2013-11-06

HA 190G: pH1N1 Vaccine Escape & Child Fatality

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 Excel for completeness in citation.

Publish Date : 2013-11-06
Last Update : 2013-11-28
Gain of Function Empiriks
by
Polymorphism
pH1N1 HA 190G

HA 190G: pH1N1 Vaccine Escape & Child Fatality
Map - Active and Detailed
18 Cases over 20 Sequences

Key Severity Indicators
Ambiguity
SegmentTypeCount
 Hemagglutinin Binary04
 Neuraminidase Binary03
 Neuraminidase Ultra01
  • CrossClade Emergent
  • Fatality Count 02
  • Vaccine Escape Count 04 (05)
  • NA UltraAmbiguity
    • [EPI213437] Singapore 2009
    • NA 296R aGG mix wt
    • NA 296R cGG mix wt
    • NA 296G mix wt

Isolate Metrics
Calendar
Sample
Year		Count
 201304
 201203
 201102
 201008
 200903
Age / Gender Dynamic
ObservationPercent
 Child or
   ChildBearing Age female		93%
 Child Aged 17 or Under73%
 Child Aged 06 or Under53%
 Child Aged 04 or Under27%
Cladistics
CladeNameCount
 UnCladed09
 Clade2:188T08
 CrossClade:
 188T_208K		02
 Clade4:128D01

HA Polymorphisms

. . . . BrazilSaoPauloSorocaba1117706_1F_2013_07_01_VxX_s (
. . . . . . . . A/Sao Paulo/11-17706/2013
. . . . . . . . Vaccinated 2013
. . . . . . . . CrossClade 188T and 208K
. . . . . . . . Deposit Report
. . . . . . . . GISAID HA EPI484739
. . . . . . . . GISAID Isolate EPI_ISL_149724
. . . . . . . . 25 Polymorphisms (13 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . 46R [pH1N1 Rare: 24 Cases over 29 Sequences (map),
. . . . . . . . . . . . . . 100% CrossClade: 2013 Cases,
. . . . . . . . . . . . . . . . . Delaware 2013-08-02,
. . . . . . . . . . . . . . TamiFlu Resistance,
. . . . . . . . . . . . . . Vaccine Escape Count 03,
. . . . . . . . . . . . . . Fatality 2009,
. . . . . . . . . . . . . . Hospitalisation 2009,
. . . . . . . . . . . . . . Age / Gender Dynamic:
. . . . . . . . . . . . . . . . . 89% = Child or ChildBearing Age Female
. . . . . . . . . . . . . . . . . 61% = Child Age 14 or Under
. . . . . . . . . . . . . . . . . 44% = Child Age 04 or Under],
. . . . . . . . . [avH1N1farm],
. . . . . . . . . [H6N1],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 119M [Emergent H7N9],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G [pH1N1 Rare: 17 Cases over 19 Sequences
. . . . . . . . . . . . . . . . . . Fatalities,
. . . . . . . . . . . . . . . . . . Vaccine Escapes,
. . . . . . . . . . . . . . . . . . Infants],
. . . . . . . . syn195Y (TAc),
. . . . . . . . 208K,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . 289V [pH1N1 with HA 230I],
. . . . . . . . . . . . [H5N1],
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn379T (ACc),
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn464G (GGg),
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . 530A [H5N1],
. . . . . . . . . . . . [H9N2])

. . . . SouthAustralia19_M1_xF_2013_05_24 (
. . . . . . . . A/SOUTH AUSTRALIA/19/2013
. . . . . . . . CrossClade 188T and 208K
. . . . . . . . GISAID HA EPI466097
. . . . . . . . GISAID Isolate EPI_ISL_145316
. . . . . . . . 23 Polymorphisms (10 Amino and 13 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 119M [Emergent H7N9],
. . . . . . . . syn161Y (TAt),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . 208K,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn323N (AAc),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn459N (AAc),
. . . . . . . . 502K,
. . . . . . . . syn507K (AAa))

. . . . NewMexico02_4M_2013_01_06 (
. . . . . . . . A/New Mexico/02/2013
. . . . . . . . GISAID HA EPI443685
. . . . . . . . GISAID Isolate EPI_ISL_139490
. . . . . . . . 22 Polymorphisms (10 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn161Y (TAt),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa),
. . . . . . . . 280A [avH1N1farm],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 452I,
. . . . . . . . 454N,
. . . . . . . . 502K)

. . . . NewMexico02_M1C2_4M_2013_01_06_VxX (
. . . . . . . . A/New Mexico/02/2013
. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . GISAID HA EPI439239
. . . . . . . . GISAID Isolate EPI_ISL_138664
. . . . . . . . 23 Polymorphisms (11 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 158E,
. . . . . . . . syn161Y (TAt),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa),
. . . . . . . . 280A [avH1N1farm],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 452I [H13N2],
. . . . . . . . 454N,
. . . . . . . . 502K)

. . . . Minnesota34_M1C1_1M_2012_12_20_VxX (
. . . . . . . . A/Minnesota/34/2012
. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . GISAID HA EPI426455
. . . . . . . . GISAID Isolate EPI_ISL_136468
. . . . . . . . 22 Polymorphisms (10 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 124I [H9N2],
. . . . . . . . 158E,
. . . . . . . . syn161Y (TAt),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa),
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K)

. . . . Minnesota26_C1_31F_2012_12_13 (
. . . . . . . . A/Minnesota/26/2012
. . . . . . . . GISAID HA EPI409917
. . . . . . . . GISAID Isolate EPI_ISL_133162
. . . . . . . . 21 Polymorphisms (8 Amino and 13 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn161Y (TAt),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa),
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn472H (CAt),
. . . . . . . . 502K)

. . . . Washington2961_PMK1_24F_2012_03_25 (
. . . . . . . . A/Washington/2961/2012
. . . . . . . . United States Air Force: Probable Vaccination
. . . . . . . . GISAID HA EPI377070
. . . . . . . . GISAID Isolate EPI_ISL_121766
. . . . . . . . 16 Polymorphisms (10 Amino and 6 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 57R [H7N7 Passerine],
. . . . . . . . . . [zH3N2],
. . . . . . . . 72T,
. . . . . . . . syn84E (GAg),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 149E,
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . 200T,
. . . . . . . . 219M [pH1N1 with HA 230I],
. . . . . . . . 263D,
. . . . . . . . syn296Q (CAa),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . HA Truncated after aa386)

. . . . Paraguay191_X1C1_25F_2011_11_17_VxX (
. . . . . . . . A/Paraguay/191/2011
. . . . . . . . Vaccine Escape Genotype HA 159D
. . . . . . . . GISAID HA EPI349352
. . . . . . . . GISAID Isolate EPI_ISL_101589
. . . . . . . . 18 Polymorphisms (11 Amino and 7 Silent)
. . . . . . . . 3T,
. . . . . . . . 73P,
. . . . . . . . syn88S (TCt),
. . . . . . . . 100N,
. . . . . . . . syn158G (GGg),
. . . . . . . . 159D [Emergent H7N9 wt],
. . . . . . . . syn167S (TCa),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . 218E [H7N7 Avian and Sea Mammal],
. . . . . . . . syn255R (AGg),
. . . . . . . . syn339F (TTt),
. . . . . . . . 377K,
. . . . . . . . 406G mix wt,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 513T [H5N1])

. . . . CameroonLEID03111573_M2M2_xM_2011_03_01_VxX (
. . . . . . . . A/Cameroon/LEID/03/11/1573/2011
. . . . . . . . Vaccine Escape Genotype HA 158E mix wt
. . . . . . . . GISAID HA EPI346687
. . . . . . . . GISAID Isolate EPI_ISL_99919
. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . syn157K (AAg),
. . . . . . . . 158E mix wt,
. . . . . . . . syn173G (GGa),
. . . . . . . . 190G,
. . . . . . . . 205E mix wt [H7N7 Rare],
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A [Emergent H7N9 wt],
. . . . . . . . syn286K (AAa),
. . . . . . . . syn334G (GGa),
. . . . . . . . 377K,
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)

. . . . UKEngland04640543_2010_11_14_f (
. . . . . . . . A/England/04640543/2010
. . . . . . . . GISAID HA EPI403847
. . . . . . . . GISAID Isolate EPI_ISL_131605
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . UKEngland4640543_2010_11_14_f (
. . . . . . . . A/England/4640543/2010
. . . . . . . . GISAID HA EPI295754
. . . . . . . . GISAID Isolate EPI_ISL_84274
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . AustraliaDarwin156_6M_2010_10_26 (
. . . . . . . . A/DARWIN/156/2010
. . . . . . . . Clade4: HA 128D
. . . . . . . . GISAID HA EPI294354
. . . . . . . . GISAID Isolate EPI_ISL_83873
. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)
. . . . . . . . syn60I (ATc),
. . . . . . . . 128D,
. . . . . . . . syn132N (AAt),
. . . . . . . . 190G,
. . . . . . . . syn306C (TGc),
. . . . . . . . 377K,
. . . . . . . . syn469E (GAg),
. . . . . . . . syn501E (GAg))

. . . . BrazilSaoPaulo29269_6M_2010_05_03_f (
. . . . . . . . A/Sao Paulo/29269/2010
. . . . . . . . GISAID HA EPI335466
. . . . . . . . GISAID Isolate EPI_ISL_95941
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . syn132N (AAt),
. . . . . . . . 190G,
. . . . . . . . 274Q,
. . . . . . . . 377K,
. . . . . . . . syn547Q (CAa))

. . . . ChinaShanghaiPudongxinSWL1335_C3_17M_2010_03_18 (
. . . . . . . . A/Shanghai-Pudongxin/SWL1335/2010
. . . . . . . . GISAID HA EPI258224
. . . . . . . . GISAID Isolate EPI_ISL_75083
. . . . . . . . 7 Polymorphisms (6 Amino and 1 Silent)
. . . . . . . . 131P,
. . . . . . . . 141N,
. . . . . . . . 190G,
. . . . . . . . 205E mix wt [H7N7 Rare],
. . . . . . . . 377K,
. . . . . . . . syn408E (GAa),
. . . . . . . . 409S)

. . . . JapanNagasakiHA109_M_0F_2010_01_18 (
. . . . . . . . A/Nagasaki/HA-10-9/2010
. . . . . . . . GISAID HA EPI249903
. . . . . . . . GISAID Isolate EPI_ISL_71907
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . syn16T (ACt),
. . . . . . . . 174R [GreeceKavala470_46M_2011_02_01_f],
. . . . . . . . 190G,
. . . . . . . . 200T)

. . . . JapanNagasakiHA106_M_2M_2010_01_12 (
. . . . . . . . A/Nagasaki/HA-10-6/2010
. . . . . . . . GISAID HA EPI249900
. . . . . . . . GISAID Isolate EPI_ISL_71904
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . syn134G (GGc),
. . . . . . . . 190G,
. . . . . . . . 206S,
. . . . . . . . syn292S (AGt),
. . . . . . . . syn413K (AAg),
. . . . . . . . syn482V (GTa),
. . . . . . . . 550K)

. . . . JapanNagasakiHA105_M_13F_2010_01_12 (
. . . . . . . . A/Nagasaki/HA-10-5/2010
. . . . . . . . GISAID HA EPI249899
. . . . . . . . GISAID Isolate EPI_ISL_71903
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn94Y (TAt),
. . . . . . . . 142D [pH1N1 Rare: Count 50 on 46 Cases (map),
. . . . . . . . . . . . BrazilSaoPauloJaboticabal630177_1M_2013_09_30_s,
. . . . . . . . . . . . Deposit Report],
. . . . . . . . 190G,
. . . . . . . . syn193S (AGc),
. . . . . . . . 298V,
. . . . . . . . 307S [H9N2],
. . . . . . . . syn471Y (TAt))

. . . . ChinaQingdao1215_15M_2009_09_12 (
. . . . . . . . A/Qingdao/1215/2009
. . . . . . . . GISAID HA EPI272697
. . . . . . . . GISAID Isolate EPI_ISL_77396
. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)
. . . . . . . . syn#6L (CTa),
. . . . . . . . 13D [pH1N1 Rare: Count 04],
. . . . . . . . 25R [Emergent H7N9 wt],
. . . . . . . . . . [H7N7],
. . . . . . . . . . [H5N1],
. . . . . . . . syn27V (GTg),
. . . . . . . . syn44L (tTA),
. . . . . . . . 190G,
. . . . . . . . 293P,
. . . . . . . . syn318A (GCt),
. . . . . . . . syn325P (CCt),
. . . . . . . . syn378I (ATc))

. . . . SingaporeON1138_P1_2009_07_13 (
. . . . . . . . A/Singapore/ON1138/2009
. . . . . . . . UltraAmbiguity Neuraminidase
. . . . . . . . GISAID HA EPI213435
. . . . . . . . GISAID Isolate EPI_ISL_61427
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . syn181G (GGt),
. . . . . . . . 190G)

. . . . Pennsylvania08_C1_31M_2009_05_02 (
. . . . . . . . A/Pennsylvania/08/2009
. . . . . . . . GISAID HA EPI221156
. . . . . . . . GISAID Isolate EPI_ISL_31576
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],
. . . . . . . . 190G,
. . . . . . . . 206S,
. . . . . . . . syn346G (GGa),
. . . . . . . . syn456L (cTA))

NA Polymorphisms

. . . . SouthAustralia19_M1_xF_2013_05_24 (
. . . . . . . . A/SOUTH AUSTRALIA/19/2013
. . . . . . . . CrossClade 188T and 208K
. . . . . . . . GISAID NA EPI466096
. . . . . . . . GISAID Isolate EPI_ISL_145316
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg),
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn307N (AAt),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . NewMexico02_4M_2013_01_06 (
. . . . . . . . A/New Mexico/02/2013
. . . . . . . . GISAID NA EPI442693
. . . . . . . . GISAID Isolate EPI_ISL_139490
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg),
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn274Y (TAc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . NewMexico02_M1C2_4M_2013_01_06_VxX (
. . . . . . . . A/New Mexico/02/2013
. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . GISAID NA EPI439238
. . . . . . . . GISAID Isolate EPI_ISL_138664
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg),
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt),
. . . . . . . . 224V,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn274Y (TAc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Minnesota34_M1C1_1M_2012_12_20_VxX (
. . . . . . . . A/Minnesota/34/2012
. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . GISAID NA EPI426454
. . . . . . . . GISAID Isolate EPI_ISL_136468
. . . . . . . . 17 Polymorphisms (9 Amino and 8 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . 38T [H5N1],
. . . . . . . . 44S,
. . . . . . . . syn55T (ACc),
. . . . . . . . 56H [H6N1],
. . . . . . . . 66H mix wt [H6N1],
. . . . . . . . 67A [avH1N1farm],
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg),
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Minnesota26_C1_31F_2012_12_13 (
. . . . . . . . A/Minnesota/26/2012
. . . . . . . . GISAID NA EPI409916
. . . . . . . . GISAID Isolate EPI_ISL_133162
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg),
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 317M mix wt,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Paraguay191_X1C1_25F_2011_11_17_VxX (
. . . . . . . . A/Paraguay/191/2011
. . . . . . . . Vaccine Escape Genotype HA 159D
. . . . . . . . GISAID NA EPI349351
. . . . . . . . GISAID Isolate EPI_ISL_101589
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 62I [H6N1],
. . . . . . . . syn111K (AAa),
. . . . . . . . syn162P (CCc),
. . . . . . . . 188F,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 272S [H9N2],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn387F (TTt),
. . . . . . . . 396M mix wt [avH1N1farm],
. . . . . . . . syn416D (GAc),
. . . . . . . . syn438T (ACc))

. . . . CameroonLEID03111573_M2M2_xM_2011_03_01_VxX (
. . . . . . . . A/Cameroon/LEID/03/11/1573/2011
. . . . . . . . Vaccine Escape Genotype HA 158E mix wt
. . . . . . . . GISAID NA EPI346688
. . . . . . . . GISAID Isolate EPI_ISL_99919
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn6K (AAa),
. . . . . . . . syn22L (cTA),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa))

. . . . UKEngland04640543_2010_11_14_f (
. . . . . . . . A/England/04640543/2010
. . . . . . . . GISAID NA EPI403849
. . . . . . . . GISAID Isolate EPI_ISL_131605
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . AustraliaDarwin156_6M_2010_10_26 (
. . . . . . . . A/DARWIN/156/2010
. . . . . . . . Clade4: HA 128D
. . . . . . . . GISAID NA EPI294353
. . . . . . . . GISAID Isolate EPI_ISL_83873
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn4N (AAt),
. . . . . . . . syn5Q (CAg),
. . . . . . . . syn85L (cTA),
. . . . . . . . syn354G (GGa),
. . . . . . . . 394I [H5N1],
. . . . . . . . . . [avH1N1farm],
. . . . . . . . 397K,
. . . . . . . . NA Truncated after aa465)

. . . . ChinaShanghaiPudongxinSWL1335_C3_17M_2010_03_18 (
. . . . . . . . A/Shanghai-Pudongxin/SWL1335/2010
. . . . . . . . GISAID NA EPI258223
. . . . . . . . GISAID Isolate EPI_ISL_75083
. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)
. . . . . . . . syn110S (TCa),
. . . . . . . . syn281C (TGc),
. . . . . . . . syn315G (GGg),
. . . . . . . . syn330D (GAc),
. . . . . . . . syn339S (TCa),
. . . . . . . . syn446C (TGc))

. . . . ChinaQingdao1215_15M_2009_09_12 (
. . . . . . . . A/Qingdao/1215/2009
. . . . . . . . GISAID NA EPI272698
. . . . . . . . GISAID Isolate EPI_ISL_77396
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 6T [H5N1],
. . . . . . . . syn22L (TTg) [H5N1],
. . . . . . . . 81I [avH1N1farm],
. . . . . . . . 105N [H5N1],
. . . . . . . . syn444S (TCt))

. . . . SingaporeON1138_P1_2009_07_13 (
. . . . . . . . A/Singapore/ON1138/2009
. . . . . . . . UltraAmbiguity Neuraminidase
. . . . . . . . GISAID NA EPI213437
. . . . . . . . GISAID Isolate EPI_ISL_61427
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . NA Truncated before aa6,
. . . . . . . . 296R (aGG) mix wt,
. . . . . . . . 296R (cGG) mix wt,
. . . . . . . . 296G (gGG) mix wt)

. . . . Pennsylvania08_C1_31M_2009_05_02 (
. . . . . . . . A/Pennsylvania/08/2009
. . . . . . . . GISAID NA EPI184376
. . . . . . . . GISAID Isolate EPI_ISL_31576
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . 95G,
. . . . . . . . 106V,
. . . . . . . . 248N)

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pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-11-01-01_21_33_806820 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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