First Guangdong Human Case Acquires Antigenic H3N2 HA 128A

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 : 2013-12-05
Last Update : 2014-04-07

On 2013-10-05, the Guangzhou Medical University in China released a complete set of human Emergent H7N9 sequences at GISAID.  The Hemagglutinin carries markers from previous Emergent H7N9 human cases, including HA 277D from the sentinel case.  The acquisition of HA 128A, an antigenic revision from the circulating human seasonal H3N2 that set Hospitalisation and Fatality records last season, merits close examination for human infectivity.

Although the Neuraminidase is stock (trend for many human H7N9 sequences), the Polymerase Complex defines a novel ReAssortment with H9N2 at the Polymerase Basic 2 (PB2) and Polymerase Basic 1 (PB1) segments.  Additionally, segment 3, Polymerase Acidic (PA), is on an Emergent H7N9 background with novel polymorphisms from H5N1, PA 343T, and from H9N2, PA 519T.

For additional case information, including presentation dates and clinical progressions, the Guangdong Huizhou patient is indexed as Case #136 on the 2013 H7N9 Human Case List maintained by the crowd-sourced FluTrackers.com.

The Emergent H7N9 reservoir continues to cast a wide net for genetic acquisition in movements toward higher human infectivity.

HA Polymorphisms

. . . . ChinaGuangdongHuizhou1_51F_2013_08_10_s (

. . . . . . . . A/Guangdong/1/2013
. . . . . . . . Novel Hemagglutinin

. . . . . . . . GISAID HA EPI476697

. . . . . . . . GISAID Isolate EPI_ISL_148417

. . . . . . . . 105 Polymorphisms (19 Amino and 86 Silent)

. . . . . . . . 11I [#4I] [zH3N2],

. . . . . . . . 65K [51K],

. . . . . . . . 130A [118A],

. . . . . . . . 140A [128A] [Emergent H7N9 Novel],
. . . . . . . . . . . . . . . . . [H3N2 Human Seasonal],

. . . . . . . . 183S [174S] [zH3N2],

. . . . . . . . 188V [179V] [zH3N2],

. . . . . . . . 195V [186V],

. . . . . . . . 198A [189A],

. . . . . . . . 211V [202V] [zH3N2],

. . . . . . . . 217N [208N],

. . . . . . . . 235L [226L] [zH3N2],

. . . . . . . . 285D [277D] [Sentinel Emergent H7N9],
. . . . . . . . . . . . . . . . . [pH1N1],
. . . . . . . . . . . . . . . . . [H5N1],

. . . . . . . . 307D [299D],

. . . . . . . . 321R [313R] [H9N2],

. . . . . . . . 410N [401N],

. . . . . . . . 427I [418I],

. . . . . . . . 455D [446D],

. . . . . . . . 462K [453K] [zH3N2],

. . . . . . . . 541V [533V])

NA Polymorphisms

. . . . ChinaGuangdongHuizhou1_51F_2013_08_10_s (

. . . . . . . . A/Guangdong/1/2013

. . . . . . . . GISAID NA EPI476703

. . . . . . . . GISAID Isolate EPI_ISL_148417

. . . . . . . . 32 Polymorphisms (10 Amino and 22 Silent)

. . . . . . . . 16I [16I],

. . . . . . . . 19A [19A],

. . . . . . . . 40G [40G],

. . . . . . . . 53T [53T],

. . . . . . . . 81T [80T],

. . . . . . . . 84N [83N],

. . . . . . . . 112S [111S],

. . . . . . . . 335I [332I],

. . . . . . . . 359A [355A],

. . . . . . . . 401A [397A])

PB2 Polymorphisms

. . . . ChinaGuangdongHuizhou1_51F_2013_08_10_s (

. . . . . . . . A/Guangdong/1/2013

. . . . . . . . ~ H9N2

. . . . . . . . GISAID PB2 EPI476698

. . . . . . . . GISAID Isolate EPI_ISL_148417

. . . . . . . . 83 Polymorphisms (5 Amino and 78 Silent)

. . . . . . . . 139I [pH1N1 Rare: Early Emergence],

. . . . . . . . 191E [pH1N1 Wild Type],

. . . . . . . . 559T,

. . . . . . . . 570I,

. . . . . . . . 676V)

PB1 Polymorphisms

. . . . ChinaGuangdongHuizhou1_51F_2013_08_10_s (

. . . . . . . . A/Guangdong/1/2013

. . . . . . . . ~ H9N2

. . . . . . . . GISAID PB1 EPI476699

. . . . . . . . GISAID Isolate EPI_ISL_148417

. . . . . . . . 62 Polymorphisms (5 Amino and 57 Silent)

. . . . . . . . 171V,

. . . . . . . . 374V,

. . . . . . . . 397M,

. . . . . . . . 525I,

. . . . . . . . 694S)

PA Polymorphisms

. . . . ChinaGuangdongHuizhou1_51F_2013_08_10_s (

. . . . . . . . A/Guangdong/1/2013
. . . . . . . . Novel Polymerase Acidic

. . . . . . . . GISAID PA EPI476700

. . . . . . . . GISAID Isolate EPI_ISL_148417

. . . . . . . . 8 Polymorphisms (2 Amino and 6 Silent)

. . . . . . . . syn57R (CGt) [H7N9 Novel],

. . . . . . . . syn58G (GGc) [neH7N9],
. . . . . . . . . . . . . . . . . [H5N1],

. . . . . . . . syn73K (AAg) [neH7N9],

. . . . . . . . syn90V (GTa) [neH7N9],

. . . . . . . . 343T [H7N9 Novel],
. . . . . . . . . . . . [pH1N1 Count 210],
. . . . . . . . . . . . [H5N1 Human Fatality:
. . . . . . . . . . . . . . . VietnamNinhBinhUT31413II_M2_27M_2008_02_13_f

. . . . . . . . . . . . . . . . . . . GenBank PA HM114608],
. . . . . . . . . . . . [H5N1 Vietnam Commercial Poultry 2008],
. . . . . . . . . . . . [H9N2 China 2003],
. . . . . . . . syn414A (GCa) [Emergent H7N9 Fatality],
. . . . . . . . . . . . . . . . . .[neH7N9],
. . . . . . . . . . . . . . . . . .[H5N1],
. . . . . . . . . . . . . . . . . .[H9N2],

. . . . . . . . syn516D (GAt) [Emergent H7N9],
. . . . . . . . . . . . . . . . . .[neH7N9],
. . . . . . . . . . . . . . . . . .[H5N1],
. . . . . . . . . . . . . . . . . .[H9N2],

. . . . . . . . 519T [H7N9 Novel],
. . . . . . . . . . . . [H9N2 Hong Kong Avian 2010])

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eH7N9 Influenza PolymeraseBasic2, PolymeraseBasic1, PolymeraseAcidic, Hemagglutinin & Neuraminidase Segments
elucidated at 2013-10-11-03_38_08_019530 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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