2014-01-06

pH1N1 Child Vaccine Escape: CDC Early 2013

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 : 2014-01-06
Last Update : 2014-01-06

pH1N1 Child Vaccine Escape: CDC Early 2013
Geographic Distribution
41 Cases over 43 Sequences

In the 30 days covering 2013-02-28 to 2013-03-29, the United States CDC released a total of 43 pH1N1 sequences at GISAID on 41 human cases sampled from October 2012 to February 2013. Geographic surveillance includes America, Africa, Asia and Russia. Although pH1N1 in most locales during the 2012-2013 season was the minority serotype, the sequences in this Analytic Report describe a high level of human-infective diversity and an ease of avian genetic acquisition, including multiple instances demonstrating concentrated transport of High-CFR pH1N1 Upsilon polymorphisms onto single sequences.

Widely recognised Immune Escape parameters are seen in 13 of the sequences, 7 from children aged 10 years old or younger. CrossClade events occur on 6 sequences across 4 distinct clade combinations. Host Switching polymorphisms are observed in this set. Co-infection and / or quasi-species are suggested by 47 instances of ambiguity on the Hemagglutinin and Neuraminidase segments.

As a minority strain, pH1N1 continued to aggressively mature and diversify by conglomerating early pandemic severity markers (geographically dispersed in 2009) onto single lineages in 2013 setting the stage for the late summer 2013 upwelling.  Those highly avian pH1N1 lineages that developed during a minority phase in the 2012 season are now escaping vaccines, evading diagnostics and resisting antivirals at a season-tilting rate.

Expect flashfires as in Texas with extended illnesses, systemic morbidity and excess focal mortality.

Key Severity Indicators
Host Transition
Status
 PROBABLE 

Vaccine Escape Diversity
GenoTypeCount
 VxX 156E01
 VxX 157E01
 VxX 158E03
 VxX 218T01
 VxX 219V02
 VxX 225G04
Ambiguity
SegmentTypeCount
 Hemagglutinin  Binary 32
 Neuraminidase  Binary 15
Receptor Binding Variance
RevisionCount
 HA 187N 01
 HA 190G 02
 HA 193R 01
 HA 194I 02
 HA 198T 01
 HA 225G 04
 HA 226R 05
Vaccine Escape Sequences
Sample
Date		NameFindingID
 2013_01_22  California09_E3_10F_VxX HA 225G EPI439223 
 2013_01_22  NewYork02_E3_28M_VxX HA 225G EPI439220 
 2013_01_09  Japan1419_E3_29M_VxX HA 225G EPI439994 
 2013_01_06  NewMexico02_M1C2_4M_VxX Low Reactor EPI439239 
 2013_01_05  HongKong101_C3C1_2M_VxX Low Reactor EPI439254 
 2012_12_20  Minnesota34_M1C1_1M_VxX Low Reactor EPI426455 
 2012_12_19  Tanzania2131_C2_1F_VxX Low Reactor EPI440929 
 2012_12_18  HongKong9232_C5C1_49F_VxX  Low Reactor EPI439312 
 2012_12_05  Tanzania326_E3_2M_VxX HA 225G EPI440003 
 2012_11_28  Tanzania309_C2_3M_VxX Low Reactor EPI426450 
 2012_11_27  Tanzania307_E3_36F_VxX HA 225G EPI439242 
 2012_10_16  CoteDIvoire1186_C2_xF_VxX Low Reactor EPI426441 
 2012_10_16  CoteDIvoire1186_xF_VxX =Low Reactor  EPI432618 

CrossClade Analytics
pH1N1
CrossClade CDC Sequences in Winter 2012-2013
Sample
Date		NameClade
Name		ID
 2013_02_05  Missouri03_C1_20F CrossClade:
 188T_208K		 EPI439225 
 2013_01_10  HongKong145_C3C1_61M  CrossClade:
 186P_188T_208K 		 EPI439214 
 2013_01_09  Japan1419_E3_29M_VxX  CrossClade:
 186P_188T		 EPI439994 
 2013_01_04  NewMexico01_M1C2_35F CrossClade:
 188T_208K		 EPI439231 
 2013_01_03  Oman21_C2_24F CrossClade:
 188T_189T		 EPI439465 
 2012_12_31  Oman03_C2_17F CrossClade:
 188T_189T		 EPI439515 

Isolate Metrics
Calendar
Sample
Month		Count
 2013 February 11
 2013 January 15
 2012 December 09
 2012 November 06
 2012 October 02
Cladistics
CladeNameCount
 Clade2:188T35
 CrossClade:
  188T_208K		02
 CrossClade:
  188T_189T		02
 UnCladed02
 CrossClade:
  186P_188T_208K 		01
 CrossClade:
  186P_188T		01
Age / Gender Dynamic
ObservationPercent
 Child or
   ChildBearing Age female		71%
 Child Aged 17 or Under47%
 Child Aged 12 or Under42%
 Child Aged 04 or Under31%


HA Polymorphisms

. . . . Alabama04_C1C1_54M_2013_02_25 (
. . . . . . . . Novel Hemagglutinin
. . . . . . . . A/Alabama/04/2013
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439517
. . . . . . . . GISAID Isolate EPI_ISL_138730
. . . . . . . . 20 Polymorphisms (8 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 92P mix wt [pH1N1 Novel],
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn466G (GGt) [zH3N2],
. . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . RussiaStPetersburg42_C1C1_2013_02_20 (
. . . . . . . . A/St. Petersburg/42/2013
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439481
. . . . . . . . GISAID Isolate EPI_ISL_138735
. . . . . . . . 19 Polymorphisms (8 Amino and 11 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . 9S,
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . RussiaStPetersburg37_C1C1_58x_2013_02_20 (
. . . . . . . . A/St. Petersburg/37/2013
. . . . . . . . H7N9 Correlation HA 10H
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439471
. . . . . . . . GISAID Isolate EPI_ISL_138731
. . . . . . . . 19 Polymorphisms (9 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . 10H [Emergent H7N9 wild type],
. . . . . . . . syn58C (TGc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 144T [pH1N1 Upsilon],
. . . . . . . . . . . [zH3N2],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Pennsylvania04_C1_52M_2013_02_14 (
. . . . . . . . A/Pennsylvania/04/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Novel Neuraminidase
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439458
. . . . . . . . GISAID Isolate EPI_ISL_138724
. . . . . . . . 21 Polymorphisms (8 Amino and 13 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . syn182I (ATc),
. . . . . . . . 188T,
. . . . . . . . syn211K (AAa),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918],
. . . . . . . . syn547Q (CAa))

. . . . NorthCarolina03_C1_66M_2013_02_13 (
. . . . . . . . A/North Carolina/03/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439473
. . . . . . . . GISAID Isolate EPI_ISL_138732
. . . . . . . . 22 Polymorphisms (8 Amino and 14 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . syn182I (ATc),
. . . . . . . . 188T,
. . . . . . . . syn211K (AAa),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . syn266S (TCc) [H7N9 Avian United States:
. . . . . . . . . . . . . . . . . . . . . . Third Base Donor 266V GTc],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918],
. . . . . . . . syn547Q (CAa))

. . . . RussiaStPetersburg19_E2E1_1x_2013_02_13 (
. . . . . . . . A/St. Petersburg/19/2013
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439463
. . . . . . . . GISAID Isolate EPI_ISL_138726
. . . . . . . . 20 Polymorphisms (8 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 226R,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn461K (AAa) [H5N1],
. . . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Kentucky02_M1C1_12M_2013_02_08 (
. . . . . . . . A/Kentucky/02/2013
. . . . . . . . H7N9 Correlation NA 199N
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439255
. . . . . . . . GISAID Isolate EPI_ISL_138673
. . . . . . . . 22 Polymorphisms (12 Amino and 10 Silent)
. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],
. . . . . . . . 3T [pH1N1 Kyrgyzstan220_C1_2013_01_08],
. . . . . . . . syn34N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . 39E [pH1N1 Upsilon],
. . . . . . . . . . [H9N2],
. . . . . . . . 87G [H6N1],
. . . . . . . . syn122K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 141N [Emergent H7N9 wild type First Base Donor AGA],
. . . . . . . . 146G,
. . . . . . . . 166I [H5N1],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn258F (TTt),
. . . . . . . . syn275V (GTt) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn337A (GCt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn488D (GAt),
. . . . . . . . 523A,
. . . . . . . . syn524A (GCt),
. . . . . . . . syn538F (TTt))

. . . . Nebraska05_C1_1F_2013_02_06 (
. . . . . . . . A/Nebraska/05/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439475
. . . . . . . . GISAID Isolate EPI_ISL_138733
. . . . . . . . 24 Polymorphisms (8 Amino and 16 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn112S (TCc) [avH1N1],
. . . . . . . . syn124S (AGc) [zH3N2],
. . . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn141H (CAc) [H5N1],
. . . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . syn182I (ATc),
. . . . . . . . 188T,
. . . . . . . . syn211K (AAa),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn335A (GCt) [H7N7],
. . . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918],
. . . . . . . . syn547Q (CAa))

. . . . Missouri03_C1_20F_2013_02_05 (
. . . . . . . . A/Missouri/03/2013
. . . . . . . . H7N9 Correlation HA 119M
. . . . . . . . CrossClade: 188T & 208K
. . . . . . . . GISAID HA EPI439225
. . . . . . . . GISAID Isolate EPI_ISL_138659
. . . . . . . . 19 Polymorphisms (9 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 119M [Emergent H7N9 wild type],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn193S (AGc),
. . . . . . . . 208K [H7N9 Avian wild type],
. . . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . . . . [H7N7],
. . . . . . . . . . . [zH3N2],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Utah04_C1_2M_2013_02_03 (
. . . . . . . . A/Utah/04/2013
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439245
. . . . . . . . GISAID Isolate EPI_ISL_138667
. . . . . . . . 20 Polymorphisms (7 Amino and 13 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn350G (GGg),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn424Y (TAt),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Indiana03_M1C1_4M_2013_02_02 (
. . . . . . . . A/Indiana/03/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439467
. . . . . . . . GISAID Isolate EPI_ISL_138728
. . . . . . . . 21 Polymorphisms (7 Amino and 14 Silent)
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . syn182I (ATc),
. . . . . . . . 188T,
. . . . . . . . syn211K (AAa),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918],
. . . . . . . . syn547Q (CAa))

. . . . California09_E3_10F_2013_01_22_VxX (
. . . . . . . . A/California/09/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . Novel Hemagglutinin
. . . . . . . . US Military - Probable Vaccination
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439223
. . . . . . . . GISAID Isolate EPI_ISL_138658
. . . . . . . . 23 Polymorphisms (11 Amino and 12 Silent)
. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],
. . . . . . . . syn34N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . 87G [H6N1],
. . . . . . . . syn122K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn127P (CCa),
. . . . . . . . 146G,
. . . . . . . . 166I [H5N1],
. . . . . . . . syn171D (GAc),
. . . . . . . . 188T,
. . . . . . . . 200T mix wt,
. . . . . . . . 225G mix wt,
. . . . . . . . 226R mix wt,
. . . . . . . . syn258F (TTt),
. . . . . . . . syn275V (GTt) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn337A (GCt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn488D (GAt),
. . . . . . . . 523A,
. . . . . . . . syn524A (GCt),
. . . . . . . . syn538F (TTt))

. . . . NewYork02_E3_28M_2013_01_22_VxX (
. . . . . . . . A/New York/02/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Novel Hemagglutinin
. . . . . . . . US Military Cluster, 2 Adults & 2 Children
. . . . . . . . US Military - Probable Vaccination
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439220
. . . . . . . . GISAID Isolate EPI_ISL_138657
. . . . . . . . 25 Polymorphisms (9 Amino and 16 Silent)
. . . . . . . . syn34N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . 166Q [avH1N1],
. . . . . . . . syn179L (CTg),
. . . . . . . . syn182I (ATc),
. . . . . . . . 188T,
. . . . . . . . syn211K (AAa),
. . . . . . . . 225G,
. . . . . . . . syn244T (ACg),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn297N (AAc) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [zH3N2],
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918],
. . . . . . . . syn547Q (CAa))

. . . . Washington05_E3_21F_2013_01_18 (
. . . . . . . . A/Washington/05/2013
. . . . . . . . US Military - Probable Vaccination
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439217
. . . . . . . . GISAID Isolate EPI_ISL_138656
. . . . . . . . 21 Polymorphisms (9 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . 3S [H5N1],
. . . . . . . . syn31H (CAt) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn77S (AGt) [avH1N1],
. . . . . . . . syn135V (GTg) [H5N1],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 166N [avH1N1farm],
. . . . . . . . . . . [Prediction: CrossClade with HA 166N],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 226R,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn476N (AAt),
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . [H7N7])

. . . . Indiana02_C1_23F_2013_01_14 (
. . . . . . . . A/Indiana/02/2013
. . . . . . . . H7N9 Correlation NA 45H and 52N
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439249
. . . . . . . . GISAID Isolate EPI_ISL_138669
. . . . . . . . 26 Polymorphisms (9 Amino and 17 Silent)
. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],
. . . . . . . . syn#5L (CTg) [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn34N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . 87G [H6N1],
. . . . . . . . syn102E (GAa),
. . . . . . . . syn122K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 141Q [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . [Emergent H7N9 wild type Third Base Donor AGA],
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . syn189A (GCc) [Emergent H7N9 wild type],
. . . . . . . . 200T,
. . . . . . . . syn212K (AAa) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn223V (GTa) [Emergent H7N9 wild type],
. . . . . . . . syn258F (TTt),
. . . . . . . . 272E [pH1N1 Rare: 1 Case over 1 Sequence 2010-01-04],
. . . . . . . . . . [H5N1],
. . . . . . . . syn330R (AGg) [H7N7],
. . . . . . . . . . . . . [zH3N2],
. . . . . . . . syn337A (GCt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn515Q (CAa) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn524A (GCt) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . syn538F (TTt) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . syn546L (tTA) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm])

. . . . ThailandSuratThani16_C1C1_xM_2013_01_11 (
. . . . . . . . A/Surat Thani/16/2013
. . . . . . . . H7N9 Correlation HA 141R
. . . . . . . . H7N9 Correlation HA 300S
. . . . . . . . H7N9 Correlation NA 11S
. . . . . . . . H7N9 Correlation NA 385S
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439228
. . . . . . . . GISAID Isolate EPI_ISL_138660
. . . . . . . . 22 Polymorphisms (11 Amino and 11 Silent)
. . . . . . . . #8L [H5N1],
. . . . . . . . syn30T (ACt) [zH3N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn58C (TGc),
. . . . . . . . syn61A (GCg) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . syn87S (AGc) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . 100N,
. . . . . . . . syn118E (GAa) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 122N [zH3N2, H5N1],
. . . . . . . . 141R [Emergent H7N9 Amino wild type],
. . . . . . . . . . . [zH3N2],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 252L [pH1N1 Clade5: 208K_219V],
. . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . 300S [Emergent H7N9 Amino wild type],
. . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . syn334G (GGa) [pH1N1 Upsilon],
. . . . . . . . syn338G (GGc),
. . . . . . . . syn375I (ATc),
. . . . . . . . 377K,
. . . . . . . . syn379T (ACc),
. . . . . . . . 446E [Emergent H7N9 wild type First Base Donor GAC],
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 523A)

. . . . HongKong145_C3C1_61M_2013_01_10 (
. . . . . . . . A/Hong Kong/145/2013
. . . . . . . . H7N9 Correlation HA 14S
. . . . . . . . CrossClade: 186P, 188T & 208K
. . . . . . . . GISAID HA EPI439214
. . . . . . . . GISAID Isolate EPI_ISL_138655
. . . . . . . . 24 Polymorphisms (12 Amino and 12 Silent)
. . . . . . . . #6M [H9N2 Human],
. . . . . . . . . . . [H9N2 Pheasant, Pigeon, Quail],
. . . . . . . . . . . [H9N2 Commercial Poultry],
. . . . . . . . 14S mix wt [Emergent H7N9 Amino wild type],
. . . . . . . . syn34N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . 87G [H6N1],
. . . . . . . . syn122K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn127P (CCa),
. . . . . . . . 146G,
. . . . . . . . 166I [H5N1],
. . . . . . . . syn171D (GAc),
. . . . . . . . 186P mix wt,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 208K [H7N9 Avian wild type],
. . . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . . . . [H7N7],
. . . . . . . . . . . [zH3N2],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn258F (TTt),
. . . . . . . . syn275V (GTt) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn337A (GCt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn488D (GAt),
. . . . . . . . 523A,
. . . . . . . . syn524A (GCt),
. . . . . . . . syn538F (TTt))

. . . . Japan1419_E3_29M_2013_01_09_VxX (
. . . . . . . . A/Japan/1419/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . H7N9 Correlation HA 44I
. . . . . . . . US Military - Probable Vaccination
. . . . . . . . CrossClade: 186P & 188T
. . . . . . . . GISAID HA EPI439994
. . . . . . . . GISAID Isolate EPI_ISL_138662
. . . . . . . . 30 Polymorphisms (13 Amino and 17 Silent)
. . . . . . . . #12E mix wt [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn#6L (tTG),
. . . . . . . . syn34N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . 44I [Emergent H7N9 wild type],
. . . . . . . . syn53L (TTa),
. . . . . . . . syn56G (GGa) [H7N9 Avian wild type],
. . . . . . . . 146G,
. . . . . . . . syn150N (AAc),
. . . . . . . . 166N [avH1N1farm],
. . . . . . . . . . . [Prediction: CrossClade with HA 166N],
. . . . . . . . 186P mix wt,
. . . . . . . . 188T,
. . . . . . . . syn190D (GAt),
. . . . . . . . syn196Q (CAa),
. . . . . . . . 200T,
. . . . . . . . 225G mix wt,
. . . . . . . . syn236L (CTg),
. . . . . . . . 274T,
. . . . . . . . syn293L (CTa),
. . . . . . . . syn309Y (TAc),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn397G (GGc) mix wt [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn440Y (TAt),
. . . . . . . . syn443S (TCg),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . 477M,
. . . . . . . . syn482V (GTt),
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn538F (TTt))

. . . . Tennessee01_C1_37M_2013_01_09 (
. . . . . . . . A/Tennessee/01/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI426458
. . . . . . . . GISAID Isolate EPI_ISL_136469
. . . . . . . . 21 Polymorphisms (8 Amino and 13 Silent)
. . . . . . . . syn35L (CTc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . syn182I (ATc),
. . . . . . . . 188T,
. . . . . . . . syn211K (AAa),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918],
. . . . . . . . syn547Q (CAa))

. . . . Kyrgyzstan220_C1_2013_01_08 (
. . . . . . . . A/Kyrgyzstan/220/2013
. . . . . . . . H7N9 Correlation HA 482I
. . . . . . . . H7N9 Correlation NA 313H
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439478
. . . . . . . . GISAID Isolate EPI_ISL_138734
. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . 3T,
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn361G (GGa) [pH1N1 Upsilon],
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 482I [Emergent H7N9 wild type],
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn507K (AAa))

. . . . NewMexico02_M1C2_4M_2013_01_06_VxX (
. . . . . . . . A/New Mexico/02/2013
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . HA 190G GoFE
. . . . . . . . ~ HA Minnesota34_M1C1_1M_2012_12_20_VxX [EPI426455]
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439239
. . . . . . . . GISAID Isolate EPI_ISL_138664
. . . . . . . . 23 Polymorphisms (11 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 158E,
. . . . . . . . syn161Y (TAt),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G [pH1N1 Rare: 17 Cases over 19 Sequences (map),
. . . . . . . . . . . . . . . . . . Fatalities,
. . . . . . . . . . . . . . . . . . Vaccine Escapes,
. . . . . . . . . . . . . . . . . . Infants],
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 280A [pH1N1 with HA 230I],
. . . . . . . . . . [avH1N1farm],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 452I [pH1N1 ReEmergent 2013],
. . . . . . . . . . [pH1N1 Rare: 25 Cases over 27 Sequences,
. . . . . . . . . . . . . . . . . . Vaccine Escape HA 158E Count 02,
. . . . . . . . . . . . . . . . . . Vaccine Escape HA 225G,
. . . . . . . . . . . . . . . . . . Vaccine Escape HA 225N,
. . . . . . . . . . . . . . . . . . US Military,
. . . . . . . . . . . . . . . . . . Child 6 or Under Count 05],
. . . . . . . . . . [H13N2],
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . HongKong101_C3C1_2M_2013_01_05_VxX (
. . . . . . . . A/Hong Kong/101/2013
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . HA with Strong Avian Influence
. . . . . . . . HA Identity 19/22 [EPI426460]
. . . . . . . . . . . . . KoreaGyeongnam3526_C2C2_13F_2012_12_19
. . . . . . . . NA Identity 16/17 [EPI426459]
. . . . . . . . . . . . . KoreaGyeongnam3526_C2C2_13F_2012_12_19
. . . . . . . . NA Identity with High-CFR pH1N1 Upsilon
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439254
. . . . . . . . GISAID Isolate EPI_ISL_138672
. . . . . . . . 22 Polymorphisms (8 Amino and 14 Silent)
. . . . . . . . syn34N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . 38G [Emergent H7N9 wild type Second Base Donor CGA],
. . . . . . . . . . [avH1N1],
. . . . . . . . syn47L (CTg) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn91G (GGg) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn103E (GAa) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn105R (AGg) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [H10N7],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn181G (GGa),
. . . . . . . . syn183H (CAt),
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 218T mix wt [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . syn338G (GGc),
. . . . . . . . syn352Y (TAt),
. . . . . . . . 377K,
. . . . . . . . syn378I (ATc) [pH1N1 Upsilon],
. . . . . . . . syn384S (TCa) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn447N (AAt),
. . . . . . . . 454N,
. . . . . . . . 463T [Emergent H7N9 LookAsided2 wild type],
. . . . . . . . syn465N (AAt),
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn538F (TTt))

. . . . Texas07_C1_1F_2013_01_05 (
. . . . . . . . A/Texas/07/2013
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase nu
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI426447
. . . . . . . . GISAID Isolate EPI_ISL_136465
. . . . . . . . 19 Polymorphisms (9 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 127L [pH1N1 Rare: 4 Cases over 4 Sequences (2009-2010)],
. . . . . . . . . . . [H5N1],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . 265E [H1N1 WilsonSmith 1933],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn361G (GGa) [pH1N1 Upsilon],
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Maryland02_CXC1_25F_2013_01_04 (
. . . . . . . . A/Maryland/02/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439251
. . . . . . . . GISAID Isolate EPI_ISL_138670
. . . . . . . . 21 Polymorphisms (8 Amino and 13 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . syn182I (ATc),
. . . . . . . . 188T,
. . . . . . . . syn211K (AAa),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918],
. . . . . . . . syn547Q (CAa))

. . . . NewMexico01_M1C2_35F_2013_01_04 (
. . . . . . . . A/New Mexico/01/2013
. . . . . . . . H7N9 Correlation HA 119M
. . . . . . . . CrossClade: 188T & 208K
. . . . . . . . ~ CaliforniaNHRC386820_2013_01_07 [EPI493739]
. . . . . . . . GISAID HA EPI439231
. . . . . . . . GISAID Isolate EPI_ISL_138661
. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 119M [Emergent H7N9],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 198T [ReEmergent 2013 on new background],
. . . . . . . . . . . . [pH1N1 Rare: 7 Cases over 9 Sequences,
. . . . . . . . . . . . . . . 3 US Military in 3 geographies on 2 backgrounds],
. . . . . . . . 208K [H7N9 Avian wild type],
. . . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . . . . [H7N7],
. . . . . . . . . . . [zH3N2],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Oman21_C2_24F_2013_01_03 (
. . . . . . . . A/Oman/21/2013
. . . . . . . . CrossClade: 188T & 189T
. . . . . . . . GISAID HA EPI439465
. . . . . . . . GISAID Isolate EPI_ISL_138727
. . . . . . . . 20 Polymorphisms (10 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . 210C mix wt,
. . . . . . . . 212T mix wt,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn313T (ACc) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Oman03_C2_17F_2012_12_31 (
. . . . . . . . A/Oman/03/2012
. . . . . . . . CrossClade: 188T & 189T
. . . . . . . . GISAID HA EPI439515
. . . . . . . . GISAID Isolate EPI_ISL_138729
. . . . . . . . 20 Polymorphisms (10 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . 218V [pH1N1 Upsilon],
. . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . . . [H9N2],
. . . . . . . . . . [avH1N1farm],
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn313T (ACc) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . 437I mix wt [Emergent H7N9 LookAsided wild type],
. . . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Kentucky23_M1C1_37M_2012_12_25 (
. . . . . . . . A/Kentucky/23/2012
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . H7N9 Correlation HA #2L
. . . . . . . . H7N9 Correlation NA 313H
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI426444
. . . . . . . . GISAID Isolate EPI_ISL_136464
. . . . . . . . 22 Polymorphisms (8 Amino and 14 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . #2L [H7N9 Avian North America],
. . . . . . . . . .[pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . .[avH1N1],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn111V (GTa) [avH1N1farm, zH3N2],
. . . . . . . . syn158G (GGg),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn301I (ATt),
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn361G (GGa) [pH1N1 Upsilon],
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn507K (AAa))

. . . . India2192_C3_2012_12_22 (
. . . . . . . . A/India/2192/2012
. . . . . . . . H7N9 Correlation HA 298V
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439347
. . . . . . . . GISAID Isolate EPI_ISL_138692
. . . . . . . . 19 Polymorphisms (9 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . 54N [zH3N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . 298V [Emergent H7N9],
. . . . . . . . . . [zH3N2],
. . . . . . . . . . [H9N2],
. . . . . . . . . . [avH1N1farm],
. . . . . . . . syn308K (AAg),
. . . . . . . . syn321L (TTa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Minnesota34_M1C1_1M_2012_12_20_VxX (
. . . . . . . . A/Minnesota/34/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . HA 190G GoFE
. . . . . . . . ~ HA NewMexico02_M1C2_4M_2013_01_06_VxX [EPI439239]
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI426455
. . . . . . . . GISAID Isolate EPI_ISL_136468
. . . . . . . . 22 Polymorphisms (10 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 124I [H9N2],
. . . . . . . . 158E,
. . . . . . . . syn161Y (TAt),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 190G [pH1N1 Rare: 17 Cases over 19 Sequences (map),
. . . . . . . . . . . . . . . . . . Fatalities,
. . . . . . . . . . . . . . . . . . Vaccine Escapes,
. . . . . . . . . . . . . . . . . . Infants],
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Tanzania2131_1F_2012_12_19 (
. . . . . . . . A/Tanzania/2131/2012
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI432620
. . . . . . . . GISAID Isolate EPI_ISL_137434
. . . . . . . . 18 Polymorphisms (7 Amino and 11 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Tanzania2131_C2_1F_2012_12_19_VxX (
. . . . . . . . A/Tanzania/2131/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI440929
. . . . . . . . GISAID Isolate EPI_ISL_136467
. . . . . . . . 21 Polymorphisms (10 Amino and 11 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 157E mix wt [H10N7],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 219M mix wt [Emergent H7N9 wild type Third Base Donor GCG],
. . . . . . . . . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . 364H mix wt,
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . KoreaGyeongnam3526_C2C2_13F_2012_12_19 (
. . . . . . . . A/Gyeongnam/3526/2012
. . . . . . . . Deep Lung Binding Enhancer HA 194I
. . . . . . . . Host Transition HA 106K
. . . . . . . . HA with Strong Avian Influence
. . . . . . . . HA Identity 19/23 [EPI439254]
. . . . . . . . . . . . . HongKong101_C3C1_2M_2013_01_05_VxX
. . . . . . . . NA Identity 16/19 [EPI440004]
. . . . . . . . . . . . . HongKong101_C3C1_2M_2013_01_05_VxX
. . . . . . . . NA Identity with High-CFR pH1N1 Upsilon
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI426460
. . . . . . . . GISAID Isolate EPI_ISL_136470
. . . . . . . . 23 Polymorphisms (8 Amino and 15 Silent)
. . . . . . . . syn34N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . syn47L (CTg) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn103E (GAa) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn105R (AGg) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [H10N7],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 106K mix wt [H7N7 Equine Host Switching],
. . . . . . . . syn181G (GGa),
. . . . . . . . syn183H (CAt),
. . . . . . . . 188T,
. . . . . . . . 194I mix wt [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 200T,
. . . . . . . . syn223V (GTa) [Emergent H7N9 wild type],
. . . . . . . . syn338G (GGc),
. . . . . . . . syn352Y (TAt),
. . . . . . . . 377K,
. . . . . . . . syn378I (ATc) [pH1N1 Upsilon],
. . . . . . . . syn384S (TCa) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn436R (AGg) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn447N (AAt),
. . . . . . . . 454N,
. . . . . . . . 463T [Emergent H7N9 LookAsided2 wild type],
. . . . . . . . syn465N (AAt),
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn538F (TTt))

. . . . HongKong9232_C5C1_49F_2012_12_18_VxX (
. . . . . . . . A/Hong Kong/9232/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . H7N9 Correlation HA 141R
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439312
. . . . . . . . GISAID Isolate EPI_ISL_138683
. . . . . . . . 20 Polymorphisms (10 Amino and 10 Silent)
. . . . . . . . #12E [pH1N1 Upsilon],
. . . . . . . . . . [H5N1],
. . . . . . . . . . [H9N2],  
. . . . . . . . . . [avH1N1farm],
. . . . . . . . 41D [H7N9 Avian First Base Donor GTC, GTT],
. . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . syn61A (GCg) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . 100N,
. . . . . . . . syn118E (GAa) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 141R [Emergent H7N9 Amino wild type],
. . . . . . . . . . . [zH3N2],
. . . . . . . . 158E mix wt,
. . . . . . . . syn169I (ATc),
. . . . . . . . syn179L (CTg),
. . . . . . . . syn184H (CAc) [pH1N1 Upsilon],
. . . . . . . . 187N mix wt [H5N1],
. . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 188T,
. . . . . . . . 252L [pH1N1 Clade5: 208K_219V],
. . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . syn257A (GCt),
. . . . . . . . syn334G (GGa) [pH1N1 Upsilon],
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454T,
. . . . . . . . syn511T (ACg))

. . . . Tanzania326_E3_2M_2012_12_05_VxX (
. . . . . . . . A/Tanzania/326/2012
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . H7N9 Correlation HA 476D
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI440003
. . . . . . . . GISAID Isolate EPI_ISL_138671
. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 225G mix wt,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 476D [Emergent H7N9 wild type],
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Tanzania315_E3_30F_2012_11_30 (
. . . . . . . . A/Tanzania/315/2012
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439247
. . . . . . . . GISAID Isolate EPI_ISL_138668
. . . . . . . . 20 Polymorphisms (8 Amino and 12 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 130E [H5N1],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn346G (GGa) [pH1N1 Upsilon],
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Kenya2917_X1C1_9F_2012_11_28 (
. . . . . . . . A/Kenya/2917/2012
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439460
. . . . . . . . GISAID Isolate EPI_ISL_138725
. . . . . . . . 17 Polymorphisms (7 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn33V (GTc) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Tanzania309_C2_3M_2012_11_28_VxX (
. . . . . . . . A/Tanzania/309/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . Deep Lung Binding Enhancer HA 193R
. . . . . . . . Host Transition HA 193R
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI426450
. . . . . . . . GISAID Isolate EPI_ISL_136466
. . . . . . . . 19 Polymorphisms (9 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 156E mix wt,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 193R mix wt [H7N7 Host Switching:
. . . . . . . . . . . . . . . . . . . . . . Equine & Sea Mammal],
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn305K (AAg) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Tanzania307_E3_36F_2012_11_27_VxX (
. . . . . . . . A/Tanzania/307/2012
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . Deep Lung Binding Enhancer HA 194I
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439242
. . . . . . . . GISAID Isolate EPI_ISL_138666
. . . . . . . . 21 Polymorphisms (10 Amino and 11 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn39K (AAa) mix wt [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 194I mix wt [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 225G mix wt,
. . . . . . . . 226R mix wt,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa) mix wt [pH1N1 Upsilon],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Tanzania308_E3_35M_2012_11_27 (
. . . . . . . . A/Tanzania/308/2012
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439241
. . . . . . . . GISAID Isolate EPI_ISL_138665
. . . . . . . . 18 Polymorphisms (8 Amino and 10 Silent)
. . . . . . . . syn#4Y (TAc),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 226R,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn305K (AAg) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa) [pH1N1 Upsilon],
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ])

. . . . Laos839_C1C2_12F_2012_11_12 (
. . . . . . . . A/Laos/839/2012
. . . . . . . . H7N9 Correlation HA 141R
. . . . . . . . Clade2: 188T
. . . . . . . . GISAID HA EPI439236
. . . . . . . . GISAID Isolate EPI_ISL_138663
. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)
. . . . . . . . #2L [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . ,[avH1N1],
. . . . . . . . . ,[H7N7],
. . . . . . . . syn30T (ACt) [zH3N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn61A (GCg) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . 100N,
. . . . . . . . syn118E (GAa) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 141R [Emergent H7N9 Amino wild type],
. . . . . . . . . . . [zH3N2],
. . . . . . . . 163M mix wt [Emergent H7N9 LookAsided wild type],
. . . . . . . . syn173G (GGa) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 205E mix wt [H7N7],
. . . . . . . . 252L [pH1N1 Clade5: 208K_219V],
. . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . 263S mix wt [Emergent H7N9 Amino wild type],
. . . . . . . . syn291T (ACt),
. . . . . . . . syn334G (GGa) [pH1N1 Upsilon],
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . CoteDIvoire1186_xF_2012_10_16_VxX (
. . . . . . . . A/Cote D'Ivoire/1186/2012
. . . . . . . . Perfect Identity to
. . . . . . . . . . . . Vaccine Escape HI Assay Low Reactor [EPI426441]
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Host Transition HA syn99I (ATt)
. . . . . . . . Off-Clade
. . . . . . . . GISAID HA EPI432618
. . . . . . . . GISAID Isolate EPI_ISL_137433
. . . . . . . . 34 Polymorphisms (11 Amino and 23 Silent)
. . . . . . . . 35I [avH1N1, zH3N2, H5N1],
. . . . . . . . syn54H (CAc),
. . . . . . . . syn56G (GGc) [Emergent H7N9],
. . . . . . . . 89E [pH1N1 Rare: 17 Cases over 19 Sequences],
. . . . . . . . . [avH1N1farm, zH3N2, 1918],
. . . . . . . . syn99I (ATt) [Host Switching Potential],
. . . . . . . . . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7 Sea Mammal],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn122K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 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],
. . . . . . . . . . . [WilsonSmith 1933],
. . . . . . . . . . . [1918],
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . 219V [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . syn244T (ACt),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K [Emergent H7N9 wild type],
. . . . . . . . 266A [H7N9 Avian United States:
. . . . . . . . . . . . . . . . First Base Donor 266V gTC, gTT],
. . . . . . . . syn276H (CAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . .  [avH1N1farm],
. . . . . . . . syn295F (TTc) [H7N9 Avian wild type],
. . . . . . . . syn301I (ATt),
. . . . . . . . syn331G (GGt),
. . . . . . . . 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) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [zH3N2],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . . [H10N7],
. . . . . . . . 497R [avH1N1farm, zH5N1, H9N2],
. . . . . . . . syn505G (GGa),
. . . . . . . . 523A,
. . . . . . . . syn526S (TCc),
. . . . . . . . syn527L (TTa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1])

. . . . CoteDIvoire1186_C2_xF_2012_10_16_VxX (
. . . . . . . . A/Cote D'Ivoire/1186/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Host Transition HA syn99I (ATt)
. . . . . . . . Off-Clade
. . . . . . . . GISAID HA EPI426441
. . . . . . . . GISAID Isolate EPI_ISL_136463
. . . . . . . . 34 Polymorphisms (11 Amino and 23 Silent)
. . . . . . . . 35I [avH1N1, zH3N2, H5N1],
. . . . . . . . syn54H (CAc),
. . . . . . . . syn56G (GGc) [Emergent H7N9],
. . . . . . . . 89E [pH1N1 Rare: 17 Cases over 19 Sequences],
. . . . . . . . . [avH1N1farm, zH3N2, 1918],
. . . . . . . . syn99I (ATt) [Host Switching Potential],
. . . . . . . . . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . [H7N7 Sea Mammal],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn122K (AAa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 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],
. . . . . . . . . . . [WilsonSmith 1933],
. . . . . . . . . . . [1918],
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . 219V [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . syn244T (ACt),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K [Emergent H7N9 wild type],
. . . . . . . . 266A [H7N9 Avian United States:
. . . . . . . . . . . . . . . . First Base Donor 266V gTC, gTT],
. . . . . . . . syn276H (CAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . .  [avH1N1farm],
. . . . . . . . syn295F (TTc) [H7N9 Avian wild type],
. . . . . . . . syn301I (ATt),
. . . . . . . . syn331G (GGt),
. . . . . . . . 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) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [zH3N2],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H7N7],
. . . . . . . . . . . . . . . . . . [H10N7],
. . . . . . . . 497R [avH1N1farm, zH5N1, H9N2],
. . . . . . . . syn505G (GGa),
. . . . . . . . 523A,
. . . . . . . . syn526S (TCc),
. . . . . . . . syn527L (TTa) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1])

NA Polymorphisms

. . . . Alabama04_C1C1_54M_2013_02_25 (
. . . . . . . . Novel Hemagglutinin
. . . . . . . . A/Alabama/04/2013
. . . . . . . . GISAID NA EPI439516
. . . . . . . . GISAID Isolate EPI_ISL_138730
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn349F (TTc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . RussiaStPetersburg42_C1C1_2013_02_20 (
. . . . . . . . A/St. Petersburg/42/2013
. . . . . . . . Novel Hemagglutinin
. . . . . . . . GISAID NA EPI439521
. . . . . . . . GISAID Isolate EPI_ISL_138735
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . syn76A (GCc),
. . . . . . . . 106V,
. . . . . . . . 155F,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . RussiaStPetersburg37_C1C1_58x_2013_02_20 (
. . . . . . . . A/St. Petersburg/37/2013
. . . . . . . . H7N9 Correlation HA 10H
. . . . . . . . GISAID NA EPI442700
. . . . . . . . GISAID Isolate EPI_ISL_138731
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn415L (tTG))

. . . . Pennsylvania04_C1_52M_2013_02_14 (
. . . . . . . . A/Pennsylvania/04/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Novel Neuraminidase
. . . . . . . . GISAID NA EPI439457
. . . . . . . . GISAID Isolate EPI_ISL_138724
. . . . . . . . 16 Polymorphisms (9 Amino and 7 Silent)
. . . . . . . . 32M [H5N1],
. . . . . . . . 44S,
. . . . . . . . 48A [H7N9 Avian],
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 220K [pH1N1 with HA 230I],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn221N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn248D (GAc),
. . . . . . . . syn257R (cGA),
. . . . . . . . 321V [Emergent H7N9 wild type],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H6N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . NorthCarolina03_C1_66M_2013_02_13 (
. . . . . . . . A/North Carolina/03/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . GISAID NA EPI440936
. . . . . . . . GISAID Isolate EPI_ISL_138732
. . . . . . . . 15 Polymorphisms (8 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 48A [H7N9 Avian],
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 220K [pH1N1 with HA 230I],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn221N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn248D (GAc),
. . . . . . . . syn257R (cGA),
. . . . . . . . 321V [Emergent H7N9 wild type],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H6N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . RussiaStPetersburg19_E2E1_1x_2013_02_13 (
. . . . . . . . A/St. Petersburg/19/2013
. . . . . . . . GISAID NA EPI439462
. . . . . . . . GISAID Isolate EPI_ISL_138726
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Kentucky02_M1C1_12M_2013_02_08 (
. . . . . . . . A/Kentucky/02/2013
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . H7N9 Correlation NA 199N
. . . . . . . . GISAID NA EPI440006
. . . . . . . . GISAID Isolate EPI_ISL_138673
. . . . . . . . 16 Polymorphisms (9 Amino and 7 Silent)
. . . . . . . . 40V [Emergent H7N9 wild type First Base Donor GGC],
. . . . . . . . 44S,
. . . . . . . . syn77G (GGg),
. . . . . . . . 79P,
. . . . . . . . 106V,
. . . . . . . . syn153S (AGt),
. . . . . . . . 199N [Emergent H7N9 wild type],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . 200S,
. . . . . . . . 222D [avH1N1],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn439S (AGt),
. . . . . . . . syn452T (ACc))

. . . . Nebraska05_C1_1F_2013_02_06 (
. . . . . . . . A/Nebraska/05/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . GISAID NA EPI440940
. . . . . . . . GISAID Isolate EPI_ISL_138733
. . . . . . . . 16 Polymorphisms (8 Amino and 8 Silent)
. . . . . . . . 44S,
. . . . . . . . 48A [H7N9 Avian],
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 220K [pH1N1 with HA 230I],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn221N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn248D (GAc),
. . . . . . . . syn257R (cGA),
. . . . . . . . 321V [Emergent H7N9 wild type],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H6N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn456S (TCc))

. . . . Missouri03_C1_20F_2013_02_05 (
. . . . . . . . A/Missouri/03/2013
. . . . . . . . H7N9 Correlation HA 119M
. . . . . . . . CrossClade: 188T & 208K
. . . . . . . . GISAID NA EPI439995
. . . . . . . . GISAID Isolate EPI_ISL_138659
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . syn73N (AAt),
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Utah04_C1_2M_2013_02_03 (
. . . . . . . . A/Utah/04/2013
. . . . . . . . GISAID NA EPI439244
. . . . . . . . GISAID Isolate EPI_ISL_138667
. . . . . . . . 13 Polymorphisms (5 Amino and 8 Silent)
. . . . . . . . 44S,
. . . . . . . . syn66Y (TAc),
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn420P (CCc))

. . . . Indiana03_M1C1_4M_2013_02_02 (
. . . . . . . . A/Indiana/03/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . GISAID NA EPI440928
. . . . . . . . GISAID Isolate EPI_ISL_138728
. . . . . . . . 17 Polymorphisms (9 Amino and 8 Silent)
. . . . . . . . syn28N (AAt) [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 30T [H5N1 China Human 2009
. . . . . . . . . . . . . . . . Guizhou Wet Market
. . . . . . . . . . . . . . . . . . . . with NA 321V],
. . . . . . . . . . . [pH1N1 Rare: 19 Cases over 20 Sequences,
. . . . . . . . . . . . . . . . Vermont03_M1C2_29M_2013_04_08
. . . . . . . . . . . . . . . . . . . . GISAID HA EPI454439
. . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_142575
. . . . . . . . . . . . . . . . . . . . . . . with HA 225N,
. . . . . . . . . . . . . . . . TamiFlu Resistance:
. . . . . . . . . . . . . . . . KoreaSeoul1870_3F_2009_12_18
. . . . . . . . . . . . . . . . . . . . GISAID HA EPI254674
. . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_74109
. . . . . . . . . . . . . . . . . . . . . . . with NA 275Y],
. . . . . . . . 44S,
. . . . . . . . 48A [H7N9 Avian],
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 220K [pH1N1 with HA 230I],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn221N (AAt) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn248D (GAc),
. . . . . . . . syn257R (cGA),
. . . . . . . . 321V [Emergent H7N9 wild type],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H6N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . California09_E3_10F_2013_01_22_VxX (
. . . . . . . . A/California/09/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Identical NA [EPI450894]
. . . . . . . . . . . . . JapanIbaraki15_M3+2_2013_01_15
. . . . . . . . . . . . . . . . [EPI450885]
. . . . . . . . . . . . . JapanKanagawa54_M2+1_2013_01_22
. . . . . . . . US Military - Probable Vaccination
. . . . . . . . GISAID NA EPI439222
. . . . . . . . GISAID Isolate EPI_ISL_138658
. . . . . . . . 14 Polymorphisms (8 Amino and 6 Silent)
. . . . . . . . 40V [Emergent H7N9 wild type First Base Donor GGC],
. . . . . . . . 44S,
. . . . . . . . 76V [pH1N1 Upsilon],
. . . . . . . . . . [H5N1],
. . . . . . . . syn77G (GGg),
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . 222D [avH1N1],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn426L (tTA),
. . . . . . . . syn439S (AGt))

. . . . NewYork02_E3_28M_2013_01_22_VxX (
. . . . . . . . A/New York/02/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . Novel Hemagglutinin
. . . . . . . . US Military Cluster, 2 Adults & 2 Children
. . . . . . . . US Military - Probable Vaccination
. . . . . . . . GISAID NA EPI439219
. . . . . . . . GISAID Isolate EPI_ISL_138657
. . . . . . . . 16 Polymorphisms (8 Amino and 8 Silent)
. . . . . . . . 44S,
. . . . . . . . 48A [H7N9 Avian],
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 220K [pH1N1 with HA 230I],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn221N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn248D (GAc),
. . . . . . . . syn257R (cGA),
. . . . . . . . 321V [Emergent H7N9 wild type],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H6N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn404G (GGa))

. . . . Washington05_E3_21F_2013_01_18 (
. . . . . . . . A/Washington/05/2013
. . . . . . . . US Military - Probable Vaccination
. . . . . . . . GISAID NA EPI439216
. . . . . . . . GISAID Isolate EPI_ISL_138656
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Indiana02_C1_23F_2013_01_14 (
. . . . . . . . A/Indiana/02/2013
. . . . . . . . H7N9 Correlation NA 45H and 52N
. . . . . . . . Identical NA to [EPI466203]
. . . . . . . . . . . . . AustraliaTownsville34_M4_23F_2013_04_03
. . . . . . . . GISAID NA EPI440000
. . . . . . . . GISAID Isolate EPI_ISL_138669
. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)
. . . . . . . . syn30I (ATt),
. . . . . . . . 44S,
. . . . . . . . 45H [Emergent H7N9 wild type],
. . . . . . . . 52N [Emergent H7N9 wild type],
. . . . . . . . 84N [Emergent H7N9 LookAsideud wild type],
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . 389T [H7N9 LookAsideu North America],
. . . . . . . . syn391Q (CAg))

. . . . ThailandSuratThani16_C1C1_xM_2013_01_11 (
. . . . . . . . A/Surat Thani/16/2013
. . . . . . . . H7N9 Correlation HA 141R
. . . . . . . . H7N9 Correlation HA 300S
. . . . . . . . H7N9 Correlation NA 11S
. . . . . . . . H7N9 Correlation NA 385S
. . . . . . . . GISAID NA EPI439227
. . . . . . . . GISAID Isolate EPI_ISL_138660
. . . . . . . . 17 Polymorphisms (9 Amino and 8 Silent)
. . . . . . . . 5R [H5N1],
. . . . . . . . 11S [Emergent H7N9 Amino wild type],
. . . . . . . . 93L [H5N1],
. . . . . . . . syn158L (tTA),
. . . . . . . . syn172S (TCg),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 264I [pH1N1 Upsilon],
. . . . . . . . . . [H5N1],
. . . . . . . . . . [Emergent H7N9 LookAsideu wild type],
. . . . . . . . syn338V (GTg),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 385S [Emergent H7N9 Amino wild type],
. . . . . . . . . . [pH1N1 with HA 230I],
. . . . . . . . 386S [pH1N1 Upsilon],
. . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . [H9N2],
. . . . . . . . syn393I (ATt),
. . . . . . . . syn416D (GAc),
. . . . . . . . syn439S (AGt),
. . . . . . . . 451G [pH1N1 Upsilon],
. . . . . . . . . . [avH1N1farm],
. . . . . . . . . . [H9N2])

. . . . HongKong145_C3C1_61M_2013_01_10 (
. . . . . . . . A/Hong Kong/145/2013
. . . . . . . . H7N9 Correlation HA 14S
. . . . . . . . CrossClade: 186P, 188T & 208K
. . . . . . . . GISAID NA EPI439213
. . . . . . . . GISAID Isolate EPI_ISL_138655
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . 40V [Emergent H7N9 wild type First Base Donor GGC],
. . . . . . . . 44S,
. . . . . . . . syn77G (GGg),
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn426L (tTA),
. . . . . . . . syn439S (AGt))

. . . . Japan1419_E3_29M_2013_01_09_VxX (
. . . . . . . . A/Japan/1419/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . H7N9 Correlation HA 44I
. . . . . . . . US Military - Probable Vaccination
. . . . . . . . CrossClade: 186P & 188T
. . . . . . . . GISAID NA EPI439233
. . . . . . . . GISAID Isolate EPI_ISL_138662
. . . . . . . . 17 Polymorphisms (7 Amino and 10 Silent)
. . . . . . . . 13I [Emergent H7N9 wild type First Base Donor ACT],
. . . . . . . . . [pH1N1 China 2009 with NA 30T],
. . . . . . . . 44S,
. . . . . . . . syn75A (GCa),
. . . . . . . . syn82S (TCt),
. . . . . . . . syn96G (GGg),
. . . . . . . . syn103D (GAt),
. . . . . . . . syn118R (AGa),
. . . . . . . . syn125S (TCt),
. . . . . . . . 211V [H9N2],
. . . . . . . . syn237S (TCa),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 389T [H7N9 LookAsideu North America],
. . . . . . . . syn430R (aGA),
. . . . . . . . 469N)

. . . . Tennessee01_C1_37M_2013_01_09 (
. . . . . . . . A/Tennessee/01/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . GISAID NA EPI426457
. . . . . . . . GISAID Isolate EPI_ISL_136469
. . . . . . . . 15 Polymorphisms (8 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 48A [H7N9 Avian],
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 220K [pH1N1 with HA 230I],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn221N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn248D (GAc),
. . . . . . . . syn257R (cGA),
. . . . . . . . 321V [Emergent H7N9 wild type],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H6N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Kyrgyzstan220_C1_2013_01_08 (
. . . . . . . . A/Kyrgyzstan/220/2013
. . . . . . . . H7N9 Correlation HA 482I
. . . . . . . . H7N9 Correlation NA 313H
. . . . . . . . GISAID NA EPI439477
. . . . . . . . GISAID Isolate EPI_ISL_138734
. . . . . . . . 14 Polymorphisms (6 Amino and 8 Silent)
. . . . . . . . syn30I (ATa),
. . . . . . . . 44S,
. . . . . . . . syn70S (AGt),
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 313H [Emergent H7N9 wild type],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . 411K mix wt [H9N2])

. . . . NewMexico02_M1C2_4M_2013_01_06_VxX (
. . . . . . . . A/New Mexico/02/2013
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . HA 190G GoFE
. . . . . . . . GISAID NA EPI439238
. . . . . . . . GISAID Isolate EPI_ISL_138664
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 224V [pH1N1 Novel],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn274Y (TAc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . HongKong101_C3C1_2M_2013_01_05_VxX (
. . . . . . . . A/Hong Kong/101/2013
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . HA with Strong Avian Influence
. . . . . . . . HA Identity 19/22 [EPI426460]
. . . . . . . . . . . . . KoreaGyeongnam3526_C2C2_13F_2012_12_19
. . . . . . . . NA Identity 16/17 [EPI426459]
. . . . . . . . . . . . . KoreaGyeongnam3526_C2C2_13F_2012_12_19
. . . . . . . . NA Identity with High-CFR pH1N1 Upsilon
. . . . . . . . GISAID NA EPI440004
. . . . . . . . GISAID Isolate EPI_ISL_138672
. . . . . . . . 17 Polymorphisms (5 Amino and 12 Silent)
. . . . . . . . syn40L (CTc),
. . . . . . . . 44S [pH1N1 Upsilon],
. . . . . . . . 48I [pH1N1 Upsilon],
. . . . . . . . . [H9N2],
. . . . . . . . . [avH1N1farm],
. . . . . . . . syn81V (GTc) [pH1N1 Upsilon],
. . . . . . . . syn125S (TCa) [avH1N1farm],
. . . . . . . . syn177V (GTt) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn197G (GGt) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn240T (ACc) [pH1N1 Upsilon],
. . . . . . . . 241I [pH1N1 Upsilon],
. . . . . . . . syn267V (GTt) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 287K [H7N9 Avian First Base Donor AGT],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn299S (TCa) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn356G (GGc) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 369K [pH1N1 Upsilon],
. . . . . . . . syn376D (GAc) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn377P (CCa) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn465F (TTc) [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm])

. . . . Texas07_C1_1F_2013_01_05 (
. . . . . . . . A/Texas/07/2013
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase nu
. . . . . . . . GISAID NA EPI426446
. . . . . . . . GISAID Isolate EPI_ISL_136465
. . . . . . . . 14 Polymorphisms (5 Amino and 9 Silent)
. . . . . . . . 44S,
. . . . . . . . syn70S (AGt),
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn363K (AAg) [pH1N1 Upsilon],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn448V (GTc) mix wt)

. . . . Maryland02_CXC1_25F_2013_01_04 (
. . . . . . . . A/Maryland/02/2013
. . . . . . . . H7N9 Correlation NA 48A and 321V
. . . . . . . . GISAID NA EPI440001
. . . . . . . . GISAID Isolate EPI_ISL_138670
. . . . . . . . 15 Polymorphisms (8 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 48A [H7N9 Avian],
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 220K [pH1N1 with HA 230I],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn221N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn248D (GAc),
. . . . . . . . syn257R (cGA),
. . . . . . . . 321V [Emergent H7N9 wild type],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H6N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . NA Truncated after aa466)

. . . . NewMexico01_M1C2_35F_2013_01_04 (
. . . . . . . . A/New Mexico/01/2013
. . . . . . . . H7N9 Correlation HA 119M
. . . . . . . . CrossClade: 188T & 208K
. . . . . . . . GISAID NA EPI439230
. . . . . . . . GISAID Isolate EPI_ISL_138661
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . syn191L (tTA) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Oman21_C2_24F_2013_01_03 (
. . . . . . . . A/Oman/21/2013
. . . . . . . . CrossClade: 188T & 189T
. . . . . . . . GISAID NA EPI439520
. . . . . . . . GISAID Isolate EPI_ISL_138727
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 66C mix wt,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Oman03_C2_17F_2012_12_31 (
. . . . . . . . A/Oman/03/2012
. . . . . . . . CrossClade: 188T & 189T
. . . . . . . . GISAID NA EPI439514
. . . . . . . . GISAID Isolate EPI_ISL_138729
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn168S (TCc),
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . 430Q [avH1N1farm],
. . . . . . . . . . . [H5N1])

. . . . Kentucky23_M1C1_37M_2012_12_25 (
. . . . . . . . A/Kentucky/23/2012
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . H7N9 Correlation HA #2L
. . . . . . . . H7N9 Correlation NA 313H
. . . . . . . . GISAID NA EPI426443
. . . . . . . . GISAID Isolate EPI_ISL_136464
. . . . . . . . 16 Polymorphisms (9 Amino and 7 Silent)
. . . . . . . . 19I [H5N1],
. . . . . . . . . [avH1N1farm],
. . . . . . . . 44S,
. . . . . . . . 46T [Emergent H7N9 wild type:
. . . . . . . . . . . . . .  Second Base Donor TCA],
. . . . . . . . syn70S (AGt),
. . . . . . . . 106V,
. . . . . . . . 128G mix wt [pH1N1 Rare: 16 Cases over 21 Sequences,
. . . . . . . . . . . . . . . . . . . . . . . . Vaccine Escape Genotype HA 156E mix wt,
. . . . . . . . . . . . . . . . . . . . . . . . Vaccine Escape Genotype HA 157E mix wt,
. . . . . . . . . . . . . . . . . . . . . . . . CrossClade: 188T & 189T,
. . . . . . . . . . . . . . . . . . . . . . . . TamiFlu Resistance NA 275Y Count 02],
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 313H [Emergent H7N9 wild type],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . India2192_C3_2012_12_22 (
. . . . . . . . A/India/2192/2012
. . . . . . . . H7N9 Correlation HA 298V
. . . . . . . . GISAID NA EPI439346
. . . . . . . . GISAID Isolate EPI_ISL_138692
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn436I (ATt))

. . . . Minnesota34_M1C1_1M_2012_12_20_VxX (
. . . . . . . . A/Minnesota/34/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . HA 190G GoFE
. . . . . . . . GISAID NA EPI426454
. . . . . . . . GISAID Isolate EPI_ISL_136468
. . . . . . . . 17 Polymorphisms (9 Amino and 8 Silent)
. . . . . . . . syn20A (GCc) [pH1N1 Upsilon],
. . . . . . . . 38T [H5N1],
. . . . . . . . 44S,
. . . . . . . . syn55T (ACc),
. . . . . . . . 56H [H6N1],
. . . . . . . . 66H mix wt [H6N1],
. . . . . . . . 67A [avH1N1farm],
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Tanzania2131_1F_2012_12_19 (
. . . . . . . . A/Tanzania/2131/2012
. . . . . . . . GISAID NA EPI432619
. . . . . . . . GISAID Isolate EPI_ISL_137434
. . . . . . . . 13 Polymorphisms (5 Amino and 8 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn131T (ACa) mix wt,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn432K (AAg))

. . . . Tanzania2131_C2_1F_2012_12_19_VxX (
. . . . . . . . A/Tanzania/2131/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . GISAID NA EPI426452
. . . . . . . . GISAID Isolate EPI_ISL_136467
. . . . . . . . 15 Polymorphisms (7 Amino and 8 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn131T (ACa),
. . . . . . . . 151N mix wt,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . 217R mix wt [H5N1],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn432K (AAg))

. . . . KoreaGyeongnam3526_C2C2_13F_2012_12_19 (
. . . . . . . . A/Gyeongnam/3526/2012
. . . . . . . . Host Transition HA 106K
. . . . . . . . HA with Strong Avian Influence
. . . . . . . . HA Identity 19/23 [EPI439254]
. . . . . . . . . . . . . HongKong101_C3C1_2M_2013_01_05_VxX
. . . . . . . . NA Identity 16/19 [EPI440004]
. . . . . . . . . . . . . HongKong101_C3C1_2M_2013_01_05_VxX
. . . . . . . . NA Identity with High-CFR pH1N1 Upsilon
. . . . . . . . GISAID NA EPI426459
. . . . . . . . GISAID Isolate EPI_ISL_136470
. . . . . . . . 19 Polymorphisms (5 Amino and 14 Silent)
. . . . . . . . syn40L (CTc),
. . . . . . . . 44S [pH1N1 Upsilon],
. . . . . . . . syn81V (GTc) [pH1N1 Upsilon],
. . . . . . . . syn94V (GTc) [avH1N1],
. . . . . . . . syn125S (TCa) [avH1N1farm],
. . . . . . . . syn177V (GTt) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn197G (GGt) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn234V (GTg) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn240T (ACc) [pH1N1 Upsilon],
. . . . . . . . 241I [pH1N1 Upsilon],
. . . . . . . . syn267V (GTt) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 287K [H7N9 Avian First Base Donor AGT],
. . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn299S (TCa) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 341D mix wt [Emergent H7N9 LookAsided 2013-10-14],
. . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn356G (GGc) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 369K [pH1N1 Upsilon],
. . . . . . . . syn376D (GAc) [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn377P (CCa) [pH1N1 Upsilon],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . syn465F (TTc) [H5N1],
. . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . [avH1N1farm])

. . . . HongKong9232_C5C1_49F_2012_12_18_VxX (
. . . . . . . . A/Hong Kong/9232/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . H7N9 Correlation HA 141R
. . . . . . . . GISAID NA EPI439311
. . . . . . . . GISAID Isolate EPI_ISL_138683
. . . . . . . . 17 Polymorphisms (7 Amino and 10 Silent)
. . . . . . . . syn42N (AAc),
. . . . . . . . syn68N (AAt),
. . . . . . . . 83L,
. . . . . . . . syn92C (TGt),
. . . . . . . . syn95S (AGc),
. . . . . . . . 122V,
. . . . . . . . syn158L (tTA),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn251A (GCt),
. . . . . . . . syn306F (TTt),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn385N (AAc),
. . . . . . . . 386S [pH1N1 Upsilon],
. . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . [H9N2],
. . . . . . . . 416N,
. . . . . . . . 451G [pH1N1 Upsilon],
. . . . . . . . . . [avH1N1farm],
. . . . . . . . . . [H9N2])

. . . . Tanzania326_E3_2M_2012_12_05_VxX (
. . . . . . . . A/Tanzania/326/2012
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . H7N9 Correlation HA 476D
. . . . . . . . GISAID NA EPI440002
. . . . . . . . GISAID Isolate EPI_ISL_138671
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn432K (AAg))

. . . . Tanzania315_E3_30F_2012_11_30 (
. . . . . . . . A/Tanzania/315/2012
. . . . . . . . GISAID NA EPI439999
. . . . . . . . GISAID Isolate EPI_ISL_138668
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 321L,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Kenya2917_X1C1_9F_2012_11_28 (
. . . . . . . . A/Kenya/2917/2012
. . . . . . . . GISAID NA EPI439459
. . . . . . . . GISAID Isolate EPI_ISL_138725
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn439S (AGt))

. . . . Tanzania309_C2_3M_2012_11_28_VxX (
. . . . . . . . A/Tanzania/309/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . Host Transition HA 193R
. . . . . . . . GISAID NA EPI426449
. . . . . . . . GISAID Isolate EPI_ISL_136466
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 313K [H5N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Tanzania307_E3_36F_2012_11_27_VxX (
. . . . . . . . A/Tanzania/307/2012
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . GISAID NA EPI439998
. . . . . . . . GISAID Isolate EPI_ISL_138666
. . . . . . . . 16 Polymorphisms (6 Amino and 10 Silent)
. . . . . . . . syn28N (AAt) mix wt [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn224L (TTa) mix wt [H5N1],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn312Y (TAc) mix wt [H5N1],
. . . . . . . . 313K mix wt [H5N1],
. . . . . . . . syn341N (AAc) mix wt [H5N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Tanzania308_E3_35M_2012_11_27 (
. . . . . . . . A/Tanzania/308/2012
. . . . . . . . GISAID NA EPI439240
. . . . . . . . GISAID Isolate EPI_ISL_138665
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . 44S,
. . . . . . . . 106V,
. . . . . . . . syn176S (TCg) [pH1N1 Upsilon],
. . . . . . . . 200S,
. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . . . . [H6N1],
. . . . . . . . syn209N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 313K [H5N1],
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . Laos839_C1C2_12F_2012_11_12 (
. . . . . . . . A/Laos/839/2012
. . . . . . . . H7N9 Correlation HA 141R
. . . . . . . . GISAID NA EPI439235
. . . . . . . . GISAID Isolate EPI_ISL_138663
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . 66H mix wt,
. . . . . . . . syn158L (tTA),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . 386S [pH1N1 Upsilon],
. . . . . . . . . . [pH1N1 with NA 247N TamiFlu Resistance],
. . . . . . . . . . [H9N2],
. . . . . . . . syn416D (GAc),
. . . . . . . . 451G [pH1N1 Upsilon],
. . . . . . . . . . [avH1N1farm],
. . . . . . . . . . [H9N2])

. . . . CoteDIvoire1186_xF_2012_10_16_VxX (
. . . . . . . . A/Cote D'Ivoire/1186/2012
. . . . . . . . Perfect Identity to
. . . . . . . . . . . . Vaccine Escape HI Assay Low Reactor [EPI426441]
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID NA EPI432617
. . . . . . . . GISAID Isolate EPI_ISL_137433
. . . . . . . . 17 Polymorphisms (4 Amino and 13 Silent)
. . . . . . . . syn20A (GCc) [pH1N1 Upsilon],
. . . . . . . . syn34I (ATc),
. . . . . . . . syn36H (CAt),
. . . . . . . . 74V,
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn127L (cTG),
. . . . . . . . syn173R (cGA),
. . . . . . . . syn183A (GCc),
. . . . . . . . syn224L (cTG),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn369N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K [Emergent H7N9 wild type],
. . . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . . [H9N2],
. . . . . . . . syn431P (CCa),
. . . . . . . . syn433E (GAa))

. . . . CoteDIvoire1186_C2_xF_2012_10_16_VxX (
. . . . . . . . A/Cote D'Ivoire/1186/2012
. . . . . . . . Vaccine Escape HI Assay Low Reactor
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID NA EPI426440
. . . . . . . . GISAID Isolate EPI_ISL_136463
. . . . . . . . 17 Polymorphisms (4 Amino and 13 Silent)
. . . . . . . . syn20A (GCc) [pH1N1 Upsilon],
. . . . . . . . syn34I (ATc),
. . . . . . . . syn36H (CAt),
. . . . . . . . 74V,
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn127L (cTG),
. . . . . . . . syn173R (cGA),
. . . . . . . . syn183A (GCc),
. . . . . . . . syn224L (cTG),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn369N (AAt) [pH1N1 Upsilon],
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K [Emergent H7N9 wild type],
. . . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . . [H9N2],
. . . . . . . . syn431P (CCa),
. . . . . . . . syn433E (GAa))

Supporting Sequences

. . . . Vermont03_M1C2_29M_2013_04_08 (
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . GISAID HA EPI454439
. . . . . . . . GISAID Isolate EPI_ISL_142575
. . . . . . . . 21 Polymorphisms (8 Amino and 13 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . syn182I (ATc),
. . . . . . . . 188T,
. . . . . . . . syn211K (AAa),
. . . . . . . . 225N mix wt,
. . . . . . . . 259T,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K,
. . . . . . . . syn537S (AGc),
. . . . . . . . syn547Q (CAa))

. . . . Vermont03_M1C2_29M_2013_04_08 (
. . . . . . . . Novel Hemagglutinin
. . . . . . . . Novel Neuraminidase
. . . . . . . . GISAID NA EPI454438
. . . . . . . . GISAID Isolate EPI_ISL_142575
. . . . . . . . 18 Polymorphisms (10 Amino and 8 Silent)
. . . . . . . . 30T,
. . . . . . . . 44S,
. . . . . . . . 48A,
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . syn209N (AAt),
. . . . . . . . 220K,
. . . . . . . . syn221N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn248D (GAc),
. . . . . . . . syn257R (cGA),
. . . . . . . . 289I [Emergent H7N9 LookAsideu wild type],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 321V,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . syn398E (GAa) [pH1N1 with NA 247N TamiFlu Resistance])

PB2 Polymorphisms

. . . . India2192_C3_2012_12_22 (
. . . . . . . . A/India/2192/2012
. . . . . . . . GISAID PB2 EPI439345
. . . . . . . . GISAID Isolate EPI_ISL_138692
. . . . . . . . 25 Polymorphisms (10 Amino and 15 Silent)
. . . . . . . . 54K,
. . . . . . . . 66I,
. . . . . . . . 114I,
. . . . . . . . 155S,
. . . . . . . . 195N,
. . . . . . . . syn222G (GGt),
. . . . . . . . syn291G (GGt),
. . . . . . . . syn292V (GTg),
. . . . . . . . 293K,
. . . . . . . . syn319I (ATc),
. . . . . . . . 344M,
. . . . . . . . syn348N (AAt),
. . . . . . . . 354L,
. . . . . . . . syn383Q (CAa),
. . . . . . . . syn384L (TTa),
. . . . . . . . syn396E (GAa),
. . . . . . . . syn427R (aGA),
. . . . . . . . syn482K (AAg),
. . . . . . . . syn489S (TCa),
. . . . . . . . 518I,
. . . . . . . . syn555R (AGa),
. . . . . . . . syn573N (AAt),
. . . . . . . . syn646R (AGa),
. . . . . . . . syn697L (TTa),
. . . . . . . . 731I)

PB1 Polymorphisms

. . . . India2192_C3_2012_12_22 (
. . . . . . . . A/India/2192/2012
. . . . . . . . GISAID PB1 EPI440007
. . . . . . . . GISAID Isolate EPI_ISL_138692
. . . . . . . . 23 Polymorphisms (3 Amino and 20 Silent)
. . . . . . . . syn14A (GCa),
. . . . . . . . syn56T (ACa),
. . . . . . . . syn105N (AAt),
. . . . . . . . syn122L (CTg),
. . . . . . . . 154D,
. . . . . . . . syn158N (AAc),
. . . . . . . . syn210Q (CAg),
. . . . . . . . syn270G (GGa),
. . . . . . . . syn295D (GAt),
. . . . . . . . syn333F (TTt),
. . . . . . . . syn346N (AAt),
. . . . . . . . syn377D (GAt),
. . . . . . . . syn396L (tTA),
. . . . . . . . 397M,
. . . . . . . . 435T,
. . . . . . . . syn573S (TCa),
. . . . . . . . syn632V (GTa),
. . . . . . . . syn635K (AAg),
. . . . . . . . syn692C (TGt),
. . . . . . . . syn701P (CCa),
. . . . . . . . syn719V (GTa),
. . . . . . . . syn730F (TTt),
. . . . . . . . syn734R (CGa))

PA Polymorphisms

. . . . India2192_C3_2012_12_22 (
. . . . . . . . A/India/2192/2012
. . . . . . . . GISAID PA EPI439344
. . . . . . . . GISAID Isolate EPI_ISL_138692
. . . . . . . . 27 Polymorphisms (2 Amino and 25 Silent)
. . . . . . . . syn33N (AAt),
. . . . . . . . syn112Y (TAt),
. . . . . . . . syn115N (AAt),
. . . . . . . . syn145I (ATc),
. . . . . . . . syn154E (GAa),
. . . . . . . . syn169A (GCg),
. . . . . . . . syn221P (CCa),
. . . . . . . . syn291S (AGc),
. . . . . . . . syn312K (AAa),
. . . . . . . . 321K,
. . . . . . . . syn335L (CTa),
. . . . . . . . 343T,
. . . . . . . . syn358K (AAa),
. . . . . . . . syn390L (CTc),
. . . . . . . . syn398P (CCc),
. . . . . . . . syn443R (AGa),
. . . . . . . . syn476A (GCt),
. . . . . . . . syn508R (AGa),
. . . . . . . . syn534P (CCa),
. . . . . . . . syn544E (GAg),
. . . . . . . . syn563L (tTA),
. . . . . . . . syn592I (ATc),
. . . . . . . . syn608T (ACt),
. . . . . . . . syn645V (GTg),
. . . . . . . . syn662S (TCa),
. . . . . . . . syn673R (AGa),
. . . . . . . . syn705S (TCc))

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pH1N1 Influenza PolymeraseBasic2, PolymeraseBasic1, PolymeraseAcidic, Hemagglutinin & Neuraminidase Segments
elucidated at 2013-12-19-02_04_33_556030 by GeneWurx see.PolyDetector v0, Copyright 2007-2014.

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