcome of rrT demonstrates the presence of wild type D225 with both 225G and 225N, hypermorphism at a single amino acid position.  Overall, ten of the fourteen sequences demonstrate a mixed peak (ambiguity) at one or more nucleotides that build aa225.  MexicoCityINER3_NP_47M_2009_10_15 [EPI341034] illustrates the highly variant nature of the pH1N1 reservoir Receptor Binding Site aa225 with two rare values, 225A and 225V, in a mixture without wild type (D225) and with no additional polymorphisms.

Sequences

. . . . MexicoCityINER14_NP_xF_2010_04_05 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341023
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn71E (GAg) mix wt [H6N1],
. . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn100D (GAc) [H1N1 Avian Farm],
. . . . . . . . 165N,
. . . . . . . . 181S,
. . . . . . . . 189T,
. . . . . . . . syn198A (GCg) mix wt,
. . . . . . . . syn213F (TTt),
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER13_NP_48F_2010_03_25 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341024
. . . . . . . . 6 Polymorphisms (5 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 225G mix wt,
. . . . . . . . 225N mix wt,
. . . . . . . . 225S mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER12_NP_37M_2010_03_23 (
. . . . . . . . GISAID HA EPI341025
. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 122R,
. . . . . . . . 225N,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER11_NP_34F_2010_02_09 (
. . . . . . . . GISAID HA EPI341026
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn214K (AAa) [H9N2],
. . . . . . . . . . . . . . . . . . [H13N2 Avian],
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER10_NP_39M_2010_02_09 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341027
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn58C (TGc) [H2N3, H3N8, H4, H6],
. . . . . . . . . . . . . . . . . [H7N3, H7N7],
. . . . . . . . . . . . . . . . . [H9N2, H11],
. . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER8_NP_23F_2009_11_23 (
. . . . . . . . GISAID HA EPI341029
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn106E (GAa) [H1N1 Avian],
. . . . . . . . syn189A (GCc),
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER9_NP_49M_2010_01_18 (
. . . . . . . . GISAID HA EPI341028
. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER7_NP_54F_2009_11_09 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341030
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 157T,
. . . . . . . . 165N,
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER6_NP_22F_2009_11_06 (
. . . . . . . . GISAID HA EPI341031
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn106E (GAa) [H1N1 Avian],
. . . . . . . . syn189A (GCc),
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER5_NP_52F_2009_10_27 (
. . . . . . . . GISAID HA EPI341032
. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER4_NP_xM_2009_10_16 (
. . . . . . . . GISAID HA EPI341033
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn145K (AAg),
. . . . . . . . 225G mix wt,
. . . . . . . . 225N mix wt,
. . . . . . . . 225S mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER3_NP_47M_2009_10_15 (
. . . . . . . . GISAID HA EPI341034
. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 225A mix,
. . . . . . . . 225V mix,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER2_NP_44F_2009_10_12 (
. . . . . . . . GISAID HA EPI341035
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 225G mix wt,
. . . . . . . . 225N mix wt,
. . . . . . . . 225S mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER1_NP_40M_2009_10_01 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341036
. . . . . . . . 4 Polymorphisms (4 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 165N,
. . . . . . . . 225G mix wt,
. . . . . . . . 225N mix wt,
. . . . . . . . 225S mix wt,
. . . . . . . . HA Truncated after aa269)

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Morocco Reports Hypermorphism on pH1N1 HA and NA Fragments

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

Last Update
2011-11-03

On 2011-10-25, the Institute Pasteur of Morocco deposited a group of human pH1N1 sequences at GenBank and GISAID.  HA segments include 14 fragments.  The NA segment is represented with 15 fragments, 7 that are related to a deposited HA fragment.  All sequences are marked geographically as Casablanca.  The sample dates span 2010-12-20 to 2011-04-01 with no specification of treatment protocol, clinical progression or clinical outcome.

Hypermorphic behaviour is found on 71% of the sequences that have both HA and NA segments, notwithstanding the fact that both segments are fragments across this deposit.  These 5 hypermorphic representatives are on two separate lineages. Additionally, the NA fragment of  MoroccoCasablanca69_11F_2011_01_26  [EPI340865] demonstrates significant, rare zoonotic homology to Avian H1N1, H5N1 and Avian H9N2.

Multi-clade hypermorphism in a single geography and within a contemporaneous time span merits careful evaluation.

Zoonoses of Polymorphisms

The mammal and avian database of Influenza A H13 covering all Neuraminidase forms comprises only 93 sequences, yet shares homology to pH1N1 human polymorphisms on Clade1.Upsilon as well as rare and novel pH1N1 human polymorphisms on Clade2, Clade4 and Clade5 sequences in this Moroccan deposit.  Several of these shared polymorphisms, e.g. markers for Clade5 (HA 219V and HA 252L), are previously uncharacterised as to potential Ultimate Origin.  The identification of multi-clade hypermorphism in this geography with wide homology to a single candidate animal reservoir (A/H13) solidifies the clear requirement for higher levels of avian surveillance.

Cladistics

10 - Clade2: 188T
01 - Clade4: 128D [EPI340861]
03 - Clade5: 208K_219V [EPI340881], [EPI340860], [EPI340876]

HA   84 Polymorphisms Averaging ~6.0 per Segment Fragment
NA 118 Polymorphisms Averaging ~7.9 per Segment Fragment

HA and NA 202 Total Polymorphisms Averaging ~13.9 per Sequence (Fragments)

Diversity

HA Superset – 36 Distinct Values
NA Superset - 47 Distinct Values

Two Receptor Binding Site items of interest are syn221P and 224K.  No indication is found of revisions at aa225, aa226 or aa230.  The Clade5 sequence bearing HA syn221P is contemporary in timing and homology to a small group of European Clade5 sequences.  A hypermorphic, Clade2 Moroccan sequence bears HA 224K, a polymorphism previously found in pH1N1 swine Clade5, suggesting a potential cross-clade transfer or compatibility.  The HA 224K may signal tissue tropism issues, having been documented on a lethal, neurotropic experimental strain (WSN_1933).

• [EPI340860] MoroccoCasablanca91_15mM_2011_02_02 – HA syn221P
• [EPI340866] MoroccoCasablanca69_11F_2011_01_26    – HA 224K

Hypermorphic Behaviour

04 HA Fragments >= 7 polymorphisms (29%)
13 NA Segments  >= 7 polymorphisms (87%)

Combined Polymorphic Count >= 15
5 of 7 Sequences with HA and NA Fragments (71%)
Total (HA / NA)

• 16 (HA 09 / NA 07): [EPI340881] MoroccoCasablanca117_10m_2011_02_15
• 16 (HA 07 / NA 09): [EPI340860] MoroccoCasablanca91_15mM_2011_02_02
• 16 (HA 05 / NA 11): [EPI340866] MoroccoCasablanca69_11F_2011_01_26
• 16 (HA 09 / NA 07): [EPI340876] MoroccoCasablanca23_3F_2011_01_13
• 15 (HA 09 / NA 07): [EPI340868] MoroccoCasablanca63_47F_2011_01_20

Sequences

. . . . MoroccoCasablanca124_5M_2011_04_01 (
. . . . . . . . GISAID NA EPI340879
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . NA Truncated before aa36,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . NA Truncated after aa453)

. . . . MoroccoCasablanca211_15M_2010_12_20 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340885
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa354)

. . . . MoroccoCasablanca117_10m_2011_02_15 (
. . . . . . . . Clade5: 208K_219V crossing with
. . . . . . . . . . . Clade2: 188T Defining Marker syn338G
. . . . . . . . GISAID HA EPI340881
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn47L (CTg) [H1N1 Avian],
. . . . . . . . syn82I (ATc) [H5N2 Avian],
. . . . . . . . syn93C (TGc) [H5N1 Avian Domestic & Wild],
. . . . . . . . . . . . . . . . . [H9N2 Avian Emergent 2009],
. . . . . . . . . . . . . . . . . [H13N2 Mammal],
. . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . 100N [H5N1 Egypt Avian 2009-2010
. . . . . . . . . . . . . . . with syn40H, syn55L, 192I, 196K],
. . . . . . . . . . . . [H5N1 Egypt Avian 2008 with syn40H, syn55L],
. . . . . . . . . . . . [H5N2 Italy Avian 2005-2007],
. . . . . . . . . . . . [H7N3, H7N7, H9N2],
. . . . . . . . . . . . [H13N2 Mammal],
. . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 141Q (CAa) [H13 Avian (gAa, gga)],
. . . . . . . . syn170N (AAc) [H5N1 Egypt Human 2009],
. . . . . . . . . . . . . . . . . . [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . . . . [H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . . . with 225G & 252L],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . 208K (AaA) [pH1N1 Canine 2009],
. . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . [H3N2 Avian 2006, 2009],
. . . . . . . . 219V (gTA) [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . . [H13N2, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . syn338G (GGc) [Clade2, Rare to Clade5],
. . . . . . . . HA Truncated after aa342)

. . . . MoroccoCasablanca117_10m_2011_02_15 (
. . . . . . . . GISAID NA EPI340880
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . NA Truncated before aa33,
. . . . . . . . syn89S (TCt) [H1N1 Avian],
. . . . . . . . syn126P (CCt) [H1N1 Avian (Cat)],
. . . . . . . . . . . . . . . . . .[H9N2 Avian (Ctt)],
. . . . . . . . syn229S (TCc) [H1N1 Avian],
. . . . . . . . syn236G (GGc) [H1N1 Avian],
. . . . . . . . syn241V (GTg) [H1N1 Avian],
. . . . . . . . 299A,
. . . . . . . . 454V [Rare to pH1N1 (1)],
. . . . . . . . NA Truncated after aa454)

. . . . MoroccoCasablanca110_3F_2011_02_09 (
. . . . . . . . GISAID NA EPI340882
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa38,
. . . . . . . . 38V [H9N2 Avian],
. . . . . . . . syn60T (ACc) [H1N1 Avian Farm],
. . . . . . . . 81A [H1N1 Avian],
. . . . . . . . syn138A (GCt) [H1N1 Avian],
. . . . . . . . . . . . . . . . . . [H9N2 Avian],
. . . . . . . . 192N [H9N2 Avian (cac)],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . NA Truncated after aa453)

. . . . MoroccoCasablanca107_xF_2011_02_09 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340883
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa#4,
. . . . . . . . 100N,
. . . . . . . . 173R,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa341)

. . . . MoroccoCasablanca103_5M_2011_02_07 (
. . . . . . . . GISAID HA EPI340884
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa#7,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 324D [Novel to pH1N1],
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa350)

. . . . MoroccoCasablanca92_52F_2011_02_02 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340858
. . . . . . . . 8 Polymorphisms (6 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa#3,
. . . . . . . . 22E [Novel to pH1N1],
. . . . . . . . 34T [Novel to pH1N1 2011],
. . . . . . . . 47Q [Novel to pH1N1],
. . . . . . . . 60V [H1N1 Avian],
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa341)

. . . . MoroccoCasablanca91_15mM_2011_02_02 (
. . . . . . . . Clade5: 208K_219V
. . . . . . . . GISAID HA EPI340860
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa82,
. . . . . . . . 100F [Novel to pH1N1],
. . . . . . . . syn102E (GAa) [H5N1 wt],
. . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . syn170N (AAc) [H5N1 Egypt Human 2009],
. . . . . . . . . . . . . . . . . . [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . . . . [H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . . . with 225G & 252L],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . 208K (AaA) [pH1N1 Canine 2009],
. . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . [H3N2 Avian 2006, 2009],
. . . . . . . . 219V (gTA) [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . . [H13N2, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . syn221P (CCt) [H3N2 Avian
. . . . . . . . . . . . . . . . . . . . . with 157S, 159S, syn287G],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human and Avian (tCt)],
. . . . . . . . . . . . . . . . . . [H5N1 Nigeria Avian (tCt)],
. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],
. . . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive Upsilon polymorphisms],
. . . . . . . . 252L (tTG) [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],
. . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],
. . . . . . . . HA Truncated after aa352)

. . . . MoroccoCasablanca91_15mM_2011_02_02 (
. . . . . . . . GISAID NA EPI340859
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa36,
. . . . . . . . 69V [H1N1 Avian],
. . . . . . . . 81A [H1N1 Avian],
. . . . . . . . 106M,
. . . . . . . . syn138A (GCt) [H1N1 Avian],
. . . . . . . . . . . . . . . . . . [H9N2 Avian],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn395G (GGg),
. . . . . . . . NA Truncated after aa452)

. . . . MoroccoCasablanca76_13M_2011_01_26 (
. . . . . . . . Clade4: 128D
. . . . . . . . GISAID HA EPI340861
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa13,
. . . . . . . . 28P [Novel to pH1N1.Clade4],
. . . . . . . . . . . [pH1N1 with Avian Influence (3)],
. . . . . . . . . . . [H13N2 Mammal
. . . . . . . . . . . . . . with 188T, syn210S, 225G & 252L],
. . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . with 188T, syn210S, 225G & 252L],
. . . . . . . . syn60I (ATc) [H9N2 Human and Avian Emergent],
. . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6,
. . . . . . . . . . . . . . . . . . . H13N8, H13N9 Avian (tTc)
. . . . . . . . . . . . . . . . . . . . . . with 28P, 188T, syn210S],
. . . . . . . . . . . . . . . . [1918],
. . . . . . . . 128D,
. . . . . . . . syn210S (AGt) [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . . . with 28P, 188T, 225G & 252L],
. . . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . . . with 28P, 188T, 225G & 252L],
. . . . . . . . 298V [H3N2 Avian, Canine, Feline & Mink],
. . . . . . . . . . . [H3N8],
. . . . . . . . . . . [H5 Avian, H6 Avian],
. . . . . . . . . . . [H9N2],
. . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . HA Truncated after aa341)

. . . . MoroccoCasablanca73_43F_2011_01_26 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340863
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa0,
. . . . . . . . 11L [Novel to pH1N1],
. . . . . . . . . . . [H13N2 Mammal
. . . . . . . . . . . . . . with 28P, 188T, syn210S, 225G & 252L],
. . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . with 28P, 188T, syn210S, 225G & 252L],
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 259T [Recently Novel to pH1N1υ],
. . . . . . . . . . . . [H9N2 Avian and Human (att)
. . . . . . . . . . . . . . . . with syn40H],
. . . . . . . . . . . . [Not Found in H1N1 Swine with 124N],
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa338)

. . . . MoroccoCasablanca73_43F_2011_01_26 (
. . . . . . . . GISAID NA EPI340862
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . NA Truncated before aa44,
. . . . . . . . syn126P (CCa),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn293R (AGa) [H1N1 Avian Farm],
. . . . . . . . . . . . . . . . . . . [H5N1 Avian],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . NA Truncated after aa453)

. . . . MoroccoCasablanca69_11F_2011_01_26 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340866
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa#5,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 224K [swine pH1N1.Clade5]
. . . . . . . . . . . . [WSN_1933],
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa339)

. . . . MoroccoCasablanca69_11F_2011_01_26 (
. . . . . . . . GISAID NA EPI340865
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . NA Truncated before aa35,
. . . . . . . . 70N [H1N1 Avian],
. . . . . . . . syn137G (GGa) [H1N1 Avian],
. . . . . . . . syn215T (ACa) [H1N1 Avian],
. . . . . . . . 235D [H9N2 Avian],
. . . . . . . . syn240T (ACc) [H1N1 Avian],
. . . . . . . . 241I [H1N1 Avian],
. . . . . . . . 260R [H1N1 Avian],
. . . . . . . . 369K [H1N1 Avian],
. . . . . . . . syn377P (CCa) [H1N1 Avian],
. . . . . . . . syn386N (AAt) [H1N1 Environment],
. . . . . . . . syn416D (GAc) [H5N1 wt],
. . . . . . . . NA Truncated after aa453)

. . . . MoroccoCasablanca63_47F_2011_01_20 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340868
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa3,
. . . . . . . . syn90N (AAc) [Rare to pH1N1],
. . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa339)

. . . . MoroccoCasablanca63_47F_2011_01_20 (
. . . . . . . . GISAID NA EPI340867
. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa20,
. . . . . . . . syn89S (TCt) [H1N1 Avian],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 262N,
. . . . . . . . 263V [H1N1 Avian],
. . . . . . . . . . . . [H5N1 wt],
. . . . . . . . . . . . [H9N2 Avian],
. . . . . . . . 269I [H5N1 (tTa)],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . 420C,
. . . . . . . . NA Truncated after aa453)

. . . . MoroccoCasablanca60_43F_2011_01_20 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340869
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa#3,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn205G (GGa),
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa338)

. . . . MoroccoCasablanca54_23F_2011_01_20 (
. . . . . . . . GISAID NA EPI340870
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa17,
. . . . . . . . 54L,
. . . . . . . . 81A [H1N1 Avian],
. . . . . . . . syn138A (GCt) [H1N1 Avian],
. . . . . . . . . . . . . . . . . . [H9N2 Avian],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn395G (GGg),
. . . . . . . . NA Truncated after aa454)

. . . . MoroccoCasablanca52_25F_2011_01_20 (
. . . . . . . . GISAID NA EPI340871
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . NA Truncated before aa19,
. . . . . . . . 43R,
. . . . . . . . 44T,
. . . . . . . . 45L,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . NA Truncated after aa452)

. . . . MoroccoCasablanca28_10M_2011_01_13 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340873
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa#6,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 340M,
. . . . . . . . HA Truncated after aa340)

. . . . MoroccoCasablanca28_10M_2011_01_13 (
. . . . . . . . GISAID NA EPI340872
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . NA Truncated before aa21,
. . . . . . . . 54V [H1N1 Avian],
. . . . . . . . . . [H9N2 Avian],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . 454V [Rare to pH1N1 (1)],
. . . . . . . . NA Truncated after aa454)

. . . . MoroccoCasablanca26_24M_2011_01_13 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340874
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . syn136T (ACt),
. . . . . . . . 176I,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa353)

. . . . MoroccoCasablanca23_3F_2011_01_13 (
. . . . . . . . Clade5: 208K_219V
. . . . . . . . GISAID HA EPI340876
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . HA Truncated before aa#7,
. . . . . . . . syn36L (tTA) [H5N1 Avian (tTg)],
. . . . . . . . syn47L (CTg) [H1N1 Avian],
. . . . . . . . 100N [H5N1 Egypt Avian 2009-2010
. . . . . . . . . . . . . . . . . with syn40H, syn55L, 192I, 196K],
. . . . . . . . . . . . [H5N1 Egypt Avian 2008 with syn40H, syn55L],
. . . . . . . . . . . . [H5N2 Italy Avian 2005-2007],
. . . . . . . . . . . . [H7N3, H7N7, H9N2],
. . . . . . . . . . . . [H13N2 Mammal],
. . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn102E (GAa) [H5N1 wt],
. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . syn170N (AAc) [H5N1 Egypt Human 2009],
. . . . . . . . . . . . . . . . . . [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . . . . [H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . . . with 225G & 252L],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . syn184H (CAc) [Early pH1N1 Highly Zoonotic]
. . . . . . . . . . . . . . . . . . [swine pH1N1.Clade5],
. . . . . . . . . . . . . . . . . . [H2N3, H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Fatality 2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009],
. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . . . . . . . . . . . [H13N2 Mammal],
. . . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 208K (AaA) [pH1N1 Canine 2009],
. . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . [H3N2 Avian 2006, 2009],
. . . . . . . . 219V (gTA) [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . . . . . . . . . [H13N2, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . with 188T, 225G & 252L],
. . . . . . . . 252L (tTG) [H13N2 Mammal
. . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],
. . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian
. . . . . . . . . . . . . . . . . . . with 188T, 219V & 225G],
. . . . . . . . HA Truncated after aa335)

. . . . MoroccoCasablanca23_3F_2011_01_13 (
. . . . . . . . GISAID NA EPI340875
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa39,
. . . . . . . . syn87G (GGg) [H9N2 Avian (aag)],
. . . . . . . . syn138A (GCt) [H1N1 Avian],
. . . . . . . . . . . . . . . . . . [H9N2 Avian],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 242V [H9N2 Avian],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . NA Truncated after aa455)

. . . . MoroccoCasablanca17_12F_2011_01_07 (
. . . . . . . . GISAID NA EPI340877
. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)
. . . . . . . . NA Truncated before aa35,
. . . . . . . . syn176S (TCg) [H1N1 Avian],
. . . . . . . . 213K,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn338V (GTg) [H1N1 Avian],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . NA Truncated after aa453)

. . . . MoroccoCasablanca15_35F_2011_01_06 (
. . . . . . . . GISAID NA EPI340878
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa35,
. . . . . . . . syn126P (CCa),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 263V [H1N1 Avian],
. . . . . . . . . . . . [H5N1 wt],
. . . . . . . . . . . . [H9N2 Avian],
. . . . . . . . 269I [H5N1 (tTa)],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . NA Truncated after aa454)

. . . . MoroccoCasablanca07_23F_2011_01_05 (
. . . . . . . . GISAID NA EPI340864
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . NA Truncated before aa34,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . 419S,
. . . . . . . . 420A,
. . . . . . . . 428I,
. . . . . . . . NA Truncated after aa453)

. . . . MoroccoCasablanca210_2010_12_20 (
. . . . . . . . GISAID NA EPI340886
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa17,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn273N (AAc) [H1N1 Avian],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . NA Truncated after aa457)

Supporting Sequences

. . . . NewYork7420_2010_01_02 (
. . . . . . . . GenBank HA CY065067
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . 35I [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . syn80S (TCt) [H5N1 Egypt Human 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . . . [H6N1, H7N3, H9N2, H11],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn31H,
. . . . . . . . . . . . . . . . . . . . . . . . syn40H, syn42G, 72L,
. . . . . . . . . . . . . . . . . . . . . . . . syn81Y, syn82I, 87N
. . . . . . . . . . . . . . . . . . . . . . . . syn118E, 144E, 158E,
. . . . . . . . . . . . . . . . . . . . . . . . 189T, 200T, 218S, 218V,
. . . . . . . . . . . . . . . . . . . . . . . . 237I, syn287G, syn346G,
. . . . . . . . . . . . . . . . . . . . . . . . 453K, 502K, 523A, 523I],
. . . . . . . . syn159N (AAc) [H3N8 Avian & Equine],
. . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn184H (CAc) [Early pH1N1 Highly Zoonotic]
. . . . . . . . . . . . . . . . . . [swine pH1N1.Clade5],
. . . . . . . . . . . . . . . . . . [H2N3, H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Fatality 2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009],
. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . 236I [H3N8],
. . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],
. . . . . . . . . . . . [H6, H7N7, H9N2 2009, H11],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn441H (CAt) [H1N1 Avian, H2, H5N1, H6, H9N2, H11])

. . . . NewYork7425_2009_12_20 (
. . . . . . . . GenBank HA CY065091
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . 35I [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . syn113S (TCg) [1918],
. . . . . . . . syn159N (AAc) [H3N8 Avian & Equine],
. . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn184H (CAc) [Early pH1N1 Highly Zoonotic]
. . . . . . . . . . . . . . . . . . [swine pH1N1.Clade5],
. . . . . . . . . . . . . . . . . . [H2N3, H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Fatality 2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009],
. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . 236I [H3N8],
. . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],
. . . . . . . . . . . . [H6, H7N7, H9N2 2009, H11],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn441H (CAt) [H1N1 Avian, H2, H5N1, H6, H9N2, H11])

. . . . Texas43242018_2009_07_24 (
. . . . . . . . GenBank HA CY051823
. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)
. . . . . . . . syn184H (CAc) [Early pH1N1 Highly Zoonotic]
. . . . . . . . . . . . . . . . . . [swine pH1N1.Clade5],
. . . . . . . . . . . . . . . . . . [H2N3, H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Fatality 2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009],
. . . . . . . . . . . . . . . . . . [H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . syn239P (CCt) [H1N1 Avian],
. . . . . . . . syn297N (AAc) [H3N2 Asia Avian 1975-1977 with 159S, 453K],
. . . . . . . . . . . . . . . . . . [H3N8 Avian],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2 Human, Avian, Equine and Seal wt],
. . . . . . . . . . . . . . . . . . [H9N2 Avian 2009],
. . . . . . . . syn453R (AGg) [H1N1 Avian],
. . . . . . . . syn525S (AGc) [H1N1 Avian])

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Japan Demonstrates 2011 pH1N1 Multi-Segment Hypermorphism

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

Last Update
2011-10-27

On 2011-10-19, the Japanese Influenza Collaborative Study Group based at Niigata University released a group of human pH1N1 sequences at GenBank and GISAID including 46 HA fragments and 46 full NA segments.  The sample dates span 2011-01-04 to 2011-03-08.  Seven geographic areas of Japan are covered with no specification of subject age, subject gender, treatment protocol, clinical progression or clinical outcome notated.

Cladistics

Clade2: 188T is represented on 44 sequences crossing all geographic divisions and Clade3: 186P is found once each in Niigata and Osaka.  Although cladding is clear, perhaps due to publication bias, overall diversity is high. That diversity and the sheer polymorphic count demonstrate the instability of human pH1N1 as the reservoir continues to undergo revision.

HA 320 Polymorphisms Averaging ~7.0 per Segment Fragment
NA 352 Polymorphisms Averaging ~7.6 per Segment

HA and NA 672 Total Polymorphisms Averaging ~14.6 per Sequence (HA Fragments)

Diversity

The HA superset producing 77 distinct values includes 4 polymorphisms (syn31H, syn42G, 189T, syn287G) that appear on the High CFR Clade1.Upsilon revision set.  Polymorphic sets shared across pH1N1 clades suggest cross-clade compatibility.  H5N1 involvement is notated on JapanOsaka10K362_2011_02_15, [EPI340541].  Notably absent in this deposit are Receptor Binding Site changes at HA aa225.  The NA superset produces 85 distinct values.  No mixed peaks (ambiguity) are found on any segment though significant zoonoses are represented.

Hypermorphic Behaviour

14 HA Fragments >= 8 polymorphisms (30%)
20 NA Segments >= 8 polymorphisms (43%)

Combined Polymorphic Count >= 17
Total (HA / NA)

• 21 (HA 11 / NA 10): [EPI340579] JapanHokkaido10H054_2011_02_07
• 21 (HA 11 / NA 10): [EPI340574] JapanHyogo10K055_2011_01_24
• 19 (HA 11 / NA 08): [EPI340549] JapanNiigata10F257_2011_02_03
• 18 (HA 10 / NA 08): [EPI340551] JapanNiigata10F202_2011_01_31
• 18 (HA 10 / NA 08): [EPI340552] JapanNiigata10F117_2011_01_25
• 18 (HA 07 / NA 11): [EPI340548] JapanNiigata10F306_2011_02_05
• 18 (HA 11 / NA 07): [EPI340543] JapanOsaka10K346_2011_02_07
• 17 (HA 07 / NA 10): [EPI340555] JapanNagasaki10N103_2011_02_10
• 17 (HA 08 / NA 09): [EPI340561] JapanKyoto10K385_2011_02_22
• 17 (HA 09 / NA 08): [EPI340568] JapanHyogo10K308_2011_02_14

TamiFlu Resistance

Two TamiFlu Resistant sequences (NA 275Y) each feature on Clade2: 188T backgrounds having significant HA and NA homology with Avian H1N1.

• [EPI340570] JapanHyogo10K291_2011_02_07_TmX
• [EPI340564] JapanKyoto10K124_2011_01_28_TmX

Sequences

. . . . JapanNiigata10F557_2011_03_08 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340547
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . HA Truncated after aa329)

. . . . JapanNiigata10F557_2011_03_08 (
. . . . . . . . GISAID NA EPI340662
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn304V (GTa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . JapanKyoto10K393_2011_02_25 (
. . . . . . . . GISAID HA EPI340560
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn#6L (tTG),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn53L (TTa),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . HA Truncated after aa329)

. . . . JapanKyoto10K393_2011_02_25 (
. . . . . . . . GISAID NA EPI340675
. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . 62I,
. . . . . . . . syn237S (TCa),
. . . . . . . . 240I,
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . JapanKyoto10K385_2011_02_22 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340561
. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn130D (GAt),
. . . . . . . . 146G,
. . . . . . . . syn162P (CCg),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn321L (TTa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanKyoto10K385_2011_02_22 (
. . . . . . . . GISAID NA EPI340676
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 62L,
. . . . . . . . 127S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn427I (ATa),
. . . . . . . . 431S)

. . . . JapanOsaka10K366_2011_02_21 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340539
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . syn#12K (AAa),
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 156T,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . HA Truncated after aa329)

. . . . JapanOsaka10K366_2011_02_21 (
. . . . . . . . GISAID NA EPI340654
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . 13A,
. . . . . . . . 44S,
. . . . . . . . syn64Q (CAa),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . JapanNagasaki10N088_2011_02_19 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340556
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn258F (TTt),
. . . . . . . . HA Truncated after aa329)

. . . . JapanNagasaki10N088_2011_02_19 (
. . . . . . . . GISAID NA EPI340671
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 86T,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . JapanOsaka10K363_2011_02_16 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340540
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 288S,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanOsaka10K363_2011_02_16 (
. . . . . . . . GISAID NA EPI340655
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn157T (ACa),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanOsaka10K362_2011_02_15 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340541
. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . 33I,
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 305E [H5N1 wt],
. . . . . . . . HA Truncated after aa329)

. . . . JapanOsaka10K362_2011_02_15 (
. . . . . . . . GISAID NA EPI340656
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . 44S,
. . . . . . . . syn121F (TTt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn304V (GTa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . JapanHyogo10K308_2011_02_14 (
. . . . . . . . Clade2: 188T crossed with 189T from Clade1
. . . . . . . . GISAID HA EPI340568
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . syn10Y (TAc) [H1N1 Avian],
. . . . . . . . syn34N (AAt) [H1N1 Avian],
. . . . . . . . syn98F (TTt) [H1N1 Avian],
. . . . . . . . syn122K (AAa) [H1N1 Avian],
. . . . . . . . 146G,
. . . . . . . . 166T,
. . . . . . . . 188T [H1N1 Avian],
. . . . . . . . 189T [pH1N1 Clade1.Upsilon],
. . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 200T [H1N1 Avian],
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K308_2011_02_14 (
. . . . . . . . GISAID NA EPI340683
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . 44S,
. . . . . . . . syn104N (AAt) [H1N1 Avian],
. . . . . . . . syn240T [H1N1 Avian],
. . . . . . . . 241I [H1N1 Avian],
. . . . . . . . syn287E (GAg) [H1N1 Avian],
. . . . . . . . 369K [H1N1 Avian],
. . . . . . . . syn377P (CCa) [H1N1 Avian],
. . . . . . . . 451N [H3N8 Equine, Canine, Swine (aAa)])

. . . . JapanHokkaido10H073_2011_02_14 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340578
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn223V (GTa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanHokkaido10H073_2011_02_14 (
. . . . . . . . GISAID NA EPI340693
. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 140V,
. . . . . . . . 224F,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn304V (GTa),
. . . . . . . . 309D,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 392N)

. . . . JapanOsaka10K358_2011_02_12 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340542
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . HA Truncated after aa329)

. . . . JapanOsaka10K358_2011_02_12 (
. . . . . . . . GISAID NA EPI340657
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn304V (GTa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . JapanHyogo10K302_2011_02_12 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340569
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn#12K (AAa),
. . . . . . . . syn31H (CAt) [pH1N1 Clade1.Upsilon],
. . . . . . . . syn34N (AAt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K302_2011_02_12 (
. . . . . . . . GISAID NA EPI340684
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn301R (CGg),
. . . . . . . . syn326P (CCg),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M,
. . . . . . . . 454D)

. . . . JapanNagasaki10N103_2011_02_10 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340555
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],
. . . . . . . . syn50V (GTt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . 297D,
. . . . . . . . HA Truncated after aa329)

. . . . JapanNagasaki10N103_2011_02_10 (
. . . . . . . . GISAID NA EPI340670
. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)
. . . . . . . . syn42N (AAc),
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 257K,
. . . . . . . . 351Y,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M,
. . . . . . . . 416G)

. . . . JapanNagasaki10N073_2011_02_09 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340557
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanNagasaki10N073_2011_02_09 (
. . . . . . . . GISAID NA EPI340672
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn28N (AAt),
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanOsaka10K346_2011_02_07 (
. . . . . . . . Clade3: 186P
. . . . . . . . GISAID HA EPI340543
. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)
. . . . . . . . syn#12K (AAa),
. . . . . . . . 41T,
. . . . . . . . 135A,
. . . . . . . . 137T,
. . . . . . . . 144S,
. . . . . . . . syn163K (AAa),
. . . . . . . . 186P,
. . . . . . . . syn251L (CTg),
. . . . . . . . syn287G (GGg) [pH1N1 Clade1.Upsilon],
. . . . . . . . syn293L (CTt),
. . . . . . . . 298V,
. . . . . . . . HA Truncated after aa329)

. . . . JapanOsaka10K346_2011_02_07 (
. . . . . . . . GISAID NA EPI340658
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 46T,
. . . . . . . . syn126P (CCt),
. . . . . . . . syn187G (GGt),
. . . . . . . . 313R,
. . . . . . . . 394I,
. . . . . . . . syn430R (CGg),
. . . . . . . . 467V)

. . . . JapanHyogo10K291_2011_02_07_TmX (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340570
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 17G,
. . . . . . . . syn34N (AAt) [H1N1 Avian],
. . . . . . . . 188T [H1N1 Avian],
. . . . . . . . 200T [H1N1 Avian],
. . . . . . . . syn296Q [H1N1 Avian],
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K291_2011_02_07_TmX (
. . . . . . . . GISAID NA EPI340685
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 47G [H1N1 Avian Farm],
. . . . . . . . syn126P (CCt),
. . . . . . . . syn240T [H1N1 Avian],
. . . . . . . . 241I [H1N1 Avian],
. . . . . . . . 275Y,
. . . . . . . . 369K [H1N1 Avian],
. . . . . . . . syn377P (CCa) [H1N1 Avian],
. . . . . . . . 415M [H1N1 Avian Farm])

. . . . JapanHokkaido10H054_2011_02_07 (
. . . . . . . . Clade 2: 188T
. . . . . . . . GISAID HA EPI340579
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . syn174K (AAg),
. . . . . . . . syn177L (CTt),
. . . . . . . . syn185P (CCg),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 218E,
. . . . . . . . 253A,
. . . . . . . . HA Truncated after aa329)

. . . . JapanHokkaido10H054_2011_02_07 (
. . . . . . . . GISAID NA EPI340694
. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)
. . . . . . . . 44S,
. . . . . . . . syn152R (AGa),
. . . . . . . . syn234V (GTg),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn392D (GAc),
. . . . . . . . 396T,
. . . . . . . . 469N)

. . . . JapanNiigata10F306_2011_02_05 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340548
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . syn22V (GTc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . 297D,
. . . . . . . . HA Truncated after aa329)

. . . . JapanNiigata10F306_2011_02_05 (
. . . . . . . . GISAID NA EPI340663
. . . . . . . . 11 Polymorphisms (8 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 58Y,
. . . . . . . . 67I,
. . . . . . . . 86V,
. . . . . . . . syn224L (cTG),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . 371Y,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanOsaka10K340_2011_02_04 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340544
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn239P (CCa),
. . . . . . . . syn259A (GCg),
. . . . . . . . 264T,
. . . . . . . . HA Truncated after aa329)

. . . . JapanOsaka10K340_2011_02_04 (
. . . . . . . . GISAID NA EPI340659
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 62I,
. . . . . . . . 77V,
. . . . . . . . 90T,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn366S (AGc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . JapanHyogo10K283_2011_02_04 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340571
. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 205E,
. . . . . . . . 276Q,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K283_2011_02_04 (
. . . . . . . . GISAID NA EPI340686
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 38F,
. . . . . . . . 44S,
. . . . . . . . 143N,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn251A (GCt),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanKyoto10K250_2011_02_04 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340562
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . HA Truncated after aa329)

. . . . JapanKyoto10K250_2011_02_04 (
. . . . . . . . GISAID NA EPI340677
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . 415M)

. . . . JapanNiigata10F257_2011_02_03 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340549
. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn50V (GTg),
. . . . . . . . 89N,
. . . . . . . . syn98F (TTt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn293L (CTt),
. . . . . . . . HA Truncated after aa329)

. . . . JapanNiigata10F257_2011_02_03 (
. . . . . . . . GISAID NA EPI340664
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 13I,
. . . . . . . . 44S,
. . . . . . . . syn104N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 451N)

. . . . JapanKyoto10K243_2011_02_02 (
. . . . . . . . GISAID HA EPI340563
. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)
. . . . . . . . syn33V (GTc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],
. . . . . . . . syn96G (GGg),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn205G (GGa),
. . . . . . . . syn214K (AAa),
. . . . . . . . syn296Q (CAa),
. . . . . . . . 297D,
. . . . . . . . HA Truncated after aa329)

. . . . JapanKyoto10K243_2011_02_02 (
. . . . . . . . GISAID NA EPI340678
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanNiigata10F228_2011_02_01 (
. . . . . . . . GISAID HA EPI340550
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . syn162P (CCt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . HA Truncated after aa329)

. . . . JapanNiigata10F228_2011_02_01 (
. . . . . . . . GISAID NA EPI340665
. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)
. . . . . . . . syn12S (TCa),
. . . . . . . . 44S,
. . . . . . . . syn148T (ACt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn304V (GTa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . JapanGunma10G021_2011_02_01 (
. . . . . . . . GISAID HA EPI340582
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn211K (AAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanGunma10G021_2011_02_01 (
. . . . . . . . GISAID NA EPI340697
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn304V (GTa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . JapanOsaka10K332_2011_01_31 (
. . . . . . . . GISAID HA EPI340545
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanOsaka10K332_2011_01_31 (
. . . . . . . . GISAID NA EPI340660
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn382G (GGa),
. . . . . . . . 415M)

. . . . JapanHyogo10K275_2011_01_31 (
. . . . . . . . GISAID HA EPI340572
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 205E,
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K275_2011_01_31 (
. . . . . . . . GISAID NA EPI340687
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 143N,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn304V (GTa),
. . . . . . . . 364N,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . JapanNiigata10F202_2011_01_31 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340551
. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn50V (GTg),
. . . . . . . . syn98F (TTt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn293L (CTt),
. . . . . . . . HA Truncated after aa329)

. . . . JapanNiigata10F202_2011_01_31 (
. . . . . . . . GISAID NA EPI340666
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . 44S,
. . . . . . . . syn104N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn243T (ACa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 451N)

. . . . JapanHokkaido10H041_2011_01_31 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340580
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanHokkaido10H041_2011_01_31 (
. . . . . . . . GISAID NA EPI340695
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 100H,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn252S (TCg),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanKyoto10K124_2011_01_28_TmX (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340564
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn34N (AAt) [H1N1 Avian],
. . . . . . . . syn37E (GAg) [H1N1 Avian Farm],
. . . . . . . . 146G [H3N8 Avian],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K, 275I],
. . . . . . . . 188T [H1N1 Avian],
. . . . . . . . 200T [H1N1 Avian],
. . . . . . . . syn259A (GCg) [H1N1 Avian],
. . . . . . . . HA Truncated after aa329)

. . . . JapanKyoto10K124_2011_01_28_TmX (
. . . . . . . . GISAID NA EPI340679
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 43H [H1N1 Avian],
. . . . . . . . 44S [H1N1 Avian],
. . . . . . . . syn240T [H1N1 Avian],
. . . . . . . . 241I [H1N1 Avian],
. . . . . . . . 275Y,
. . . . . . . . syn366S (AGc) [H1N1 Avian],
. . . . . . . . 369K [H1N1 Avian],
. . . . . . . . syn377P (CCa) [H1N1 Avian],
. . . . . . . . 381A)

. . . . JapanNiigata10F117_2011_01_25 (
. . . . . . . . Clade3: 186P
. . . . . . . . GISAID HA EPI340552
. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 137T,
. . . . . . . . 144S,
. . . . . . . . 146G,
. . . . . . . . syn163K (AAa),
. . . . . . . . 186P,
. . . . . . . . syn251L (CTg),
. . . . . . . . syn287G (GGg) [pH1N1 Clade1.Upsilon],
. . . . . . . . syn293L (CTt),
. . . . . . . . 298V,
. . . . . . . . HA Truncated after aa329)

. . . . JapanNiigata10F117_2011_01_25 (
. . . . . . . . GISAID NA EPI340667
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 32V,
. . . . . . . . 46T,
. . . . . . . . syn126P (CCt),
. . . . . . . . syn187G (GGt),
. . . . . . . . 313R,
. . . . . . . . 394I,
. . . . . . . . syn430R (CGg),
. . . . . . . . 467V)

. . . . JapanHyogo10K061_2011_01_25 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340573
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 166N,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 288S,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K061_2011_01_25 (
. . . . . . . . GISAID NA EPI340688
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn157T (ACa),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanGunma10G013_2011_01_25 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340583
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanGunma10G013_2011_01_25 (
. . . . . . . . GISAID NA EPI340698
. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 288V,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanOsaka10K323_2011_01_24 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340546
. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)
. . . . . . . . syn#8V (GTg),
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn130D (GAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn280T (ACc),
. . . . . . . . HA Truncated after aa329)

. . . . JapanOsaka10K323_2011_01_24 (
. . . . . . . . GISAID NA EPI340661
. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)
. . . . . . . . 44S,
. . . . . . . . 127S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn315G (GGg),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn382G (GGa),
. . . . . . . . 432T,
. . . . . . . . syn436I (ATt))

. . . . JapanHyogo10K055_2011_01_24 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340574
. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn33V (GTc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 86F,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn116R (AGa),
. . . . . . . . 123A,
. . . . . . . . 146G,
. . . . . . . . 169V,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K055_2011_01_24 (
. . . . . . . . GISAID NA EPI340689
. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . syn139L (cTG),
. . . . . . . . syn158L (tTA),
. . . . . . . . syn183A (GCc),
. . . . . . . . syn195I (ATc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn246P (CCg),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . JapanGunma10G004_2011_01_21 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340584
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanGunma10G004_2011_01_21 (
. . . . . . . . GISAID NA EPI340699
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanHyogo10K045_2011_01_20 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340575
. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn205G (GGa),
. . . . . . . . syn214K (AAa),
. . . . . . . . syn296Q (CAa),
. . . . . . . . 297D,
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K045_2011_01_20 (
. . . . . . . . GISAID NA EPI340690
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanKyoto10K025_2011_01_18 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340565
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanKyoto10K025_2011_01_18 (
. . . . . . . . GISAID NA EPI340680
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanNiigata10F025_2011_01_18 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340553
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa) [pH1N1 Clade1.Upsilon],
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . 297D,
. . . . . . . . HA Truncated after aa329)

. . . . JapanNiigata10F025_2011_01_18 (
. . . . . . . . GISAID NA EPI340668
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanHyogo10K037_2011_01_17 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340576
. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)
. . . . . . . . syn33V (GTc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn205G (GGa),
. . . . . . . . syn214K (AAa),
. . . . . . . . syn296Q (CAa),
. . . . . . . . 297D,
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K037_2011_01_17 (
. . . . . . . . GISAID NA EPI340691
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M,
. . . . . . . . syn460G (GGc))

. . . . JapanHokkaido10H031_2011_01_17 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340581
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . #1E,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanHokkaido10H031_2011_01_17 (
. . . . . . . . GISAID NA EPI340696
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn330D (GAc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanNiigata10F012_2011_01_17 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340554
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn240G (GGg),
. . . . . . . . syn258F (TTt),
. . . . . . . . syn299H (CAc),
. . . . . . . . HA Truncated after aa329)

. . . . JapanNiigata10F012_2011_01_17 (
. . . . . . . . GISAID NA EPI340669
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . 44S,
. . . . . . . . syn210G (GGa),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . JapanKyoto10K012_2011_01_15 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340566
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn212K (AAa),
. . . . . . . . 289M,
. . . . . . . . HA Truncated after aa329)

. . . . JapanKyoto10K012_2011_01_15 (
. . . . . . . . GISAID NA EPI340681
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 46V,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn449N (AAt))

. . . . JapanHyogo10K029_2011_01_13 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340577
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn42G (GGa),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanHyogo10K029_2011_01_13 (
. . . . . . . . GISAID NA EPI340692
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanKyoto10K002_2011_01_12 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340567
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn31H (CAt) [pH1N1 Clade1.Upsilon],
. . . . . . . . syn34N (AAt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanKyoto10K002_2011_01_12 (
. . . . . . . . GISAID NA EPI340682
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanNagasaki10N010_2011_01_11 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340558
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 143E,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanNagasaki10N010_2011_01_11 (
. . . . . . . . GISAID NA EPI340673
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn28N (AAt),
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

. . . . JapanNagasaki10N005_2011_01_04 (
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI340559
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn36L (tTA),
. . . . . . . . 163M,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 238K,
. . . . . . . . syn296Q (CAa),
. . . . . . . . HA Truncated after aa329)

. . . . JapanNagasaki10N005_2011_01_04 (
. . . . . . . . GISAID NA EPI340674
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn28N (AAt),
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 415M)

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