Pandemic Influenza H1N1 Genetic Acquisitions: 2013-11

2013-11-28

Prediction Demonstrated in USA of Triple Polymorphism pH1N1 HA 166N, 188T & 189T

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

Publish Date : 2013-11-28
Last Update : 2013-11-29

1 Predicted Sequence

The United States CDC published a sequence on 2013-09-09 with Clade Crossing evidence sampled on 2013-08-13 from a 57 year old male in Indiana. This Indiana22_C2_57M_2013_08_13 sequence fulfills the triple polymorphism genetic change and timing of the prediction published on 2013-02-26 titled HA 166N Polymorphism Potential on pH1N1 Cross-Clade Background with Both 188T and 189T.

No clinical progression, treatment annotation or clinical outcome has yet been published corresponding to this very important case that originated from the Indiana State Department of Health Laboratories.

HA Polymorphisms

. . . . Indiana22_C2_57M_2013_08_13 (

. . . . . . . . A/Indiana/22/2013
. . . . . . . . H7N9 Correlation NA 94I
. . . . . . . . Host Transition Indication NA 94I
. . . . . . . . CrossClade 188T and 189T
. . . . . . . . GISAID HA EPI467365

. . . . . . . . GISAID Isolate EPI_ISL_145658

. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)

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

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

. . . . . . . . 100N,

. . . . . . . . 166N,

. . . . . . . . syn174K (AAg),

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

. . . . . . . . 188T,

. . . . . . . . 189T,

. . . . . . . . 237I,

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . syn500R (AGg) [pH1N1 Rare],

. . . . . . . . . . . . . . . . . . [H7N9 Avian],

. . . . . . . . 502K)

NA Polymorphisms

. . . . Indiana22_C2_57M_2013_08_13 (

. . . . . . . . A/Indiana/22/2013
. . . . . . . . H7N9 Correlation NA 94I
. . . . . . . . Host Transition Indication NA 94I
. . . . . . . . CrossClade 188T and 208K
. . . . . . . . GISAID NA EPI467364

. . . . . . . . GISAID Isolate EPI_ISL_145658

. . . . . . . . 14 Polymorphisms (6 Amino and 8 Silent)

. . . . . . . . 44S,

. . . . . . . . 94I [pH1N1 Rare:
. . . . . . . . . . . . . 10(9) Cases over 10 Sequences,
. . . . . . . . . . . . . . . . . 2013 - Count 02
. . . . . . . . . . . . . . . . . 2012 - Count 02
. . . . . . . . . . . . . . . . . 2011 - Count 00
. . . . . . . . . . . . . . . . . 2010 - Count 04
. . . . . . . . . . . . . . . . . 2009 - Count 02],
. . . . . . . . . . [Emergent H7N9 wild type],
. . . . . . . . . . [Host Transition Indication:
. . . . . . . . . . . . . H7N1 Passerine Starling England,
. . . . . . . . . . . . . H7N1 Parrot Ireland,
. . . . . . . . . . . . . H7N1 Ostrich South Africa],

. . . . . . . . . . [H5N1 China Human wild type],
. . . . . . . . . . [s2007 H1N1],
. . . . . . . . 106V,

. . . . . . . . syn156R (CGg),

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

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

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1 wild type],
. . . . . . . . . . . . . . . . . . [H6N1],

. . . . . . . . syn209N (AAt) [H5N1 wild type],

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

. . . . . . . . 241I [H5N1],

. . . . . . . . syn243T (ACt) [H5N1 China Human wild type],

. . . . . . . . . . . . . . . . . . [H7N9 Avian],

. . . . . . . . 369K,

. . . . . . . . syn377P (CCa) [H5N1 wild type],

. . . . . . . . syn378N (AAt) [H5N1 wild type])

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

pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-09-10-23_00_00_621110 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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

2013-11-21

Burkina Faso Off-Clade pH1N1 Sequences with Strong Homology to H7N9 Vaccine Candidate

Burkina Faso

3 Sequences

Three Off-Clade Pandemic H1N1 sequences sampled from Burkina Faso were published recently at GISAID by the United States CDC. These West African sequences group with a small set of highly divergent sequences we have been following that carries an unusually strong polymorphic homology to H7N9. The set of distinct pH1N1 HA polymorphisms also displays a 51% homology to zoonotic H3N2 and a rather high 44% homology to the H7 serotypes.

On Wednesday, November 20, 2013, the National Institute of Infectious Diseases of Japan produced the details at GISAID of an Investigational Vaccine Candidate for Emergent H7N9 based on the Anhui1 base sequence. Evidently, when their candidate culturing process was modified with an initial Lewis Lung Carcinoma passage, a novel polymorphism to Emergent H7N9 manifested [Deposit Report].

That H7N9 host switching revision, HA 131T, also features on this group of avian-centric human pH1N1 sequences we have been following. The HA 131T has previously been seen in H7N9 Avian, the H7N7 human fatality, current H3N2 Human Seasonal (wild type), H1N1 Seasonal 2008, H1N1 Variant Human and in 1918. Two of the fatalities from the 2006 Egyptian H5N1 HA 230I-bearing Gharbiyah cluster carry this HA 131T. Animal occurrences include H3N2, avH1N1, H5N1 (including a parrot) and H6N1.

We note when a Group 1 serotype (H1) develops contemporaneous homology with Group 2 serotypes (H3 & H7). Identifying a reservoir for this small, but persisting, Off-Clade pH1N1 set found primarily in western Africa would be useful in understanding the factors involved for minority strain maturation.

The Burkina Faso details are annotated at the polymorphism level in the following sequence list.

HA Polymorphisms

. . . . BurkinaFaso875_C2_2013_02_26 (

. . . . . . . . A/Burkina Faso/875/2013

. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade

. . . . . . . . GISAID HA EPI482169

. . . . . . . . GISAID Isolate EPI_ISL_149349

. . . . . . . . 38 Polymorphisms (11 Amino and 27 Silent)

. . . . . . . . #11T [avH1N1, zH3N2, H9N2],

. . . . . . . . 35I [avH1N1, zH3N2, H5N1],

. . . . . . . . syn56G (GGc) [Emergent H7N9 Avian],

. . . . . . . . 89E [avH1N1_farm, zH3N2, 1918],

. . . . . . . . syn99I (ATt),

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

. . . . . . . . 131T [Emergent H7N9

. . . . . . . . . . . . . . . Investigational Vaccine Candidate:

. . . . . . . . . . . . . . . ChinaAnhuiChuzhou1_LLC1E3_35F_2013_03_15_f

. . . . . . . . . . . . . . . . . . . A/Anhui/1/2013 NIIDRG-10.1

. . . . . . . . . . . . . . . . . . . Deposit Report
. . . . . . . . . . . . . . . . . . . GISAID HA EPI486492

. . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150198

. . . . . . . . . . . . . . . Japan NIID Lab-Derived,

. . . . . . . . . . . . . . . Initial Passage in Lewis Lung Carcinoma culture],

. . . . . . . . . . . [H7N9 Avian],

. . . . . . . . . . . [H7N7 Human Fatality],
. . . . . . . . . . . [H3N2 Human Seasonal],

. . . . . . . . . . . [H1N1 Human Seasonal 2008],

. . . . . . . . . . . [H1N1 Variant Human 2007, 2011, 2012, 2013],

. . . . . . . . . . . [H1N1 Variant Swine 2011, 2012, 2013],

. . . . . . . . . . . [H1N1 Variant Mink 2012],

. . . . . . . . . . . [1918],

. . . . . . . . syn152I (ATt),

. . . . . . . . syn154L (CTg),

. . . . . . . . syn164L (CTt) [pH1N1 Upsilon],

. . . . . . . . 173R [H7N9 Avian],

. . . . . . . . 206S,

. . . . . . . . syn214K (AAa),

. . . . . . . . syn215P (CCa),

. . . . . . . . syn219I (ATt),

. . . . . . . . syn239P (CCa),

. . . . . . . . syn254P (CCa),

. . . . . . . . 262K [Emergent H7N9 wild type],

. . . . . . . . 266A [H7N9 Avian United States:

. . . . . . . . . . . . . . . . First Base Donor 266V gTC, gTT],

. . . . . . . . syn276H (CAt),

. . . . . . . . syn295F (TTc),

. . . . . . . . syn301I (ATt),

. . . . . . . . syn326S (TCc),

. . . . . . . . syn331G (GGt) [H7N9 Avian],

. . . . . . . . syn337A (GCt) [H7N9 Avian United States],

. . . . . . . . . . . . . . . . . [Pennsylvania07_C1_1F_2013_10_02

. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI485754

. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150035

. . . . . . . . . . . . . . . . . DominicanRep7626_C2_34F_2013_06_15_TmX_VxX

. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI477445

. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_148743],

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

. . . . . . . . 377K,

. . . . . . . . syn379T (ACc),

. . . . . . . . syn433E (GAg) [Emergent H7N9 wild type],

. . . . . . . . syn451K (AAa),

. . . . . . . . syn456L (cTA),

. . . . . . . . 463V [H6N1],

. . . . . . . . syn475D (GAc),

. . . . . . . . syn486T (ACc) [Emergent H7N9 wild type],

. . . . . . . . . . . . . . . . . . [zH3N2],

. . . . . . . . . . . . . . . . . . [H3N8 Avian],

. . . . . . . . syn505G (GGa),

. . . . . . . . 523A,

. . . . . . . . syn526S (TCc),

. . . . . . . . syn527L (TTa))

. . . . BurkinaFaso876_C2_2013_02_26_VxX (

. . . . . . . . A/Burkina Faso/876/2013

. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade

. . . . . . . . GISAID HA EPI482162

. . . . . . . . GISAID Isolate EPI_ISL_149346

. . . . . . . . 39 Polymorphisms (12 Amino and 27 Silent)

. . . . . . . . #11T [avH1N1, zH3N2, H9N2],

. . . . . . . . 13T [H5N1, H9N2, H13],

. . . . . . . . 35I [avH1N1, zH3N2, H5N1],

. . . . . . . . syn56G (GGc) [Emergent H7N9 Avian],

. . . . . . . . 89E [avH1N1_farm, zH3N2, 1918],

. . . . . . . . syn99I (ATt),

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

. . . . . . . . 131T [Emergent H7N9

. . . . . . . . . . . . . . . Investigational Vaccine Candidate:

. . . . . . . . . . . . . . . ChinaAnhuiChuzhou1_LLC1E3_35F_2013_03_15_f

. . . . . . . . . . . . . . . . . . . A/Anhui/1/2013 NIIDRG-10.1
. . . . . . . . . . . . . . . . . . . Deposit Report

. . . . . . . . . . . . . . . . . . . GISAID HA EPI486492

. . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150198

. . . . . . . . . . . . . . . Japan NIID Lab-Derived,

. . . . . . . . . . . . . . . Initial Passage in Lewis Lung Carcinoma culture],

. . . . . . . . . . . [H7N9 Avian],

. . . . . . . . . . . [H7N7 Human Fatality],
. . . . . . . . . . . [H3N2 Human Seasonal],

. . . . . . . . . . . [H1N1 Human Seasonal 2008],

. . . . . . . . . . . [H1N1 Variant Human 2007, 2011, 2012, 2013],

. . . . . . . . . . . [H1N1 Variant Swine 2011, 2012, 2013],

. . . . . . . . . . . [H1N1 Variant Mink 2012],

. . . . . . . . . . . [1918],

. . . . . . . . syn152I (ATt),

. . . . . . . . syn154L (CTg),

. . . . . . . . 158E,

. . . . . . . . 206S,

. . . . . . . . syn214K (AAa),

. . . . . . . . syn215P (CCa),

. . . . . . . . syn219I (ATt),

. . . . . . . . syn239P (CCa),

. . . . . . . . syn254P (CCa),

. . . . . . . . 262K [Emergent H7N9 wild type],

. . . . . . . . 266A [H7N9 Avian United States:

. . . . . . . . . . . . . . . . First Base Donor 266V gTC, gTT],

. . . . . . . . syn276H (CAt),

. . . . . . . . syn295F (TTc),

. . . . . . . . syn301I (ATt),

. . . . . . . . syn326S (TCc),

. . . . . . . . syn331G (GGt) [H7N9 Avian],

. . . . . . . . syn337A (GCt) [H7N9 Avian United States],

. . . . . . . . . . . . . . . . . [Pennsylvania07_C1_1F_2013_10_02

. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI485754

. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150035

. . . . . . . . . . . . . . . . . DominicanRep7626_C2_34F_2013_06_15_TmX_VxX

. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI477445

. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_148743],

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

. . . . . . . . 377K,

. . . . . . . . syn379T (ACc),

. . . . . . . . syn425N (AAc) [H7N9 Avian],

. . . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],

. . . . . . . . syn433E (GAg) [Emergent H7N9 wild type],

. . . . . . . . syn451K (AAa),

. . . . . . . . syn456L (cTA),

. . . . . . . . 463V [H6N1],

. . . . . . . . syn475D (GAc),

. . . . . . . . syn486T (ACc) [Emergent H7N9 wild type],

. . . . . . . . . . . . . . . . . . [zH3N2],

. . . . . . . . . . . . . . . . . . [H3N8 Avian],

. . . . . . . . syn505G (GGa),

. . . . . . . . 523A,

. . . . . . . . syn526S (TCc),

. . . . . . . . syn527L (TTa))

. . . . BurkinaFaso859_C1_2013_02_18 (

. . . . . . . . A/Burkina Faso/859/2013

. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade

. . . . . . . . GISAID HA EPI484718

. . . . . . . . GISAID Isolate EPI_ISL_148736

. . . . . . . . 37 Polymorphisms (10 Amino and 27 Silent)

. . . . . . . . #11T [avH1N1, zH3N2, H9N2],

. . . . . . . . 35I [avH1N1, zH3N2, H5N1],

. . . . . . . . syn56G (GGc) [Emergent H7N9 Avian],

. . . . . . . . 89E [avH1N1_farm, zH3N2, 1918],

. . . . . . . . syn99I (ATt),

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

. . . . . . . . 131T [Emergent H7N9

. . . . . . . . . . . . . . . Investigational Vaccine Candidate:

. . . . . . . . . . . . . . . ChinaAnhuiChuzhou1_LLC1E3_35F_2013_03_15_f

. . . . . . . . . . . . . . . . . . . A/Anhui/1/2013 NIIDRG-10.1
. . . . . . . . . . . . . . . . . . . Deposit Report

. . . . . . . . . . . . . . . . . . . GISAID HA EPI486492

. . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150198

. . . . . . . . . . . . . . . Japan NIID Lab-Derived,

. . . . . . . . . . . . . . . Initial Passage in Lewis Lung Carcinoma culture],

. . . . . . . . . . . [H7N9 Avian],

. . . . . . . . . . . [H7N7 Human Fatality],
. . . . . . . . . . . [H3N2 Human Seasonal],

. . . . . . . . . . . [H1N1 Human Seasonal 2008],

. . . . . . . . . . . [H1N1 Variant Human 2007, 2011, 2012, 2013],

. . . . . . . . . . . [H1N1 Variant Swine 2011, 2012, 2013],

. . . . . . . . . . . [H1N1 Variant Mink 2012],

. . . . . . . . . . . [1918],

. . . . . . . . syn152I (ATt),

. . . . . . . . syn154L (CTg),

. . . . . . . . 206S,

. . . . . . . . syn214K (AAa),

. . . . . . . . syn215P (CCa),

. . . . . . . . syn219I (ATt),

. . . . . . . . syn239P (CCa),

. . . . . . . . syn254P (CCa),

. . . . . . . . 262K [Emergent H7N9 wild type],

. . . . . . . . 266A [H7N9 Avian United States:

. . . . . . . . . . . . . . . . First Base Donor 266V gTC, gTT],

. . . . . . . . syn276H (CAt),

. . . . . . . . syn295F (TTc),

. . . . . . . . syn301I (ATt),

. . . . . . . . syn326S (TCc),

. . . . . . . . syn331G (GGt) [H7N9 Avian],

. . . . . . . . syn337A (GCt) [H7N9 Avian United States],

. . . . . . . . . . . . . . . . . [Pennsylvania07_C1_1F_2013_10_02

. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI485754

. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150035

. . . . . . . . . . . . . . . . . DominicanRep7626_C2_34F_2013_06_15_TmX_VxX

. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI477445

. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_148743],

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

. . . . . . . . 377K,

. . . . . . . . syn379T (ACc),

. . . . . . . . syn425N (AAc) [H7N9 Avian],

. . . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],

. . . . . . . . syn433E (GAg) [Emergent H7N9 wild type],

. . . . . . . . syn451K (AAa),

. . . . . . . . syn456L (cTA),

. . . . . . . . 463V [H6N1],

. . . . . . . . syn475D (GAc),

. . . . . . . . syn486T (ACc) [Emergent H7N9 wild type],

. . . . . . . . . . . . . . . . . . [zH3N2],

. . . . . . . . . . . . . . . . . . [H3N8 Avian],

. . . . . . . . syn505G (GGa),

. . . . . . . . 523A,

. . . . . . . . syn526S (TCc),

. . . . . . . . syn527L (TTa))

NA Polymorphisms

. . . . BurkinaFaso875_C2_2013_02_26 (

. . . . . . . . A/Burkina Faso/875/2013

. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID NA EPI482168

. . . . . . . . GISAID Isolate EPI_ISL_149349

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

. . . . . . . . 13I [Emergent H7N9 wild type
. . . . . . . . . . . . . . First Base Donor ACc, ACT, Atg],
. . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [H6N1],

. . . . . . . . syn20A (GCc),

. . . . . . . . 74V,

. . . . . . . . syn89S (TCt),

. . . . . . . . 106V,

. . . . . . . . syn127L (cTG),

. . . . . . . . syn183A (GCc),

. . . . . . . . syn192T (ACc),

. . . . . . . . syn304V (GTt),

. . . . . . . . syn370G (GGg),

. . . . . . . . syn382G (GGa),

. . . . . . . . 385T,

. . . . . . . . 386K [Emergent H7N9 wild type],

. . . . . . . . . . . . [pH1N1 Upsilon],

. . . . . . . . . . . . [H9N2],

. . . . . . . . syn433E (GAa))

. . . . BurkinaFaso876_C2_2013_02_26_VxX (

. . . . . . . . A/Burkina Faso/876/2013

. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID NA EPI482161

. . . . . . . . GISAID Isolate EPI_ISL_149346

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

. . . . . . . . syn20A (GCc),

. . . . . . . . 74V,

. . . . . . . . syn89S (TCt),

. . . . . . . . 106V,

. . . . . . . . syn127L (cTG),

. . . . . . . . syn140L (tTA),

. . . . . . . . syn183A (GCc),

. . . . . . . . syn192T (ACc),

. . . . . . . . syn304V (GTt),

. . . . . . . . syn370G (GGg),

. . . . . . . . syn382G (GGa),

. . . . . . . . 385T,

. . . . . . . . 386K [Emergent H7N9 wild type],

. . . . . . . . . . . . [pH1N1 Upsilon],

. . . . . . . . . . . . [H9N2],

. . . . . . . . syn433E (GAa))

. . . . BurkinaFaso859_C1_2013_02_18 (

. . . . . . . . A/Burkina Faso/859/2013

. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID NA EPI477427

. . . . . . . . GISAID Isolate EPI_ISL_148736

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

. . . . . . . . syn20A (GCc),

. . . . . . . . syn47E (GAg),

. . . . . . . . 74V,

. . . . . . . . syn89S (TCt),

. . . . . . . . 106V,

. . . . . . . . syn127L (cTG),

. . . . . . . . syn183A (GCc),

. . . . . . . . syn192T (ACc),

. . . . . . . . syn304V (GTt),

. . . . . . . . syn370G (GGg),

. . . . . . . . syn382G (GGa),

. . . . . . . . 385T,

. . . . . . . . 386K [Emergent H7N9 wild type],

. . . . . . . . . . . . [pH1N1 Upsilon],

. . . . . . . . . . . . [H9N2],

. . . . . . . . syn433E (GAa))

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

pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-11-20-01_51_10_493570 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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

2013-11-09

HA 142D: pH1N1 Vaccine Escape Diversity

Gain of Function Empiriks

Polymorphism

pH1N1 HA 142D

Map - Active and Detailed

Clinical and Genetic Features

48 Cases over 52 Sequences

Key Severity Indicators

Status
Host Transition
PROBABLE

GenoType	Count
Vaccine Escape Diversity
VxX 156E	01
VxX 158E	01
VxX 159D	02
VxX 225G	04
VxX 225Y	01

Segment	Type	Count
Ambiguity
Hemagglutinin	Binary	17
Neuraminidase	Binary	03

Revision	Count
Receptor Binding Variance
HA 189D	01
HA 190G	01
HA 193R	01
HA 194I	01
HA 225G	04
HA 225Y	01
HA 233H	10

Human Variant Observations

Name	ID
Variant Human H1N1 2011
Wisconsin28_55M_2011_12_01	EPI346731
Wisconsin28_C1_55M_2011_12_01	EPI346916

Notable pH1N1 Samples

Name	ID
Severe and Fatal Disease Study
ChinaShenzhen33_xM_2009_09_08	EPI348003
ChinaShenzhen28_xF_2009_08_31	EPI348125

Name	ID
H7N9 Correlation HA
PuertoRico05_C2_45M_2013_06_14_VxX	EPI465269
Luxembourg20130134_2013_01_22	EPI457408
Virginia13_M1C1_46F_2012_08_21	EPI404817
Tanzania2085_E3_30F_2012_12_10	EPI422630
India2005_E3_2012_11_24	EPI422601
BelgiumG860_M1_xF_2012_11_08	EPI417116
JapanSaitama289_M2+1_2011_04_02_VxX	EPI329107
ChinaShenzhen33_xM_2009_09_08	EPI348003
ChinaShenzhen28_xF_2009_08_31	EPI348125

Cross SeroType Analytics

SeroType	Count	Percent
HA Set Polymorphic Homology
H5N1	76	45%
H7N7	60	36%

SeroType
Origin-Seeking HA 142D
H5N1 2nd Base Donor 142Q (CAG)
H9N2

Isolate Metrics

Sample Year	Count
Calendar
2013	19
2012	05
2011	04
2010	14
2009	10

Observation	Per Cent
Age Dynamic
Child Aged 17 or Under	50%
Child Aged 07 or Under	25%

Clade Name	Count
Cladistics
Clade2:188T	27
UnCladed	23
Clade1:189T	01
Clade5:208K_219V	01

HA Polymorphisms

. . . . BrazilSaoPauloJaboticabal630177_1M_2013_09_30_s (

. . . . . . . . A/Sao Paulo/6-30177/2013
. . . . . . . . Treatment by Oseltamivir
. . . . . . . . Deposit Report
. . . . . . . . GISAID HA EPI484748

. . . . . . . . GISAID Isolate EPI_ISL_149732

. . . . . . . . 27 Polymorphisms (12 Amino and 15 Silent)

. . . . . . . . #1T,

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

. . . . . . . . 100N,

. . . . . . . . 115K [pH1N1 with HA 230I],

. . . . . . . . . . . . [H7N7 Equine: Host Transition],

. . . . . . . . . . . . [H5N1],

. . . . . . . . . . . . [H9N2],

. . . . . . . . syn141H (CAc) [H5N1],

. . . . . . . . 142D [pH1N1 Rare: 46 Cases over 50 Sequences,

. . . . . . . . . . . . . JapanNagasakiHA105_M_13F_2010_01_12

. . . . . . . . . . . . . . . . . . . . . . . . . with HA 190G],
. . . . . . . . . . . . . [Propensity to Children:
. . . . . . . . . . . . . . . . . . 52% - Age 17 or Under],

. . . . . . . . . . . . . [Co-location pH1N1_υ Polymorphisms (15)],

. . . . . . . . . . . . . [Co-location pH1N1 VxX indicators

. . . . . . . . . . . . . . . . . . . . . HA 158E mix, 159D mix],

. . . . . . . . . . . . . [Co-location pH1N1 HA 166Q],

. . . . . . . . . . . . . [Co-location pH1N1 HA 189D, 189T_xL, 190G],

. . . . . . . . . . . . . [Co-location pH1N1 RBS 225G (2), 226R, 233H],

. . . . . . . . . . . . . [Co-location early pH1N1 HA 237I],

. . . . . . . . . . . . . [Co-location pH1N1 Isolated from Blood (Serum)],

. . . . . . . . . . . . . [Studied with pH1N1 Severe and Fatal cases],

. . . . . . . . . . . . . [Wisconsin28_55M_2011_12_01

. . . . . . . . . . . . . . . . swine-like human H1N1 variant case

. . . . . . . . . . . . . . . . . . with pH1N1 PA & M gene segments],
. . . . . . . . . . . . . [H5N1 2^nd Base Donor 142Q (CAG)],

. . . . . . . . . . . . . [H9N2],

. . . . . . . . . . . . . [H13 LookAside_u],

. . . . . . . . . . . . . [zH3N2 LookAside_d2],

. . . . . . . . . . . . . [zH6N1 LookAside_d2],

. . . . . . . . syn156K (AAg),

. . . . . . . . 166Q [avH1N1

. . . . . . . . . . . . . . . with HA #1T, syn34N (AAt), syn77S (AGt),
. . . . . . . . . . . . . . . . . . . syn102E (GAa), syn156K (AAg),
. . . . . . . . . . . . . . . . . . . 188T, syn258F (TTt), syn285P (CCt), syn306C (TGc),
. . . . . . . . . . . . . . . . . . . 324I, syn333F (TTc), syn372Q (CAa), syn396V (GTg),
. . . . . . . . . . . . . . . . . . . syn465N (AAt)],
. . . . . . . . . . . . .[Virginia13_M1C1_46F_2012_08_21
. . . . . . . . . . . . . . . . . . . . . . . . with HA 142D, 188T, syn223V (GTa),
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn338G (GGc), 377K, 454N],

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

. . . . . . . . 188T,

. . . . . . . . syn223V (GTa),

. . . . . . . . syn236L (tTA),

. . . . . . . . 259T [pH1N1 Upsilon US Military],

. . . . . . . . syn285P (CCt),

. . . . . . . . 286E,

. . . . . . . . syn306C (TGc),

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

. . . . . . . . 324I [pH1N1 with HA 230I],

. . . . . . . . . . . . [Wilson-Smith],

. . . . . . . . . . . . [1918],

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K [pH1N1 Upsilon],

. . . . . . . . . . . . [avH1N1_farm],

. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],

. . . . . . . . . . . . [H5N1],

. . . . . . . . . . . . [H9N2],

. . . . . . . . . . . . [WSN, WSZ],

. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I]

. . . . . . . . . . . . . . . . . . [1918])

. . . . Bolivia1351_C2_46M_2013_07_31_VxX (

. . . . . . . . A/Bolivia/1351/2013

. . . . . . . . Vaccine Escape Genotype HA 225Y
. . . . . . . . GISAID HA EPI467387

. . . . . . . . GISAID Isolate EPI_ISL_145666

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

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

. . . . . . . . syn177L (CTa),

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

. . . . . . . . 225Y,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454K,

. . . . . . . . 502K)

. . . . ChileSantiago46965_C2C1_28M_2013_07_15 (

. . . . . . . . A/Santiago/46965/2013

. . . . . . . . GISAID HA EPI467229

. . . . . . . . GISAID Isolate EPI_ISL_145635

. . . . . . . . 26 Polymorphisms (9 Amino and 17 Silent)

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

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

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

. . . . . . . . syn94Y (TAt),

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . syn455Q (CAa),

. . . . . . . . 502K)

. . . . Florida20_C1_47M_2013_07_07 (

. . . . . . . . A/Florida/20/2013

. . . . . . . . GeoCombination of South America and Puerto Rico
. . . . . . . . GISAID HA EPI465254

. . . . . . . . GISAID Isolate EPI_ISL_145023

. . . . . . . . 26 Polymorphisms (10 Amino and 16 Silent)

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn352Y (TAt),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 475N mix wt [pH1N1 Rare ~ 40 Sequences],
. . . . . . . . . . . . . . . . . [sH1N1 2009],
. . . . . . . . . . . . . . . . . [sH3N2 2013],
. . . . . . . . . . . . . . . . . [zH3N2 Hong Kong Passerine 2009],
. . . . . . . . . . . . . . . . . [H3N8 Guangxi Commercial Poultry 2010],
. . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . [H5 Avian],
. . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . . . . . . . . . . [H13],

. . . . . . . . 502K,

. . . . . . . . syn548C (TGc))

. . . . ArgentinaMarDelPlata10091_C1C1_xM_2013_07_04 (

. . . . . . . . A/Mar Del Plata/10091/2013

. . . . . . . . GISAID HA EPI467370

. . . . . . . . GISAID Isolate EPI_ISL_145660

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

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K)

. . . . Argentina911_C1C1_60F_2013_07_02 (

. . . . . . . . A/Argentina/911/2013

. . . . . . . . GISAID HA EPI465495

. . . . . . . . GISAID Isolate EPI_ISL_145105

. . . . . . . . 24 Polymorphisms (9 Amino and 15 Silent)

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

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

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

. . . . . . . . 100N,

. . . . . . . . syn120F (TTt),

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K)

. . . . Paraguay17_C1C1_55F_2013_07_01 (

. . . . . . . . A/Paraguay/17/2013

. . . . . . . . GISAID HA EPI484969

. . . . . . . . GISAID Isolate EPI_ISL_149777

. . . . . . . . 26 Polymorphisms (11 Amino and 15 Silent)

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

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

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

. . . . . . . . 87I,

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

. . . . . . . . syn419L (tTG) [avH1N1_farm],

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

. . . . . . . . 454N,

. . . . . . . . 502K,

. . . . . . . . 528I [H7N7 wild type],

. . . . . . . . . . . [H7N9 LookAside_u],

. . . . . . . . . . . [avH1N1])

. . . . Uruguay279_C1_xM_2013_06_21 (

. . . . . . . . A/Uruguay/279/2013

. . . . . . . . GISAID HA EPI467206

. . . . . . . . GISAID Isolate EPI_ISL_145630

. . . . . . . . 26 Polymorphisms (12 Amino and 14 Silent)

. . . . . . . . #10M mix wt [H5N1],

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

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

. . . . . . . . 57N [Argentina508_S1C1_62M_2013_06_16],
. . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . [H10N7],

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 269F [Argentina508_S1C1_62M_2013_06_16],
. . . . . . . . . . . . [H6N1],

. . . . . . . . . . . . [H13],
. . . . . . . . 286E,

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

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K)

. . . . Argentina508_S1C1_62M_2013_06_16 (

. . . . . . . . A/Argentina/508/2013

. . . . . . . . GISAID HA EPI465257

. . . . . . . . GISAID Isolate EPI_ISL_145024

. . . . . . . . 27 Polymorphisms (12 Amino and 15 Silent)

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

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

. . . . . . . . 57N [Uruguay279_C1_xM_2013_06_21],
. . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . [H10N7],

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

. . . . . . . . 100N,

. . . . . . . . syn129H (CAc),

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 264D [pH1N1 Rare: 26 Cases over 28 Sequences,
. . . . . . . . . . . . . . . ReEmergent Singular 2013,
. . . . . . . . . . . . . . . Last in China 2010-01-04,
. . . . . . . . . . . . . . . HA 225E Count 03,
. . . . . . . . . . . . . . . US Military Count 11:
. . . . . . . . . . . . . . . . . . First pH1N1 HA 230I,
. . . . . . . . . . . . . . . . . . HA 225N],
. . . . . . . . . . . . [H6N1],

. . . . . . . . 269F [Uruguay279_C1_xM_2013_06_21],
. . . . . . . . . . . . [H6N1],

. . . . . . . . . . . . [H13],

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K)

. . . . PuertoRico01_C2_13F_2013_06_14 (

. . . . . . . . A/Puerto Rico/01/2013

. . . . . . . . GISAID HA EPI468085

. . . . . . . . GISAID Isolate EPI_ISL_145509

. . . . . . . . 25 Polymorphisms (9 Amino and 16 Silent)

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn352Y (TAt),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K,

. . . . . . . . syn548C (TGc))

. . . . PuertoRico03_E3_7M_2013_06_14 (

. . . . . . . . A/Puerto Rico/03/2013

. . . . . . . . GISAID HA EPI465459

. . . . . . . . GISAID Isolate EPI_ISL_145090

. . . . . . . . 26 Polymorphisms (10 Amino and 16 Silent)

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

. . . . . . . . 226R,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn352Y (TAt),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K,

. . . . . . . . syn548C (TGc))

. . . . PuertoRico01_E3_13F_2013_06_14_VxX (

. . . . . . . . A/Puerto Rico/01/2013

. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . GISAID HA EPI465455

. . . . . . . . GISAID Isolate EPI_ISL_145088

. . . . . . . . 26 Polymorphisms (10 Amino and 16 Silent)

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

. . . . . . . . 225G,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn352Y (TAt),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K,

. . . . . . . . syn548C (TGc))

. . . . PuertoRico05_C2_45M_2013_06_14_VxX (

. . . . . . . . A/Puerto Rico/05/2013

. . . . . . . . Vaccine Escape Genotype HA 159D
. . . . . . . . Emergent H7N9 Correlation
. . . . . . . . GISAID HA EPI465269

. . . . . . . . GISAID Isolate EPI_ISL_145028

. . . . . . . . 26 Polymorphisms (10 Amino and 16 Silent)

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

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

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

. . . . . . . . 100N,

. . . . . . . . 130E [H5N1 wild type],

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

. . . . . . . . 142D,

. . . . . . . . 159D mix wt [Emergent H7N9 wild type],

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

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

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

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

. . . . . . . . syn352Y (TAt),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K,

. . . . . . . . syn548C (TGc))

. . . . PuertoRico03_C1_7M_2013_06_14 (

. . . . . . . . A/Puerto Rico/03/2013

. . . . . . . . GISAID HA EPI465102

. . . . . . . . GISAID Isolate EPI_ISL_144967

. . . . . . . . 26 Polymorphisms (10 Amino and 16 Silent)

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn352Y (TAt),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

. . . . . . . . 437N mix wt [pH1N1 Rare: 21 Cases over 22 Sequences,
. . . . . . . . . . . . . . . . . . . . Fatality Russia 2009:

. . . . . . . . . . . . . . . . . . . . . . RussiaArkhangelsk_CRIEGNY_2009_11_25_xL_f,
. . . . . . . . . . . . . . . . . . . . . . Deposit Report
. . . . . . . . . . . . . . . . . . . . TamiFlu Resistance Taiwan 2011,
. . . . . . . . . . . . . . . . . . . . Probable Youth Marker],

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

. . . . . . . . 454N,

. . . . . . . . 502K,

. . . . . . . . syn548C (TGc))

. . . . PuertoRico01_C1_13F_2013_06_14 (

. . . . . . . . A/Puerto Rico/01/2013

. . . . . . . . GISAID HA EPI465070

. . . . . . . . GISAID Isolate EPI_ISL_144956

. . . . . . . . 26 Polymorphisms (10 Amino and 16 Silent)

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn352Y (TAt),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

. . . . . . . . 440H mix wt,

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

. . . . . . . . 454N,

. . . . . . . . 502K,

. . . . . . . . syn548C (TGc))

. . . . Argentina168_S1C1_xM_2013_06_04_VxX (

. . . . . . . . A/Argentina/168/2013

. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . GISAID HA EPI465453

. . . . . . . . GISAID Isolate EPI_ISL_145087

. . . . . . . . 26 Polymorphisms (11 Amino and 15 Silent)

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

. . . . . . . . 225G,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

. . . . . . . . 324A mix wt,

. . . . . . . . syn326S (TCc) mix wt,

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K)

. . . . Argentina102_C1C1_56F_2013_05_30 (

. . . . . . . . A/Argentina/102/2013

. . . . . . . . GISAID HA EPI465711

. . . . . . . . GISAID Isolate EPI_ISL_145086

. . . . . . . . 24 Polymorphisms (10 Amino and 14 Silent)

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

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

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

. . . . . . . . 100N,

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

. . . . . . . . 142D,

. . . . . . . . 166I,

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

. . . . . . . . syn185P (CCg),

. . . . . . . . 188T,

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

. . . . . . . . 237I,

. . . . . . . . syn239P (CCa),

. . . . . . . . 286E,

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

. . . . . . . . 324A,

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

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

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

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

. . . . . . . . 454N,

. . . . . . . . 502K)

. . . . Hungary17_M1E5M1_xF_2013_02_15_VxX (

. . . . . . . . A/Hungary/17/2013

. . . . . . . . Vaccine Escape Genotype HA 156E
. . . . . . . . GISAID HA EPI462037

. . . . . . . . GISAID Isolate EPI_ISL_144056

. . . . . . . . 24 Polymorphisms (10 Amino and 14 Silent)

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

. . . . . . . . syn47L (tTA),

. . . . . . . . syn58C (TGc),

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

. . . . . . . . 100N,

. . . . . . . . 142D,

. . . . . . . . 156E,

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

. . . . . . . . 188T,

. . . . . . . . 193R,

. . . . . . . . 237I,

. . . . . . . . 286E,

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

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

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

. . . . . . . . syn361G (GGa),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

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

. . . . . . . . syn403L (tTG),

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

. . . . . . . . 454N,

. . . . . . . . 502K,

. . . . . . . . syn527L (TTa))

. . . . Luxembourg20130134_2013_01_22 (

. . . . . . . . A/Luxembourg/20130134/2013
. . . . . . . . H7N9 Correlation

. . . . . . . . GISAID HA EPI457408

. . . . . . . . GISAID Isolate EPI_ISL_142843

. . . . . . . . 26 Polymorphisms (11 Amino and 15 Silent)

. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],

. . . . . . . . syn#5L (CTg) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . . . . . . . . . . .[H7N7 Passerine],

. . . . . . . . #2L [neH7N9 wild type],
. . . . . . . . . . . [H7N7 Rare: Sea Mammal & Anser],
. . . . . . . . . . . [H7N3 Pheasant],
. . . . . . . . . . . [H7N3 Commercial Poultry],
. . . . . . . . . . . [H7N2 Ratite],
. . . . . . . . . . . [H7N1 Ratite],

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

. . . . . . . . 87G,

. . . . . . . . syn102E (GAa),

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

. . . . . . . . 142D,

. . . . . . . . 146G,

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . syn223V (GTa),

. . . . . . . . syn228G (GGa),

. . . . . . . . syn240G (GGg),

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

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

. . . . . . . . 377K,

. . . . . . . . syn396V (GTg) mix wt,

. . . . . . . . syn420D (GAt) mix wt,

. . . . . . . . 435D mix wt, [pH1N1 Rare: 1 Case,
. . . . . . . . . . . . . . . . . . . . . . Singapore 2010],

. . . . . . . . syn448L (TTg) mix wt,

. . . . . . . . 454N,

. . . . . . . . syn465N (AAt) mix wt,

. . . . . . . . 502K mix wt,

. . . . . . . . syn515Q (CAa) mix wt,

. . . . . . . . syn524A (GCt),

. . . . . . . . HA Truncated after aa528)

. . . . Tanzania2085_E3_30F_2012_12_10 (

. . . . . . . . A/Tanzania/2085/2012

. . . . . . . . Clade2:188T with Diverse Hemagglutinin

. . . . . . . . H7N9 Correlation
. . . . . . . . GISAID HA EPI422630

. . . . . . . . GISAID Isolate EPI_ISL_135825

. . . . . . . . 26 Polymorphisms (12 Amino and 14 Silent)

. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],

. . . . . . . . syn#5L (CTg) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . . . . . . . . . . .[H7N7 Passerine],

. . . . . . . . syn22V (GTg),

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

. . . . . . . . 87G,

. . . . . . . . syn102E (GAa),

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

. . . . . . . . 142D,

. . . . . . . . 146G,

. . . . . . . . 172R,

. . . . . . . . 175K,

. . . . . . . . 188T,

. . . . . . . . 189D,

. . . . . . . . 200T,

. . . . . . . . syn223V (GTa),

. . . . . . . . 226R,

. . . . . . . . syn240G (GGg),

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

. . . . . . . . syn301I (ATa),

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

. . . . . . . . 377K,

. . . . . . . . 454N,

. . . . . . . . syn465N (AAt),

. . . . . . . . syn515Q (CAa),

. . . . . . . . syn524A (GCt),

. . . . . . . . syn538F (TTt))

. . . . India2005_E3_2012_11_24 (

. . . . . . . . A/India/2005/2012
. . . . . . . . H7N9 Correlation

. . . . . . . . GISAID HA EPI422601

. . . . . . . . GISAID Isolate EPI_ISL_135815

. . . . . . . . 23 Polymorphisms (10 Amino and 13 Silent)

. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],

. . . . . . . . syn#5L (CTg) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . . . . . . . . . . .[H7N7 Passerine],

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

. . . . . . . . syn66G (GGg),

. . . . . . . . 87G,

. . . . . . . . syn102E (GAa),

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

. . . . . . . . 142D,

. . . . . . . . 146G,

. . . . . . . . 188T,

. . . . . . . . 194I,

. . . . . . . . 200T,

. . . . . . . . syn223V (GTa),

. . . . . . . . syn240G (GGg),

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

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

. . . . . . . . 377K,

. . . . . . . . 430I [H7N9 2011]

. . . . . . . . 454N,

. . . . . . . . syn465N (AAt),

. . . . . . . . syn515Q (CAa),

. . . . . . . . syn524A (GCt),

. . . . . . . . syn538F (TTt))

. . . . BelgiumG860_M1_xF_2012_11_08 (

. . . . . . . . A/Belgium/G860/2012
. . . . . . . . H7N9 Correlation

. . . . . . . . GISAID HA EPI417116

. . . . . . . . GISAID Isolate EPI_ISL_134396

. . . . . . . . 24 Polymorphisms (8 Amino and 16 Silent)

. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],

. . . . . . . . syn#5L (CTg) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . . . . . . . . . . .[H7N7 Passerine],

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

. . . . . . . . syn44L (CTg),

. . . . . . . . 87G,

. . . . . . . . syn102E (GAa),

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

. . . . . . . . 142D,

. . . . . . . . 146G,

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . syn223V (GTa),

. . . . . . . . syn228G (GGa),

. . . . . . . . syn240G (GGg),

. . . . . . . . syn252V (GTa),

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

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

. . . . . . . . 377K,

. . . . . . . . syn420D (GAt),

. . . . . . . . 454N,

. . . . . . . . syn465N (AAt),

. . . . . . . . syn515Q (CAa),

. . . . . . . . syn524A (GCt),

. . . . . . . . syn538F (TTt))

. . . . IndiaLKO2577_2012_09_22 (

. . . . . . . . A/India/LKO2577/2012

. . . . . . . . GISAID HA EPI441661

. . . . . . . . GISAID Isolate EPI_ISL_139281

. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)

. . . . . . . . HA Truncated before aa132,

. . . . . . . . 142D,

. . . . . . . . 146G,

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . syn223V (GTa),

. . . . . . . . syn240G (GGg),

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

. . . . . . . . HA Truncated after aa269)

. . . . Virginia13_M1C1_46F_2012_08_21 (

. . . . . . . . A/Virginia/13/2012
. . . . . . . . H7N9 Correlation
. . . . . . . . Distant to Relative:
. . . . . . . . . . ~ India2005_E3_2012_11_24
. . . . . . . . . . [EPI422601]

. . . . . . . . . . 09 Nucleotides
. . . . . . . . GISAID HA EPI404817

. . . . . . . . GISAID Isolate EPI_ISL_131789

. . . . . . . . 26 Polymorphisms (11 Amino and 15 Silent)

. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],

. . . . . . . . syn#5L (CTg) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . . . . . . . . . . .[H7N7 Passerine],

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

. . . . . . . . 87G,

. . . . . . . . syn102E (GAa),

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

. . . . . . . . 132D,

. . . . . . . . 142D,

. . . . . . . . 146G,

. . . . . . . . 166Q [avH1N1

. . . . . . . . . . . . . . . with HA #1T, syn34N (AAt), syn77S (AGt),
. . . . . . . . . . . . . . . . . . . syn102E (GAa), syn156K (AAg),
. . . . . . . . . . . . . . . . . . . 188T, syn258F (TTt), syn285P (CCt), syn306C (TGc),
. . . . . . . . . . . . . . . . . . . 324I, syn333F (TTc), syn372Q (CAa), syn396V (GTg),
. . . . . . . . . . . . . . . . . . . syn465N (AAt)],
. . . . . . . . . . . . .[BrazilSaoPauloJaboticabal630177_1M_2013_09_30_s
. . . . . . . . . . . . . . . . . . . . . . . . with HA 142D, 188T, syn223V (GTa),
. . . . . . . . . . . . . . . . . . . . . . . . . . . syn338G (GGc), 377K, 454N],
. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . syn223V (GTa),

. . . . . . . . syn238E (GAa),

. . . . . . . . syn240G (GGg),

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

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

. . . . . . . . 377K,

. . . . . . . . 381T mix wt [H7N7],

. . . . . . . . syn403L (tTG),

. . . . . . . . 454N,

. . . . . . . . syn465N (AAt),

. . . . . . . . syn515Q (CAa),

. . . . . . . . syn524A (GCt) [H5N1],

. . . . . . . . syn530V (GTg) [H6N1],

. . . . . . . . syn538F (TTt) [H5N1])

. . . . SouthAfricaJohannesburg150_M1M1_46F_2011_07_10 (

. . . . . . . . A/Johannesburg/150/2011

. . . . . . . . Clade5:208K_219V

. . . . . . . . GISAID HA EPI346655

. . . . . . . . GISAID Isolate EPI_ISL_99903

. . . . . . . . 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))

. . . . AustraliaBrisbane139_M4_59M_2011_04_07_VxX (

. . . . . . . . A/BRISBANE/139/2011

. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . GISAID HA EPI332676

. . . . . . . . GISAID Isolate EPI_ISL_95091

. . . . . . . . 15 Polymorphisms (7 Amino and 8 Silent)

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

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

. . . . . . . . 142D,

. . . . . . . . 146G,

. . . . . . . . 158E mix wt,

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . syn316R (AGg),

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

. . . . . . . . 377K,

. . . . . . . . syn417G (GGg),

. . . . . . . . syn439D (GAt),

. . . . . . . . 454N,

. . . . . . . . syn465N (AAt),

. . . . . . . . syn538F (TTt),

. . . . . . . . HA Truncated after aa548)

. . . . JapanSaitama289_M2+1_2011_04_02_VxX (

. . . . . . . . A/SAITAMA/289/2011

. . . . . . . . Vaccine Escape Genotype HA 159D
. . . . . . . . Emergent H7N9 Correlation
. . . . . . . . GISAID HA EPI329107

. . . . . . . . GISAID Isolate EPI_ISL_94426

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

. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],

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

. . . . . . . . 76T,

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

. . . . . . . . 123A,

. . . . . . . . 142D,

. . . . . . . . 146G,

. . . . . . . . 159D mix wt [Emergent H7N9 wild type],

. . . . . . . . syn178V (GTa),

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . syn292S (AGt),

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

. . . . . . . . HA Truncated after aa348)

. . . . AustraliaVictoriaRythdale512_M1_46M_2011_02_04 (

. . . . . . . . A/VICTORIA/512/2011

. . . . . . . . GISAID HA EPI331324

. . . . . . . . GISAID Isolate EPI_ISL_94794

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

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . 188T,

. . . . . . . . 200T,

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

. . . . . . . . syn343G (GGa),

. . . . . . . . 377K,

. . . . . . . . syn398K (AAg),

. . . . . . . . 454N,

. . . . . . . . syn465N (AAt),

. . . . . . . . syn538F (TTt))

. . . . SingaporeKK376_C2_14F_2010_06_07 (

. . . . . . . . A/Singapore/KK376/2010

. . . . . . . . GISAID HA EPI385493

. . . . . . . . GISAID Isolate EPI_ISL_124750

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

. . . . . . . . syn18T (ACc),

. . . . . . . . syn107Q (CAg),

. . . . . . . . 115K [pH1N1 with HA 230I,
. . . . . . . . . . . . . BrazilSaoPauloJaboticabal630177_1M_2013_09_30_s
. . . . . . . . . . . . . . . . . . . . . . . . . with HA 142D, 377K, syn537S (AGc)],

. . . . . . . . . . . . [H7N7 Equine: Host Transition],

. . . . . . . . . . . . [H5N1],

. . . . . . . . . . . . [H9N2],

. . . . . . . . 142D,

. . . . . . . . syn160S (TCc),

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . SingaporeGP2864_3F_2010_06_03 (

. . . . . . . . A/Singapore/GP2864/2010

. . . . . . . . Sepsis - Isolated from Blood

. . . . . . . . GISAID HA EPI385439

. . . . . . . . GISAID Isolate EPI_ISL_124731

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . SingaporeSS34_C1_75F_2010_06_03_VxX (

. . . . . . . . A/Singapore/SS34/2010

. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . GISAID HA EPI385418

. . . . . . . . GISAID Isolate EPI_ISL_124723

. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . syn160S (TCc),

. . . . . . . . 225G,

. . . . . . . . 233H,

. . . . . . . . syn272D (GAc),

. . . . . . . . syn339F (TTt),

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . SingaporeGP2301_17F_2010_05_17 (

. . . . . . . . A/Singapore/GP2301/2010

. . . . . . . . GISAID HA EPI385347

. . . . . . . . GISAID Isolate EPI_ISL_124700

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

. . . . . . . . syn62G (GGa),

. . . . . . . . syn64I (ATt),

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . syn160S (TCc),

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . SingaporeGP1684_11M_2010_04_28 (

. . . . . . . . A/Singapore/GP1684/2010

. . . . . . . . GISAID HA EPI385211

. . . . . . . . GISAID Isolate EPI_ISL_124656

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

. . . . . . . . 0A,

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . syn160S (TCc),

. . . . . . . . 208K,

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . SingaporeTT150_C2_2010_04_26_VxX (

. . . . . . . . A/Singapore/TT150/2010

. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . GISAID HA EPI385172

. . . . . . . . GISAID Isolate EPI_ISL_124641

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

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . syn160S (TCc),

. . . . . . . . 225G,

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn482V (GTt),

. . . . . . . . syn537S (AGc))

. . . . SingaporeGP1212_C1_19F_2010_04_12 (

. . . . . . . . A/Singapore/GP1212/2010

. . . . . . . . GISAID HA EPI385256

. . . . . . . . GISAID Isolate EPI_ISL_124669

. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . syn155V (GTc),

. . . . . . . . syn160S (TCc),

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . SingaporeKK111_C1_11M_2010_03_31 (

. . . . . . . . A/Singapore/KK111/2010

. . . . . . . . GISAID HA EPI385125

. . . . . . . . GISAID Isolate EPI_ISL_124627

. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . syn160S (TCc),

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . SingaporeKK98_C1_4F_2010_03_08 (

. . . . . . . . A/Singapore/KK98/2010

. . . . . . . . GISAID HA EPI385142

. . . . . . . . GISAID Isolate EPI_ISL_124632

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . SingaporeKK90_C1_5M_2010_03_02 (

. . . . . . . . A/Singapore/KK90/2010

. . . . . . . . GISAID HA EPI385157

. . . . . . . . GISAID Isolate EPI_ISL_124637

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . syn107Q (CAg),

. . . . . . . . 142D,

. . . . . . . . 233H,

. . . . . . . . 377K,

. . . . . . . . syn537S (AGc))

. . . . JapanNagasakiHA1010_M_13F_2010_01_18 (

. . . . . . . . A/Nagasaki/HA-10-10/2010

. . . . . . . . GISAID HA EPI249892

. . . . . . . . GISAID Isolate EPI_ISL_71896

. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)

. . . . . . . . syn94Y (TAt),

. . . . . . . . 142D,

. . . . . . . . syn193S (AGc),

. . . . . . . . 298V,

. . . . . . . . 307S [H9N2],

. . . . . . . . syn471Y (TAt))

. . . . ChinaGuangxiLonganSWL1921_C1_15M_2010_01_14 (

. . . . . . . . A/Guangxi-Longan/SWL1921/2010

. . . . . . . . GISAID HA EPI258140

. . . . . . . . GISAID Isolate EPI_ISL_75063

. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)

. . . . . . . . 142D,

. . . . . . . . syn175E (GAg),

. . . . . . . . 502K,

. . . . . . . . syn541C (TGt))

. . . . JapanNagasakiHA105_M_13F_2010_01_12 (

. . . . . . . . A/Nagasaki/HA-10-5/2010

. . . . . . . . GISAID HA EPI249899

. . . . . . . . GISAID Isolate EPI_ISL_71903

. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)

. . . . . . . . syn94Y (TAt),

. . . . . . . . 142D [pH1N1 Rare: 46 Cases over 50 Sequences,

. . . . . . . . . . . . BrazilSaoPauloJaboticabal630177_1M_2013_09_30_s,
. . . . . . . . . . . . Deposit Report],

. . . . . . . . 190G [pH1N1 Rare: 17 Cases over 19 Sequences (map),
. . . . . . . . . . . . . . . . . . Fatalities,
. . . . . . . . . . . . . . . . . . Vaccine Escapes,
. . . . . . . . . . . . . . . . . . Infants],

. . . . . . . . syn193S (AGc),

. . . . . . . . 298V,

. . . . . . . . 307S [H9N2],

. . . . . . . . syn471Y (TAt))

. . . . JapanNagasakiHA104_M_4F_2010_01_04 (

. . . . . . . . A/Nagasaki/HA-10-4/2010

. . . . . . . . GISAID HA EPI249898

. . . . . . . . GISAID Isolate EPI_ISL_71902

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

. . . . . . . . syn94Y (TAt),

. . . . . . . . 142D,

. . . . . . . . syn193S (AGc),

. . . . . . . . 298V,

. . . . . . . . 307S [H9N2],

. . . . . . . . 340L,

. . . . . . . . 346E,

. . . . . . . . syn471Y (TAt))

. . . . TexasHoustonJMS392_xM_2009_12_25 (

. . . . . . . . A/Texas/JMS392/2009

. . . . . . . . Potential

Military

. . . . . . . . GISAID HA EPI252938

. . . . . . . . GISAID Isolate EPI_ISL_73523

. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)

. . . . . . . . 142D,

. . . . . . . . 377K)

. . . . WashingtonDCAF2182_PMK1_29M_2009_12_02 (

. . . . . . . . A/District of Columbia/AF2182/2009

. . . . . . . . US Air Force

. . . . . . . . GISAID HA EPI276604

. . . . . . . . GISAID Isolate EPI_ISL_78483

. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)

. . . . . . . . 100N,

. . . . . . . . syn137A (GCt),

. . . . . . . . 142D,

. . . . . . . . 237I,

. . . . . . . . syn270I (ATc),

. . . . . . . . 377K,

. . . . . . . . HA Truncated after aa386)

. . . . JapanTottoriST450_M_2009_12 (

. . . . . . . . A/Tottori/ST450/2009

. . . . . . . . GISAID HA EPI394485

. . . . . . . . GISAID Isolate EPI_ISL_128769

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . 142D,

. . . . . . . . 377V,

. . . . . . . . syn413K (AAg),

. . . . . . . . syn426A (GCa),

. . . . . . . . 440F)

. . . . UKEnglandGerrardsCross94560148_E338_2009_11_04 (

. . . . . . . . A/England/94560148/2009

. . . . . . . . GISAID HA EPI336314

. . . . . . . . GISAID Isolate EPI_ISL_96338

. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)

. . . . . . . . syn8I (ATc),

. . . . . . . . 142D,

. . . . . . . . syn428L (tTG))

. . . . UKEnglandGerrardsCross94560148_E390_2009_11_04 (

. . . . . . . . A/ENG/94560148/2009

. . . . . . . . GISAID HA EPI276511

. . . . . . . . GISAID Isolate EPI_ISL_78390

. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)

. . . . . . . . syn8I (ATc),

. . . . . . . . 142D,

. . . . . . . . syn428L (tTG))

. . . . Wisconsin51_C1C1_5F_2009_09_27 (

. . . . . . . . A/Wisconsin/51/2009

. . . . . . . . Clade1:189T

. . . . . . . . GISAID HA EPI217263

. . . . . . . . GISAID Isolate EPI_ISL_62361

. . . . . . . . 5 Polymorphisms (4 Amino and 1 Silent)

. . . . . . . . 142D,

. . . . . . . . 189T,

. . . . . . . . 324I,

. . . . . . . . syn413K (AAg),

. . . . . . . . 499K [H5N1])

. . . . ChinaShenzhen33_xM_2009_09_08 (

. . . . . . . . A/Shenzhen/33/2009

. . . . . . . . Severe or Fatal disease study
. . . . . . . . H7N9 Correlation

. . . . . . . . GISAID HA EPI348003

. . . . . . . . GISAID Isolate EPI_ISL_100954

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . 40N [H7N9 wild type],

. . . . . . . . 56D [H9N2],
. . . . . . . . . . . [H10N7],

. . . . . . . . 142D,

. . . . . . . . syn251L (tTA),

. . . . . . . . syn507K (AAa))

. . . . ChinaShenzhen28_xF_2009_08_31 (

. . . . . . . . A/Shenzhen/28/2009

. . . . . . . . Severe or Fatal disease study

. . . . . . . . H7N9 Correlation
. . . . . . . . GISAID HA EPI348125

. . . . . . . . GISAID Isolate EPI_ISL_101194

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . 40N [H7N9 wild type],

. . . . . . . . 56D [H9N2],
. . . . . . . . . . . [H10N7],

. . . . . . . . 142D,

. . . . . . . . syn251L (tTA),

. . . . . . . . syn507K (AAa))

. . . . BrazilSaoPaulo70311_7F_2009_08_28 (

. . . . . . . . A/Sao Paulo/70311/2009

. . . . . . . . GISAID HA EPI335488

. . . . . . . . GISAID Isolate EPI_ISL_95963

. . . . . . . . 5 Polymorphisms (4 Amino and 1 Silent)

. . . . . . . . #12E,

. . . . . . . . 142D,

. . . . . . . . 206S,

. . . . . . . . 296H,

. . . . . . . . syn480E (GAg))

. . . . SlovakiaModra1156_2009_07_27 (

. . . . . . . . A/Modra/1156/2009

. . . . . . . . GISAID HA EPI210532

. . . . . . . . GISAID Isolate EPI_ISL_60278

. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)

. . . . . . . . 142D,

. . . . . . . . HA Truncated after aa389)

NA Polymorphisms

. . . . Bolivia1351_C2_46M_2013_07_31_VxX (

. . . . . . . . A/Bolivia/1351/2013

. . . . . . . . GISAID NA EPI467386

. . . . . . . . GISAID Isolate EPI_ISL_145666

. . . . . . . . 15 Polymorphisms (7 Amino and 8 Silent)

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

. . . . . . . . 232T,

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

. . . . . . . . 241I,

. . . . . . . . 331N,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . ChileSantiago46965_C2C1_28M_2013_07_15 (

. . . . . . . . A/Santiago/46965/2013

. . . . . . . . GISAID NA EPI467228

. . . . . . . . GISAID Isolate EPI_ISL_145635

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

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . Florida20_C1_47M_2013_07_07 (

. . . . . . . . A/Florida/20/2013

. . . . . . . . GISAID NA EPI465253

. . . . . . . . GISAID Isolate EPI_ISL_145023

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

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn201G (GGa),

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . ArgentinaMarDelPlata10091_C1C1_xM_2013_07_04 (

. . . . . . . . A/Mar Del Plata/10091/2013

. . . . . . . . GISAID NA EPI467369

. . . . . . . . GISAID Isolate EPI_ISL_145660

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

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . Argentina911_C1C1_60F_2013_07_02 (

. . . . . . . . A/Argentina/911/2013

. . . . . . . . GISAID NA EPI465494

. . . . . . . . GISAID Isolate EPI_ISL_145105

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

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . Paraguay17_C1C1_55F_2013_07_01 (

. . . . . . . . A/Paraguay/17/2013

. . . . . . . . GISAID NA EPI484968

. . . . . . . . GISAID Isolate EPI_ISL_149777

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

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . Uruguay279_C1_xM_2013_06_21 (

. . . . . . . . A/Uruguay/279/2013

. . . . . . . . GISAID NA EPI467205

. . . . . . . . GISAID Isolate EPI_ISL_145630

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

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . Argentina508_S1C1_62M_2013_06_16 (

. . . . . . . . A/Argentina/508/2013

. . . . . . . . GISAID NA EPI465256

. . . . . . . . GISAID Isolate EPI_ISL_145024

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

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . PuertoRico01_C2_13F_2013_06_14 (

. . . . . . . . A/Puerto Rico/01/2013

. . . . . . . . GISAID NA EPI466914

. . . . . . . . GISAID Isolate EPI_ISL_145509

. . . . . . . . 14 Polymorphisms (6 Amino and 8 Silent)

. . . . . . . . 44S,

. . . . . . . . 72I,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . PuertoRico03_E3_7M_2013_06_14 (

. . . . . . . . A/Puerto Rico/03/2013

. . . . . . . . GISAID NA EPI465458

. . . . . . . . GISAID Isolate EPI_ISL_145090

. . . . . . . . 14 Polymorphisms (6 Amino and 8 Silent)

. . . . . . . . 44S,

. . . . . . . . 72I,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . PuertoRico01_E3_13F_2013_06_14_VxX (

. . . . . . . . A/Puerto Rico/01/2013

. . . . . . . . GISAID NA EPI465454

. . . . . . . . GISAID Isolate EPI_ISL_145088

. . . . . . . . 14 Polymorphisms (6 Amino and 8 Silent)

. . . . . . . . 44S,

. . . . . . . . 72I,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . PuertoRico05_C2_45M_2013_06_14_VxX (

. . . . . . . . A/Puerto Rico/05/2013

. . . . . . . . GISAID NA EPI465268

. . . . . . . . GISAID Isolate EPI_ISL_145028

. . . . . . . . 15 Polymorphisms (6 Amino and 9 Silent)

. . . . . . . . 44S,

. . . . . . . . 72I,

. . . . . . . . 106V,

. . . . . . . . syn171N (AAt),

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . PuertoRico03_C1_7M_2013_06_14 (

. . . . . . . . A/Puerto Rico/03/2013

. . . . . . . . GISAID NA EPI465101

. . . . . . . . GISAID Isolate EPI_ISL_144967

. . . . . . . . 14 Polymorphisms (6 Amino and 8 Silent)

. . . . . . . . 44S,

. . . . . . . . 72I,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . PuertoRico01_C1_13F_2013_06_14 (

. . . . . . . . A/Puerto Rico/01/2013

. . . . . . . . GISAID NA EPI465069

. . . . . . . . GISAID Isolate EPI_ISL_144956

. . . . . . . . 15 Polymorphisms (7 Amino and 8 Silent)

. . . . . . . . 44S,

. . . . . . . . 72I,

. . . . . . . . 106V,

. . . . . . . . 151N mix wt,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . Argentina168_S1C1_xM_2013_06_04_VxX (

. . . . . . . . A/Argentina/168/2013

. . . . . . . . GISAID NA EPI465452

. . . . . . . . GISAID Isolate EPI_ISL_145087

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

. . . . . . . . 44S,

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . Argentina102_C1C1_56F_2013_05_30 (

. . . . . . . . A/Argentina/102/2013

. . . . . . . . GISAID NA EPI465450

. . . . . . . . GISAID Isolate EPI_ISL_145086

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

. . . . . . . . 44S,

. . . . . . . . syn52S (AGt),

. . . . . . . . 106V,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

. . . . . . . . syn213T (ACg),

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

. . . . . . . . 241I,

. . . . . . . . syn349F (TTc),

. . . . . . . . 369K,

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

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

. . . . Hungary17_M1E5M1_xF_2013_02_15_VxX (

. . . . . . . . A/Hungary/17/2013

. . . . . . . . GISAID NA EPI462038

. . . . . . . . GISAID Isolate EPI_ISL_144056

. . . . . . . . 15 Polymorphisms (8 Amino and 7 Silent)

. . . . . . . . 11S [Emergent H7N9 Amino wild type 11S TCA],

. . . . . . . . 44S,

. . . . . . . . syn70S (AGt),

. . . . . . . . 93S mix wt [avH1N1_farm],
. . . . . . . . . . . . . . . . [H6N1],

. . . . . . . . 106V,

. . . . . . . . 126S,

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

. . . . . . . . 200S,

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],

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

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

. . . . . . . . 241I,

. . . . . . . . 369K,

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

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

. . . . Luxembourg20130134_2013_01_22 (

. . . . . . . . A/Luxembourg/20130134/2013

. . . . . . . . GISAID NA EPI457407

. . . . . . . . GISAID Isolate EPI_ISL_142843

. . . . . . . . 14 Polymorphisms (8 Amino and 6 Silent)

. . . . . . . . 44S,

. . . . . . . . 79P,

. . . . . . . . 106V,

. . . . . . . . syn131T (ACa),

. . . . . . . . 191I [Emergent H7N9 wild type
. . . . . . . . . . . . . . . First Base Donor ATG],

. . . . . . . . 200S,

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

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

. . . . . . . . 241I,

. . . . . . . . syn274Y (TAc),

. . . . . . . . 369K,

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

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

. . . . Tanzania2085_E3_30F_2012_12_10 (

. . . . . . . . A/Tanzania/2085/2012

. . . . . . . . GISAID NA EPI422629

. . . . . . . . GISAID Isolate EPI_ISL_135825

. . . . . . . . 14 Polymorphisms (7 Amino and 7 Silent)

. . . . . . . . 44S,

. . . . . . . . syn67V (GTc),

. . . . . . . . syn96G (GGg),

. . . . . . . . 106V,

. . . . . . . . 200S,

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

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

. . . . . . . . 241I,

. . . . . . . . 321V,

. . . . . . . . syn325N (AAc),

. . . . . . . . 354S,

. . . . . . . . 369K,

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

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

. . . . India2005_E3_2012_11_24 (

. . . . . . . . A/India/2005/2012

. . . . . . . . GISAID NA EPI422600

. . . . . . . . GISAID Isolate EPI_ISL_135815

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

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

. . . . . . . . 42D,

. . . . . . . . 44S,

. . . . . . . . 106V,

. . . . . . . . syn162P (CCc),

. . . . . . . . 200S,

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

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

. . . . . . . . 241I,

. . . . . . . . 369K,

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

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

. . . . . . . . 454D)

. . . . BelgiumG860_M1_xF_2012_11_08 (

. . . . . . . . A/Belgium/G860/2012

. . . . . . . . GISAID NA EPI417117

. . . . . . . . GISAID Isolate EPI_ISL_134396

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

. . . . . . . . 44S,

. . . . . . . . 106V,

. . . . . . . . syn145S (TCt),

. . . . . . . . 163V,

. . . . . . . . 200S,

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

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

. . . . . . . . 241I,

. . . . . . . . 369K,

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

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

. . . . Virginia13_M1C1_46F_2012_08_21 (

. . . . . . . . A/Virginia/13/2012

. . . . . . . . GISAID NA EPI404816

. . . . . . . . GISAID Isolate EPI_ISL_131789

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

. . . . . . . . 44S,

. . . . . . . . 106V,

. . . . . . . . 200S,

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

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

. . . . . . . . 241I,

. . . . . . . . syn307N (AAt),

. . . . . . . . 369K,

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

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

. . . . . . . . syn466T (ACt))

. . . . SouthAfricaJohannesburg150_M1M1_46F_2011_07_10 (

. . . . . . . . A/Johannesburg/150/2011

. . . . . . . . GISAID NA EPI346656

. . . . . . . . GISAID Isolate EPI_ISL_99903

. . . . . . . . 9 Polymorphisms (2 Amino and 7 Silent)

. . . . . . . . syn79S (TCg),

. . . . . . . . syn89S (TCt),

. . . . . . . . syn126P (CCt),

. . . . . . . . syn229S (TCc),

. . . . . . . . syn236G (GGc),

. . . . . . . . 269I mix wt [SingaporeKK376_C2_14F_2010_06_07],

. . . . . . . . 299A,

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

. . . . . . . . syn405S (AGc))

. . . . AustraliaBrisbane139_M4_59M_2011_04_07_VxX (

. . . . . . . . A/BRISBANE/139/2011

. . . . . . . . GISAID NA EPI332675

. . . . . . . . GISAID Isolate EPI_ISL_95091

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

. . . . . . . . syn4N (AAt),

. . . . . . . . syn5Q (CAg),

. . . . . . . . syn32I (ATt),

. . . . . . . . 44S,

. . . . . . . . 145F,

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

. . . . . . . . 241I,

. . . . . . . . 369K,

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

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

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

. . . . JapanSaitama289_M2+1_2011_04_02_VxX (

. . . . . . . . A/SAITAMA/289/2011

. . . . . . . . GISAID NA EPI334515

. . . . . . . . GISAID Isolate EPI_ISL_94426

. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)

. . . . . . . . syn14C (TGc),

. . . . . . . . syn41G (GGa),

. . . . . . . . 44S,

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

. . . . . . . . 241I,

. . . . . . . . syn281C (TGc),

. . . . . . . . 369K,

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

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

. . . . AustraliaVictoriaRythdale512_M1_46M_2011_02_04 (

. . . . . . . . A/VICTORIA/512/2011

. . . . . . . . GISAID NA EPI331323

. . . . . . . . GISAID Isolate EPI_ISL_94794

. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)

. . . . . . . . syn4N (AAt),

. . . . . . . . syn5Q (CAg),

. . . . . . . . 23M,

. . . . . . . . 44S,

. . . . . . . . 220K,

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

. . . . . . . . 241I,

. . . . . . . . 369K,

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

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

. . . . SingaporeKK376_C2_14F_2010_06_07 (

. . . . . . . . A/Singapore/KK376/2010

. . . . . . . . GISAID NA EPI385494

. . . . . . . . GISAID Isolate EPI_ISL_124750

. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa),

. . . . . . . . 269I [SouthAfricaJohannesburg150_M1M1_46F_2011_07_10])

. . . . SingaporeGP2864_3F_2010_06_03 (

. . . . . . . . A/Singapore/GP2864/2010

. . . . . . . . Sepsis - Isolated from Blood

. . . . . . . . GISAID NA EPI385440

. . . . . . . . GISAID Isolate EPI_ISL_124731

. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa))

. . . . SingaporeSS34_C1_75F_2010_06_03_VxX (

. . . . . . . . A/Singapore/SS34/2010

. . . . . . . . GISAID NA EPI385420

. . . . . . . . GISAID Isolate EPI_ISL_124723

. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa))

. . . . SingaporeGP2301_17F_2010_05_17 (

. . . . . . . . A/Singapore/GP2301/2010

. . . . . . . . GISAID NA EPI385348

. . . . . . . . GISAID Isolate EPI_ISL_124700

. . . . . . . . 3 Polymorphisms (0 Amino and 3 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa),

. . . . . . . . syn430R (aGA))

. . . . SingaporeGP1684_11M_2010_04_28 (

. . . . . . . . A/Singapore/GP1684/2010

. . . . . . . . GISAID NA EPI385212

. . . . . . . . GISAID Isolate EPI_ISL_124656

. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa),

. . . . . . . . 412Q)

. . . . SingaporeTT150_C2_2010_04_26_VxX (

. . . . . . . . A/Singapore/TT150/2010

. . . . . . . . GISAID NA EPI385174

. . . . . . . . GISAID Isolate EPI_ISL_124641

. . . . . . . . 3 Polymorphisms (0 Amino and 3 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa),

. . . . . . . . syn295N (AAt))

. . . . SingaporeGP1212_C1_19F_2010_04_12 (

. . . . . . . . A/Singapore/GP1212/2010

. . . . . . . . GISAID NA EPI385258

. . . . . . . . GISAID Isolate EPI_ISL_124669

. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa))

. . . . SingaporeKK111_C1_11M_2010_03_31 (

. . . . . . . . A/Singapore/KK111/2010

. . . . . . . . GISAID NA EPI385126

. . . . . . . . GISAID Isolate EPI_ISL_124627

. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa))

. . . . SingaporeKK98_C1_4F_2010_03_08 (

. . . . . . . . A/Singapore/KK98/2010

. . . . . . . . GISAID NA EPI385143

. . . . . . . . GISAID Isolate EPI_ISL_124632

. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa))

. . . . SingaporeKK90_C1_5M_2010_03_02 (

. . . . . . . . A/Singapore/KK90/2010

. . . . . . . . GISAID NA EPI385158

. . . . . . . . GISAID Isolate EPI_ISL_124637

. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)

. . . . . . . . syn86A (GCt),

. . . . . . . . syn207K (AAa))

. . . . ChinaGuangxiLonganSWL1921_C1_15M_2010_01_14 (

. . . . . . . . A/Guangxi-Longan/SWL1921/2010

. . . . . . . . GISAID NA EPI258139

. . . . . . . . GISAID Isolate EPI_ISL_75063

. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)

. . . . . . . . syn275H (CAt),

. . . . . . . . syn398E (GAa))

. . . . TexasHoustonJMS392_xM_2009_12_25 (

. . . . . . . . A/Texas/JMS392/2009

. . . . . . . . Potential

Military

. . . . . . . . GISAID NA EPI252940

. . . . . . . . GISAID Isolate EPI_ISL_73523

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . syn132F (TTt),

. . . . . . . . 241I,

. . . . . . . . 366N)

. . . . Wisconsin51_C1C1_5F_2009_09_27 (

. . . . . . . . A/Wisconsin/51/2009

. . . . . . . . GISAID NA EPI217262

. . . . . . . . GISAID Isolate EPI_ISL_62361

. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)

. . . . . . . . 382E,

. . . . . . . . syn407V (GTc))

. . . . SlovakiaModra1156_2009_07_27 (

. . . . . . . . A/Modra/1156/2009

. . . . . . . . GISAID NA EPI210533

. . . . . . . . GISAID Isolate EPI_ISL_60278

. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)

. . . . . . . . syn64Q (CAa))

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

pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-11-08-02_14_41_307200 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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

2013-11-28

Prediction Demonstrated in USA of Triple Polymorphism pH1N1 HA 166N, 188T & 189T

2013-11-21

Burkina Faso Off-Clade pH1N1 Sequences with Strong Homology to H7N9 Vaccine Candidate

2013-11-09

HA 142D: pH1N1 Vaccine Escape Diversity

Fund

Search pH1N1 Genetics

pH1N1 Articles

Labels

Fellow Investigators

Author