2013-09-26

Emergent H7N9 Homology in Fatal Human pH1N1 Case Near Caspian Sea

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 workbook for completeness in citation.

Publish Date : 2013-09-26
Last Update : 2013-11-04
Emergent H7N9 Homology in Fatal Human pH1N1 Case Near Caspian Sea
Geographic Distribution

On 2013-09-25, the Rospotrebnadzor of Moscow, Russia released a set of human pH1N1 sequences without age or gender at GISAID, including 6 Fatal cases. The Neuraminidase segments were not released.

One HA segment sampled in late January 2013 from Astrakhan [map], near the Caspian Sea, [EPI471830] strongly suggests Emergent H7N9 involvement.   This Astrakhan H7N9-related viral Hemagglutinin displays a standard Emergent H7N9 amino at 179V on a pH1N1 Clade2:188T background.  The HA 179V is Novel to pH1N1 after more than 4 years of pH1N1 circulation in humans.  HA 89G, found in the H7N9 reservoir, is co-located on this same pH1N1 sequence.  Polymorphisms at two antigenic amino positions practically adjacent, HA 129Q and HA 131L, provide grist for the Host-Transition mill.

Contemporary sequences from Spain carry homology as well as an unusual change adjacent to these odd aa129 and aa131 positions from the Russian Federation:
  • HA 477M SpainCatalonia5925S_29F_2013_02_05
  • HA 132S  SpainMurcia164_80F_2013_01_30_s
Furthermore, SpainMurcia164_80F_2013_01_30_s, an In-Patient case, is on a cross-clade background (HA 188T & 189T) and features a polymorphism at aa89 (HA 89N)

HA 219T, also seen in the H7N9 reservoir, is demonstrated in Kazan [map], [EPI471827].

HA 225G continues to inform Fatal pH1N1 cases:
Hemagglutinin Sequences

. . . . RussiaVolgogradCRIE25_2013_02_28_VxX_f (
. . . . . . . . A/Volgograd/CRIE-25/2013
. . . . . . . . GISAID HA EPI471832
. . . . . . . . GISAID Isolate EPI_ISL_146874
. . . . . . . . 22 Polymorphisms (8 Amino and 14 Silent)
. . . . . . . . syn39K (AAa),
. . . . . . . . syn77S (AGt),
. . . . . . . . syn99I (ATa),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa),
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn461K (AAa),
. . . . . . . . 502K,
. . . . . . . . syn546L (tTg),
. . . . . . . . syn548C (TGc))

. . . . RussiaOrenburgCRIE26_2013_02_13_f (
. . . . . . . . A/Orenburg/CRIE-26/2013
. . . . . . . . GISAID HA EPI471833
. . . . . . . . GISAID Isolate EPI_ISL_146875
. . . . . . . . 23 Polymorphisms (8 Amino and 15 Silent)
. . . . . . . . syn39K (AAa),
. . . . . . . . syn61A (GCa),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 166I,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa),
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn417G (GGc),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K,
. . . . . . . . syn542S (TCc),
. . . . . . . . syn546L (tTg),
. . . . . . . . syn548C (TGc))

. . . . RussiaAstrakhanCRIE18_2013_02_05_f (
. . . . . . . . A/Astrakhan/CRIE-18/2013
. . . . . . . . GISAID HA EPI471831
. . . . . . . . GISAID Isolate EPI_ISL_146873
. . . . . . . . 20 Polymorphisms (8 Amino and 12 Silent)
. . . . . . . . syn39K (AAa),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . 166I,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa),
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K,
. . . . . . . . syn542S (TCc),
. . . . . . . . syn546L (tTg),
. . . . . . . . syn548C (TGc))

. . . . RussiaAstrakhanCRIE17_2013_01_28_f (
. . . . . . . . A/Astrakhan/CRIE-17/2013
. . . . . . . . GISAID HA EPI471830
. . . . . . . . GISAID Isolate EPI_ISL_146872
. . . . . . . . 23 Polymorphisms (13 Amino and 10 Silent)
. . . . . . . . syn16T (ACg),
. . . . . . . . 77I [avH1N1],
. . . . . . . . 89G [H7N9 wt],
. . . . . . . . 100N,
. . . . . . . . 129Q,
. . . . . . . . 131L,
. . . . . . . . syn162P (CCt),
. . . . . . . . 179V [pH1N1 Novel],
. . . . . . . . . . . . [Emergent H7N9 wt],
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 477M [SpainCatalonia5925S_29F_2013_02_05 (PhyloTree)],
. . . . . . . . . . . . [sH1N1],
. . . . . . . . syn497K (AAg),
. . . . . . . . 502K,
. . . . . . . . syn546L (tTg),
. . . . . . . . syn548C (TGc))

. . . . RussiaMoscowOblastCRIE08_2013_01_28_VxX_f (
. . . . . . . . A/Moscow-Oblast/CRIE-08/2013
. . . . . . . . GISAID HA EPI471828
. . . . . . . . GISAID Isolate EPI_ISL_146870
. . . . . . . . 23 Polymorphisms (8 Amino and 15 Silent)
. . . . . . . . syn64I (ATt),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn111V (GTa),
. . . . . . . . syn141H (CAc),
. . . . . . . . 188T,
. . . . . . . . syn223V (GTa),
. . . . . . . . 225G,
. . . . . . . . 259T,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn402H (CAt),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K,
. . . . . . . . syn542S (TCc),
. . . . . . . . syn546L (tTg),
. . . . . . . . syn548C (TGc))

. . . . RussiaAstrakhanCRIE16_2013_01_26_f (
. . . . . . . . A/Astrakhan/CRIE-16/2013
. . . . . . . . GISAID HA EPI471829
. . . . . . . . GISAID Isolate EPI_ISL_146871
. . . . . . . . 20 Polymorphisms (9 Amino and 11 Silent)
. . . . . . . . syn16T (ACg),
. . . . . . . . 77I,
. . . . . . . . 89G,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 237I,
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . syn497K (AAg),
. . . . . . . . 502K,
. . . . . . . . syn542S (TCc),
. . . . . . . . syn546L (tTg),
. . . . . . . . syn548C (TGc))

. . . . RussiaKazanCRIE01_2012_12_29 (
. . . . . . . . A/Kazan/CRIE-01/2012
. . . . . . . . GISAID HA EPI471827
. . . . . . . . GISAID Isolate EPI_ISL_146869
. . . . . . . . 21 Polymorphisms (8 Amino and 13 Silent)
. . . . . . . . syn39K (AAa),
. . . . . . . . syn77S (AGt),
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 219T [H7N9],
. . . . . . . . 237I,
. . . . . . . . syn239P (CCa),
. . . . . . . . 286E,
. . . . . . . . syn308K (AAg),
. . . . . . . . syn333F (TTc),
. . . . . . . . syn338G (GGc),
. . . . . . . . syn372Q (CAa),
. . . . . . . . 377K,
. . . . . . . . syn396V (GTg),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N,
. . . . . . . . 502K,
. . . . . . . . syn542S (TCc),
. . . . . . . . syn546L (tTg),
. . . . . . . . syn548C (TGc))

This analysis catalysed with ingenuity from 2 lead Professors of Group10 at Ion203.  We never cease to find inspiration in your halls of instruction.


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pH1N1 Influenza Hemagglutinin Segments elucidated at 2013-09-26-00_39_36_150170  by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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