2013-11-06

HA 263S: Emergent H7N9 & pH1N1 Receptor Binding Dynamic

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

Publish Date : 2013-11-06
Last Update : 2013-11-25
Gain of Function Empiriks
by
Polymorphism
pH1N1 HA 263S

Emergent H7N9 & pH1N1 Receptor Binding Dynamic: HA 263S
Map - Active and Detailed
8 Cases over 10 Sequences

Receptor Binding Site Variance
pH1N1
100% Receptor Binding Site Revision for 2013
Sample
Date		NameRBS
Revision		ID
 2013-10-05  BrazilSaoPauloRibeiraoPreto630359_44M_VxX_s HA 225G EPI484749 
 2013-02-20  Ukraine5794_C2M1_18F HA 227G EPI462073 

Cross SeroType Analytics
HA Set Polymorphic Homology
SeroTypeCountPercent
 H5N13049%
 H7N71931%
Origin-Seeking HA 263S
SeroType
 Emergent H7N9 Amino wild type
 H7N7 Human Fatality Amino
 H7N7 Amino wild type
 avH1N1 Amino wild type

Isolate Metrics
Calendar
Sample
Year		Count
 201302
 201200
 201101
 201001
 200906
Age Dynamic
ObservationPer
Cent
 Child Aged 18 or Under60%
Cladistics
CladeNameCount
 UnCladed07
 Clade2:188T03

HA Polymorphisms

. . . . BrazilSaoPauloRibeiraoPreto630359_44M_2013_10_05_VxX_s (
. . . . . . . . A/Sao Paulo/6-30359/2013
. . . . . . . . Vaccine Escape Genotype HA 225G
. . . . . . . . Treatment by Oseltamivir
. . . . . . . . Deposit Report
. . . . . . . . GISAID HA EPI484749
. . . . . . . . GISAID Isolate EPI_ISL_149733
. . . . . . . . 24 Polymorphisms (10 Amino and 14 Silent)
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn141H (CAc),
. . . . . . . . syn156K (AAg),
. . . . . . . . 166Q,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn236L (tTA),
. . . . . . . . syn237V (GTg),
. . . . . . . . 259T [pH1N1 Upsilon US Military],
. . . . . . . . 263S [pH1N1 Rare: Count 09 on 07 Cases,
. . . . . . . . . . . . . . . . . . Ukraine5794_C2M1_18F_2013_02_20
. . . . . . . . . . . . . . . . . . . . . . .  with HA 227G and NA 222D,
. . . . . . . . . . . . . . . . . . US Air Force 2009],
. . . . . . . . . . . . [Emergent H7N9 Amino wt],
. . . . . . . . . . . . [H7N7 Human Fatality Amino wt],
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K [pH1N1 Upsilon],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [H7N7 Passerine, Anser & Galliformes],
. . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . [WSN, WSZ],
. . . . . . . . syn513I (ATc),
. . . . . . . . syn537S (AGc) [pH1N1 with HA 230I],
. . . . . . . . . . . . . . . . . . [1918])

. . . . Ukraine5794_C2M1_18F_2013_02_20 (
. . . . . . . . A/Ukraine/5794/2013
. . . . . . . . Receptor Binding Variance HA 227G
. . . . . . . . GISAID HA EPI462073
. . . . . . . . GISAID Isolate EPI_ISL_144074
. . . . . . . . 25 Polymorphisms (11 Amino and 14 Silent)
. . . . . . . . #6M,
. . . . . . . . syn34N (AAt),
. . . . . . . . 87G,
. . . . . . . . syn122K (AAa),
. . . . . . . . syn127P (CCa),
. . . . . . . . 146G,
. . . . . . . . 166I,
. . . . . . . . syn171D (GAc),
. . . . . . . . 188T,
. . . . . . . . syn189A (GCa),
. . . . . . . . 200T,
. . . . . . . . syn224R (AGa),
. . . . . . . . 227G [FranceLorraine1176_50x_2011_02_23_TmX],
. . . . . . . . . . . . [H5N1],
. . . . . . . . syn258F (TTt),
. . . . . . . . 263S,
. . . . . . . . syn275V (GTt),
. . . . . . . . syn337A (GCt),
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn488D (GAt),
. . . . . . . . 523A,
. . . . . . . . syn524A (GCt),
. . . . . . . . syn538F (TTt))

. . . . JapanSuita99_2011_01 (
. . . . . . . . A/Suita/99/2011
. . . . . . . . GISAID HA EPI416353
. . . . . . . . GISAID Isolate EPI_ISL_134103
. . . . . . . . 13 Polymorphisms (7 Amino and 6 Silent)
. . . . . . . . HA Truncated before aa2,
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 71D,
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 263S,
. . . . . . . . syn338G (GGc),
. . . . . . . . syn360Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn445V (GTt),
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . HA Truncated after aa535)

. . . . SingaporeGP1112_C2_9M_2010_04_06 (
. . . . . . . . A/Singapore/GP1112/2010
. . . . . . . . GISAID HA EPI385245
. . . . . . . . GISAID Isolate EPI_ISL_124666
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . syn#9L (tTA),
. . . . . . . . syn53L (cTG),
. . . . . . . . syn107Q (CAg),
. . . . . . . . 145R,
. . . . . . . . 208K,
. . . . . . . . 263S)

. . . . UKEnglandLondon863_C1_E275_2009_11_24 (
. . . . . . . . A/England/863/2009
. . . . . . . . GISAID HA EPI336251
. . . . . . . . GISAID Isolate EPI_ISL_96275
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn#2F (TTc),
. . . . . . . . 35I,
. . . . . . . . syn53L (cTG),
. . . . . . . . 263S,
. . . . . . . . syn490P (CCc))

. . . . UKEnglandLondon863_C1_2009_11_24 (
. . . . . . . . A/ENG/863/2009
. . . . . . . . GISAID HA EPI276501
. . . . . . . . GISAID Isolate EPI_ISL_78380
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn#2F (TTc),
. . . . . . . . 35I,
. . . . . . . . syn53L (cTG),
. . . . . . . . 263S,
. . . . . . . . syn490P (CCc))

. . . . SpainLaRiojaRR6490_15F_2009_11_03 (
. . . . . . . . A/LaRioja/RR6490/2009
. . . . . . . . GISAID HA EPI304878
. . . . . . . . GISAID Isolate EPI_ISL_86857
. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa20,
. . . . . . . . 263S,
. . . . . . . . 291I [Emergent H7N9 LookAsideu]
. . . . . . . . HA Truncated after aa335)

. . . . MarylandAF2452_PMK1_38M_2009_10_27 (
. . . . . . . . A/Maryland/AF2452/2009
. . . . . . . . GISAID HA EPI278242
. . . . . . . . GISAID Isolate EPI_ISL_79000
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn137A (GCt),
. . . . . . . . 263S,
. . . . . . . . syn270I (ATc),
. . . . . . . . 377K,
. . . . . . . . HA Truncated after aa386)

. . . . UKEnglandLambeth1081_C1_E403_2009_10_16 (
. . . . . . . . A/England/1081/2009
. . . . . . . . GISAID HA EPI336379
. . . . . . . . GISAID Isolate EPI_ISL_96403
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 24K [zH3N2],
. . . . . . . . 35I,
. . . . . . . . 263S,
. . . . . . . . syn490P (CCc))

. . . . UKEnglandLambeth1081_C1_2009_10_16 (
. . . . . . . . A/ENG/1081/2009
. . . . . . . . GISAID HA EPI276392
. . . . . . . . GISAID Isolate EPI_ISL_78271
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 24K [zH3N2],
. . . . . . . . 35I,
. . . . . . . . 263S,
. . . . . . . . syn490P (CCc))

NA Polymorphisms

. . . . Ukraine5794_C2M1_18F_2013_02_20 (
. . . . . . . . A/Ukraine/5794/2013
. . . . . . . . GISAID NA EPI462074
. . . . . . . . GISAID Isolate EPI_ISL_144074
. . . . . . . . 15 Polymorphisms (9 Amino and 6 Silent)
. . . . . . . . 40V,
. . . . . . . . 44S,
. . . . . . . . 76V,
. . . . . . . . syn77G (GGg),
. . . . . . . . 106V,
. . . . . . . . 200S,
. . . . . . . . 222D [Youth Age Dynamic],
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt),
. . . . . . . . 416N,
. . . . . . . . syn426L (tTA),
. . . . . . . . syn439S (AGt))

. . . . SingaporeGP1112_C2_9M_2010_04_06 (
. . . . . . . . A/Singapore/GP1112/2010
. . . . . . . . GISAID NA EPI385247
. . . . . . . . GISAID Isolate EPI_ISL_124666
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . syn114V (GTa),
. . . . . . . . 257K,
. . . . . . . . syn323G (GGg))

. . . . SpainLaRiojaRR6490_15F_2009_11_03 (
. . . . . . . . A/LaRioja/RR6490/2009
. . . . . . . . GISAID NA EPI305244
. . . . . . . . GISAID Isolate EPI_ISL_86857
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . NA Truncated before aa198,
. . . . . . . . syn369N (AAt),
. . . . . . . . 393V,
. . . . . . . . NA Truncated after aa418)

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pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-11-04-16_34_55_129670 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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