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.

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