High-CFR Clade1.Upsilon Markers Cross to pH1N1.Clade2 on 70% of Spain's Recent pH1N1 Hospitalisations

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 PDF for completeness in citation.

Publish Date : 2013-03-04
Last Update : 2013-03-08

The most widespread Pandemic Influenza H1N1 clade is actively inheriting virulence factors from the most dangerous sub-clade (Upsilon with a minimum 5% Fatality Rate).  Friday’s genetic sequences from Spain confirmed our predictions of further spread from the highest fatality sub-clade onto the widest circulating strain.  This batch of sequences also shows significant inclusion of antigen donations at the nucleotide level from recent H5N1 Avian Influenza.

Spain’s 2013-03-01 GISAID pH1N1 deposit of 17 HA Fragments and 3 NA Fragments from 2013 cases carries 258 polymorphisms from the pH1N1 Origin Reference.  61 Distinct Polymorphisms appear among the HA fragments and 15 across the NA fragments.  All sequences are on a Clade2:188T background.

Five of the seven severe cases (70%) involve Clade Crossing with Clade1.Upsilon, (pH1N1_υ).  Four of the seven severe cases demonstrate antigenic variation.  Twelve of the seventeen Clade2:188T HA fragments carry pH1N1_υ polymorphisms, a significant rate of Clade Crossing.  60% of the NA Polymorphisms from this deposit are found within the pH1N1_υ NA subset.

• Hemagglutinin – Average 13.0 polymorphisms Per Fragment
• Neuraminidase – Average 12.3 polymorphisms Per Fragment

Hypermorphic behaviour with a tendency toward homology with H5N1 and Avian H1N1 continues to be present in the development toward a future state of Pandemic H1N1 Omega (pH1N1_Ω) as demonstrated in SpainCatalonia5925S_29F_2013_02_05 [EPI427227] from a 29 year old female with 36 combined polymorphisms (22 HA / 14 NA) though both gene segments are fragments.

Please refer to the GeneWurx PolyPlus PhyloGenetic tree for a rapid assessment of details concerning sequence relationships, passage history, age, gender, clinical outcome and individual polymorphisms (amino and 'silent').

The SpainGalicia207_M_6mF_2013_01_25_s [EPI427246] disease that hospitalised a 6 month old baby girl at the end of January  carries an HA 166N change that we have predicted to translate onto a lower branch of the tree that is annotated with ‘75A, 176I, 189T’.  Further severity is expected in babies and young children infected with the predicted strain.

HA and NA Polymorphisms by Sequence

. . . . SpainCatalonia2076930NS_59M_2013_02_18 (

. . . . . . . . GISAID HA EPI427229

. . . . . . . . 18 Polymorphisms (8 Amino and 10 Silent)

. . . . . . . . HA Truncated before aa11,

. . . . . . . . syn39K (AAa),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . 144T [pH1N1_υ],

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa) [pH1N1_υ],

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . syn372Q (CAa) [pH1N1_υ],

. . . . . . . . 377K,

. . . . . . . . syn396V (GTg),

. . . . . . . . syn448L (TTg),

. . . . . . . . 454N,

. . . . . . . . 502K [pH1N1_υ],

. . . . . . . . HA Truncated after aa541)

. . . . SpainCatalonia2076930NS_59M_2013_02_18 (

. . . . . . . . GISAID NA EPI427230

. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)

. . . . . . . . NA Truncated before aa35,

. . . . . . . . 44S,

. . . . . . . . 52N,

. . . . . . . . 106V,

. . . . . . . . syn176S (TCg),

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa),

. . . . . . . . syn209N (AAt),

. . . . . . . . syn240T (ACc),

. . . . . . . . 241I,

. . . . . . . . 369K,

. . . . . . . . syn377P (CCa),

. . . . . . . . syn378N (AAt),

. . . . . . . . NA Truncated after aa465)

. . . . SpainMadrid196_70F_2013_02_05_s (

. . . . . . . . GISAID HA EPI427247

. . . . . . . . 12 Polymorphisms (4 Amino and 8 Silent)

. . . . . . . . HA Truncated before aa#3,

. . . . . . . . syn16T (ACg),

. . . . . . . . syn55L (TTa) [pH1N1_υ],

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn162P (CCt),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa342)

. . . . SpainCatalonia5925S_29F_2013_02_05 (

. . . . . . . . GISAID HA EPI427227

. . . . . . . . 22 Polymorphisms (8 Amino and 14 Silent)

. . . . . . . . HA Truncated before aa11,

. . . . . . . . syn39K (AAa) [avH7, avH10],

. . . . . . . . syn77S (AGt) [avH1N1, H5N1 syn],

. . . . . . . . 100N [avH1N1, H5N1],

. . . . . . . . syn158G (GGg) [pH1N1_υ],

. . . . . . . . syn179L (CTg) [H5N1],

. . . . . . . . 188T [avH1N1, H5N1],

. . . . . . . . syn215P (CCa) [avH1N1, H5N1],

. . . . . . . . 237I [avH1N1, H5N1 LookAside_upstream wt, H10],

. . . . . . . . syn239P (CCa) [pH1N1_υ],

. . . . . . . . 286E [H6N1],

. . . . . . . . syn308K (AAg) [avH1N1, H5N1],

. . . . . . . . syn333F (TTc) [avH1N1, H5N1],

. . . . . . . . syn337A (GCt) [pH1N1_υ syn],

. . . . . . . . syn338G (GGc) [avH1N1, H5N1],

. . . . . . . . syn372Q (CAa) [pH1N1_υ],

. . . . . . . . 377K [pH1N1_υ],

. . . . . . . . syn396V (GTg) [avH1N1, H5N1 syn],

. . . . . . . . syn417G (GGg) [avH1N1, H5N1],

. . . . . . . . syn448L (TTg) [pH1N1_υ],

. . . . . . . . 454N [pH1N1_υ],

. . . . . . . . 477M [pH1N1 avian],

. . . . . . . . 502K [pH1N1_υ],

. . . . . . . . HA Truncated after aa508)

. . . . SpainCatalonia5925S_29F_2013_02_05 (

. . . . . . . . GISAID NA EPI427228

. . . . . . . . 14 Polymorphisms (5 Amino and 9 Silent)

. . . . . . . . NA Truncated before aa35,

. . . . . . . . 44S [pH1N1_υ],

. . . . . . . . 106V [pH1N1_υ],

. . . . . . . . syn176S (TCg) [pH1N1_υ],

. . . . . . . . 200S [avH1N1, H5N1],

. . . . . . . . syn205V (GTa)  [avH1N1, H5N1],

. . . . . . . . syn209N (AAt) [pH1N1_υ],

. . . . . . . . syn228E (GAa)  [avH1N1, H5N1],

. . . . . . . . syn240T (ACc) [pH1N1_υ],

. . . . . . . . 241I [pH1N1_υ],

. . . . . . . . syn264V (GTt) [avH1N1, H5N1],

. . . . . . . . 369K [pH1N1_υ],

. . . . . . . . syn377P (CCa) [pH1N1_υ],

. . . . . . . . syn378N (AAt) [avH1N1, H5N1],

. . . . . . . . syn393I (ATt) [pH1N1_υ],

. . . . . . . . NA Truncated after aa462)

. . . . SpainNavarra193_15F_2013_02_04 (

. . . . . . . . GISAID HA EPI427248

. . . . . . . . 13 Polymorphisms (7 Amino and 6 Silent)

. . . . . . . . HA Truncated before aa#10,

. . . . . . . . syn#4Y (TAc),

. . . . . . . . 75A,

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . 176I,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 189T [pH1N1_υ],

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa345)

. . . . SpainMurcia165_39F_2013_01_30_s (

. . . . . . . . GISAID HA EPI427252

. . . . . . . . 13 Polymorphisms (8 Amino and 5 Silent)

. . . . . . . . HA Truncated before aa27,

. . . . . . . . 75A,

. . . . . . . . syn77S (AGt),

. . . . . . . . 89N,

. . . . . . . . 100N,

. . . . . . . . 176I,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 189T [pH1N1_υ],

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa344)

. . . . SpainMurcia164_80F_2013_01_30_s (

. . . . . . . . GISAID HA EPI427242

. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)

. . . . . . . . HA Truncated before aa3,

. . . . . . . . 75A,

. . . . . . . . syn77S (AGt),

. . . . . . . . 89N,

. . . . . . . . 100N,

. . . . . . . . 132S,

. . . . . . . . 176I,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 189T [pH1N1_υ],

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa346)

. . . . SpainPaisVasco187_M_42F_2013_01_29 (

. . . . . . . . GISAID HA EPI427251

. . . . . . . . 12 Polymorphisms (4 Amino and 8 Silent)

. . . . . . . . HA Truncated before aa#9,

. . . . . . . . syn#4Y (TAc),

. . . . . . . . syn39K (AAa),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa) [pH1N1_υ],

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa344)

. . . . SpainPaisVasco185_M_38M_2013_01_29 (

. . . . . . . . GISAID HA EPI427250

. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)

. . . . . . . . HA Truncated before aa1,

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn140P (CCc),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa344)

. . . . SpainGalicia208_5M_2013_01_29_s (

. . . . . . . . GISAID HA EPI427245

. . . . . . . . 12 Polymorphisms (4 Amino and 8 Silent)

. . . . . . . . HA Truncated before aa27,

. . . . . . . . syn39K (AAa),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa) [pH1N1_υ],

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn329S (TCc) [pH1N1_υ],

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa346)

. . . . SpainBaleares168_58M_2013_01_29_s (

. . . . . . . . GISAID HA EPI427244

. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)

. . . . . . . . HA Truncated before aa5,

. . . . . . . . syn16T (ACg),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn162P (CCt),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa346)

. . . . SpainPaisVasco184_M_4mM_2013_01_28 (

. . . . . . . . GISAID HA EPI427249

. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)

. . . . . . . . HA Truncated before aa1,

. . . . . . . . syn64I (ATa),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa344)

. . . . SpainGalicia207_M_6mF_2013_01_25_s (

. . . . . . . . GISAID HA EPI427246

. . . . . . . . 15 Polymorphisms (5 Amino and 10 Silent)

. . . . . . . . HA Truncated before aa#3,

. . . . . . . . syn34N (AAt),

. . . . . . . . syn53L (TTa),

. . . . . . . . syn56G (GGa),

. . . . . . . . 146G,

. . . . . . . . syn150N (AAc),

. . . . . . . . 166N,

. . . . . . . . 188T,

. . . . . . . . syn190D (GAt),

. . . . . . . . syn196Q (CAa),

. . . . . . . . 200T,

. . . . . . . . syn236L (CTg),

. . . . . . . . 274T,

. . . . . . . . syn293L (CTa),

. . . . . . . . syn309Y (TAc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa346)

. . . . SpainBaleares167_3M_2013_01_25 (

. . . . . . . . GISAID HA EPI427243

. . . . . . . . 12 Polymorphisms (4 Amino and 8 Silent)

. . . . . . . . HA Truncated before aa#3,

. . . . . . . . syn39K (AAa),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . syn212K (AAa),

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa) [pH1N1_υ],

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa344)

. . . . SpainBaleares167_3M_2013_01_25 (

. . . . . . . . GISAID NA EPI427285

. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)

. . . . . . . . 44S,

. . . . . . . . 106V,

. . . . . . . . syn176S (TCg),

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa),

. . . . . . . . syn209N (AAt),

. . . . . . . . syn240T (ACc),

. . . . . . . . 241I,

. . . . . . . . 369K,

. . . . . . . . syn377P (CCa),

. . . . . . . . syn378N (AAt),

. . . . . . . . NA Truncated after aa462)

. . . . SpainPaisVasco132_M_62F_2013_01_19_s (

. . . . . . . . GISAID HA EPI427241

. . . . . . . . 14 Polymorphisms (5 Amino and 9 Silent)

. . . . . . . . HA Truncated before aa6,

. . . . . . . . syn34N (AAt),

. . . . . . . . 87G,

. . . . . . . . syn104L (tTA) [pH1N1_υ syn],

. . . . . . . . syn122K (AAa),

. . . . . . . . syn127P (CCa),

. . . . . . . . 146G,

. . . . . . . . 166I,

. . . . . . . . syn171D (GAc),

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . syn258F (TTt),

. . . . . . . . syn275V (GTt) [pH1N1_υ],

. . . . . . . . syn337A (GCt) [pH1N1_υ syn],

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa342)

. . . . SpainPaisVasco138_M_3mM_2013_01_18 (

. . . . . . . . GISAID HA EPI427240

. . . . . . . . 14 Polymorphisms (5 Amino and 9 Silent)

. . . . . . . . HA Truncated before aa7,

. . . . . . . . syn34N (AAt),

. . . . . . . . 87G,

. . . . . . . . syn122K (AAa),

. . . . . . . . syn127P (CCa),

. . . . . . . . 146G,

. . . . . . . . 166I,

. . . . . . . . syn171D (GAc),

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . syn252V (GTa) [pH1N1_υ],

. . . . . . . . syn258F (TTt),

. . . . . . . . syn275V (GTt) [pH1N1_υ],

. . . . . . . . syn337A (GCt) [pH1N1_υ syn],

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa342)

. . . . SpainNavarra108_M_52F_2013_01_14 (

. . . . . . . . GISAID HA EPI427239

. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)

. . . . . . . . HA Truncated before aa#10,

. . . . . . . . syn#4Y (TAc),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn136T (ACa),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . HA Truncated after aa342)

. . . . SpainBaleares100_M_59F_2013_01_14 (

. . . . . . . . GISAID HA EPI427238

. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)

. . . . . . . . HA Truncated before aa2,

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 237I,

. . . . . . . . syn262R (AGg),

. . . . . . . . 286E,

. . . . . . . . 289L,

. . . . . . . . HA Truncated after aa296)

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pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-03-01-15_26_05_537900 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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Morocco Reports Hypermorphism on pH1N1 HA and NA Fragments

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

Last Update
2011-11-03

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

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

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

Zoonoses of Polymorphisms

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

Cladistics

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

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

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

Diversity

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

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

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

Hypermorphic Behaviour

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

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

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

Sequences

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Supporting Sequences

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

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

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

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Brasil Shows 94% Avian Zoonotic Potential on Diverse Early Pandemic Sequences

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

Last Update
2011-10-18

On 2011-08-30, a group of researchers from Instituto Adolfo Lutz Sao Paulo in Brasil, including Santos,C.L.S.; Oliveira,M.I.; Borborema,S.E.T.; Ferreira,J.L.P. and Paiva,T.M., deposited a large group of early Pandemic H1N1 sequences at GenBank and GISAID.  For this analysis, 7 HA sequences were selected for review due to their high affinity for polymorphisms homologous to Avian sequences.

The set of HA polymorphisms spans the gene segment.  23 distinct values are demonstrated.  Of the 35 total HA polymorphisms found across the 7 selected sequences, 33 trace to Avian Influenza A serotypes (H1N1, H3N8, H5N1 & H9N2).  The remaining 2 changes (HA 225N) are from mixed traces that resulted in HA 225G & 225N.  These non-Avian, Receptor Binding Site 225N values are wild-type, Human H3N2 homologies.  This early, large scale acquisition (94%) of disparate Avian polymorphisms across multiple backgrounds is suggestive that the basic Pandemic H1N1 background is related to Avian progenitors or is highly attractant to Avian genetic data upon co-infection.

Co-infection is known to produce mixed peaks on sequencing traces.  The mixed trace sequences in this selection carry H5N1 homology.  100% of the polymorphisms on BrasilSaoPaulo64519_2009_08_18 are mixed, as are the early changes on BrasilMatoGrossoDoSul64045_2009_08_13.  Each sequence carries recognised fatality markers.  Evidence supports the probability of H5N1 influence on the human carriers of the mixed trace sequences or on a progenitor animal that subsequently transported the H5N1 genetic material into proximity with the human subjects from Brasil.

. . . . BrasilSaoPaulo2227_2010_01_13 (
. . . . . . . . GISAID HA EPI335469
. . . . . . . . 6 Polymorphisms (1 Amino and 5 Silent)
. . . . . . . . HA Truncated before aa92,
. . . . . . . . syn301I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn338G (GGc) [H3N2 Avian, Canine, Feline],
. . . . . . . . . . . . . . . . . . [H3N8, H4, H5N1 Avian 2010, H6, sw],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [H3N2 Human & Avian wt],
. . . . . . . . . . . . . . . . . . [H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Preschool 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . . . [H6N2, H6N4],
. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],
. . . . . . . . syn366A (GCt) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 377K [H9N2 Avian and Human],
. . . . . . . . syn548C (TGc) [H1N1 Avian wt])

. . . . BrasilSaoPaulo91656_2009_10_23 (
. . . . . . . . GISAID HA EPI335471
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn354Y (TAc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn486T (ACc) [H3N8 Avian])

. . . . BrasilSaoPaulo89876_2009_10_19 (
. . . . . . . . GISAID HA EPI335473
. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)
. . . . . . . . syn68P (CCg) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn202V (GTc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn446K (AAa) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilSaoPaulo83218_2009_09_27 (
. . . . . . . . GISAID HA EPI335474
. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)
. . . . . . . . syn41N (AAt) [H5N1 Egypt Human 2007],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2008],
. . . . . . . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn140P (CCc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn356H (CAc) [H5N1 Human Egypt 2009],
. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn375I (ATc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn461K (AAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilSaoPaulo64519_2009_08_18 (
. . . . . . . . GISAID HA EPI335504
. . . . . . . . GenBank HA HQ595254
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 34D mix wt [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . syn53L (TTa) mix wt [H5N1 Human, Avian, Civet],
. . . . . . . . . . . . . . . . . . . . . . [H6N1 Avian],
. . . . . . . . . . . . . . . . . . . . . . [H2 Avian]
. . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 225G mix wt [pH1N1 Fatality Marker],
. . . . . . . . . . . . . . . . . [H5N1 Avian wt],
. . . . . . . . . . . . . . . . . [1918],
. . . . . . . . 225N mix wt [pH1N1 Fatality Marker],
. . . . . . . . syn413K (AAg) mix wt [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) mix wt [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 523A mix wt [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilMatoGrossoDoSul64045_2009_08_13 (
. . . . . . . . GISAID HA EPI335505
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 34D mix wt [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . 225G mix wt [pH1N1 Fatality Marker],
. . . . . . . . . . . . . . . . . [H5N1 Avian wt],
. . . . . . . . . . . . . . . . . [1918],
. . . . . . . . 225N mix wt [pH1N1 Fatality Marker],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . [H1N1 Avian])

. . . . BrasilSaoPaulo52142_2009_07_30 (
. . . . . . . . GISAID HA EPI335518
. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . [H1N1 Avian])

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Arizona 2011 on a Pandemic Background with an Observed 5% Case Fatality Rate

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

Last Update
2011-07-20

On 2011-06-21, the lead public health agency from the United States released 50 sequences at GISAID containing a subset from a heavily zoonotic sub-clade that is circulating across a worldwide geography in Americans and in individuals of at least 11 other nationalities.  Eight matched pairs (HA and NA segments) from the emergent sub-clade are found in this deposit.

This Pandemic H1N1 Upsilon Sub-Clade is termed as pH1N1_υ for reference brevity and encompasses the 230I-Permissive, 189T-Bearing Hydra that has emerged from January 2010 to April 2011 across 62 HA and 53 NA sequences defining a clinical subset of 58 cases, including fatalities, vaccine escape situations and TamiFlu resistance.  Across the HA segments (19 Fragments), 745 polymorphisms are found (93 distinct).  The NA is less volatile, but does lead other sub-clades with 251 polymorphisms spread over 68 distinct codons. 

Although complete clinical outcomes are not forthcoming, the Case Fatality Rate for pH1N1_υ cases remains at or above 5% for a number of reasons, including very high Zoonotic Potential scores indicating rapid acquisition of genetic material from animal reservoirs.  This sub-clade displays hypermorphic behaviour, carrying an average of 12 changes per HA and 4.7 per NA.  At this analysis, GeneWurx investigates the potential donor reservoirs for the late season 2011 sequence that bears the highest count of pH1N1_υ HA polymorphisms, Arizona02_43F_2011_03_08.  The HA polymorphism count of 19 (7 Amino and 12 Silent) and 6 for the NA (0 Amino and 6 Silent) ranks this sequence within the ultimate decile of cladded pH1N1 sequences.

Four HA revisions novel to pH1N1_υ demonstrate a continued genetic re-seeding though the base of this sub-clade is founded on a significant immune escape charge.  A triad of novelties (210N, syn334G, syn337A) are found individually and grouped on various animal reservoirs closely related to the change pattern for pH1N1_υ, H2N2 and H6N1.  The fourth novelty, 516V, appears within H2N2. The 210N and syn337A have recently appeared on pH1N1 Clade 2: 188T.

Sequences

Clade 1.Upsilon:
34D, 165N, 189T, syn213F, syn305K

. . . . Arizona02_43F_2011_03_08 (
. . . . . . . . Zoonotic Potential: 100%
. . . . . . . . GISAID HA EPI319994
. . . . . . . . 19 Polymorphisms (7 Amino and 12 Silent)
. . . . . . . . syn31H (CAt) [H2N2 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H2N3 with syn40H],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2009],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2009],
. . . . . . . . . . . . . . . . . [H5N1 Europe Avian 1999-2009
. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],
. . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2002-2008
. . . . . . . . . . . . . . . . . . . . with 34D, syn40H, syn42G],
. . . . . . . . . . . . . . . . . [H5N1 Africa Avian 2004-2008],
. . . . . . . . . . . . . . . . . [H9N2 Avian and Human wt],
. . . . . . . . . . . . . . . . . [H1N1 Human Seasonal 1988-1989
. . . . . . . . . . . . . . . . . . . . . with 219K, 225G, 230I, syn397G],
. . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn42G, 72L,
. . . . . . . . . . . . . . . . . . . . . syn80S, syn82I, 87N, syn118E,
. . . . . . . . . . . . . . . . . . . . . 156E, 158E, 200T, 218V,
. . . . . . . . . . . . . . . . . . . . . syn228G, 231S,
. . . . . . . . . . . . . . . . . . . . . syn287G, syn346G,
. . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K],
. . . . . . . . . . . . . . . . . [WSN_1933],
. . . . . . . . 34D [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . .  [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . .  [H5N1 Egypt Equine 2009],
. . . . . . . . . . .  [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . .  [H2N2 Human and Avian wt],
. . . . . . . . syn55L (TTa) [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . .  [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . .  [H5N1 Azerbaijan Human 2006],
. . . . . . . . . . . . . . . . .  [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . .  [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . .  [H5N1 Feline with syn40H, syn469E],
. . . . . . . . . . . . . . . . .  [H2N2 Avian with syn184H, 189T],
. . . . . . . . . . . . . . . . .  [H2N2 Human and Avian (cTa)],
. . . . . . . . syn118E (GAa) [H3N8 Equine wt, Canine wt, Swine wt],
. . . . . . . . . . . . . . . . . . [H3N8 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2009-2010 (cAa):
. . . . . . . . . . . . . . . . . . . . . . ckEgypt1055_2010_02,
. . . . . . . . . . . . . . . . . . . . . . dkEgypt0972NLQP_2009_04],
. . . . . . . . . . . . . . . . . . [H4, H6N1],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with #1T, 8V, 22I, syn31H,
. . . . . . . . . . . . . . . . . . . . . . . . syn40H, syn42G, 72L,
. . . . . . . . . . . . . . . . . . . . . . . . syn80S, syn81Y, syn82I, 87N,
. . . . . . . . . . . . . . . . . . . . . . . . 144K, 156E, 158E, 158N, 159G,
. . . . . . . . . . . . . . . . . . . . . . . . 200T, 218S, 218V,
. . . . . . . . . . . . . . . . . . . . . . . . syn228G, 230I, 231S,
. . . . . . . . . . . . . . . . . . . . . . . . 275I, syn287G, 313I, syn346G,
. . . . . . . . . . . . . . . . . . . . . . . . 450D, 453K, 502K, 523A, 523I],
. . . . . . . . . . . . . . . . . . [S8, 1918],
. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933],
. . . . . . . . . . . . . . . . . . [swBelgium1_1998],
. . . . . . . . syn140P (CCa) [H5N1 Egypt Human 2007-2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . 149N [H3N8 Equine, Canine, Avian, Swine (Agc)],
. . . . . . . . . . . . [H3N2 Avian (Agc)
. . . . . . . . . . . . . . . . with 165N, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 238K, 275I],
. . . . . . . . . . . . [H3N2 Avian (cgc)],
. . . . . . . . . . . . [H4 Avian],
. . . . . . . . 165N [H6N1 Avian
. . . . . . . . . . . . . . . . with 188T, 225G, 230I, 275I,
. . . . . . . . . . . . . . . . . . syn334G, syn346G, 377K, syn390N,
. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Avian Emergent
. . . . . . . . . . . . . . . . with 39E, syn40H, syn93C,
. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I,
. . . . . . . . . . . . . . . . . . . syn294P, 296H, syn404E],
. . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N, syn177L,
. . . . . . . . . . . . . . . . . . . 188T, syn207S, syn213F, syn221P,
. . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . [H3N2 Human with 225N, 230I],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline, Mink
. . . . . . . . . . . . . . . . with 225G, 230I],
. . . . . . . . . . . . [WSZ_1933],
. . . . . . . . 189T [H3N2 Human (aaa, aag, agg)]
. . . . . . . . . . . . [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . [H5N1 Egypt Avian 2007-2009],
. . . . . . . . . . . . [H6N1 Avian
. . . . . . . . . . . . . . . . with 165K, 188T, 225G, 230I,
. . . . . . . . . . . . . . . . . . 275I, syn334G, syn346G, syn390N,
. . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Avian
. . . . . . . . . . . . . . . . with 39E, syn40H, syn42G, syn93C,
. . . . . . . . . . . . . . . . . . . syn181G, 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,
. . . . . . . . . . . . . . . . . . . syn399E, syn404E, 453K, 502K],
. . . . . . . . . . . . [H9N2 Human
. . . . . . . . . . . . . . . . with 189T, 190E,
. . . . . . . . . . . . . . . . . . . 225G, 230I, syn294P, 296H,
. . . . . . . . . . . . . . . . . . . syn399E, 453K, 502K],
. . . . . . . . . . . . [H1N1 Avian Europe 2009
. . . . . . . . . . . . . . . . with #1T, syn42G, 72L, syn81Y, syn82I, 87N,
. . . . . . . . . . . . . . . . . . . 159T, 186P, 188T, syn346G],
. . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . with #1T, syn40H, syn42G,
. . . . . . . . . . . . . . . . . . . 72L, syn80S, syn81Y, 87N
. . . . . . . . . . . . . . . . . . . 144E, 158E, 186P,
. . . . . . . . . . . . . . . . . . . 230I, 237I, syn346G, 523A],
. . . . . . . . . . . . [H2N2 Human, Avian
. . . . . . . . . . . . . . . . with 200T, 208K, 225E,
. . . . . . . . . . . . . . . . . . 225G, 238D, 238K, 253A],
. . . . . . . . . . . . [1918 with 186P, 208K, 219A, 225G, 252I],
. . . . . . . . 210N mix wt [Novel to pH1N1_υ],
. . . . . . . . . . . . . . . . .  [pH1N1 Clade 2: 188T with 128D],
. . . . . . . . . . . . . . . . .  [H1N1 Avian wt],
. . . . . . . . . . . . . . . . .  [H2N2 Human],
. . . . . . . . . . . . . . . . .  [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn#1A, syn31H, 42E, syn147F,
. . . . . . . . . . . . . . . . . . . . . . . . . .188A, 189T, 190E, 200T,
. . . . . . . . . . . . . . . . . . . . . . . . . .210N, 225G, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . .  238K, 240N, syn346G],
. . . . . . . . . . . . . . . . .  [H6N1 Avian wt],
. . . . . . . . . . . . . . . . . .[1918, WSN_1933, WSZ_1933],
. . . . . . . . syn213F (TTt) [H5N1, H7N3, H7N7, H9N2],
. . . . . . . . . . . . . . . . .  [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . .  [H1N1 Avian],
. . . . . . . . 275I [H6N1 Avian wt],
. . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . . . . . [H3N2 Human 2011
. . . . . . . . . . . . . . . . with 165N, 225N, 230I, 238K],
. . . . . . . . . . . . [H3N2 Avian, Canine, Feline
. . . . . . . . . . . . . . . . with 165N, 190E, 225G, 230I, 238K],
. . . . . . . . syn287G (GGg) [H3N2 Avian with 159S],
. . . . . . . . . . . . . . . . . . [H3N2 Canine & Feline],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2007-2010],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2008-2010],
. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E, syn104L,
. . . . . . . . . . . . . . . . . . . . . . . . . 166R, syn184H,
. . . . . . . . . . . . . . . . . . . . . . . . . 189T, 225G, 238K, syn346G]
. . . . . . . . . . . . . . . . . . [H2N2 Human
. . . . . . . . . . . . . . . . . . . . . . with 42E, 189T, 225G, 238D, 253A],
. . . . . . . . . . . . . . . . . . [swBelgium1_1998],
. . . . . . . . syn305K (AAg) [H2N2 Avian & Human (gAg)],
. . . . . . . . . . . . . . . . . . [H2N3 Avian wt],
. . . . . . . . . . . . . . . . . . [H3N8 Avian (gcg)],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Gharbiyah/Qena Avian 2008 (AAa)],
. . . . . . . . . . . . . . . . . . [H5N1 Human VietJP4207_2005 (gAg)],
. . . . . . . . . . . . . . . . . . [H5N1 Asia Avian 2001-2006 (gAg)],
. . . . . . . . . . . . . . . . . . [H7N3, H7N7],
. . . . . . . . . . . . . . . . . . [H1N1 Avian (gAg)],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt (gAg)
. . . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S,
. . . . . . . . . . . . . . . . . . . . . . . . . . 219K, 225G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn397G, syn494E],
. . . . . . . . . . . . . . . . . . [H1N1 swine
. . . . . . . . . . . . . . . . . . . . . . . with #1S, 219K, 225G, 230I, 491R],
. . . . . . . . . . . . . . . . . . [1918 (gAg)],
. . . . . . . . . . . . . . . . . . [WSN_1933, WSZ_1933 (gAg)],
. . . . . . . . syn334G (GGa) [Novel to pH1N1_υ],
. . . . . . . . . . . . . . . . . . [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with syn31H, 42E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 189T, 200T, 208K, 210N,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 238K, syn287G, syn346G],
. . . . . . . . . . . . . . . . . . [H6N1 Avian wt],
. . . . . . . . . . . . . . . . . . [H10N7 Avian wt
. . . . . . . . . . . . . . . . . . . . . . . with 156E, syn213F, syn346G, et al],
. . . . . . . . . . . . . . . . . . [1918, WSN_1933, WSZ_1933],
. . . . . . . . syn337A (GCa) [Novel to pH1N1_υ],
. . . . . . . . . . . . . . . . . . [pH1N1 Clade 2: 188T with 158E],
. . . . . . . . . . . . . . . . . . [H2N2 Avian
. . . . . . . . . . . . . . . . . . . . . . . with syn#1A, syn31H, syn147F, 166R
. . . . . . . . . . . . . . . . . . . . . . . . . . 188A, 190E, 200T,
. . . . . . . . . . . . . . . . . . . . . . . . . . 210N, 225G, syn228G,
. . . . . . . . . . . . . . . . . . . . . . . . . . 238K, 240N, syn346G],
. . . . . . . . . . . . . . . . . .  [H6N1 Avian wt],
. . . . . . . . syn346G (GGa) [H2N2 Human and Avian wt],
. . . . . . . . . . . . . . . . . . [H3N2 Human & Avian wt],
. . . . . . . . . . . . . . . . . . [H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Preschool 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . . . [H6N1, H6N2, H6N4 Avian],
. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],
. . . . . . . . syn391T (ACg) [H3N2 Human wt (gag)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine, Feline (gag)],
. . . . . . . . . . . . . . . . . . [H4 Avian wt (gag)],
. . . . . . . . . . . . . . . . . . [H7N3 Avian wt (cag)],
. . . . . . . . . . . . . . . . . . [H7N7 Avian, Equine, Marine Mammal (cag)],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 (Aag)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian 2011 (Aag)],
. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . [H11 Avian extensive],
. . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn397G (GGc) [H6N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with 165N, syn181G, 188T, 190E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 210N, 225G, 230I, 275I,
. . . . . . . . . . . . . . . . . . . . . . . . . . 313K, syn334G, syn337A, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn399E, 453K, 502K],
. . . . . . . . . . . . . . . . . . [H7N3 Avian (Gac)],
. . . . . . . . . . . . . . . . . . [H7N7 Human & Avian (Gac)],
. . . . . . . . . . . . . . . . . . [H9N2 Human (Gac)],
. . . . . . . . . . . . . . . . . . [H9N2 Avian Emergent (Gac)
. . . . . . . . . . . . . . . . . . . . . . . with 39E, syn40H, 296H, syn404E],
. . . . . . . . . . . . . . . . . . [H1N1 Human Seasonal wt
. . . . . . . . . . . . . . . . . . . . . . . with syn12A, syn42G, 48K, syn84E,
. . . . . . . . . . . . . . . . . . . . . . . . . syn218A, 218T, 218S,
. . . . . . . . . . . . . . . . . . . . . . . . . 219K, syn220R, 225G, 230I,
. . . . . . . . . . . . . . . . . . . . . . . . . syn494E],
. . . . . . . . . . . . . . . . . . [H1N1 Avian 2009],
. . . . . . . . . . . . . . . . . . [S8], [swBelgium1_1998],
. . . . . . . . 516V [Novel to pH1N1_υ],
. . . . . . . . . . . . [H2N2 Avian with 17N])

. . . . Arizona02_43F_2011_03_08 (
. . . . . . . . GISAID NA EPI319993
. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn139L (TTa),
. . . . . . . . syn300N (AAc),
. . . . . . . . syn327R (CGt),
. . . . . . . . syn330D (GAc),
. . . . . . . . syn453V (GTt))

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