Prediction Demonstrated of Antigenic Dual Geography sH3N2 HA 140K

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 : 2013-12-02
Last Update : 2013-12-04

Map - Dual Geography Prediction

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2 Predicted Human Sequences

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The United States CDC and the UK National Institute for Medical Research published sequences at GISAID respectively on 2013-06-21 (CDC) and 2013-06-26 (NIMR) that fulfill the dual geography genetic change and timing of the GeneWurx spread prediction published on 2013-02-08 titled sH3N2 HA 140K Antigen Polymorphism Potential in Europe and North America.

Antigenic Variance

sH3N2 Antigen Revision Demonstrated As Predicted Sample Date Name Antigen Revision ID  2013-04-24   Alaska04_C2_44M  HA 140K  EPI459829   2013-03-12   RussiaSamara73_C1St1_17F  HA 140K  EPI460558

The Alaska04_C2_44M_2013_04_24 sequence was antigenically characterised as a Victoria361-like vaccine match.

Vaccine Candidate Investigation

On 2013-12-02 the United States CDC produced 3 lab-derived, HA 140K sequences dated 2013-11-29 and 2013-12-02 (2) at GISAID that originated at New York Medical College and are coded similarly to previous Investigational Vaccine Candidates (X-233 & X-233A).  The 3 lab-developed sequences appear to be based on the Hemagglutinin & Neuraminidase of the fixed form derived / purified from an early ambiguous HA 140K emergence, A/New York/39/2012.

That New York sample taken on 2012-10-20 was published with a submission date and update date of 2012-12-07 on a C1 passage with HA 140I, then on an E3 passage with ambiguity at HA aa140.  Those C1 and E3 passages were each antigenically characterised as Victoria361-like vaccine matches, although that E3 passage showed some trace of ambiguity resolving to HA 140K.

In a publication dated 2013-03-14, an E4 passage derived the HA 140K.  An E5 passage of A/New York/39/2012 with ambiguity resolving to HA 140K was added to GISAID today, 2013-12-02, by the United States CDC to join the outcomes of various other passage strategies for a total of 9 sequences on deposit from this New York sample.

Vaccine Candidate Investigation

sH3N2 Investigational NewYork39_2012_10_20 Passage Strategies Publish Date Name aa140 Antigen ID  2013-12-02   NewYork39_EXIR_5M_X233A_2012_10_20  HA 140K  EPI490080   2013-12-02   NewYork39_EXIR_5M_X233_2012_10_20  HA 140K  EPI490077   2013-11-29   NewYork39_E4E8E1_5M_X233_2012_10_20  HA 140K  EPI489319   2013-12-02   NewYork39_E5_5M_2012_10_20  HA 140K mix wt  EPI490093   2013-05-08   NewYork39_C2_5M_2012_10_20  HA 140I  EPI445712   2013-03-14   NewYork39_E4_5M_2012_10_20  HA 140K  EPI436261   2013-02-25   NewYork39_C3_5M_2012_10_20  HA 140I  EPI426140   2012-12-07   NewYork39_E3_5M_2012_10_20  HA 140K mix wt  EPI404965   2012-12-07   NewYork39_C1_5M_2012_10_20  HA 140I  EPI404927

MetaData

Our researchers very much appreciate that age and gender information are annotated for each base HA 140K sequence via the originating / submitting organisation's chain of custody.

Although 1 of the 2 HA 140K prediction demonstration sequences was updated subsequent to the original submission, no clinical progression, treatment annotation or clinical outcome has yet been made public corresponding to these very important cases that originated respectively from the Alaska State Virology Lab and WHO National Influenza Centre of Saint Petersburg, Russia.

HA Polymorphisms

. . . . Alaska04_C2_44M_2013_04_24 (

. . . . . . . . A/Alaska/04/2013
. . . . . . . . Emergent H7N9 Correlation HA 131A

. . . . . . . . GISAID HA EPI459829

. . . . . . . . GISAID Isolate EPI_ISL_143267

. . . . . . . . 18 Polymorphisms (10 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 131A [Emergent H7N9 wild type],

. . . . . . . . 140K,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . 186G,

. . . . . . . . 190D,

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

. . . . . . . . 278K,

. . . . . . . . syn402V (GTa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn481I (ATa),

. . . . . . . . 489N,

. . . . . . . . syn490V (GTg),

. . . . . . . . syn492R (AGg))

. . . . RussiaSamara73_C1St1_17F_2013_03_12 (

. . . . . . . . A/Samara/73/2013

. . . . . . . . Emergent H7N9 Correlation HA 128A
. . . . . . . . GISAID HA EPI460558

. . . . . . . . GISAID Isolate EPI_ISL_143568

. . . . . . . . 19 Polymorphisms (10 Amino and 9 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn36V (GTc),

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A [Emergent H7N9 Count 02:
. . . . . . . . . . . . . . . HongKong5942_M_36F_2013_11_30_s

. . . . . . . . . . . . . . . . . . . Deposit Report
. . . . . . . . . . . . . . . . . . . GISAID HA EPI490882

. . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_151417,

. . . . . . . . . . . . . . . ChinaGuangdongHuizhou1_51F_2013_08_10_s
. . . . . . . . . . . . . . . . . . . Deposit Report

. . . . . . . . . . . . . . . . . . . GISAID HA EPI476697

. . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_148417],

. . . . . . . . 140K,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn175D (GAt),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 278K,

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn479G (GGg),

. . . . . . . . syn492R (AGg))

NA Polymorphisms

. . . . Alaska04_C2_44M_2013_04_24 (

. . . . . . . . A/Alaska/04/2013

. . . . . . . . GISAID NA EPI459828

. . . . . . . . GISAID Isolate EPI_ISL_143267

. . . . . . . . 15 Polymorphisms (6 Amino and 9 Silent)

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . syn28I (ATt),

. . . . . . . . syn68L (tTa),

. . . . . . . . syn106I (ATt),

. . . . . . . . 151N mix wt,

. . . . . . . . syn167F (TTc),

. . . . . . . . 197N,

. . . . . . . . 221D,

. . . . . . . . syn248G (GGg),

. . . . . . . . 258E,

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . 392T,

. . . . . . . . syn439T (ACc))

. . . . RussiaSamara73_C1St1_17F_2013_03_12 (

. . . . . . . . A/Samara/73/2013

. . . . . . . . GISAID NA EPI460559

. . . . . . . . GISAID Isolate EPI_ISL_143568

. . . . . . . . 13 Polymorphisms (4 Amino and 9 Silent)

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 64K,

. . . . . . . . syn106I (ATt),

. . . . . . . . syn108L (CTa),

. . . . . . . . syn128K (AAa),

. . . . . . . . syn234N (AAc),

. . . . . . . . 258E,

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn395Q (CAg),

. . . . . . . . 427T,

. . . . . . . . syn439T (ACc))

Supporting Sequences

HA Polymorphisms

. . . . NewYork39_EXIR_5M_X233A_2012_10_20 (

. . . . . . . . A/New York/39/2012 X-233A

. . . . . . . . Original Submission: 2013-12-02

. . . . . . . . GISAID HA EPI490080

. . . . . . . . GISAID Isolate EPI_ISL_151399

. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 140K,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 194P,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

. . . . NewYork39_EXIR_5M_X233_2012_10_20 (

. . . . . . . . A/New York/39/2012 X-233

. . . . . . . . Original Submission: 2013-12-02

. . . . . . . . GISAID HA EPI490077

. . . . . . . . GISAID Isolate EPI_ISL_151398

. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 140K,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 194P,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

. . . . NewYork39_E4E8E1_5M_X233_2012_10_20 (

. . . . . . . . A/New York/39/2012 X-233

. . . . . . . . Original Submission: 2013-11-29

. . . . . . . . GISAID HA EPI489319

. . . . . . . . GISAID Isolate EPI_ISL_151026

. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 140K,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 194P,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

. . . . NewYork39_E5_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2013-12-02

. . . . . . . . GISAID HA EPI490093

. . . . . . . . GISAID Isolate EPI_ISL_151400

. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 140K mix wt,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 194P mix wt,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

. . . . NewYork39_C2_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2013-05-08

. . . . . . . . GISAID HA EPI445712

. . . . . . . . GISAID Isolate EPI_ISL_140279

. . . . . . . . 17 Polymorphisms (9 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

. . . . NewYork39_E4_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2013-03-14

. . . . . . . . GISAID HA EPI436261

. . . . . . . . GISAID Isolate EPI_ISL_138001

. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 140K,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 194P mix wt,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

. . . . NewYork39_C3_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2013-02-25

. . . . . . . . GISAID HA EPI426140

. . . . . . . . GISAID Isolate EPI_ISL_136409

. . . . . . . . 17 Polymorphisms (9 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

. . . . NewYork39_E3_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2012-12-07

. . . . . . . . GISAID HA EPI404965

. . . . . . . . GISAID Isolate EPI_ISL_131823

. . . . . . . . 19 Polymorphisms (11 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 140K mix wt,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G mix wt,

. . . . . . . . 190D,

. . . . . . . . 219Y mix wt,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

. . . . NewYork39_C1_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2012-12-07

. . . . . . . . GISAID HA EPI404927

. . . . . . . . GISAID Isolate EPI_ISL_131810

. . . . . . . . 17 Polymorphisms (9 Amino and 8 Silent)

. . . . . . . . #7Y,

. . . . . . . . syn8N (AAt),

. . . . . . . . 33R,

. . . . . . . . syn79F (TTt),

. . . . . . . . 128A,

. . . . . . . . 142G,

. . . . . . . . 145S,

. . . . . . . . 156H,

. . . . . . . . syn172E (GAg),

. . . . . . . . 186G,

. . . . . . . . 190D,

. . . . . . . . 278K,

. . . . . . . . syn281C (TGt),

. . . . . . . . syn402V (GTa),

. . . . . . . . syn416T (ACa),

. . . . . . . . syn455L (CTg),

. . . . . . . . syn492R (AGg))

NA Polymorphisms

. . . . NewYork39_EXIR_5M_X233A_2012_10_20 (

. . . . . . . . A/New York/39/2012 X-233A

. . . . . . . . Original Submission: 2013-12-02

. . . . . . . . GISAID NA EPI490079

. . . . . . . . GISAID Isolate EPI_ISL_151399

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

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 43D,

. . . . . . . . syn106I (ATt),

. . . . . . . . 258E,

. . . . . . . . syn275V (GTt),

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn439T (ACc),

. . . . . . . . syn465N (AAc))

. . . . NewYork39_EXIR_5M_X233_2012_10_20 (

. . . . . . . . A/New York/39/2012 X-233

. . . . . . . . Original Submission: 2013-12-02

. . . . . . . . GISAID NA EPI490076

. . . . . . . . GISAID Isolate EPI_ISL_151398

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

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 43D,

. . . . . . . . syn106I (ATt),

. . . . . . . . 258E,

. . . . . . . . syn275V (GTt),

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn439T (ACc),

. . . . . . . . syn465N (AAc))

. . . . NewYork39_E5_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2013-12-02

. . . . . . . . GISAID NA EPI490092

. . . . . . . . GISAID Isolate EPI_ISL_151400

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

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 43D,

. . . . . . . . syn106I (ATt),

. . . . . . . . 258E,

. . . . . . . . syn275V (GTt),

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn439T (ACc),

. . . . . . . . syn465N (AAc))

. . . . NewYork39_C2_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2013-05-08

. . . . . . . . GISAID NA EPI445711

. . . . . . . . GISAID Isolate EPI_ISL_140279

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

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 43D,

. . . . . . . . syn106I (ATt),

. . . . . . . . 151N mix wt,

. . . . . . . . 258E,

. . . . . . . . syn275V (GTt),

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn439T (ACc),

. . . . . . . . syn465N (AAc))

. . . . NewYork39_E4_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2013-03-14

. . . . . . . . GISAID NA EPI436260

. . . . . . . . GISAID Isolate EPI_ISL_138001

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

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 43D,

. . . . . . . . syn106I (ATt),

. . . . . . . . 258E,

. . . . . . . . syn275V (GTt),

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn439T (ACc),

. . . . . . . . syn465N (AAc))

. . . . NewYork39_C3_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2013-02-25

. . . . . . . . GISAID NA EPI465202

. . . . . . . . GISAID Isolate EPI_ISL_136409

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

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 43D,

. . . . . . . . syn106I (ATt),

. . . . . . . . 151N mix wt,

. . . . . . . . 258E,

. . . . . . . . syn275V (GTt),

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn439T (ACc),

. . . . . . . . syn465N (AAc))

. . . . NewYork39_E3_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2012-12-07

. . . . . . . . GISAID NA EPI404964

. . . . . . . . GISAID Isolate EPI_ISL_131823

. . . . . . . . 11 Polymorphisms (3 Amino and 8 Silent)

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 43D,

. . . . . . . . syn106I (ATt),

. . . . . . . . syn116V (GTa) mix wt,

. . . . . . . . 258E,

. . . . . . . . syn275V (GTt),

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn439T (ACc),

. . . . . . . . syn465N (AAc))

. . . . NewYork39_C1_5M_2012_10_20 (

. . . . . . . . A/New York/39/2012

. . . . . . . . Original Submission: 2012-12-07

. . . . . . . . GISAID NA EPI404926

. . . . . . . . GISAID Isolate EPI_ISL_131810

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

. . . . . . . . syn11G (GGc),

. . . . . . . . syn18S (TCc),

. . . . . . . . 43D,

. . . . . . . . syn106I (ATt),

. . . . . . . . 258E,

. . . . . . . . syn275V (GTt),

. . . . . . . . syn300R (cGG),

. . . . . . . . 329N,

. . . . . . . . syn439T (ACc),

. . . . . . . . syn465N (AAc))

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

sH3N2 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-12-02-23_34_14_375380 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.
Supporting Influenza HA & NA Segments elucidated at 2013-12-03-03_05_27_920970 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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