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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