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)

Please visit GeneWurx.com for insight into the latest published studies.

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

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

HA 166N Polymorphism Potential on pH1N1 Cross-Clade Background with Both 188T and 189T

Current trending indicates a reportable potential for the K166N polymorphism spreading on the Hemagglutinin of pH1N1. This change may enhance Vaccine Escape from the currently selected vaccine target candidate, CA/07 X181. 

The GeneWurx RnR model approximates that HA 166N may appear on a pH1N1 cross-clade background carrying both 188T and 189T, according to the following probabilities.

• 28% probability sampled by 2013-04-30.
• 52% probability sampled by 2013-09-30.

If the HA 166N does appear on a cross-clade background having both 188T and 189T, hospitalisation of subjects under 12 years of age is a potential scenario.

These probabilities will be updated as additional data is made public.  Transparency at this post-pandemic stage is essential to formulate viable responses for the risk groups.  Release of sequences and clinical data of a finer detail and higher quantity will allow information-based decisions.

Please visit GeneWurx.com for insight into the latest published studies.

sH3N2 HA 140K Antigen Polymorphism Potential in Europe and North America

Current trending indicates a reportable potential for the I140K polymorphism spreading on the Hemagglutinin of sH3N2. This Antigenic Domain A change may enhance Vaccine Escape from the currently selected vaccine target, Victoria361 X-217.

The GeneWurx RnR model approximates that HA I140K will appear in sH3N2 Northern Hemisphere Seasons 2012-2013 and 2013-2014 according to the following probabilities.

• 60% probability in either Europe or North America sampled by 2013-12-31.
• 38% probability in both Europe and North America sampled by 2013-12-31.

• 05% or less probability of HA 140K conserving across sH3N2 by 2013-12-31.
• 12% or less probability of HA 140K conserving on one Hydra by 2013-12-31.

These probabilities will be updated as additional data is made public.  Transparency at this High Mortality stage is essential to formulate viable responses for the risk groups.  Release of sequences and clinical data of a finer detail and higher quantity will allow information-based decisions.

Please visit GeneWurx.com for insight into the latest published studies.

Avian Homology on High Diversity Sequences Distinguished Across Globe

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.

Publish Date : 2011-12-21
Last Update : 2012-01-27

On 2011-12-20, the UK National Institute of Medical Research released a group of human pH1N1 sequences at GISAID including 46 full HA and 45 full NA segments.  The sample dates cover 2010-12-15 to 2011-08-11 (44 during 2011).  Fifteen originating labs provided the samples though no specification of clinical outcome is notated within the NIMR deposit.  The cases produced 968 total polymorphisms on the Hemagglutinin and Neuraminidase gene segments (HA 638 / NA 330) averaging over 20 polymorphisms per full sequence (HA 13.9 / NA 7.3).

The superset of polymorphisms demonstrates notable non-swine, zoonotic homology according to the GeneWurx Zoonoses Listing (GZL) assessment with an 85% minimum of the 350 combined distinct HA and NA polymorphisms being found on non-swine, animal sequences (primarily avian).  Trans-Zoonotic Serotype Analyses (TZSA), [HA] / [NA], provide the detail beneath the GZL.  Additionally, GeneWurx LookAside analysis (Upstream & Downstream Distances of 1 Amino Acid each) demonstrates potential influencer relationships for pH1N1 HA polymorphisms that have not yet shown direct zoonotic homology.

The volume and span of the deposit demonstrates the ongoing significant rate of genetic acquisition onto 4 of the established clades, alongside several uncladed sequences.  Four sequences carry clade-defining elements from multiple clades.  Ambiguity in the traces is high with 44 mixed traces, 34 HA and 10 NA. 

A certain population of geographically-dispersed sequences shows a combined HA and NA total of 25 or more revisions (10 sequences, 22% of the deposit).  This deposit brings the first pH1N1 sequence with a combined 40 polymorphisms (HA and NA) on the highly avian-influenced, SenegalDakar14_1x_2011_04_14 (HA 29 / NA 11) [EPI346724].  On that Dakar HA, 23 of 29 polymorphisms (79%) are found within Avian H1N1, while at least 90% are identifiable in non-swine zoonotic reservoirs (26 of 29 HA).  This single human sequence from a very young child carries 13 amino homologies to H5N1 (9 HA / 4 NA), 13 to H9N2 (9 HA / 4 NA) and 18 to H6N1 (10 HA / 8 NA). Dakar homology to TamiFlu Resistant strains due to NA 247N is significant with 14 matches (8 HA / 6 NA).

Enhanced acquisition of avian genetic data and convergence of polymorphisms found on High-CFR and highly-zoonotic pH1N1 strains are quantified.  Variant clades appear to be gaining data from the same sources as the pH1N1 HA 230I strains (24 HA / 12 NA matches) and the Upsilon series (31 HA / 23 NA matches) of 84 sequences (5.33% CFR). 

Five countries (Cameroon, France, England, Iceland and Hungary) produced a subset of 9 sequences bearing 12 total polymorphisms within the aa156-aa159 range, a domain documented to produce Vaccine Escape.  Hungary7_xM_2011_01_31 (HA 11 / NA 06) [EPI346709] on Clade2: 188T with RBS 226R (Vaccine Match) applies polymorphic behaviour at 3 consecutive Vaccine Escape locations in this domain (HA 157E mix wt, 158E mix wt and 159D mix wt).

One sequence is TamiFlu Resistant with NA 275Y.  More importantly a strong gravity is indicated in the polymorphic pattern suggestive that more TmX due to NA 247N will be seen in the future on these types of strains.  Considering the HA and NA distinct polymorphic supersets on these human pandemic sequences, 96 (52 HA and 44 NA) changes (27%) appear on earlier pandemic sequences with TmX due to NA 247N and 85 (52 HA and 33 NA) changes (24%) appear on the subset of H5N1 sequences that carry the NA 247N marker.

Evaluating the 229 distinct HA changes derived from these 46 human pandemic sequences against fractional HA subsets of several animal serotypes, a minimum of 84% share homology.  Avian H1N1 leads the match count at 140 polymorphic values (103 Farm Avian H1N1), while H6N1 continues to participate at a significant level (88 matches).  Homology to Avian H9N2 (65), H13 (53) and the High-CFR H5N1 (104) demonstrates that this pandemic has ample opportunity for genetic input from the extant reservoirs to amplify clinical conditions.  GeneWurx LookAside analysis shows that 109 of the 229 distinct pH1N1 HA polymorphisms demonstrate an amino acid homology within 1 position upstream or downstream in a zoonotic reservoir for a total of 311 HA LookAside influencers.

Of 121 distinct NA polymorphisms, 104 are non-swine, zoonotic (86%) and a minimum of 89 are found on Avian H1N1 (74%) with 74 (61%) of those found on a subset of a dozen Farm Avian H1N1 sequences that have consistently matched polymorphisms coming onto the human H1N1 pandemic background since 2009.  NA homology with other non-swine, zoonotic reservoirs remains significant: Avian H6N1 (88 / 73%), Avian H9N2 (30) and the High-CFR H5N1 (54).

Though the zoonotic serotype backgrounds profiled against these human polymorphisms are entirely variant, these many codon-level homologies crossing multiple zoonotic reservoirs into the human pandemic illuminates the GeneWurx premise that the origin of the human H1N1 pandemic be reconsidered as avian.

Cladistics

Clade1: 189T - 07 Sequences
Clade2: 188T - 23 Sequences
Clade3: 186P - 05 Sequences
Clade5: 208K_219V - 06 Sequences

HA 638 Polymorphisms Averaging ~13.9 per Segment
NA 330 Polymorphisms Averaging ~ 7.3 per Segment

HA and NA 968 Total Polymorphisms Averaging ~20.0 across 45 w/ HA & NA

TamiFlu Resistance

One TamiFlu Resistant sequence (NA 275Y) features on a Clade2: 188T background and carries HA RBS 227G with the HA 158E (mixture with wild type) that has repeatedly been observed to promote Vaccine Escape.  Avian H1N1 carries homology with 9 of the 11 HA and 100% of NA polymorphisms on the TamiFlu Resistant French case.  One small population of Farm Avian H1N1 sequences matches on 7 of these 11 HA and 5 of 6 NA revisions.  TamiFlu Resistance Confluence (multiple TmX markers) is correlated due to 8 of the 11 HA markers sharing homology to the superset of pH1N1 NA 247N TamiFlu Resistant sequences and 100% of the NA changes.  Fourteen revisions (8 HA / 6 NA) pattern to the pH1N1 superset of HA 230I-bearing sequences.  Eleven changes (8 HA / 3 NA) equate to the High-CFR human pandemic Upsilon sub-clade.

• [EPI346699] FranceLorraine1176_50x_2011_02_23_TmX

Sequences


. . . . Madagascar9274_7M_2011_08_11 (
. . . . . . . . GISAID HA EPI346721
. . . . . . . . Clade2: 188T
. . . . . . . . 22 Polymorphisms (12 Amino and 10 Silent)
. . . . . . . . #6M,
. . . . . . . . #4C,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn49G (GGa),
. . . . . . . . syn122K (AAa),
. . . . . . . . 141Q,
. . . . . . . . 146G,
. . . . . . . . 169S,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 216G,
. . . . . . . . 259P,
. . . . . . . . syn304G (GGg),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 388R,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn473K (AAg),
. . . . . . . . syn512R (AGa),
. . . . . . . . syn538F (TTt),
. . . . . . . . syn546L (tTA))

. . . . Madagascar9252_23F_2011_08_10 (
. . . . . . . . GISAID HA EPI346717
. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)
. . . . . . . . Clade2: 188T
. . . . . . . . #6M,
. . . . . . . . #4C,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn49G (GGa),
. . . . . . . . syn122K (AAa),
. . . . . . . . 141Q,
. . . . . . . . 146G,
. . . . . . . . 169S,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn301I (ATa),
. . . . . . . . syn338G (GGc),
. . . . . . . . 364S,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn473K (AAg),
. . . . . . . . syn496A (GCg),
. . . . . . . . syn538F (TTt))

. . . . Madagascar9252_23F_2011_08_10 (
. . . . . . . . GISAID NA EPI346718
. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)
. . . . . . . . 126S,
. . . . . . . . syn152R (AGa),
. . . . . . . . syn225R (AGg),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn295N (AAt),
. . . . . . . . syn313Q (CAa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 416N)

. . . . Madagascar8753_xF_2011_08_02 (
. . . . . . . . GISAID HA EPI346715
. . . . . . . . Clade2: 188T
. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)
. . . . . . . . #6M,
. . . . . . . . #4C,
. . . . . . . . syn1A (GCt),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn49G (GGa),
. . . . . . . . syn122K (AAa),
. . . . . . . . 141Q,
. . . . . . . . 146G,
. . . . . . . . 169S,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 400S,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn473K (AAg),
. . . . . . . . syn514Y (TAt),
. . . . . . . . syn538F (TTt))

. . . . Madagascar8753_xF_2011_08_02 (
. . . . . . . . GISAID NA EPI346716
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 56C,
. . . . . . . . 126S,
. . . . . . . . syn225R (AGg),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn295N (AAt),
. . . . . . . . syn307N (AAt),
. . . . . . . . syn313Q (CAa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . SouthAfricaJohannesburg150_46F_2011_07_10 (
. . . . . . . . GISAID HA EPI346655
. . . . . . . . Clade5: 208K_219V
. . . . . . . . 16 Polymorphisms (8 Amino and 8 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc),
. . . . . . . . 100N,
. . . . . . . . syn131S (TCa),
. . . . . . . . 141Q,
. . . . . . . . 142D,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn307P (CCc),
. . . . . . . . 359A,
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa),
. . . . . . . . syn512R (AGa))

. . . . SouthAfricaJohannesburg150_46F_2011_07_10 (
. . . . . . . . GISAID NA EPI346656
. . . . . . . . 9 Polymorphisms (2 Amino and 7 Silent)
. . . . . . . . syn79S (TCg),
. . . . . . . . syn89S (TCt),
. . . . . . . . syn126P (CCt),
. . . . . . . . syn229S (TCc),
. . . . . . . . syn236G (GGc),
. . . . . . . . 269I mix wt,
. . . . . . . . 299A,
. . . . . . . . syn378N (AAt),
. . . . . . . . syn405S (AGc))

. . . . CameroonLEID07111870_24F_2011_07_07 (
. . . . . . . . GISAID HA EPI346647
. . . . . . . . Clade1: 189T
. . . . . . . . 13 Polymorphisms (8 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . syn168Y (TAt),
. . . . . . . . syn176V (GTt),
. . . . . . . . 189T,
. . . . . . . . 205E,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn413K (AAg),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)

. . . . CameroonLEID07111870_24F_2011_07_07 (
. . . . . . . . GISAID NA EPI346648
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn135T (ACc),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa))

. . . . SenegalDakar18_4x_2011_07_07 (
. . . . . . . . GISAID HA EPI346685
. . . . . . . . 25 Polymorphisms (8 Amino and 17 Silent)
. . . . . . . . 10H mix wt,
. . . . . . . . 35I,
. . . . . . . . 51V,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T,
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K,
. . . . . . . . syn276H (CAt),
. . . . . . . . syn295F (TTc),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn331G (GGt),
. . . . . . . . syn337A (GCt),
. . . . . . . . syn379T (ACc),
. . . . . . . . syn433E (GAg),
. . . . . . . . syn451K (AAa),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V,
. . . . . . . . syn475D (GAc),
. . . . . . . . 523A)

. . . . SenegalDakar18_4x_2011_07_07 (
. . . . . . . . GISAID NA EPI346686
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . 74V,
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn160S (AGt),
. . . . . . . . 166I mix wt,
. . . . . . . . syn275H (CAt),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K,
. . . . . . . . syn433E (GAa))

. . . . SouthAfricaJohannesburg146_xM_2011_06_29 (
. . . . . . . . GISAID HA EPI346653
. . . . . . . . Clade5: 208K_219V
. . . . . . . . 16 Polymorphisms (9 Amino and 7 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . syn75T (ACc),
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc),
. . . . . . . . 100N,
. . . . . . . . 141Q,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 218V mix wt,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . 301V mix wt,
. . . . . . . . syn307P (CCc),
. . . . . . . . 359A,
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . SouthAfricaJohannesburg146_xM_2011_06_29 (
. . . . . . . . GISAID NA EPI346654
. . . . . . . . 8 Polymorphisms (1 Amino and 7 Silent)
. . . . . . . . syn89S (TCt),
. . . . . . . . syn126P (CCt),
. . . . . . . . syn229S (TCc),
. . . . . . . . syn236G (GGc),
. . . . . . . . 299A,
. . . . . . . . syn355N (AAc),
. . . . . . . . syn405S (AGc),
. . . . . . . . syn427I (ATt))

. . . . Madagascar3520_52M_2011_06_17 (
. . . . . . . . GISAID HA EPI346719
. . . . . . . . Clade2: 188T
. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn44L (tTA),
. . . . . . . . syn122K (AAa),
. . . . . . . . 132D,
. . . . . . . . 145R,
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 237I,
. . . . . . . . syn265G (GGg),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 397S,
. . . . . . . . 452I,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn496A (GCc),
. . . . . . . . syn538F (TTt))

. . . . Madagascar3520_52M_2011_06_17 (
. . . . . . . . GISAID NA EPI346720
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . 44S,
. . . . . . . . 151N mix wt,
. . . . . . . . syn177V (GTt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 339P,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . CameroonLEID06111809_33M_2011_06_16 (
. . . . . . . . GISAID HA EPI346645
. . . . . . . . Clade1: 189T
. . . . . . . . 15 Polymorphisms (10 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . 189T,
. . . . . . . . syn210S (AGt),
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 437I mix wt,
. . . . . . . . 439N,
. . . . . . . . syn465N (AAt),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A,
. . . . . . . . 531I)

. . . . CameroonLEID06111809_33M_2011_06_16 (
. . . . . . . . GISAID NA EPI346646
. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn161C (TGc),
. . . . . . . . 262R,
. . . . . . . . syn368R (AGg),
. . . . . . . . syn398E (GAa))

. . . . ThailandNonthaburi78_2011_06_08 (
. . . . . . . . GISAID HA EPI346707
. . . . . . . . Clade2: 188T
. . . . . . . . 14 Polymorphisms (8 Amino and 6 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . syn178V (GTa),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 218E mix wt,
. . . . . . . . 218V mix wt,
. . . . . . . . syn338G (GGc),
. . . . . . . . 375V,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))

. . . . ThailandNonthaburi78_2011_06_08 (
. . . . . . . . GISAID NA EPI346708
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn14C (TGc),
. . . . . . . . 26T,
. . . . . . . . syn41G (GGa),
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . SouthAfricaJohannesburg128_1F_2011_06_07 (
. . . . . . . . GISAID HA EPI346651
. . . . . . . . Clade5: 208K_219V
. . . . . . . . 19 Polymorphisms (9 Amino and 10 Silent)
. . . . . . . . syn#6L (tTG),
. . . . . . . . syn47L (CTg),
. . . . . . . . 51T,
. . . . . . . . syn74S (TCt),
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc),
. . . . . . . . 100N,
. . . . . . . . 141Q,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn307P (CCc),
. . . . . . . . 359A,
. . . . . . . . syn366A (GCa),
. . . . . . . . 377K,
. . . . . . . . 404D,
. . . . . . . . syn446K (AAa),
. . . . . . . . syn477T (ACa))

. . . . SouthAfricaJohannesburg128_1F_2011_06_07 (
. . . . . . . . GISAID NA EPI346652
. . . . . . . . 10 Polymorphisms (2 Amino and 8 Silent)
. . . . . . . . syn89S (TCt),
. . . . . . . . syn126P (CCt),
. . . . . . . . 157A mix wt,
. . . . . . . . syn163I (ATc),
. . . . . . . . syn229S (TCc),
. . . . . . . . syn236G (GGc),
. . . . . . . . syn241V (GTg),
. . . . . . . . syn298G (GGa),
. . . . . . . . 299A,
. . . . . . . . syn342G (GGg))

. . . . HongKong3960_2M_2011_04_21 (
. . . . . . . . GISAID HA EPI346726
. . . . . . . . Clade1.Upsilon (5.33% CFR)
. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)
. . . . . . . . #12E [Novel to Upsilon],
. . . . . . . . #8I,
. . . . . . . . 34D,
. . . . . . . . syn118E (GAa),
. . . . . . . . 144E,
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 275I,
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . syn397G (GGc),
. . . . . . . . 453K,
. . . . . . . . 502K)

. . . . HongKong3960_2M_2011_04_21 (
. . . . . . . . GISAID NA EPI346727
. . . . . . . . 6 Polymorphisms (1 Amino and 5 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . 82P,
. . . . . . . . syn139L (TTa),
. . . . . . . . syn300N (AAc),
. . . . . . . . syn327R (CGt),
. . . . . . . . syn330D (GAc))


. . . . SenegalDakar14_1x_2011_04_14 (
. . . . . . . . GISAID HA EPI346724
. . . . . . . . 29 Polymorphisms (10 Amino and 19 Silent)
. . . . . . . . 16I,
. . . . . . . . 35I [H5N1 TmX247],
. . . . . . . . 89E [H1N1 Avian],
. . . . . . . . syn99I (ATt) [H1N1 Avian],
. . . . . . . . syn122K (AAa) [H5N1 Avian],
. . . . . . . . 131T [H5N1 Avian],
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg) [H9N2 Avian],
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa) [H9N2 Avian],
. . . . . . . . syn219I (ATt),
. . . . . . . . syn254P (CCa) [H9N2 Avian],
. . . . . . . . 262K [H5N1 Avian],
. . . . . . . . 266A,
. . . . . . . . syn276H (CAt) [H1N1 Avian],
. . . . . . . . syn295F (TTc) [H9N2 Avian],
. . . . . . . . syn301I (ATt),
. . . . . . . . syn331G (GGt) [H1N1 Avian],
. . . . . . . . syn337A (GCt) [H9N2 Avian],
. . . . . . . . syn338G (GGc) [H6N1 Avian],
. . . . . . . . 377K [H9N2 Avian],
. . . . . . . . syn379T (ACc) [H6N1 Avian],
. . . . . . . . syn433E (GAg) [H6N1 Avian],
. . . . . . . . syn451K (AAa) [H6N1 Avian],
. . . . . . . . syn456L (cTA) [H6N1 Avian],
. . . . . . . . 463V,
. . . . . . . . syn475D (GAc) [H6N1 Avian],
. . . . . . . . 523A [H1N1 Avian],
. . . . . . . . syn527L (TTa))

. . . . SenegalDakar14_1x_2011_04_14 (
. . . . . . . . GISAID NA EPI346725
. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)
. . . . . . . . syn20A (GCc) [H1N1 Avian],
. . . . . . . . 74V [H1N1 Avian],
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V [H1N1 Avian],
. . . . . . . . syn127L (cTG) [H1N1 Avian],
. . . . . . . . syn183A (GCc) [H1N1 Avian],
. . . . . . . . syn304V (GTt) [H1N1 Avian],
. . . . . . . . syn382G (GGa) [H1N1 Avian (Gaa)],
. . . . . . . . 385T,
. . . . . . . . 386K,
. . . . . . . . syn433E (GAa) [H1N1 Avian])

. . . . CameroonLEID04111671_1F_2011_04_12 (
. . . . . . . . GISAID HA EPI346691
. . . . . . . . Clade1: 189T
. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . syn97D (GAc),
. . . . . . . . syn130D (GAt),
. . . . . . . . 155I,
. . . . . . . . 189T,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 509D,
. . . . . . . . 523A)

. . . . CameroonLEID04111671_1F_2011_04_12 (
. . . . . . . . GISAID NA EPI346692
. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn170Y (TAt),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa),
. . . . . . . . syn421C (TGt))

. . . . SenegalDakar11_4x_2011_04_06 (
. . . . . . . . GISAID HA EPI346683
. . . . . . . . Clade3: 186P, novel sub-clade
. . . . . . . . 22 Polymorphisms (8 Amino and 14 Silent)
. . . . . . . . 12T,
. . . . . . . . 35I,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T,
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 186P,
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K,
. . . . . . . . syn276H (CAt),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn331G (GGt),
. . . . . . . . syn337A (GCt),
. . . . . . . . syn379T (ACc),
. . . . . . . . syn433E (GAg),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V,
. . . . . . . . 523A)

. . . . SenegalDakar11_4x_2011_04_06 (
. . . . . . . . GISAID NA EPI346684
. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn172S (TCt),
. . . . . . . . 259D,
. . . . . . . . syn304V (GTt),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K,
. . . . . . . . syn415L (tTG))

. . . . SenegalDakar09_3x_2011_03_25 (
. . . . . . . . GISAID HA EPI346703
. . . . . . . . 24 Polymorphisms (8 Amino and 16 Silent)
. . . . . . . . 35I,
. . . . . . . . 47I,
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T,
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K,
. . . . . . . . syn276H (CAt),
. . . . . . . . syn288A (GCc),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn325P (CCt),
. . . . . . . . syn331G (GGt),
. . . . . . . . syn337A (GCt),
. . . . . . . . syn379T (ACc),
. . . . . . . . syn433E (GAg),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V,
. . . . . . . . 481N,
. . . . . . . . 523A)

. . . . SenegalDakar09_3x_2011_03_25 (
. . . . . . . . GISAID NA EPI346704
. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn281C (TGc),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn370G (GGc),
. . . . . . . . syn371F (TTc),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K)

. . . . Iceland59_xF_2011_03_24 (
. . . . . . . . GISAID HA EPI346697
. . . . . . . . Clade3: 186P
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 137T mix wt,
. . . . . . . . 144S,
. . . . . . . . syn163K (AAa),
. . . . . . . . 186P,
. . . . . . . . syn251L (CTg),
. . . . . . . . syn287G (GGg),
. . . . . . . . syn293L (CTt),
. . . . . . . . 298V,
. . . . . . . . syn363G (GGg),
. . . . . . . . 377K,
. . . . . . . . syn455Q (CAa),
. . . . . . . . syn474C (TGt),
. . . . . . . . 482I)

. . . . Iceland59_xF_2011_03_24 (
. . . . . . . . GISAID NA EPI346698
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 46T,
. . . . . . . . syn187G (GGt),
. . . . . . . . 313R,
. . . . . . . . 321V,
. . . . . . . . 394I,
. . . . . . . . syn412L (tTA),
. . . . . . . . syn430R (CGg),
. . . . . . . . 467V)

. . . . CameroonLEID03111616_xM_2011_03_22 (
. . . . . . . . GISAID HA EPI346689
. . . . . . . . Clade1: 189T
. . . . . . . . 12 Polymorphisms (8 Amino and 4 Silent)
. . . . . . . . 1T,
. . . . . . . . 167F,
. . . . . . . . 189T,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A,
. . . . . . . . syn538F (TTt))

. . . . CameroonLEID03111616_xM_2011_03_22 (
. . . . . . . . GISAID NA EPI346690
. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn118R (AGa),
. . . . . . . . syn262K (AAa),
. . . . . . . . 386D,
. . . . . . . . syn398E (GAa))

. . . . FrancePaysdeLoire1347_12x_2011_03_22 (
. . . . . . . . GISAID HA EPI346701
. . . . . . . . Clade2: 188T
. . . . . . . . 12 Polymorphisms (4 Amino and 8 Silent)
. . . . . . . . 100N,
. . . . . . . . syn135V (GTg),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn321L (cTG),
. . . . . . . . syn336I (ATc),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn400F (TTt),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn482V (GTt))

. . . . FrancePaysdeLoire1347_12x_2011_03_22 (
. . . . . . . . GISAID NA EPI346702
. . . . . . . . 8 Polymorphisms (2 Amino and 6 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn313Q (CAa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn401G (GGg),
. . . . . . . . syn416D (GAc))

. . . . Iceland52_xM_2011_03_18 (
. . . . . . . . GISAID HA EPI346643
. . . . . . . . Clade2: 188T
. . . . . . . . 12 Polymorphisms (9 Amino and 3 Silent)
. . . . . . . . 87I,
. . . . . . . . 100N,
. . . . . . . . 158E mix wt,
. . . . . . . . 188T,
. . . . . . . . 212N mix wt,
. . . . . . . . syn304G (GGg),
. . . . . . . . syn319T (ACg),
. . . . . . . . 324I,
. . . . . . . . 377K,
. . . . . . . . 440H mix wt,
. . . . . . . . syn441H (CAt),
. . . . . . . . 454N)

. . . . Iceland52_xM_2011_03_18 (
. . . . . . . . GISAID NA EPI346644
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . UkraineDnipropetrovsk4929_21F_2011_03_10 (
. . . . . . . . GISAID HA EPI346637
. . . . . . . . Clade2: 188T
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . UkraineDnipropetrovsk4929_21F_2011_03_10 (
. . . . . . . . GISAID NA EPI346638
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . UkraineZaporizhzhya5200_31F_2011_03_09 (
. . . . . . . . GISAID HA EPI346663
. . . . . . . . Clade2: 188T
. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 326F,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 415E,
. . . . . . . . syn441H (CAt),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . UkraineZaporizhzhya5200_31F_2011_03_09 (
. . . . . . . . GISAID NA EPI346664
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 96R mix wt,
. . . . . . . . 127F,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . UkraineLuhansk5192_xF_2011_03_07 (
. . . . . . . . GISAID HA EPI346639
. . . . . . . . Clade2: 188T
. . . . . . . . . . . . crossing Clade3: 186P
. . . . . . . . 16 Polymorphisms (6 Amino and 10 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn118E (GAa),
. . . . . . . . syn130D (GAt),
. . . . . . . . 146G,
. . . . . . . . 186P mix wt,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . syn358N (Aac) mix,
. . . . . . . . syn358T mix,
. . . . . . . . 377K,
. . . . . . . . syn412K (AAg),
. . . . . . . . syn418F (TTt),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))

. . . . UkraineLuhansk5192_xF_2011_03_07 (
. . . . . . . . GISAID NA EPI346640
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 44S,
. . . . . . . . 83G,
. . . . . . . . syn206L (cTA),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . CameroonLEID03111573_xM_2011_03_01 (
. . . . . . . . GISAID HA EPI346687
. . . . . . . . 14 Polymorphisms (9 Amino and 5 Silent)
. . . . . . . . 1T,
. . . . . . . . syn157K (AAg),
. . . . . . . . 158E mix wt,
. . . . . . . . syn173G (GGa),
. . . . . . . . 190G,
. . . . . . . . 205E mix wt,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . syn334G (GGa),
. . . . . . . . 377K,
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)

. . . . CameroonLEID03111573_xM_2011_03_01 (
. . . . . . . . GISAID NA EPI346688
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn6K (AAa),
. . . . . . . . syn22L (cTA),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa))

. . . . UkraineOdessa5197_24F_2011_03_01 (
. . . . . . . . GISAID HA EPI346641
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . syn391T (ACc),
. . . . . . . . syn413K (AAg),
. . . . . . . . 415E mix wt)

. . . . UkraineOdessa5197_24F_2011_03_01 (
. . . . . . . . GISAID NA EPI346642
. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)
. . . . . . . . syn330D (GAc),
. . . . . . . . syn407V (GTc))


. . . . FranceLorraine1176_50x_2011_02_23_TmX (
. . . . . . . . GISAID HA EPI346699
. . . . . . . . Clade2: 188T
. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)
. . . . . . . . 100N,
. . . . . . . . 158E mix wt,
. . . . . . . . 188T,
. . . . . . . . 227G,
. . . . . . . . syn245F (TTt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn461K (AAa),
. . . . . . . . syn470F (TTc),
. . . . . . . . syn537S (AGc))

. . . . FranceLorraine1176_50x_2011_02_23_TmX (
. . . . . . . . GISAID NA EPI346700
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 275Y,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . LithuaniaKlaipeda1067_xF_2011_02_22 (
. . . . . . . . GISAID HA EPI346673
. . . . . . . . Clade3: 186P
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . syn279N (AAc),
. . . . . . . . syn288A (GCc),
. . . . . . . . syn352Y (TAt),
. . . . . . . . 377G,
. . . . . . . . syn408E (GAa),
. . . . . . . . syn474C (TGt),
. . . . . . . . syn475D (GAc),
. . . . . . . . 512M,
. . . . . . . . 530I)

. . . . LithuaniaKlaipeda1067_xF_2011_02_22 (
. . . . . . . . GISAID NA EPI346674
. . . . . . . . 14 Polymorphisms (3 Amino and 11 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn66Y (TAc),
. . . . . . . . syn124C (TGt),
. . . . . . . . syn130R (AGg),
. . . . . . . . syn157T (ACt),
. . . . . . . . syn175E (GAa),
. . . . . . . . 232V,
. . . . . . . . syn302P (CCa),
. . . . . . . . syn382G (GGa),
. . . . . . . . 389V,
. . . . . . . . 394I,
. . . . . . . . syn425E (GAg),
. . . . . . . . syn428R (AGg),
. . . . . . . . syn430R (CGg))

. . . . LithuaniaTelsiai1038_xM_2011_02_19 (
. . . . . . . . GISAID HA EPI346671
. . . . . . . . Clade2: 188T
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn#6L (CTa),
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . syn245F (TTt),
. . . . . . . . syn321L (cTG),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . LithuaniaTelsiai1038_xM_2011_02_19 (
. . . . . . . . GISAID NA EPI346672
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . syn436I (ATa))

. . . . LithuaniaTelsiai1037_xM_2011_02_19 (
. . . . . . . . GISAID HA EPI346669
. . . . . . . . Clade2: 188T
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn#6L (CTa),
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . syn245F (TTt),
. . . . . . . . syn321L (cTG),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . LithuaniaTelsiai1037_xM_2011_02_19 (
. . . . . . . . GISAID NA EPI346670
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . syn436I (ATa))

. . . . LithuaniaKaunas146s_xM_2011_02_17 (
. . . . . . . . GISAID HA EPI346675
. . . . . . . . Clade2: 188T
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . 152M,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . LithuaniaKaunas146s_xM_2011_02_17 (
. . . . . . . . GISAID NA EPI346676
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . 453M)

. . . . LithuaniaKaunas988_xM_2011_02_15 (
. . . . . . . . GISAID HA EPI346667
. . . . . . . . Clade2: 188T
. . . . . . . . . . . . crossed with Clade4:128D
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa) [Upsilon?],
. . . . . . . . 100N,
. . . . . . . . 128D,
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . LithuaniaKaunas988_xM_2011_02_15 (
. . . . . . . . GISAID NA EPI346668
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . FranceParis940_16x_2011_02_11 (
. . . . . . . . GISAID HA EPI346722
. . . . . . . . Clade2: 188T
. . . . . . . . 15 Polymorphisms (8 Amino and 7 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 76T,
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 205E mix wt,
. . . . . . . . 277N,
. . . . . . . . syn338G (GGc),
. . . . . . . . syn358N (AAc),
. . . . . . . . 377K,
. . . . . . . . syn418F (TTt),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))

. . . . FranceParis940_16x_2011_02_11 (
. . . . . . . . GISAID NA EPI346723
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 44S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . FranceCentre869_60x_2011_02_08 (
. . . . . . . . GISAID HA EPI346681
. . . . . . . . Clade2: 188T
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . syn31H (CAt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 205E,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . FranceCentre869_60x_2011_02_08 (
. . . . . . . . GISAID NA EPI346682
. . . . . . . . 10 Polymorphisms (3 Amino and 7 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn316Y (TAt),
. . . . . . . . 344K,
. . . . . . . . syn365I (ATc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn390K (AAa),
. . . . . . . . syn416D (GAc))

. . . . FranceHauteNormandie774_3x_2011_02_01 (
. . . . . . . . GISAID HA EPI346679
. . . . . . . . Clade5: 208K_219V
. . . . . . . . 14 Polymorphisms (7 Amino and 7 Silent)
. . . . . . . . syn41N (AAt),
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . 133E,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . syn319T (ACg),
. . . . . . . . 352F,
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . FranceHauteNormandie774_3x_2011_02_01 (
. . . . . . . . GISAID NA EPI346680
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . syn60T (ACc),
. . . . . . . . 81A,
. . . . . . . . syn138A (GCt),
. . . . . . . . 151N mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . Hungary13_xM_2011_01_31 (
. . . . . . . . GISAID HA EPI346711
. . . . . . . . Clade2: 188T
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . 157E,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 226R,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . Hungary13_xM_2011_01_31 (
. . . . . . . . GISAID NA EPI346712
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn191L (tTA),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))


. . . . Hungary7_xM_2011_01_31 (
. . . . . . . . GISAID HA EPI346709
. . . . . . . . Clade2: 188T
. . . . . . . . 11 Polymorphisms (8 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . 157E mix wt,
. . . . . . . . 158E mix wt,
. . . . . . . . 159D mix wt,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 226R,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . Hungary7_xM_2011_01_31 (
. . . . . . . . GISAID NA EPI346710
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . TurkeyMalatyaTR_29_28M_2011_01_28 (
. . . . . . . . GISAID HA EPI346659
. . . . . . . . Clade3: 186P
. . . . . . . . 11 Polymorphisms (8 Amino and 3 Silent)
. . . . . . . . syn16T (ACg),
. . . . . . . . 137T,
. . . . . . . . 167F,
. . . . . . . . 186P,
. . . . . . . . 263K,
. . . . . . . . 377G,
. . . . . . . . syn408E (GAa),
. . . . . . . . 413R mix wt,
. . . . . . . . syn474C (TGt),
. . . . . . . . 512M,
. . . . . . . . 530I)

. . . . TurkeyMalatyaTR_29_28M_2011_01_28 (
. . . . . . . . GISAID NA EPI346660
. . . . . . . . 13 Polymorphisms (4 Amino and 9 Silent)
. . . . . . . . syn20A (GCc),
. . . . . . . . syn66Y (TAc),
. . . . . . . . syn124C (TGt),
. . . . . . . . syn130R (AGg),
. . . . . . . . syn157T (ACt),
. . . . . . . . syn175E (GAa),
. . . . . . . . 232V,
. . . . . . . . 267I,
. . . . . . . . syn382G (GGa),
. . . . . . . . 389V,
. . . . . . . . 394I,
. . . . . . . . syn425E (GAg),
. . . . . . . . syn430R (CGg))

. . . . CameroonLEID01111467_28F_2011_01_27 (
. . . . . . . . GISAID HA EPI346705
. . . . . . . . Clade1: 189T
. . . . . . . . 11 Polymorphisms (7 Amino and 4 Silent)
. . . . . . . . 1T,
. . . . . . . . 189T,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . syn340I (ATc),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)

. . . . CameroonLEID01111467_28F_2011_01_27 (
. . . . . . . . GISAID NA EPI346706
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . syn262K (AAa),
. . . . . . . . syn271A (GCt),
. . . . . . . . syn398E (GAa))

. . . . Kazakhstan2081_xF_2011_01_23 (
. . . . . . . . GISAID HA EPI346713
. . . . . . . . Clade3: 186P
. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . syn297N (AAc),
. . . . . . . . syn316R (AGg),
. . . . . . . . syn326S (TCc),
. . . . . . . . syn383N (AAc),
. . . . . . . . syn388K (AAa),
. . . . . . . . 433K,
. . . . . . . . 444K,
. . . . . . . . syn474C (TGt))

. . . . Kazakhstan2081_xF_2011_01_23 (
. . . . . . . . GISAID NA EPI346714
. . . . . . . . 7 Polymorphisms (1 Amino and 6 Silent)
. . . . . . . . syn6K (AAa),
. . . . . . . . syn139L (cTG),
. . . . . . . . syn202A (GCt),
. . . . . . . . syn274Y (TAc),
. . . . . . . . syn275H (CAt),
. . . . . . . . syn372E (GAa),
. . . . . . . . 394I)

. . . . CameroonLEID01111450_3F_2011_01_19 (
. . . . . . . . GISAID HA EPI346649
. . . . . . . . Clade1: 189T
. . . . . . . . 12 Polymorphisms (9 Amino and 3 Silent)
. . . . . . . . 1T,
. . . . . . . . 159S,
. . . . . . . . 189T,
. . . . . . . . 205E,
. . . . . . . . syn238E (GAa),
. . . . . . . . 275A,
. . . . . . . . syn286K (AAa),
. . . . . . . . 377K,
. . . . . . . . syn403L (tTG),
. . . . . . . . 476D,
. . . . . . . . 477K,
. . . . . . . . 523A)

. . . . CameroonLEID01111450_3F_2011_01_19 (
. . . . . . . . GISAID NA EPI346650
. . . . . . . . 4 Polymorphisms (1 Amino and 3 Silent)
. . . . . . . . syn22L (cTA),
. . . . . . . . 59R,
. . . . . . . . syn262K (AAa),
. . . . . . . . syn398E (GAa))

. . . . Iceland9_xF_2011_01_19 (
. . . . . . . . GISAID HA EPI346695
. . . . . . . . Clade2: 188T
. . . . . . . . 15 Polymorphisms (10 Amino and 5 Silent)
. . . . . . . . 100N,
. . . . . . . . 159D,
. . . . . . . . syn179L (tTA),
. . . . . . . . 188T,
. . . . . . . . 225N,
. . . . . . . . syn245F (TTt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 437I (Atc) mix wt,
. . . . . . . . 437I (Att) mix wt,
. . . . . . . . 437N (Aac) mix wt,
. . . . . . . . 437N (Aat) mix wt,
. . . . . . . . syn437T (Acc) mix wt,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . Iceland9_xF_2011_01_19 (
. . . . . . . . GISAID NA EPI346696
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . TurkeyTokatTR_26_26M_2011_01_19 (
. . . . . . . . GISAID HA EPI346657
. . . . . . . . Clade5: 208K_219V
. . . . . . . . . . . . crossing Clade4: 128D
. . . . . . . . 14 Polymorphisms (8 Amino and 6 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . 128D,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 210I mix wt,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . syn319T (ACg),
. . . . . . . . 377K,
. . . . . . . . 431Q mix wt,
. . . . . . . . syn446K (AAa))

. . . . TurkeyTokatTR_26_26M_2011_01_19 (
. . . . . . . . GISAID NA EPI346658
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . syn60T (ACc),
. . . . . . . . 81A,
. . . . . . . . syn138A (GCt),
. . . . . . . . 211T mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . Iceland7_xM_2011_01_16 (
. . . . . . . . GISAID HA EPI346661
. . . . . . . . Clade2: 188T
. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)
. . . . . . . . #7I,
. . . . . . . . 100N,
. . . . . . . . 157N mix wt,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 449C mix wt,
. . . . . . . . 454N)

. . . . Iceland7_xM_2011_01_16 (
. . . . . . . . GISAID NA EPI346662
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . 117M,
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . Iceland3_xM_2011_01_10 (
. . . . . . . . GISAID HA EPI346677
. . . . . . . . Clade2: 188T
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn379T (ACc),
. . . . . . . . 440H,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))

. . . . Iceland3_xM_2011_01_10 (
. . . . . . . . GISAID NA EPI346678
. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)
. . . . . . . . syn38I (ATc),
. . . . . . . . 44S,
. . . . . . . . 151E mix wt,
. . . . . . . . 151K mix wt,
. . . . . . . . 151N mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn274Y (TAc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . TurkeyAnkaraTR_23_20M_2010_12_30 (
. . . . . . . . GISAID HA EPI346693
. . . . . . . . Clade5: 208K_219V
. . . . . . . . . . . . crossing Clade3: 186P
. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . 159D mix wt,
. . . . . . . . syn170N (AAc),
. . . . . . . . 186P mix wt,
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn346G (GGa),
. . . . . . . . 377K,
. . . . . . . . 426V,
. . . . . . . . syn446K (AAa),
. . . . . . . . syn507K (AAa),
. . . . . . . . 530I)

. . . . TurkeyAnkaraTR_23_20M_2010_12_30 (
. . . . . . . . GISAID NA EPI346694
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn238C (TGt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . UKEngland687_2010_12_15 (
. . . . . . . . GISAID HA EPI346665
. . . . . . . . Clade2: 188T
. . . . . . . . 11 Polymorphisms (7 Amino and 4 Silent)
. . . . . . . . syn#7V (GTc),
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa),
. . . . . . . . 100N,
. . . . . . . . 158E mix wt,
. . . . . . . . 179I,
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . UKEngland687_2010_12_15 (
. . . . . . . . GISAID NA EPI346666
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . syn161C (TGc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn398E (GAa),
. . . . . . . . syn416D (GAc))


This analysis catalysed with ingenuity from 2 lead Professors of Group10 at Ion₂₀₃.  We never cease to find inspiration in your halls of instruction.

Please visit GeneWurx.com for insight into the latest published studies.