Prediction Demonstrated in USA of Triple Polymorphism pH1N1 HA 166N, 188T & 189T

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 : 2013-11-28
Last Update : 2013-11-29

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1 Predicted Sequence

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The United States CDC published a sequence on 2013-09-09 with Clade Crossing evidence sampled on 2013-08-13 from a 57 year old male in Indiana.  This Indiana22_C2_57M_2013_08_13 sequence fulfills the triple polymorphism genetic change and timing of the prediction published on 2013-02-26 titled HA 166N Polymorphism Potential on pH1N1 Cross-Clade Background with Both 188T and 189T.

No clinical progression, treatment annotation or clinical outcome has yet been published corresponding to this very important case that originated from the Indiana State Department of Health Laboratories.

HA Polymorphisms

. . . . Indiana22_C2_57M_2013_08_13 (

. . . . . . . . A/Indiana/22/2013
. . . . . . . . H7N9 Correlation NA 94I
. . . . . . . . Host Transition Indication NA 94I
. . . . . . . . CrossClade 188T and 189T
. . . . . . . . GISAID HA EPI467365

. . . . . . . . GISAID Isolate EPI_ISL_145658

. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)

. . . . . . . . syn#4Y (TAc),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . 166N,

. . . . . . . . syn174K (AAg),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 189T,

. . . . . . . . 237I,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

. . . . . . . . syn396V (GTg),

. . . . . . . . syn448L (TTg),

. . . . . . . . 454N,

. . . . . . . . syn500R (AGg) [pH1N1 Rare],

. . . . . . . . . . . . . . . . . . [H7N9 Avian],

. . . . . . . . 502K)

NA Polymorphisms

. . . . Indiana22_C2_57M_2013_08_13 (

. . . . . . . . A/Indiana/22/2013
. . . . . . . . H7N9 Correlation NA 94I
. . . . . . . . Host Transition Indication NA 94I
. . . . . . . . CrossClade 188T and 208K
. . . . . . . . GISAID NA EPI467364

. . . . . . . . GISAID Isolate EPI_ISL_145658

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

. . . . . . . . 44S,

. . . . . . . . 94I [pH1N1 Rare:
. . . . . . . . . . . . . 10(9) Cases over 10 Sequences,
. . . . . . . . . . . . . . . . . 2013 - Count 02
. . . . . . . . . . . . . . . . . 2012 - Count 02
. . . . . . . . . . . . . . . . . 2011 - Count 00
. . . . . . . . . . . . . . . . . 2010 - Count 04
. . . . . . . . . . . . . . . . . 2009 - Count 02],
. . . . . . . . . . [Emergent H7N9 wild type],
. . . . . . . . . . [Host Transition Indication:
. . . . . . . . . . . . . H7N1 Passerine Starling England,
. . . . . . . . . . . . . H7N1 Parrot Ireland,
. . . . . . . . . . . . . H7N1 Ostrich South Africa],

. . . . . . . . . . [H5N1 China Human wild type],
. . . . . . . . . . [s2007 H1N1],
. . . . . . . . 106V,

. . . . . . . . syn156R (CGg),

. . . . . . . . syn176S (TCg),

. . . . . . . . 200S [H5N1],

. . . . . . . . syn205V (GTa) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [avH1N1_farm],
. . . . . . . . . . . . . . . . . . [H5N1 wild type],
. . . . . . . . . . . . . . . . . . [H6N1],

. . . . . . . . syn209N (AAt) [H5N1 wild type],

. . . . . . . . syn240T (ACc),

. . . . . . . . 241I [H5N1],

. . . . . . . . syn243T (ACt) [H5N1 China Human wild type],

. . . . . . . . . . . . . . . . . . [H7N9 Avian],

. . . . . . . . 369K,

. . . . . . . . syn377P (CCa) [H5N1 wild type],

. . . . . . . . syn378N (AAt) [H5N1 wild type])

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pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-09-10-23_00_00_621110 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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