China - H7N9 Human Isolates on Deposit at GISAID

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Re: China - H7N9 Human Isolates on Deposit at GISAID

Wet Market
Cross Serotype
Genetic Seeding

H9N2 Wet Market sub-segment relationships Updated

. . . . ChinaShanghai1_E1_87M_2013_02_26_f (
. . . . . . . . GISAID HA EPI439486
. . . . . . . . GISAID Isolate EPI_ISL_138737

. . . . . . . . 146S [138S],
. . . . . . . . . . . . [H9N2 Human Asia 2009 (2)],
. . . . . . . . . . . . [H9N2 China anser 2011],
. . . . . . . . . . . . [H9N2 China quail, et al Wet Market Surveillance, 2000-2005],
. . . . . . . . . . . . [H9N2 Middle East commercial poultry, 2003-2012],
. . . . . . . . . . . . [H7N7 Near-Passerine, Companion Species Singular & Distant-to-Relation],
. . . . . . . . . . . . [H7N7 Amino Residue 138T Singular equine, Distant-to-Relation, SeroType Transition with H3N8 internal involvement],
. . . . . . . . . . . . [H5N1 Human Fatality],
. . . . . . . . . . . . [H5N9 Commercial Poultry species],
. . . . . . . . . . . . [H3N2 Human Rare (95):
. . . . . . . . . . . . . . . . Re-Emergent in Coastal US:
. . . . . . . . . . . . . . . . 2013 (3):
. . . . . . . . . . . . . . . . . . . EPI442834 North Carolina05_2013_03_07,
. . . . . . . . . . . . . . . . . . . EPI441082 Oregon01_E3_19F_2013_01_11,
. . . . . . . . . . . . . . . . . . . EPI418249 Texas01_2013_01_08,
. . . . . . . . . . . . . . . . 2012 (8),
. . . . . . . . . . . . . . . . 2011 (19),
. . . . . . . . . . . . . . . . 2010 (9), 2009 (20), 2008 (20) , 2007 (15), 2006 (1)],
. . . . . . . . . . . . [avH3N2 SouthDakota],
. . . . . . . . . . . . [pH1N1 Human Rare (6)],
. . . . . . . . . . . . [zH1N1 Mammal (Mink 2012)],
. . . . . . . . . . . . [avH1N1farm: pH1N1 Ultimate Origin reservoir],
. . . . . . . . . . . . [H6N1, H10N7]

• Sequence Analysis - Open-Access, Full-Text
• GISAID Citation

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Re: China - H7N9 Human Isolates on Deposit at GISAID

GISAID Citations

Jiangsu Wet Market Surveillance
2013-04-20

Two samples from a healthy chicken and a healthy goose of the Jiangsu area were recently isolated, each producing a complete Hemagglutinin sequence placed on deposit at GISAID by the China Animal Health and Epidemiology Center on 2013-04-20. Homology is high against the recent fatality, ChinaAnhuiChuzhouCity1_E1_35F_2013_03_20_f. The chicken HA is an exact match to Anhui1; whereas, the goose varies at 65M [51M] and syn113E (GAg) [syn101E]. Each commercial poultry specimen carries the mammalian adaptation Q235L [Q226L].

The HA 65M revision is of note due to a rare polymorphism appearance at that same position in another emergent H7N9 market sample recently from Zhejiang. The ckZhejiangDTIDZJU01_2013_04 carries a revision to Lysine, 65K, matching non-emergent H7N9 2011 in 2 birds from Korea. The Zhejiang chicken appears to be the most hyper-morphic HA in the current emergent ΣH7N9 with changes at 42G, 65K, 72G, 74P, 75R & 96M.

Numbering on the following polymorphism lists is absolute (no offset), but the antigenic center of the HA can be managed to H3 numbering with a -9, e.g. 235L becomes 226L. Synonymous changes have been removed from the lists pending verification.

HA Polymorphisms

. . . . ckChinaJiangsuK89_2013_04_01 (
. . . . . . . . GISAID HA EPI442707
. . . . . . . . GISAID Isolate EPI_ISL_139496
. . . . . . . . Clinical: Healthy
. . . . . . . . 104 Polymorphisms (17 Amino and 87 Silent)
. . . . . . . . 11I,
. . . . . . . . 130A,
. . . . . . . . 183S,
. . . . . . . . 188V,
. . . . . . . . 195V,
. . . . . . . . 198A,
. . . . . . . . 211V,
. . . . . . . . 217N,
. . . . . . . . 235L,
. . . . . . . . 285N,
. . . . . . . . 307D,
. . . . . . . . 321R,
. . . . . . . . 410N,
. . . . . . . . 427I,
. . . . . . . . 455D,
. . . . . . . . 462K,
. . . . . . . . 541V)

. . . . gsChinaJiangsuK27_2013_04_01 (
. . . . . . . . GISAID HA EPI442706
. . . . . . . . GISAID Isolate EPI_ISL_139495
. . . . . . . . Clinical: Healthy
. . . . . . . . 106 Polymorphisms (18 Amino and 88 Silent)
. . . . . . . . 11I,

. . . . . . . . 65M [51M],
. . . . . . . . . . . [H7N9 Emergent Position,
. . . . . . . . . . . . . . . ckZhejiangDTIDZJU01_2013_04
. . . . . . . . . . . . . . . . . . . GenBank KC899669
. . . . . . . . . . . . . . . . . . . Hyper-morphic with HA 42G, 65K, 72G, 74P, 75R, 96M],
. . . . . . . . . . . [H7N9 Korea 2011 (2) Position, 65K],

. . . . . . . . 130A,
. . . . . . . . 183S,
. . . . . . . . 188V,
. . . . . . . . 195V,
. . . . . . . . 198A,
. . . . . . . . 211V,
. . . . . . . . 217N,
. . . . . . . . 235L,
. . . . . . . . 285N,
. . . . . . . . 307D,
. . . . . . . . 321R,
. . . . . . . . 410N,
. . . . . . . . 427I,
. . . . . . . . 455D,
. . . . . . . . 462K,
. . . . . . . . 541V)

As of 2013-04-22, GISAID shows the goose renamed as a chicken. We will watch for additional revision prior to making changes here.

H7N9 Influenza Hemagglutinin Segments elucidated at 2013-04-20-23_09_21_344970 by GeneWurx see.PolyDetector v0, Copyright 2007-2013

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Re: China - H7N9 Human Isolates on Deposit at GISAID

GISAID Citations

Zhejiang Wet Market Surveillance
2013-04-21

One sample from a chicken of the Zhejiang area was recently isolated, yielding complete genome sequences that were placed on deposit at GenBank by Zhejiang University on 2013-04-18. Though the commercial poultry specimen carries extensive diversity at the HA 5' end and the NA 3' end, one marker typically found on emergent H7N9 is absent. The HA is wildtype 235Q [226Q]. This Zhejiang chicken appears to be the most hyper-morphic HA in the current emergent ΣH7N9 with Novel or Rare changes at 42G, 65K, 72G, 74P, 75R & 96M.

Numbering on the following polymorphism lists is absolute (no offset), but the antigenic center of the HA can be managed to H3 numbering with a -9, e.g. 211V becomes 202V. Synonymous changes have been removed from the lists pending verification.

HA Polymorphisms

. . . . ckZhejiangDTIDZJU01_2013_04 (
. . . . . . . . GenBank HA KC899669
. . . . . . . . 111 Polymorphisms (22 Amino and 89 Silent)
. . . . . . . . 11I,
. . . . . . . . 42G [27G H7N7 LAu],
. . . . . . . . 65K [51K],
. . . . . . . . . . . [non-Emergent H7N9 Rare, Count 02:
. . . . . . . . . . . . . . . Korea Wild Anas 2011,
. . . . . . . . . . . . . . . . . . A3 & A9, Table (1),
. . . . . . . . . . . . . . . . . . diagonally-opposing (g/i on map), bi-coastal / estuary geographic ranging (1)],
. . . . . . . . . . . [H7N7 LAu],
. . . . . . . . . . . [H6N1 LAu],
. . . . . . . . . . . [avH1N1farm LAu: pH1N1 Ultimate Origin reservoir],
. . . . . . . . 72G [58G],
. . . . . . . . . . . [H7N7 LAd],
. . . . . . . . . . . [H6N1 LAu],
. . . . . . . . 74P [60P],
. . . . . . . . 75R [61R],
. . . . . . . . . . . [H7N9 Singular: Korea Wild Anas 2011
. . . . . . . . . . . . . . . . HA Distant-to-Relation (23 nu),
. . . . . . . . . . . . . . . . Hyper-morphic at HA 5' with polymorphisms
. . . . . . . . . . . . . . . . . . . weighted toward, but not limited to, Lysine and Arginine,
. . . . . . . . . . . . . . . . . . . . . . e.g. 51K, 124N, 131P, 137I, 173R, 179V, 190K,
. . . . . . . . . . . . . . . . . . . . . . . . . 197I, 199S, 200N, 208N, 236I, 253P, 327L and 330K,
. . . . . . . . . . . . . . . . NA Distant-to-Relation (48 nu) Hyper-morphic with NA 426M],
. . . . . . . . . . . [zH3N2 LAd],
. . . . . . . . 96M [83M],
. . . . . . . . 130A [118A],
. . . . . . . . 183S,
. . . . . . . . 188V [179V],
. . . . . . . . 195V,
. . . . . . . . 198A,
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 285N,
. . . . . . . . 307D,
. . . . . . . . 321R,
. . . . . . . . 410N,
. . . . . . . . 427I,
. . . . . . . . 455D,
. . . . . . . . 462K,
. . . . . . . . 541V)

NA Polymorphisms

. . . . ckZhejiangDTIDZJU01_2013_04 (
. . . . . . . . GenBank NA KC899671
. . . . . . . . 35 Polymorphisms (13 Amino and 22 Silent)
. . . . . . . . 16I,
. . . . . . . . 19A,
. . . . . . . . 40G,
. . . . . . . . 53T,
. . . . . . . . 81T,
. . . . . . . . 84N,
. . . . . . . . 112S,
. . . . . . . . 335I,
. . . . . . . . 359A,
. . . . . . . . 401A,
. . . . . . . . 428V [426V],
. . . . . . . . . . . . [H7N9 Singular Position: Korea Wild Anas 2011
. . . . . . . . . . . . . . . . NA Distant-to-Relation (48 nu) Hyper-morphic with NA 426M,
. . . . . . . . . . . . . . . . HA Distant-to-Relation (23 nu),
. . . . . . . . . . . . . . . . Hyper-morphic at HA 5' with polymorphisms
. . . . . . . . . . . . . . . . . . . weighted toward, but not limited to, Lysine and Arginine,
. . . . . . . . . . . . . . . . . . . . . . e.g. 51K, 124N, 131P, 137I, 173R, 179V, 190K,
. . . . . . . . . . . . . . . . . . . . . . . . . 197I, 199S, 200N, 208N, 236I, 253P, 327L and 330K],
. . . . . . . . 441A [438V],
. . . . . . . . 442G [439G],
. . . . . . . . . . . . [Emergent H7N9, ZhejiangDTIDZJU01_2013_04_03],
. . . . . . . . . . . . [pH1N1 2009-2013 Position: NA syn439S (AGt)],
. . . . . . . . . . . . [H5N1 Human Vietnam 2009 Position: NA syn439S (AGt)],
. . . . . . . . . . . . [H5N1 Myanmar Quail 2007 HiPath Position: NA syn439S (AGt)],
. . . . . . . . . . . . [H5N1 Avian Nepal 2012 Position: NA syn439S (AGt)],
. . . . . . . . . . . . [H5N1 Avian Japan 2011 HiPath, Multi-Geo / Multi-Species Position: NA syn439S (AGt)],
. . . . . . . . . . . . [zH5N1 2003-2012 Position: NA syn439S (AGt)],
. . . . . . . . . . . . [avH1N1 China Anas 2009-07 Position: NA syn439S (AGt)],
. . . . . . . . . . . . [avH12N1 Japan Anas 2012-10 Position: NA syn439S (AGt)],
. . . . . . . . . . . . [avH11N1 GeorgiaRep Gull 2010 Position: NA syn439S (AGt)],
. . . . . . . . . . . . [avH10N1 GeorgiaRep Anas 2010 Position: NA syn439S (AGt)])

H7N9 Influenza Hemagglutinin and Neuraminidase Segments elucidated at 2013-04-21-01_12_50_458610 by GeneWurx see.PolyDetector v0, Copyright 2007-2013

GISAID Citations

We acknowledge the authors, originating and submitting laboratories of the sequences from GenBank & from GISAID’s EpiFlu™ Database on which this research is based. An additional list is detailed in the linked PDF entitled "GISAID_Citations_H5N1_2011" at Is H7N9 Spreading from Human to Human in China? Post#164

We are grateful to the authors of the 2012-03-09 Journal of General Virology Original Article, "Low pathogenic H7 subtype avian influenza viruses isolated from domestic ducks in South Korea and the close association with isolates of wild birds" (Hye-Ryoung Kim, Choi-Kyu Park, Youn-Jeong Lee, Jae-Ku Oem, Hyun-Mi Kang, Jun-Gu Choi, O-Soo Lee and You-Chan Bae) from which several Homology and Geography notations were originated including the map of domestic and wild bird sampling areas, including H7N9, across Korea.

Footnotes
1. Hye-Ryoung Kim, Choi-Kyu Park, Youn-Jeong Lee, Jae-Ku Oem, Hyun-Mi Kang, Jun-Gu Choi, O-Soo Lee, and You-Chan Bae
Low pathogenic H7 subtype avian influenza viruses isolated from domestic ducks in South Korea and the close association with isolates of wild birds
J. Gen. Virol. 2012 93: 1278-1287.
JGV Link

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Re: China - H7N9 Human Isolates on Deposit at GISAID

Sequence Data
required for
Analytic Validation

As the case count century mark is crossed with a 20% CFR and fewer citizens released than deceased, expectations are justified that 100% of the confirmed cases would have been sampled twice at a minimum, upon admission and healthcare separation, yielding a minimum of ~130 HA / NA pairs and 55 to 60 full genome sequence sets.

Anything less is a misappropriation of public healthcare assets by the nations honouring themselves with the titles of "Technologically Advanced" and "Modernised Medicine" practitioners.

Please extend our previous requests with your hopeful enquiries:

• 2013-04-09: Request for sequencing and deposit of historical H7N9 freezer samples
• 2013-04-10: Request for sequencing and publication of statistically-significant 120 H7 samples between 6 countries
• 2013-04-14: Request for Species- and Location-Specific Passerine sequences

We would like to thank the men and women at the United States Geological Survey for opening their freezers and lab books with the deposit at GenBank of gs_empAlaska44063061_2006_05_23, the first historical H7N9 sequence offered since the announced beginning of the H7N9 zoonotic emergence.

The emperor goose from mid-2006 in Alaska (GenBank Taxon 119239) is of interest due to the distinct HA that is 23 nucleotides distant from the nearest relative, an H7N7 from Alaska in a different species, determined via BLAST; however, at first glance, the polymorphic pattern does not overlay with emergent H7N9 HA sequences any more than other legacy H7N9 of the same background.

Thanks to the efforts of the scientists who take to the field in pursuit of these difficult samples, we shall, in time, have the opportunity to measure if the distinctions from our emperor goose find their way into the emergent ΣH7N9.

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

GISAID Citations

Human Emergent H7N9
from
Zhejiang Province

On 2013-04-22, the Hangzhou Center for Disease Control and Prevention released two human emergent H7N9 isolates at GISAID. Both demonstrate Q226L and each carries additional non-synonymous polymorphisms. HA 51M, a revision found in Jiangsu Wet Market surveillance, is present on ChinaHangzhou3_79M_2013_04_02_s, while the HA 164I on ChinaHangzhou2_67M_2013_03_25_f is wildtype within both the H5N1 and H6N1 serotypes. Human seasonal H1N1 prior to the pandemic also supported HA 164I.

Of the 111 distinct polymorphisms found on the two Hemagglutinin sequences, 32% are previously found on zoonotic H3N2, 28% on avH1N1, 25% on H6N1, 24% on H9N2, 23% on H5N1, 17% on H10N7 and 14% on H13.

The truncated NA from ChinaHangzhou2_67M_2013_03_25_f has been completed and deposited at GenBank on 2013-05-09 [KF001514] demonstrating a pure homology to envChinaHangzhou34_2013_04_04 and the fixed components found on emergent H7N9, yielding another unremarkable segment.

Both isolates carry PB2 627K.

PB2 Polymorphisms

. . . . ChinaHangzhou3_79M_2013_04_02_s (
. . . . . . . . GISAID PB2 EPI442712
. . . . . . . . GISAID Isolate EPI_ISL_139499
. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)
. . . . . . . . syn174A (GCt) [neH7N9],
. . . . . . . . syn499D (GAc) [neH7N9],
. . . . . . . . syn507V (GTc) [neH7N9],
. . . . . . . . 740A [Novel to Emergent H7N9],
. . . . . . . . syn755R (CGa) [Novel to Emergent H7N9],
. . . . . . . . . . . . . . . . . . . [H1N1 FortDix 1976],
. . . . . . . . . . . . . . . . . . . [sH3N2],
. . . . . . . . . . . . . . . . . . . [H3N2 China Avian],
. . . . . . . . . . . . . . . . . . . [H3N8 Avian],
. . . . . . . . . . . . . . . . . . . [H9N2],
. . . . . . . . . . . . . . . . . . . [H5N1 Vietnam Avian 2011],
. . . . . . . . . . . . . . . . . . . [H5N2 China Avian 2011,
. . . . . . . . . . . . . . . . . . . . . . Korea Avian 2007,
. . . . . . . . . . . . . . . . . . . . . . Mexico Avian 1997-1998],
. . . . . . . . . . . . . . . . . . . [H6Nx China Avian extensive geography])

. . . . ChinaHangzhou2_67M_2013_03_25_f (
. . . . . . . . GISAID PB2 EPI442709
. . . . . . . . GISAID Isolate EPI_ISL_139498
. . . . . . . . 15 Polymorphisms (3 Amino and 12 Silent)
. . . . . . . . syn58T (ACa) [Emergent H7N9 ChinaShanghai1_E1_87M_2013_02_26_f],
. . . . . . . . . . . . . . . . . .[neH7N9],
. . . . . . . . . . . . . . . . . .[pH1N1],
. . . . . . . . . . . . . . . . . .[H1N1 FortDix 1976],
. . . . . . . . . . . . . . . . . .[sH1N1 including 1951],
. . . . . . . . . . . . . . . . . .[sH3N2],
. . . . . . . . . . . . . . . . . .[H3N8 Avian],
. . . . . . . . . . . . . . . . . .[H9N2 including quail],
. . . . . . . . . . . . . . . . . .[H5N1],
. . . . . . . . . . . . . . . . . .[WS1933],
. . . . . . . . . . . . . . . . . .[1918],
. . . . . . . . syn149P (CCa) [neH7N9 gsCzech (2)],
. . . . . . . . syn153D (GAc) [neH7N9],
. . . . . . . . syn160Q (CAa) [neH7N9],
. . . . . . . . syn185I (ATa) [neH7N9],
. . . . . . . . 195E [neH7N9 dk_w_spotbillKorea447_2011_04],
. . . . . . . . 197R [Emergent H7N9 pgnChinaShanghaiS1069_2013_04_02],
. . . . . . . . . . . . [neH7N9 gsCzech (2)],
. . . . . . . . syn415R (AGg) [neH7N9 ruddy_trnDelawareBay220_E1_1995_05_21],
. . . . . . . . . . . . . . . . . . [pH1N1 ChinaSichuanJiangyangSWL1165_C2_16F_2009_11_10
. . . . . . . . . . . . . . . . . . . . . . . . . . . with PB2 354V [EPI256532]],
. . . . . . . . syn490S (AGt) [neH7N9],
. . . . . . . . 559T [Emergent H7N9 ChinaShanghai1_E1_87M_2013_02_26_f & neH7N9],
. . . . . . . . syn643S (TCa) [neH7N9],
. . . . . . . . syn652N (AAc) [neH7N9],
. . . . . . . . syn653S (TCc) [neH7N9],
. . . . . . . . syn666T (ACa) [neH7N9],
. . . . . . . . syn679P (CCa) [neH7N9])

HA Polymorphisms

Non-Synonymous polymorphisms are presented in the HA and NA reports while synonymous changes are quantified in the totals.

. . . . ChinaHangzhou3_79M_2013_04_02_s (
. . . . . . . . GISAID HA EPI442713
. . . . . . . . GISAID Isolate EPI_ISL_139499
. . . . . . . . 108 Polymorphisms (18 Amino and 90 Silent)
. . . . . . . . 11I [#4I],
. . . . . . . . 65M [51M],
. . . . . . . . . . . [Emergent H7N9 gs/ckChinaJiangsuK27_2013_04_01],
. . . . . . . . syn113E (GAg) [syn101E (GAg)],
. . . . . . . . . . . . . . . . . . . [Emergent H7N9:
. . . . . . . . . . . . . . . . . . . . . . . . . TaiwanTaipei1_E1_53M_2013_04_24_s,
. . . . . . . . . . . . . . . . . . . . . . . . . gs/ckChinaJiangsuK27_2013_04_01],
. . . . . . . . syn119I (ATa) [syn107I (ATa)],
. . . . . . . . . . . . . . . . . . .[H7N7 Equine Only],
. . . . . . . . 130A [118A],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . syn226P (CCt) [syn217P (CCt)],
. . . . . . . . . . . . . . . . . . .[H7N7 Equine Only],
. . . . . . . . 235L [226L],
. . . . . . . . 285N [277N],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])

. . . . ChinaHangzhou2_67M_2013_03_25_f (
. . . . . . . . GISAID HA EPI442710
. . . . . . . . GISAID Isolate EPI_ISL_139498
. . . . . . . . 107 Polymorphisms (18 Amino and 89 Silent)
. . . . . . . . 11I [#4I],
. . . . . . . . syn79T (ACa) [syn65T (ACa)],
. . . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . . . . . . . . . . . .[sH3N2],
. . . . . . . . syn80G (GGg) [syn66G (GGg)],
. . . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . . . . . . . . . . . .[H5N1 Human Fatalities],
. . . . . . . . . . . . . . . . . . .[H9N2 China Avian:
. . . . . . . . . . . . . . . . . . . . . . . . Shanxi gal 2011,
. . . . . . . . . . . . . . . . . . . . . . . . Guangdong gal 2008,
. . . . . . . . . . . . . . . . . . . . . . . . Guangxi Sparrow 2006],
. . . . . . . . 130A [118A],
. . . . . . . . 173I [164I],
. . . . . . . . . . . . [H5N1 Egypt and Vietnam wildtype],
. . . . . . . . . . . . [H6N1 wildtype],
. . . . . . . . . . . . [pH1N1 Indonesia 2012,
. . . . . . . . . . . . . . . . . . Thailand 2012,
. . . . . . . . . . . . . . . . . . Sri Lanka 2012,
. . . . . . . . . . . . . . . . . . Europe 2011, 2012],
. . . . . . . . . . . . [H1N1 Human Seasonal],
. . . . . . . . . . . . [avH1N1 commercial poultry],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 235L [226L],
. . . . . . . . 285N [277N],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])


NA Polymorphisms

Non-Synonymous polymorphisms are presented in the HA and NA reports while synonymous changes are quantified in the totals.

. . . . ChinaHangzhou3_79M_2013_04_02_s (
. . . . . . . . GISAID NA EPI442714
. . . . . . . . GISAID Isolate EPI_ISL_139499
. . . . . . . . 33 Polymorphisms (11 Amino and 22 Silent)
. . . . . . . . 16I,
. . . . . . . . 19A,
. . . . . . . . 53T,
. . . . . . . . 81T,
. . . . . . . . 84N,
. . . . . . . . 112S,
. . . . . . . . 305V [304V],
. . . . . . . . . . . . [Emergent H7N9 ChinaZhejiangHZ1_2013_04,
. . . . . . . . . . . . . . . . . . . . . . . . ChinaNanjing1_2013_03_28,
. . . . . . . . . . . . . . . . . . . . . . . . envChinaShanghaiS1088_2013_04_03,
. . . . . . . . . . . . . . . . . . . . . . . . ckChinaShanghaiS1053_2013_04_03],
. . . . . . . . . . . . [pH1N1 WildType],
. . . . . . . . . . . . [avH1N1 WildType],
. . . . . . . . . . . . [H5N1 WildType],
. . . . . . . . . . . . [H6N1 WildType],
. . . . . . . . . . . . [H9N2 WildType],
. . . . . . . . 335I,
. . . . . . . . 345I [341I],
. . . . . . . . . . . . [Emergent H7N9 ChinaZhejiangHZ1_2013_04,
. . . . . . . . . . . . . . . . . . . . . . . . ChinaNanjing1_2013_03_28],
. . . . . . . . . . . . [H5N1 LookAside Upstream China ostrich 2003,
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . China anas 2001],
. . . . . . . . 359A,
. . . . . . . . 401A)

. . . . ChinaHangzhou2_67M_2013_03_25_f (
. . . . . . . . GISAID NA EPI442711
. . . . . . . . GISAID Isolate EPI_ISL_139498
. . . . . . . . 21 Polymorphisms (3 Amino and 18 Silent)
. . . . . . . . NA Truncated before aa137,
. . . . . . . . 335I,
. . . . . . . . 359A,
. . . . . . . . 401A)

H7N9 Influenza Hemagglutinin and Neuraminidase Segments elucidated at 2013-04-22-12_25_28_709130 by GeneWurx see.PolyDetector v0, Copyright 2007-2013

GISAID Citations

• GeneWurx Cross Serotype Homology Analysis, Open-Access, Full-Text version
• China - H7N9 Human Isolates on Deposit at GISAID, Comprehensive Genetics Discussion

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

GISAID Citations

Emergent H7N9
from
Zhejiang Environment

On 2013-04-22, the Hangzhou Center for Disease Control and Prevention released one emergent H7N9 isolate sampled from the environment at GISAID. The HA sequence demonstrates Q226L and carries a non-synonymous polymorphism. HA 51K, a revision found recently during Zhejiang Wet Market surveillance, is present on envChinaHangzhou34_2013_04_04.

Non-Synonymous polymorphisms are presented in this report and synonymous changes are quantified in the totals.

HA Polymorphisms

. . . . envChinaHangzhou34_2013_04_04 (
. . . . . . . . GISAID HA EPI442716
. . . . . . . . GISAID Isolate EPI_ISL_139500
. . . . . . . . 105 Polymorphisms (18 Amino and 87 Silent)
. . . . . . . . 11I,
. . . . . . . . 65K [51K],
. . . . . . . . . . . [Emergent H7N9 ckZhejiangDTIDZJU01_2013_04],
. . . . . . . . 130A [118A],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 235L [226L],
. . . . . . . . 285N [277N],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])


NA Polymorphisms

. . . . envChinaHangzhou34_2013_04_04 (
. . . . . . . . GISAID NA EPI442717
. . . . . . . . GISAID Isolate EPI_ISL_139500
. . . . . . . . 32 Polymorphisms (10 Amino and 22 Silent)
. . . . . . . . 16I,
. . . . . . . . 19A,
. . . . . . . . 40G,
. . . . . . . . 53T,
. . . . . . . . 81T,
. . . . . . . . 84N,
. . . . . . . . 112S,
. . . . . . . . 335I,
. . . . . . . . 359A,
. . . . . . . . 401A)

H7N9 Influenza Hemagglutinin and Neuraminidase Segments elucidated at 2013-04-22-14_50_54_707700 by GeneWurx see.PolyDetector v0, Copyright 2007-2013

GISAID Citations

• GeneWurx Cross Serotype Homology Analysis, Open-Access, Full-Text version
• China - H7N9 Human Isolates on Deposit at GISAID, Comprehensive Genetics Discussion

[Toaster2]

Re: China - H7N9 Human Isolates on Deposit at GISAID

I saw elsewhere that two new human H7N9 sequences are posted at GISAID - both with PB2 E627K

[sharon sanders]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Thanks!

For those of us who do not understand sequence talk, can someone explain the significance of PB2 E627K and Q226L?

[mixin]

Re: China - H7N9 Human Isolates on Deposit at GISAID

It's not a good thing. I'll let someone else give a better answer.

When I aligned all of the 2013 H7N9 sequence nucleotides, A/Hangzhou/2/2013 was a very good match in PB2 to the brambling. That's the first good match I've seen with any of these segments so far (unless I overlooked something). It shared 11 of 16 position changes.

It appears that most of the changes are synonymous so they all are pretty similar in the protein alignment.

Too bad we only have PB2, HA and NA with that sequence.

Thanks to Hangzhou Center for Disease Control and Prevention and Jin-Cao, Pan

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

I saw elsewhere that two new human H7N9 sequences are posted at GISAID - both with PB2 E627K

Those sequences and their related environmental sample are covered comprehensively in the two posts that are immediately precedent to your notification.

• Human Emergent H7N9 from Zhejiang Province
• Environment Emergent H7N9 from Zhejiang

Human

ChinaHangzhou3_79M_2013_04_02_s, HA & NA
ChinaHangzhou2_67M_2013_03_25_f, HA & NA

Environment

envChinaHangzhou34_2013_04_04, HA & NA

[JJackson]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Thanks!

For those of us who do not understand sequence talk, can someone explain the significance of PB2 E627K and Q226L?

I have tried to explain what the role of the various RNA strands, and the proteins they code for, in the H7N9 discussion thread and have covered the PB2 E627K change in some detail in posts #50 & 67.

Q226L is on the HA strand and implies a mutation changing the amino acid which is found at the 226th position along the Haemagglutinin protein chain from Glutamin (Q) to Leucine(L). The reason that this particular change is of interest is that this area on the protein is involved with the attachment of the virus to the cell surface prior to infection. The Q form of the protein is better suited to binding sites typically found in the guts of birds and the L form is better for the epithelial cells found in our upper respiratory tract - which is the normal port of entry for influenza in humans.

Edit:
For those that read the first draft of this apologies. NS1 kindly pointed out that I had got into the explanation of which Amino Acids were changed and started talking about E & K when I meant Q & L. I have corrected this now. Sorry all and thanks to NS1 for the rescue.

[mixin]

Re: China - H7N9 Human Isolates on Deposit at GISAID

The NEJM article is a good one.

In Table 1, I notice that 2 of the 3 patients had Hepatitis B. Is it that common in China? Those 2 also had secondary infections, while patient 1 did not; although he did receive antibiotic therapy.

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

GISAID Citations

Human Emergent H7N9
from
Zhejiang, Jiangsu and Shanghai

We are grateful for the recent GISAID deposits in these past 4 weeks totaling 12 human emergent H7N9 cases from 4 organisations during a potential building pandemic. The first 4 human sequences were profiled in an earlier Cross Serotype Homology study; the group of 2 Hangzhou sequences from 2013-04-22 was recently reviewed under separate cover. Now we undertake this sparse accumulation of the 6 remaining human sequences from the following institutions.

• 2013-04-17 Zhejiang University
• 2013-04-27 WHO Chinese National Influenza Center
• 2013-04-28 Zhejiang Provincial Center for Disease Control and Prevention

ChinaZhejiang1_37M_2013_03_24 carries the HA 226I and also a mixture on the NA prior to the 5 amino deletion creating at aa67 a potential repeat of the emergent H7N9 wildtype NA 66N. PB2 627K features on this HA 226I-bearing sequence while the geographically-related ChinaZhejiang2_64M_2013_04_03 carries the functional analog for mammalian adaptation PB2 701N that is also suspiciously found on ChinaZhejiangDTIDZJU01_xM_2013_04_03. Each of these sequences from the Zhejiang human deposit of 2013-04-28 carries at least one mixed signal on their respective PB2 segments, including UltraAmbiguity on ChinaZhejiang1_37M_2013_03_24 at PB2 682 deriving 682R and syn682G (gGg). The PB2 of ChinaZhejiang2_64M_2013_04_03 and ChinaZhejiang1_37M_2013_03_24 are both mixed at aa681 producing wildtype Glutamate (GAG) and syn681E (GAa). The PA also shows 3 mixtures each for these isolates deriving wildtype with syn299G (GGa), syn399E (GGa) and 400A.

PB2 224S is demonstrated as an additional rare polymorphism shared between ChinaZhejiang1_37M_2013_03_24 and the fatal ChinaHangzhou1_C1_38M_2013_03_24_f. The two also share PB2 syn514S (TCt), syn619L (TTg) and syn682G (GGg), none of which are found on other human H7N9. The Polymerase Acidic segments show a rare syn260F (TTc) shared with a 2006 Ohio teal. A rare synonymous revision at aa405 (396) is shared on the HA among these two and ChinaJiangsu01_E1_45F_2013_03_30_s. These three sequences also share a rare synonymous polymorphism on the Neuraminidase segment at aa142 (141).

Are we looking at a different passage of the same sample or serial samples from the same patient with different sequence names and subject ages? We have sought advice from the depositing institution as no experimental passage history metadata was included in the deposit.

Though outcome is not specified for ChinaZhejiang1_37M_2013_03_24, we will proceed under the concept of host subject identity to ChinaHangzhou1_C1_38M_2013_03_24_f, who was notated as Deceased by the Hangzhou Center for Disease Control and Prevention in their GISAID deposit of 2013-04-05.

At one month post-announcement of a 20%+ CFR zoonotic disease emergence and more than two months since cases have been genetically confirmed (2013-02-27 Fatal), the database of human sequences appears to stand at a total of eleven cases, and perhaps as few as ten, documented by no more than twelve partially annotated isolates.

For the purpose of brevity, non-synonymous polymorphisms are presented in this report while only the very rare synonymous changes are quantified beyond the totals.

HA Polymorphisms

. . . . ChinaZhejiang2_64M_2013_04_03 (
. . . . . . . . GISAID HA EPI443042
. . . . . . . . GISAID Isolate EPI_ISL_139653
. . . . . . . . Deposited 2013-04-28 by Zhejiang Provincial CDC
. . . . . . . . 104 Polymorphisms (17 Amino and 87 Silent)
. . . . . . . . 11I [#4I],
. . . . . . . . 130A [118A],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 235L [226L],
. . . . . . . . 285N [277N],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])

. . . . ChinaZhejiangDTIDZJU01_xM_2013_04_03 (
. . . . . . . . GISAID HA EPI441794
. . . . . . . . GISAID Isolate EPI_ISL_139364
. . . . . . . . Deposited 2013-04-17 by Zhejiang University
. . . . . . . . 104 Polymorphisms (17 Amino and 87 Silent)
. . . . . . . . 11I [#4I],
. . . . . . . . 130A [118A],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 235L [226L],
. . . . . . . . 285N [277N],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])

. . . . ChinaJiangsu01_E1_45F_2013_03_30_s (
. . . . . . . . GISAID HA EPI443028
. . . . . . . . GISAID Isolate EPI_ISL_139651
. . . . . . . . Deposited 2013-04-27 by WHO Chinese National Influenza Center
. . . . . . . . 105 Polymorphisms (17 Amino and 88 Silent)
. . . . . . . . 11I [#4I],
. . . . . . . . 130A [118A],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 235I [226I],
. . . . . . . . 285N [277N],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . syn405I (ATc) [syn396I (ATc)],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])

. . . . ChinaZhejiang1_37M_2013_03_24_f (
. . . . . . . . GISAID HA EPI443034
. . . . . . . . GISAID Isolate EPI_ISL_139652
. . . . . . . . Deposited 2013-04-28 by Zhejiang Provincial CDC
. . . . . . . . ~ChinaHangzhou1_C1_38M_2013_03_24_f
. . . . . . . . 105 Polymorphisms (17 Amino and 88 Silent)
. . . . . . . . 11I [#4I],
. . . . . . . . 130A [118A],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 235I [226I],
. . . . . . . . 285N [277N],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . syn405I (ATc) [syn396I (ATc)],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])

. . . . ChinaShanghai4_E1_63M_2013_03_09 (
. . . . . . . . GISAID HA EPI443025
. . . . . . . . GISAID Isolate EPI_ISL_139650
. . . . . . . . Deposited 2013-04-27 by WHO Chinese National Influenza Center
. . . . . . . . 105 Polymorphisms (17 Amino and 88 Silent)
. . . . . . . . 11I [#4I],
. . . . . . . . 130A [118A],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . syn192H (CAc) [syn183H (CAc)],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 235L [226L],
. . . . . . . . 285N [277N],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])

. . . . ChinaShanghai3_E1_73M_2013_02_27_f (
. . . . . . . . GISAID HA EPI443022
. . . . . . . . GISAID Isolate EPI_ISL_139649
. . . . . . . . Deposited 2013-04-27 by WHO Chinese National Influenza Center
. . . . . . . . 105 Polymorphisms (18 Amino and 87 Silent)
. . . . . . . . 11I [#4I],
. . . . . . . . 130A [118A],
. . . . . . . . 183S [174S],
. . . . . . . . 188V [179V],
. . . . . . . . 195V [186V],
. . . . . . . . 198A [189A],
. . . . . . . . 211V [202V],
. . . . . . . . 217N [208N],
. . . . . . . . 235L [226L],
. . . . . . . . 285N [277N],
. . . . . . . . 291H [283H],
. . . . . . . . . . . . . . [H7N7 LAd],
. . . . . . . . 307D [299D],
. . . . . . . . 321R [313R],
. . . . . . . . 410N [401N],
. . . . . . . . 427I [418I],
. . . . . . . . 455D [446D],
. . . . . . . . 462K [453K],
. . . . . . . . 541V [533V])

NA Polymorphisms

. . . . ChinaZhejiang2_64M_2013_04_03 (
. . . . . . . . GISAID NA EPI443044
. . . . . . . . GISAID Isolate EPI_ISL_139653
. . . . . . . . Deposited 2013-04-28 by Zhejiang Provincial CDC
. . . . . . . . 32 Polymorphisms (10 Amino and 22 Silent)
. . . . . . . . 16I [16I],
. . . . . . . . . . . [H5N1 Human Fatality China 2011],
. . . . . . . . . . . [H5N1 Human Cambodia 2005],
. . . . . . . . . . . [H5N1 Avian Rare (58) Scotland, Middle East and Asia]
. . . . . . . . . . . [pH1N1 Rare (35) Worldwide including Scotland and 1 US Low Reactor],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 19A [19A],
. . . . . . . . . . . [avH1N1, H9N2],
. . . . . . . . 40G [40G],
. . . . . . . . . . . [H9N2],
. . . . . . . . 53T [53T],
. . . . . . . . 81T [80T],
. . . . . . . . . . . [avH1N1],
. . . . . . . . 84N [83N],
. . . . . . . . 112S [111S],
. . . . . . . . . . . . [H9N2],
. . . . . . . . 335I [332I],
. . . . . . . . . . . .[H6N1],
. . . . . . . . 359A [355A],
. . . . . . . . 401A [397A]
. . . . . . . . . . . . [H6N1])

. . . . ChinaZhejiangDTIDZJU01_xM_2013_04_03 (
. . . . . . . . GISAID NA EPI441797
. . . . . . . . GISAID Isolate EPI_ISL_139364
. . . . . . . . Deposited 2013-04-17 by Zhejiang University
. . . . . . . . 35 Polymorphisms (13 Amino and 22 Silent)
. . . . . . . . 16I [16I],
. . . . . . . . . . . [H5N1 Human Fatality China 2011],
. . . . . . . . . . . [H5N1 Human Cambodia 2005],
. . . . . . . . . . . [H5N1 Avian Rare (58) Scotland, Middle East and Asia]
. . . . . . . . . . . [pH1N1 Rare (35) Worldwide including Scotland and 1 US Low Reactor],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 19A [19A],
. . . . . . . . . . . [avH1N1, H9N2],
. . . . . . . . 40G [40G],
. . . . . . . . . . . [H9N2],
. . . . . . . . 53T [53T],
. . . . . . . . 81T [80T],
. . . . . . . . . . . [avH1N1],
. . . . . . . . 84N [83N],
. . . . . . . . 112S [111S],
. . . . . . . . . . . . [H9N2],
. . . . . . . . 335I [332I],
. . . . . . . . . . . .[H6N1],
. . . . . . . . 359A [355A],
. . . . . . . . 401A [397A]
. . . . . . . . . . . . [H6N1],
. . . . . . . . 439L [437L],
. . . . . . . . 442G [439G],
. . . . . . . . . . . . . . [Emergent H7N9 ckZhejiangDTIDZJU01_2013_04],
. . . . . . . . 443D [440D])

. . . . ChinaJiangsu01_E1_45F_2013_03_30_s (
. . . . . . . . GISAID NA EPI443029
. . . . . . . . GISAID Isolate EPI_ISL_139651
. . . . . . . . Deposited 2013-04-27 by WHO Chinese National Influenza Center
. . . . . . . . 33 Polymorphisms (10 Amino and 23 Silent)
. . . . . . . . 16I [16I],
. . . . . . . . . . . [H5N1 Human Fatality China 2011],
. . . . . . . . . . . [H5N1 Human Cambodia 2005],
. . . . . . . . . . . [H5N1 Avian Rare (58) Scotland, Middle East and Asia]
. . . . . . . . . . . [pH1N1 Rare (35) Worldwide including Scotland and 1 US Low Reactor],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 19A [19A],
. . . . . . . . . . . [avH1N1, H9N2],
. . . . . . . . 40G [40G],
. . . . . . . . . . . [H9N2],
. . . . . . . . 53T [53T],
. . . . . . . . 81T [80T],
. . . . . . . . . . . [avH1N1],
. . . . . . . . 84N [83N],
. . . . . . . . 112S [111S],
. . . . . . . . . . . . [H9N2],
. . . . . . . . syn142R (cGA) [syn141R (cGA)],
. . . . . . . . 335I [332I],
. . . . . . . . . . . .[H6N1],
. . . . . . . . 359A [355A],
. . . . . . . . 401A [397A]
. . . . . . . . . . . . [H6N1])

. . . . ChinaZhejiang1_37M_2013_03_24_f (
. . . . . . . . GISAID NA EPI443036
. . . . . . . . GISAID Isolate EPI_ISL_139652
. . . . . . . . Deposited 2013-04-28 by Zhejiang Provincial CDC
. . . . . . . . ~ChinaHangzhou1_C1_38M_2013_03_24_f
. . . . . . . . 34 Polymorphisms (11 Amino and 23 Silent)
. . . . . . . . 16I [16I],
. . . . . . . . . . . [H5N1 Human Fatality China 2011],
. . . . . . . . . . . [H5N1 Human Cambodia 2005],
. . . . . . . . . . . [H5N1 Avian Rare (58) Scotland, Middle East and Asia]
. . . . . . . . . . . [pH1N1 Rare (35) Worldwide including Scotland and 1 US Low Reactor],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 19A [19A],
. . . . . . . . . . . [avH1N1, H9N2],
. . . . . . . . 40G [40G],
. . . . . . . . . . . [H9N2],
. . . . . . . . 53T [53T],
. . . . . . . . 67N mix wt [66N],
. . . . . . . . . . . . . . . . . . . [Emergent H7N9 Potential repeat of Upstream amino],
. . . . . . . . 81T [80T],
. . . . . . . . . . . [avH1N1],
. . . . . . . . 84N [83N],
. . . . . . . . 112S [111S],
. . . . . . . . . . . . [H9N2],
. . . . . . . . syn142R (cGA) [syn141R (cGA)],
. . . . . . . . 335I [332I],
. . . . . . . . . . . .[H6N1],
. . . . . . . . 359A [355A],
. . . . . . . . 401A [397A]
. . . . . . . . . . . . [H6N1])

. . . . ChinaShanghai4_E1_63M_2013_03_09 (
. . . . . . . . GISAID NA EPI443026
. . . . . . . . GISAID Isolate EPI_ISL_139650
. . . . . . . . Deposited 2013-04-27 by WHO Chinese National Influenza Center
. . . . . . . . 32 Polymorphisms (10 Amino and 22 Silent)
. . . . . . . . 16I [16I],
. . . . . . . . . . . [H5N1 Human Fatality China 2011],
. . . . . . . . . . . [H5N1 Human Cambodia 2005],
. . . . . . . . . . . [H5N1 Avian Rare (58) Scotland, Middle East and Asia]
. . . . . . . . . . . [pH1N1 Rare (35) Worldwide including Scotland and 1 US Low Reactor],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 19A [19A],
. . . . . . . . . . . [avH1N1, H9N2],
. . . . . . . . 40G [40G],
. . . . . . . . . . . [H9N2],
. . . . . . . . 53T [53T],
. . . . . . . . 81T [80T],
. . . . . . . . . . . [avH1N1],
. . . . . . . . 84N [83N],
. . . . . . . . 112S [111S],
. . . . . . . . . . . . [H9N2],
. . . . . . . . 335I [332I],
. . . . . . . . . . . .[H6N1],
. . . . . . . . 359A [355A],
. . . . . . . . 401A [397A]
. . . . . . . . . . . . [H6N1])

. . . . ChinaShanghai3_E1_73M_2013_02_27_f (
. . . . . . . . GISAID NA EPI443023
. . . . . . . . GISAID Isolate EPI_ISL_139649
. . . . . . . . Deposited 2013-04-27 by WHO Chinese National Influenza Center
. . . . . . . . 32 Polymorphisms (10 Amino and 22 Silent)
. . . . . . . . 16I [16I],
. . . . . . . . . . . [H5N1 Human Fatality China 2011],
. . . . . . . . . . . [H5N1 Human Cambodia 2005],
. . . . . . . . . . . [H5N1 Avian Rare (58) Scotland, Middle East and Asia]
. . . . . . . . . . . [pH1N1 Rare (35) Worldwide including Scotland and 1 US Low Reactor],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 19A [19A],
. . . . . . . . . . . [avH1N1, H9N2],
. . . . . . . . 40G [40G],
. . . . . . . . . . . [H9N2],
. . . . . . . . 53T [53T],
. . . . . . . . 81T [80T],
. . . . . . . . . . . [avH1N1],
. . . . . . . . 84N [83N],
. . . . . . . . 112S [111S],
. . . . . . . . . . . . [H9N2],
. . . . . . . . 335I [332I],
. . . . . . . . . . . .[H6N1],
. . . . . . . . 359A [355A],
. . . . . . . . 401A [397A]
. . . . . . . . . . . . [H6N1])

H7N9 Influenza Hemagglutinin and Neuraminidase Segments elucidated at 2013-04-29-03_26_24_576380 by GeneWurx see.PolyDetector v0, Copyright 2007-2013
H7N9 Influenza Hemagglutinin and Neuraminidase Segments elucidated at 2013-04-27-16_14_45_207860 by GeneWurx see.PolyDetector v0, Copyright 2007-2013
H7N9 Influenza Hemagglutinin and Neuraminidase Segments elucidated at 2013-04-23-00_30_18_809650 by GeneWurx see.PolyDetector v0, Copyright 2007-2013

GISAID Citations

• GeneWurx Cross Serotype Homology Analysis, Open-Access, Full-Text version
• Human Emergent H7N9 from Zhejiang Province
• Environment Emergent H7N9 from Zhejiang
• China - H7N9 Human Isolates on Deposit at GISAID, Comprehensive Genetics Discussion

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Passerines
Fly Higher
than Poultry

We could not diverge more rapidly from the widely-stated position that commercial poultry is the standing reservoir for emergent H7N9. If poultry were the Ultimate Origin, surely farms would be rife with fulminant samples. The numbers are not in evidence to support the claim of poultry as reservoir, but an immediate scapegoat was required during the expert consultative junket. A media-visible solution was presented to the public as an actionable progression: culling of poultry became a well-received relief.

Unfortunately, using outdated methods during critical decision-making processes may generate less than optimal results. While citizens were being instructed that spread was confined to coastal areas and wet markets (due to assumptive bias), the landlocked province of Hunan had emergent H7N9 activity before mid-month as predicted using genetic tracing. Terrestrial birds do not seed virus stock across great distances; terrestrial birds (commercial poultry) do act as primary incubators of many dangerous polymorphisms.

Passerines, on the other hand, do cover significant ranges in flight and do interact / overlap at times with commercial poultry.

One incubates in situ; another transports.

Influenza exhibits flawless utilisation of these vectors as influenza always has. Nothing new in the influenza behaviour . . . and nothing new in viral science conventional wisdom either. Perhaps in this modern age, in this 21st century, we will reinstate that once great fulcrum to science and allow observational evidence a place at the table again.

[Shannon Bennett]

Re: China - H7N9 Human Isolates on Deposit at GISAID

I cannot read the polymorphisms but I can say that as a geographer I have to agree with NS1. The virus has shown signs of passes through a remarkable number of organisms. If chickens were the fulminant species then we would see a lot higher numbers of infected poultry workers. We would find higher numbers of infected chickens. The numbers just aren't there. And the puzzle of why 20% of human victims have zero contact with poultry of any kind are sick, cannot be answered with wet market chickens as the vector. I do believe that wet markets have played a role and, I also believe that chickens can and do become sick with H7N9 and may pass the disease to humans. However, I do not believe that chickens are not infected in home flocks then somehow magically become infected spontaneously while en route to a wet market. Given the travelogue the polymorphisms indicate the possibility of many other species as a fulminat cannot and should not be ignored for the sake of calming fears and stabilizing markets.

I hope that the Chinese are fully aware and are still actively searching for the fulminant species and not still focused on chickens.