2013-11-21

Burkina Faso Off-Clade pH1N1 Sequences with Strong Homology to H7N9 Vaccine Candidate

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 : 2013-11-21
Last Update : 2013-12-18
Burkina Faso
3 Sequences

Three Off-Clade Pandemic H1N1 sequences sampled from Burkina Faso were published recently at GISAID by the United States CDC.  These West African sequences group with a small set of highly divergent sequences we have been following that carries an unusually strong polymorphic homology to H7N9.  The set of distinct pH1N1 HA polymorphisms also displays a 51% homology to zoonotic H3N2 and a rather high 44% homology to the H7 serotypes.

On Wednesday, November 20, 2013, the National Institute of Infectious Diseases of Japan produced the details at GISAID of an Investigational Vaccine Candidate for Emergent H7N9 based on the Anhui1 base sequence.  Evidently, when their candidate culturing process was modified with an initial Lewis Lung Carcinoma passage, a novel polymorphism to Emergent H7N9 manifested [Deposit Report].

That H7N9 host switching revision, HA 131T, also features on this group of avian-centric human pH1N1 sequences we have been following.  The HA 131T has previously been seen in H7N9 Avian, the H7N7 human fatality, current H3N2 Human Seasonal (wild type), H1N1 Seasonal 2008, H1N1 Variant Human and in 1918.  Two of the fatalities from the 2006 Egyptian H5N1 HA 230I-bearing Gharbiyah cluster carry this HA 131T.  Animal occurrences include H3N2, avH1N1, H5N1 (including a parrot) and H6N1.

We note when a Group 1 serotype (H1) develops contemporaneous homology with Group 2 serotypes (H3 & H7).  Identifying a reservoir for this small, but persisting, Off-Clade pH1N1 set found primarily in western Africa would be useful in understanding the factors involved for minority strain maturation.

The Burkina Faso details are annotated at the polymorphism level in the following sequence list.

HA Polymorphisms

. . . . BurkinaFaso875_C2_2013_02_26 (
. . . . . . . . A/Burkina Faso/875/2013
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID HA EPI482169
. . . . . . . . GISAID Isolate EPI_ISL_149349
. . . . . . . . 38 Polymorphisms (11 Amino and 27 Silent)
. . . . . . . . #11T [avH1N1, zH3N2, H9N2],
. . . . . . . . 35I [avH1N1, zH3N2, H5N1],
. . . . . . . . syn56G (GGc) [Emergent H7N9 Avian],
. . . . . . . . 89E [avH1N1farm, zH3N2, 1918],
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T [Emergent H7N9
. . . . . . . . . . . . . . . Investigational Vaccine Candidate:
. . . . . . . . . . . . . . . ChinaAnhuiChuzhou1_LLC1E3_35F_2013_03_15_f
. . . . . . . . . . . . . . . . . . . A/Anhui/1/2013 NIIDRG-10.1
. . . . . . . . . . . . . . . . . . . Deposit Report
. . . . . . . . . . . . . . . . . . . GISAID HA EPI486492
. . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150198
. . . . . . . . . . . . . . . Japan NIID Lab-Derived,
. . . . . . . . . . . . . . . Initial Passage in Lewis Lung Carcinoma culture],
. . . . . . . . . . . [H7N9 Avian],
. . . . . . . . . . . [H7N7 Human Fatality],
. . . . . . . . . . . [H3N2 Human Seasonal],
. . . . . . . . . . . [H1N1 Human Seasonal 2008],
. . . . . . . . . . . [H1N1 Variant Human 2007, 2011, 2012, 2013],
. . . . . . . . . . . [H1N1 Variant Swine 2011, 2012, 2013],
. . . . . . . . . . . [H1N1 Variant Mink 2012],
. . . . . . . . . . . [1918],
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . syn164L (CTt) [pH1N1 Upsilon],
. . . . . . . . 173R [H7N9 Avian],
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn215P (CCa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn239P (CCa),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K [Emergent H7N9 wild type],
. . . . . . . . 266A [H7N9 Avian United States:
. . . . . . . . . . . . . . . . First Base Donor 266V gTC, gTT],
. . . . . . . . syn276H (CAt),
. . . . . . . . syn295F (TTc),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn326S (TCc),
. . . . . . . . syn331G (GGt) [H7N9 Avian],
. . . . . . . . syn337A (GCt) [H7N9 Avian United States],
. . . . . . . . . . . . . . . . .  [Pennsylvania07_C1_1F_2013_10_02
. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI485754
. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150035
. . . . . . . . . . . . . . . . .  DominicanRep7626_C2_34F_2013_06_15_TmX_VxX
. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI477445
. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_148743],
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn379T (ACc),
. . . . . . . . syn433E (GAg) [Emergent H7N9 wild type],
. . . . . . . . syn451K (AAa),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V [H6N1],
. . . . . . . . syn475D (GAc),
. . . . . . . . syn486T (ACc) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [zH3N2],
. . . . . . . . . . . . . . . . . . [H3N8 Avian],
. . . . . . . . syn505G (GGa),
. . . . . . . . 523A,
. . . . . . . . syn526S (TCc),
. . . . . . . . syn527L (TTa))

. . . . BurkinaFaso876_C2_2013_02_26_VxX (
. . . . . . . . A/Burkina Faso/876/2013
. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID HA EPI482162
. . . . . . . . GISAID Isolate EPI_ISL_149346
. . . . . . . . 39 Polymorphisms (12 Amino and 27 Silent)
. . . . . . . . #11T [avH1N1, zH3N2, H9N2],
. . . . . . . . 13T [H5N1, H9N2, H13],
. . . . . . . . 35I [avH1N1, zH3N2, H5N1],
. . . . . . . . syn56G (GGc) [Emergent H7N9 Avian],
. . . . . . . . 89E [avH1N1farm, zH3N2, 1918],
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T [Emergent H7N9
. . . . . . . . . . . . . . . Investigational Vaccine Candidate:
. . . . . . . . . . . . . . . ChinaAnhuiChuzhou1_LLC1E3_35F_2013_03_15_f
. . . . . . . . . . . . . . . . . . . A/Anhui/1/2013 NIIDRG-10.1
. . . . . . . . . . . . . . . . . . . Deposit Report
. . . . . . . . . . . . . . . . . . . GISAID HA EPI486492
. . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150198
. . . . . . . . . . . . . . . Japan NIID Lab-Derived,
. . . . . . . . . . . . . . . Initial Passage in Lewis Lung Carcinoma culture],
. . . . . . . . . . . [H7N9 Avian],
. . . . . . . . . . . [H7N7 Human Fatality],
. . . . . . . . . . . [H3N2 Human Seasonal],
. . . . . . . . . . . [H1N1 Human Seasonal 2008],
. . . . . . . . . . . [H1N1 Variant Human 2007, 2011, 2012, 2013],
. . . . . . . . . . . [H1N1 Variant Swine 2011, 2012, 2013],
. . . . . . . . . . . [H1N1 Variant Mink 2012],
. . . . . . . . . . . [1918],
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 158E,
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn215P (CCa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn239P (CCa),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K [Emergent H7N9 wild type],
. . . . . . . . 266A [H7N9 Avian United States:
. . . . . . . . . . . . . . . . First Base Donor 266V gTC, gTT],
. . . . . . . . syn276H (CAt),
. . . . . . . . syn295F (TTc),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn326S (TCc),
. . . . . . . . syn331G (GGt) [H7N9 Avian],
. . . . . . . . syn337A (GCt) [H7N9 Avian United States],
. . . . . . . . . . . . . . . . .  [Pennsylvania07_C1_1F_2013_10_02
. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI485754
. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150035
. . . . . . . . . . . . . . . . .  DominicanRep7626_C2_34F_2013_06_15_TmX_VxX
. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI477445
. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_148743],
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn379T (ACc),
. . . . . . . . syn425N (AAc) [H7N9 Avian],
. . . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . syn433E (GAg) [Emergent H7N9 wild type],
. . . . . . . . syn451K (AAa),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V [H6N1],
. . . . . . . . syn475D (GAc),
. . . . . . . . syn486T (ACc) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [zH3N2],
. . . . . . . . . . . . . . . . . . [H3N8 Avian],
. . . . . . . . syn505G (GGa),
. . . . . . . . 523A,
. . . . . . . . syn526S (TCc),
. . . . . . . . syn527L (TTa))

. . . . BurkinaFaso859_C1_2013_02_18 (
. . . . . . . . A/Burkina Faso/859/2013
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID HA EPI484718
. . . . . . . . GISAID Isolate EPI_ISL_148736
. . . . . . . . 37 Polymorphisms (10 Amino and 27 Silent)
. . . . . . . . #11T [avH1N1, zH3N2, H9N2],
. . . . . . . . 35I [avH1N1, zH3N2, H5N1],
. . . . . . . . syn56G (GGc) [Emergent H7N9 Avian],
. . . . . . . . 89E [avH1N1farm, zH3N2, 1918],
. . . . . . . . syn99I (ATt),
. . . . . . . . syn122K (AAa),
. . . . . . . . 131T [Emergent H7N9
. . . . . . . . . . . . . . . Investigational Vaccine Candidate:
. . . . . . . . . . . . . . . ChinaAnhuiChuzhou1_LLC1E3_35F_2013_03_15_f
. . . . . . . . . . . . . . . . . . . A/Anhui/1/2013 NIIDRG-10.1
. . . . . . . . . . . . . . . . . . . Deposit Report
. . . . . . . . . . . . . . . . . . . GISAID HA EPI486492
. . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150198
. . . . . . . . . . . . . . . Japan NIID Lab-Derived,
. . . . . . . . . . . . . . . Initial Passage in Lewis Lung Carcinoma culture],
. . . . . . . . . . . [H7N9 Avian],
. . . . . . . . . . . [H7N7 Human Fatality],
. . . . . . . . . . . [H3N2 Human Seasonal],
. . . . . . . . . . . [H1N1 Human Seasonal 2008],
. . . . . . . . . . . [H1N1 Variant Human 2007, 2011, 2012, 2013],
. . . . . . . . . . . [H1N1 Variant Swine 2011, 2012, 2013],
. . . . . . . . . . . [H1N1 Variant Mink 2012],
. . . . . . . . . . . [1918],
. . . . . . . . syn152I (ATt),
. . . . . . . . syn154L (CTg),
. . . . . . . . 206S,
. . . . . . . . syn214K (AAa),
. . . . . . . . syn215P (CCa),
. . . . . . . . syn219I (ATt),
. . . . . . . . syn239P (CCa),
. . . . . . . . syn254P (CCa),
. . . . . . . . 262K [Emergent H7N9 wild type],
. . . . . . . . 266A [H7N9 Avian United States:
. . . . . . . . . . . . . . . . First Base Donor 266V gTC, gTT],
. . . . . . . . syn276H (CAt),
. . . . . . . . syn295F (TTc),
. . . . . . . . syn301I (ATt),
. . . . . . . . syn326S (TCc),
. . . . . . . . syn331G (GGt) [H7N9 Avian],
. . . . . . . . syn337A (GCt) [H7N9 Avian United States],
. . . . . . . . . . . . . . . . .  [Pennsylvania07_C1_1F_2013_10_02
. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI485754
. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_150035
. . . . . . . . . . . . . . . . .  DominicanRep7626_C2_34F_2013_06_15_TmX_VxX
. . . . . . . . . . . . . . . . . . . . . GISAID HA EPI477445
. . . . . . . . . . . . . . . . . . . . . GISAID Isolate EPI_ISL_148743],
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn379T (ACc),
. . . . . . . . syn425N (AAc) [H7N9 Avian],
. . . . . . . . . . . . . . . . . . .[H7N7 Human Fatality],
. . . . . . . . syn433E (GAg) [Emergent H7N9 wild type],
. . . . . . . . syn451K (AAa),
. . . . . . . . syn456L (cTA),
. . . . . . . . 463V [H6N1],
. . . . . . . . syn475D (GAc),
. . . . . . . . syn486T (ACc) [Emergent H7N9 wild type],
. . . . . . . . . . . . . . . . . . [zH3N2],
. . . . . . . . . . . . . . . . . . [H3N8 Avian],
. . . . . . . . syn505G (GGa),
. . . . . . . . 523A,
. . . . . . . . syn526S (TCc),
. . . . . . . . syn527L (TTa))

NA Polymorphisms

. . . . BurkinaFaso875_C2_2013_02_26 (
. . . . . . . . A/Burkina Faso/875/2013
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID NA EPI482168
. . . . . . . . GISAID Isolate EPI_ISL_149349
. . . . . . . . 14 Polymorphisms (5 Amino and 9 Silent)
. . . . . . . . 13I [Emergent H7N9 wild type
. . . . . . . . . . . . . . First Base Donor ACc, ACT, Atg],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [H6N1],
. . . . . . . . syn20A (GCc),
. . . . . . . . 74V,
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn127L (cTG),
. . . . . . . . syn183A (GCc),
. . . . . . . . syn192T (ACc),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn370G (GGg),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K [Emergent H7N9 wild type],
. . . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . . [H9N2],
. . . . . . . . syn433E (GAa))

. . . . BurkinaFaso876_C2_2013_02_26_VxX (
. . . . . . . . A/Burkina Faso/876/2013
. . . . . . . . Vaccine Escape Genotype HA 158E
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID NA EPI482161
. . . . . . . . GISAID Isolate EPI_ISL_149346
. . . . . . . . 15 Polymorphisms (5 Amino and 10 Silent)
. . . . . . . . 13I [Emergent H7N9 wild type
. . . . . . . . . . . . . . First Base Donor ACc, ACT, Atg],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [H6N1],
. . . . . . . . syn20A (GCc),
. . . . . . . . 74V,
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn127L (cTG),
. . . . . . . . syn140L (tTA),
. . . . . . . . syn183A (GCc),
. . . . . . . . syn192T (ACc),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn370G (GGg),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K [Emergent H7N9 wild type],
. . . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . . [H9N2],
. . . . . . . . syn433E (GAa))

. . . . BurkinaFaso859_C1_2013_02_18 (
. . . . . . . . A/Burkina Faso/859/2013
. . . . . . . . H7N9 Correlation HA 131T
. . . . . . . . H7N9 Correlation NA 386K
. . . . . . . . Off-Clade
. . . . . . . . GISAID NA EPI477427
. . . . . . . . GISAID Isolate EPI_ISL_148736
. . . . . . . . 15 Polymorphisms (5 Amino and 10 Silent)
. . . . . . . . 13I [Emergent H7N9 wild type
. . . . . . . . . . . . . . First Base Donor ACc, ACT, Atg],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . [H5N1],
. . . . . . . . . . . [H6N1],
. . . . . . . . syn20A (GCc),
. . . . . . . . syn47E (GAg),
. . . . . . . . 74V,
. . . . . . . . syn89S (TCt),
. . . . . . . . 106V,
. . . . . . . . syn127L (cTG),
. . . . . . . . syn183A (GCc),
. . . . . . . . syn192T (ACc),
. . . . . . . . syn304V (GTt),
. . . . . . . . syn370G (GGg),
. . . . . . . . syn382G (GGa),
. . . . . . . . 385T,
. . . . . . . . 386K [Emergent H7N9 wild type],
. . . . . . . . . . . . [pH1N1 Upsilon],
. . . . . . . . . . . . [H9N2],
. . . . . . . . syn433E (GAa))

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pH1N1 Influenza Hemagglutinin & Neuraminidase Segments elucidated at 2013-11-20-01_51_10_493570 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

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