2013-11-07

Brazil 2013: pH1N1 Extreme Variant and Infant Vaccine Escape

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 : 2013-11-07
Last Update : 2013-12-17

Brazil: pH1N1 Extreme Variant & Infant Vaccine Escape
Map - Active and Detailed
Brazil 2013-11-01: Features by SubClade
Clinical and Genetic Features
9 HA Sequences

Between 2013-10-31 and 2013-11-01, the Instituto Adolfo Lutz of Brazil did the Northern Hemisphere a great service by releasing nine pH1N1 Hemagglutinin sequences at GISAID sampled during 2013 (July to October) and covering the Federal District, Mato Grosso and Sao Paulo. No Neuraminidase segments were released.

Vaccine Escape Diversity
TypeObservationCount
 PhenoTypic Vaccinated 201303
 GenoTypic VxX 225G01

We applaud the researchers' precision and detail in annotating these very important sentinels to the Northern Hemisphere season for discussion alongside their deposit earlier this month of one Vaccine Escape in an adult.  Attention to the specific geography of each case is much appreciated in this age of woefully inadequate public health management of human Influenza investigations.

Sequences for three infant patients were notated and three patients were described as having been vaccinated in 2013, including two of the infants.  HA 225G GenoTypic Vaccine Escape is noted on a RibeiraoPreto case [EPI484749] that also carries the rare HA 263S (GoF·E), a homolog to Emergent H7N9.  The infant Vaccine Escape case from Sorocaba [EPI484739] is instructive with an aggregation of two very dangerous genetic revisions HA 46R (GoF·E) and HA 190G (GoF·E).

Receptor Binding Variance
RevisionCount
 HA 190G01
 HA 225G01

The HA segments on deposit indicate an aggressive acquisition strategy from avian influences including Emergent H7N9.  The most recent sequence, a fragment from Moji Das Cruzes in mid-October [EPI484751], demonstrates the tendency with extreme variance from amino acid positions 175 to 188, generating not only novelty in the pH1N1 reservoir, but also novelty across known Influenza serotypes.  Markers from earlier pandemic death waves are evident alongside new revisions homologous to Emergent H7N9 (HA 187S).

The infant from Jaboticabal [EPI484748] carried a Clade2:188T background with HA 142D (GoF·E), a value and position associated with mishap and malady in pH1N1. Our 2011 discussion on HA 142V, 100% Case Fatality Rate on pH1N1 Clade2 Lineage (Deposit Report), continues to hold true when HA 142V is found with NA syn204A.  This deposit's rare HA 142D variation appears to be paired for the first time in the pH1N1 reservoir with a HA syn141H (CAc), suggesting an origin of the two revisions from H5N1 with a second base donation to form HA 142D (GaT) from the H5N1 wild type Glutamine (CAG) at aa142.  The HA 142D was also seen on Wisconsin28_55M_2011_12_01, a swine-like human H1N1 variant case.

Cross SeroType Analytics
HA Set Polymorphic Homology
SeroTypeCountPercent
 avH1N14964%
 avH1N1farm3749%
 H6N13546%
 H5N13242%
 H7N72837%
 H9N22634%
 zH3N22533%
 H132128%
 H10N71621%

pH1N1υ involvement is evident in this deposit with homology to 16% of the distinct HA polymorphisms. HA syn31H (CAt) is noted at Cuiaba (36 year old male) [EPI484750] and at the Federal District (80 year old female) [EPI484747].  Eight of the nine sequences in this deposit, including these two, have adopted the Upsilon HA 259T.

This small set of Hemagglutinin sequences provides an early look at the viral reservoir and acquisition patterns as the Northern Hemisphere winter arrives.  The increased genetic variance in children and women of childbearing age is an area that merits additional research.

Isolate Metrics
Calendar 2013
Sample
Month		Count
 October 03
 September 03
 August 01
 July 02
Cladistics
CladeNameCount
 Clade2:188T07
 CrossClade:
  188T_208K		01
 UnCladed01

HA Polymorphisms

. . . . BrazilSaoPauloMojiDasCruzes78453_34M_2013_10_14_s (
. . . . . . . . A/Sao Paulo/78453/2013
. . . . . . . . H7N9 Correlation HA 187S
. . . . . . . . Extreme Variance HA aa175 to aa188
. . . . . . . . 5’ Truncated, Potential Primer MisMatch
. . . . . . . . 3’ from Widely Circulating Clade 2: 188T
. . . . . . . . Off-Clade
. . . . . . . . GISAID HA EPI484751
. . . . . . . . GISAID Isolate EPI_ISL_149735
. . . . . . . . 29 Polymorphisms (17 Amino and 12 Silent)
. . . . . . . . HA Truncated before aa159,
. . . . . . . . 166Q,
. . . . . . . . syn168Y (TAt) [pH1N1 Fatalities and HA 225G / 225N
. . . . . . . . . . . . . . . . . . . . . . . . . . Ukraine FlashFire 2009,
. . . . . . . . . . . . . . . . . . . . . . . . . . Russia],
. . . . . . . . . . . . . . . . . . . [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . . [H7N7 Rare: Sea Mammal],
. . . . . . . . . . . . . . . . . . . [H7N3 Avian
. . . . . . . . . . . . . . . . . . . . . . . . . . including US Anser 2010],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian],
. . . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . . [H1N1 Human 2008 wt],
. . . . . . . . 169V [avH1N1farm],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . . . . . [1918],
. . . . . . . . 175D [H5N1 wt],
. . . . . . . . . . . . [H7N7 Human Fatality LookAsideu],
. . . . . . . . . . . . [H7N9 Avian LookAsideu],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [H13N2],
. . . . . . . . 176I [H9N2],
. . . . . . . . 178L,
. . . . . . . . syn179L (CTg),
. . . . . . . . 180R,
. . . . . . . . 181V [H7N9 Avian LookAsided],
. . . . . . . . . . . . [zH3N2 LookAsided],
. . . . . . . . 182F,
. . . . . . . . 183L [H13N2 LookAsideu],
. . . . . . . . 184Q [H9N2],
. . . . . . . . syn185P (CCt),
. . . . . . . . 187S (tCc) [Emergent H7N9 wild type:
. . . . . . . . . . . . . . . . . . . . . HA 187S / 196S (TCA)],
. . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . 188R [avH1N1 LookAsided],
. . . . . . . . . . . . [H6N1 LookAsided],
. . . . . . . . . . . . [zH3N2 LookAsided],
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn346G (GGa) [pH1N1 Upsilon],
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn383N (AAc),
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . BrazilSaoPauloRibeiraoPreto630359_44M_2013_10_05_VxX_s (
. . . . . . . . A/Sao Paulo/6-30359/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . H7N9 Correlation HA 263S
. . . . . . . . Treatment by Oseltamivir
. . . . . . . . GISAID HA EPI484749
. . . . . . . . GISAID Isolate EPI_ISL_149733
. . . . . . . . 24 Polymorphisms (10 Amino and 14 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc) [H5N1],
. . . . . . . . syn156K (AAg),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn236L (tTA),
. . . . . . . . syn237V (GTg),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 263S [Emergent H7N9 Amino wt],
. . . . . . . . . . . . [pH1N1 Rare: 7 Cases over 9 Sequences (map),
. . . . . . . . . . . . . . . . . . Ukraine5794_C2M1_18F_2013_02_20
. . . . . . . . . . . . . . . . . . . . . . .  with HA 227G and NA 222D,
. . . . . . . . . . . . . . . . . . SingaporeGP1112_C2_9M_2010_04_06
. . . . . . . . . . . . . . . . . . . . . . .  with HA 208K and NA 257K,
. . . . . . . . . . . . . . . . . . SpainLaRiojaRR6490_15F_2009_11_03
. . . . . . . . . . . . . . . . . . . . . . .  with HA 291I and NA 393V,
. . . . . . . . . . . . . . . . . . US Air Force 2009],
. . . . . . . . . . . . [H7N7 Human Fatality Amino wt],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn513I (ATc),
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . BrazilDistritoFederalBrasilia78502_80F_2013_10_03_s (
. . . . . . . . A/Distrito Federal/78502/2013
. . . . . . . . Treatment by Oseltamivir
. . . . . . . . GISAID HA EPI484747
. . . . . . . . GISAID Isolate EPI_ISL_149731
. . . . . . . . 24 Polymorphisms (9 Amino and 15 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . #2Y,
. . . . . . . . syn31H (CAt) [pH1N1 Upsilon
 . . . . . . . . . . . . . . . . . . . . . Fatalities:
 . . . . . . . . . . . . . . . . . . . . . . . . . . US Child (2M),
 . . . . . . . . . . . . . . . . . . . . . . . . . . Mexico (29M),
 . . . . . . . . . . . . . . . . . . . . . . . . . . Ecuador (35F),
 . . . . . . . . . . . . . . . . . . . . . Hospitalised:
 . . . . . . . . . . . . . . . . . . . . . . . . . . Ecuador (34M, 51M),
 . . . . . . . . . . . . . . . . . . . . . TamiFlu Resistance: US],
. . . . . . . . . . . . . . . . . . [H5N1 China Fatality 2005 (35M)],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Child 2009 (13M)],
. . . . . . . . . . . . . . . . . . [WSN, WSZ with HA 159D],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc) [H5N1],
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . syn265G (GGg),
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn458N (AAt),
. . . . . . . . syn477T (ACt),
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . BrazilSaoPauloJaboticabal630177_1M_2013_09_30_s (
. . . . . . . . A/Sao Paulo/6-30177/2013
. . . . . . . . Treatment by Oseltamivir
. . . . . . . . GISAID HA EPI484748
. . . . . . . . GISAID Isolate EPI_ISL_149732
. . . . . . . . 27 Polymorphisms (12 Amino and 15 Silent)
. . . . . . . . #1T,
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 115K [pH1N1 with HA 230I,
. . . . . . . . . . . . . SingaporeKK376_C2_14F_2010_06_07
. . . . . . . . . . . . . . . . . . . . . . . . . with HA 142D, 377K, syn537S (AGc)],
. . . . . . . . . . . . [H7N7 Equine: Host Transition],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . syn141H (CAc) [H5N1],
. . . . . . . . 142D [pH1N1 Rare: 47 Cases over 51 Sequences (map),
. . . . . . . . . . . . . JapanNagasakiHA105_M_13F_2010_01_12
. . . . . . . . . . . . . . . . . . . . . . . . . with HA 190G],
. . . . . . . . . . . . . [Propensity to Children:
. . . . . . . . . . . . . . . . . . 52% - Age 17 or Under],
. . . . . . . . . . . . . [Co-location pH1N1υ Polymorphisms (15)],
. . . . . . . . . . . . . [Co-location pH1N1 VxX indicators
. . . . . . . . . . . . . . . . . . . . . HA 158E mix, 159D mix],
. . . . . . . . . . . . . [Co-location pH1N1 HA 166Q],
. . . . . . . . . . . . . [Co-location pH1N1 HA 189D, 189T_xL, 190G],
. . . . . . . . . . . . . [Co-location pH1N1 RBS 225G (2), 226R, 233H],
. . . . . . . . . . . . . [Co-location early pH1N1 HA 237I],
. . . . . . . . . . . . . [Co-location pH1N1 Isolated from Blood (Serum)],
. . . . . . . . . . . . . [Studied with pH1N1 Severe and Fatal cases],
. . . . . . . . . . . . . [Wisconsin28_55M_2011_12_01
. . . . . . . . . . . . . . . . swine-like human H1N1 variant case
. . . . . . . . . . . . . . . . . . with pH1N1 PA & M gene segments],
. . . . . . . . . . . . . [H5N1 2nd Base Donor 142Q (CAG)],
. . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . [H13      LookAsideu],
. . . . . . . . . . . . . [zH3N2 LookAsided2],
. . . . . . . . . . . . . [zH6N1 LookAsided2],
. . . . . . . . syn156K (AAg),
. . . . . . . . 166Q [avH1N1
. . . . . . . . . . . . . . . with HA #1T, syn34N (AAt), syn77S (AGt),
. . . . . . . . . . . . . . . . . . . syn102E (GAa), syn156K (AAg),
. . . . . . . . . . . . . . . . . . . 188T, syn258F (TTt), syn285P (CCt), syn306C (TGc),
. . . . . . . . . . . . . . . . . . . 324I, syn333F (TTc), syn372Q (CAa), syn396V (GTg),
. . . . . . . . . . . . . . . . . . . syn465N (AAt)],
. . . . . . . . . . . . .[Virginia13_M1C1_46F_2012_08_21
. . . . . . . . . . . . . . . . . . . . . . . . with HA 142D, 188T, syn223V (GTa),
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn338G (GGc), 377K, 454N],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn223V (GTa),
. . . . . . . . syn236L (tTA),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . syn285P (CCt),
. . . . . . . . 286E,
. . . . . . . . syn306C (TGc),
. . . . . . . . syn308K (AAg),
. . . . . . . . 324I [pH1N1 with HA 230I],
. . . . . . . . . . . . [Wilson-Smith],
. . . . . . . . . . . . [1918],
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I]
. . . . . . . . . . . . . . . . . . [1918])

. . . . BrazilSaoPauloAltoAlegre1314856_43M_2013_09_21_s (
. . . . . . . . A/Sao Paulo/13-14856
. . . . . . . . Treatment by Oseltamivir
. . . . . . . . GISAID HA EPI484746
. . . . . . . . GISAID Isolate EPI_ISL_149730
. . . . . . . . 28 Polymorphisms (10 Amino and 18 Silent)
. . . . . . . . #9V,
. . . . . . . . syn42G (GGt),
. . . . . . . . syn58C (TGc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn125S (TCg),
. . . . . . . . syn141H (CAc) [H5N1],
. . . . . . . . syn165S (AGt),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn294P (CCc),
. . . . . . . . syn308K (AAg),
. . . . . . . . syn318A (GCa),
. . . . . . . . 326F [pH1N1 Rare: Count 12,
. . . . . . . . . . . . . . Re-Emergent,
. . . . . . . . . . . . . . Last Noted 2011],
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn383N (AAc),
. . . . . . . . syn396V (GTg),
. . . . . . . . syn426A (GCt),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . BrazilMatoGrossoCuiaba73766_36M_2013_09_11_s (
. . . . . . . . A/Mato Grosso/73766/2013
. . . . . . . . GISAID HA EPI484750
. . . . . . . . GISAID Isolate EPI_ISL_149734
. . . . . . . . 23 Polymorphisms (8 Amino and 15 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn31H (CAt) [pH1N1 Upsilon
 . . . . . . . . . . . . . . . . . . . . . Fatalities:
 . . . . . . . . . . . . . . . . . . . . . . . . . . US Child (2M),
 . . . . . . . . . . . . . . . . . . . . . . . . . . Mexico (29M),
 . . . . . . . . . . . . . . . . . . . . . . . . . . Ecuador (35F),
 . . . . . . . . . . . . . . . . . . . . . Hospitalised:
 . . . . . . . . . . . . . . . . . . . . . . . . . . Ecuador (34M, 51M),
 . . . . . . . . . . . . . . . . . . . . . TamiFlu Resistance: US],
. . . . . . . . . . . . . . . . . . [H5N1 China Fatality 2005 (35M)],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Child 2009 (13M)],
. . . . . . . . . . . . . . . . . . [WSN, WSZ with HA 159D],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc) [H5N1],
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . syn184H (CAc),
. . . . . . . . 188T,
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . syn265G (GGg),
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn458N (AAt),
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . BrazilSaoPauloGuariba628500_6mM_2013_08_05_VxX_s (
. . . . . . . . A/Sao Paulo/6-28500/2013
. . . . . . . . Vaccinated 2013
. . . . . . . . GISAID HA EPI484744
. . . . . . . . GISAID Isolate EPI_ISL_149728
. . . . . . . . 23 Polymorphisms (9 Amino and 14 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn122K (AAa),
. . . . . . . . syn141H (CAc) [H5N1],
. . . . . . . . 155I [H5N1],
. . . . . . . . . . . [avH1N1],
. . . . . . . . syn156K (AAg),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn236L (tTA),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn382V (GTg),
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . BrazilSaoPauloBauru216961_29M_2013_07_10_VxX_s (
. . . . . . . . A/Sao Paulo/2-16961/2013
. . . . . . . . Vaccinated 2013
. . . . . . . . GISAID HA EPI484740
. . . . . . . . GISAID Isolate EPI_ISL_149725
. . . . . . . . 21 Polymorphisms (9 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc) [H5N1],
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . 326F [pH1N1 Rare: Count 12,
. . . . . . . . . . . . . . Re-Emergent,
. . . . . . . . . . . . . . Last Noted 2011],
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn458N (AAt),
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . BrazilSaoPauloSorocaba1117706_1F_2013_07_01_VxX_s (
. . . . . . . . A/Sao Paulo/11-17706/2013
. . . . . . . . Vaccinated 2013
. . . . . . . . H7N9 Correlation HA 119M
. . . . . . . . CrossClade 188T and 208K
. . . . . . . . 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,
. . . . . . . . . . . . . . Fatality 2009,
. . . . . . . . . . . . . . Hospitalisation 2009,
. . . . . . . . . . . . . . Vaccine Escape: Count 03,
. . . . . . . . . . . . . . TamiFlu Resistance,
. . . . . . . . . . . . . . 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 (map),
. . . . . . . . . . . . . . . . . . Fatalities,
. . . . . . . . . . . . . . . . . . Vaccine Escapes,
. . . . . . . . . . . . . . . . . . Infants],
. . . . . . . . syn195Y (TAc),
. . . . . . . . 208K,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . 289V [pH1N1 with HA 230I,
. . . . . . . . . . . . Ukraine123_2010_02_14_xL
. . . . . . . . . . . . . . . . with HA 186P, 208K, 230I,
. . . . . . . . . . . . UKGlascow_SC10_2009_06
. . . . . . . . . . . . . . . . with HA 225G],
. . . . . . . . . . . . [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])

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pH1N1 Influenza Hemagglutinin Segments elucidated at 2013-11-01-14_54_50_257919 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

Publication Copyright 2007-2013 GeneWurx.com, All Rights Reserved.

Posted by at

2013-11-06

HA 263S: Emergent H7N9 & pH1N1 Receptor Binding Dynamic

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 : 2013-11-25
Gain of Function Empiriks
by
Polymorphism
pH1N1 HA 263S

Emergent H7N9 & pH1N1 Receptor Binding Dynamic: HA 263S
Map - Active and Detailed
8 Cases over 10 Sequences

Receptor Binding Site Variance
pH1N1
100% Receptor Binding Site Revision for 2013
Sample
Date		NameRBS
Revision		ID
 2013-10-05  BrazilSaoPauloRibeiraoPreto630359_44M_VxX_s HA 225G EPI484749 
 2013-02-20  Ukraine5794_C2M1_18F HA 227G EPI462073 

Cross SeroType Analytics
HA Set Polymorphic Homology
SeroTypeCountPercent
 H5N13049%
 H7N71931%
Origin-Seeking HA 263S
SeroType
 Emergent H7N9 Amino wild type
 H7N7 Human Fatality Amino
 H7N7 Amino wild type
 avH1N1 Amino wild type

Isolate Metrics
Calendar
Sample
Year		Count
 201302
 201200
 201101
 201001
 200906
Age Dynamic
ObservationPer
Cent
 Child Aged 18 or Under60%
Cladistics
CladeNameCount
 UnCladed07
 Clade2:188T03

HA Polymorphisms

. . . . BrazilSaoPauloRibeiraoPreto630359_44M_2013_10_05_VxX_s (
. . . . . . . . A/Sao Paulo/6-30359/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . Treatment by Oseltamivir
. . . . . . . . Deposit Report
. . . . . . . . GISAID HA EPI484749
. . . . . . . . GISAID Isolate EPI_ISL_149733
. . . . . . . . 24 Polymorphisms (10 Amino and 14 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . syn156K (AAg),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn236L (tTA),
. . . . . . . . syn237V (GTg),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 263S [pH1N1 Rare: Count 09 on 07 Cases,
. . . . . . . . . . . . . . . . . . Ukraine5794_C2M1_18F_2013_02_20
. . . . . . . . . . . . . . . . . . . . . . .  with HA 227G and NA 222D,
. . . . . . . . . . . . . . . . . . US Air Force 2009],
. . . . . . . . . . . . [Emergent H7N9 Amino wt],
. . . . . . . . . . . . [H7N7 Human Fatality Amino wt],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn513I (ATc),
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . Ukraine5794_C2M1_18F_2013_02_20 (
. . . . . . . . A/Ukraine/5794/2013
. . . . . . . . Receptor Binding Variance HA 227G
. . . . . . . . GISAID HA EPI462073
. . . . . . . . GISAID Isolate EPI_ISL_144074
. . . . . . . . 25 Polymorphisms (11 Amino and 14 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . 87G,
. . . . . . . . syn122K (AAa),
. . . . . . . . syn127P (CCa),
. . . . . . . . 146G,
. . . . . . . . 166I,
. . . . . . . . syn171D (GAc),
. . . . . . . . 188T,
. . . . . . . . syn189A (GCa),
. . . . . . . . 200T,
. . . . . . . . syn224R (AGa),
. . . . . . . . 227G [FranceLorraine1176_50x_2011_02_23_TmX],
. . . . . . . . . . . . [H5N1],
. . . . . . . . syn258F (TTt),
. . . . . . . . 263S,
. . . . . . . . syn275V (GTt),
. . . . . . . . syn337A (GCt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn488D (GAt),
. . . . . . . . 523A,
. . . . . . . . syn524A (GCt),
. . . . . . . . syn538F (TTt))

. . . . JapanSuita99_2011_01 (
. . . . . . . . A/Suita/99/2011
. . . . . . . . GISAID HA EPI416353
. . . . . . . . GISAID Isolate EPI_ISL_134103
. . . . . . . . 13 Polymorphisms (7 Amino and 6 Silent)
. . . . . . . . HA Truncated before aa2,
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 71D,
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 263S,
. . . . . . . . syn338G (GGc),
. . . . . . . . syn360Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn445V (GTt),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . HA Truncated after aa535)

. . . . SingaporeGP1112_C2_9M_2010_04_06 (
. . . . . . . . A/Singapore/GP1112/2010
. . . . . . . . GISAID HA EPI385245
. . . . . . . . GISAID Isolate EPI_ISL_124666
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn#9L (tTA),
. . . . . . . . syn53L (cTG),
. . . . . . . . syn107Q (CAg),
. . . . . . . . 145R,
. . . . . . . . 208K,
. . . . . . . . 263S)

. . . . UKEnglandLondon863_C1_E275_2009_11_24 (
. . . . . . . . A/England/863/2009
. . . . . . . . GISAID HA EPI336251
. . . . . . . . GISAID Isolate EPI_ISL_96275
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn#2F (TTc),
. . . . . . . . 35I,
. . . . . . . . syn53L (cTG),
. . . . . . . . 263S,
. . . . . . . . syn490P (CCc))

. . . . UKEnglandLondon863_C1_2009_11_24 (
. . . . . . . . A/ENG/863/2009
. . . . . . . . GISAID HA EPI276501
. . . . . . . . GISAID Isolate EPI_ISL_78380
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn#2F (TTc),
. . . . . . . . 35I,
. . . . . . . . syn53L (cTG),
. . . . . . . . 263S,
. . . . . . . . syn490P (CCc))

. . . . SpainLaRiojaRR6490_15F_2009_11_03 (
. . . . . . . . A/LaRioja/RR6490/2009
. . . . . . . . GISAID HA EPI304878
. . . . . . . . GISAID Isolate EPI_ISL_86857
. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa20,
. . . . . . . . 263S,
. . . . . . . . 291I [Emergent H7N9 LookAsideu]
. . . . . . . . HA Truncated after aa335)

. . . . MarylandAF2452_PMK1_38M_2009_10_27 (
. . . . . . . . A/Maryland/AF2452/2009
. . . . . . . . GISAID HA EPI278242
. . . . . . . . GISAID Isolate EPI_ISL_79000
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn137A (GCt),
. . . . . . . . 263S,
. . . . . . . . syn270I (ATc),
. . . . . . . . 377K,
. . . . . . . . HA Truncated after aa386)

. . . . UKEnglandLambeth1081_C1_E403_2009_10_16 (
. . . . . . . . A/England/1081/2009
. . . . . . . . GISAID HA EPI336379
. . . . . . . . GISAID Isolate EPI_ISL_96403
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 24K [zH3N2],
. . . . . . . . 35I,
. . . . . . . . 263S,
. . . . . . . . syn490P (CCc))

. . . . UKEnglandLambeth1081_C1_2009_10_16 (
. . . . . . . . A/ENG/1081/2009
. . . . . . . . GISAID HA EPI276392
. . . . . . . . GISAID Isolate EPI_ISL_78271
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 24K [zH3N2],
. . . . . . . . 35I,
. . . . . . . . 263S,
. . . . . . . . syn490P (CCc))

NA Polymorphisms

. . . . Ukraine5794_C2M1_18F_2013_02_20 (
. . . . . . . . A/Ukraine/5794/2013
. . . . . . . . GISAID NA EPI462074
. . . . . . . . GISAID Isolate EPI_ISL_144074
. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)
. . . . . . . . 40V,
. . . . . . . . 44S,
. . . . . . . . 76V,
. . . . . . . . syn77G (GGg),
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . 222D [Youth Age Dynamic],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . 416N,
. . . . . . . . syn426L (tTA),
. . . . . . . . syn439S (AGt))

. . . . SingaporeGP1112_C2_9M_2010_04_06 (
. . . . . . . . A/Singapore/GP1112/2010
. . . . . . . . GISAID NA EPI385247
. . . . . . . . GISAID Isolate EPI_ISL_124666
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . syn114V (GTa),
. . . . . . . . 257K,
. . . . . . . . syn323G (GGg))

. . . . SpainLaRiojaRR6490_15F_2009_11_03 (
. . . . . . . . A/LaRioja/RR6490/2009
. . . . . . . . GISAID NA EPI305244
. . . . . . . . GISAID Isolate EPI_ISL_86857
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . NA Truncated before aa198,
. . . . . . . . syn369N (AAt),
. . . . . . . . 393V,
. . . . . . . . NA Truncated after aa418)

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GeneWurx.com


pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-11-04-16_34_55_129670 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

Publication Copyright 2007-2013 GeneWurx.com  · All Rights Reserved.

Posted by at

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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