Sweden Signals Rapid Zoonosis from Avian H1N1 on Emergent Tertiary SubClade

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 spreadsheet for completeness in citation.

Last Updated
2011-06-09

On 2011-06-07, the Swedish Institute for Infectious Disease Control published one pH1N1 sequence at GISAID sampled in February 2011.  Six of the HA revisions are commonly found on sequences from the historical Avian H1N1 reservoir with the HA syn221P being conserved in the Avian species across both major circulating human Influenza A serotypes, H1N1 and H3N2.  This heavily avian background appears to be transmitting well in humans with cases in Switzerland, France and Estonia that continue the avian influence pattern.

A very practical implication is that many of these Avian sequences bearing the noted individual polymorphisms from this Swedish 208K_219V pH1N1 SubClade 5 sequence also carry polymorphisms that have been demonstrated on another pH1N1 subclade, the HA 189T-bearing Upsilon with a 5.8% Case Fatality Rate.  When several of the circulating human subclades are filling with Avian polymorphisms that are multiply co-located on single Avian reservoir sequences, expectations of zoonoses onto pH1N1 are heightened while the currently documented polymorphism-jumping between these very attractant pH1N1 dominant subclades is ensured.

Viable permutations rise.

“Everything that rises must converge.”

. . . . SwedenLinkoping8_20F_2011_02_17 (
. . . . . . . . GISAID HA EPI319566
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . syn47L (CTg) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 100N [H1N1 Avian
. . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn102E (GAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn170N (AAc) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 208K [H1N1 Avian
. . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt) [H3N2 Avian
. . . . . . . . . . . . . . . . . . . . . . with 157S, 159S, syn287G],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 252L,
. . . . . . . . syn319T (ACg),
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . SwedenLinkoping8_20F _2011_02_17 (
. . . . . . . . GISAID NA EPI319567
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . syn60T (ACc),
. . . . . . . . 81A,
. . . . . . . . syn138A (GCt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

Supporting Sequences

. . . . Estonia55306_3F_2011_03_03 (
. . . . . . . . GISAID HA EPI319465
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . syn254P (CCa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn319T (ACg),
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . Estonia55306_3F_2011_03_03 (
. . . . . . . . GISAID NA EPI319466
. . . . . . . . 6 Polymorphisms (2 Amino and 4 Silent)
. . . . . . . . syn119E (GAg),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . Estonia54375_51F_2011_02_11 (
. . . . . . . . GISAID HA EPI319459
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . syn319T (ACg),
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . Estonia54375_51F_2011_02_11 (
. . . . . . . . GISAID NA EPI319460
. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)
. . . . . . . . syn60T (ACc),
. . . . . . . . syn67V (GTc),
. . . . . . . . 81A,
. . . . . . . . syn138A (GCt),
. . . . . . . . syn221N (AAt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . Estonia54132_18F_2011_02_08 (
. . . . . . . . GISAID HA EPI319457
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . syn319T (ACg),
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . Estonia54132_18F_2011_02_08 (
. . . . . . . . GISAID NA EPI319458
. . . . . . . . 8 Polymorphisms (3 Amino and 5 Silent)
. . . . . . . . syn24L (TTg),
. . . . . . . . 81A,
. . . . . . . . syn138A (GCt),
. . . . . . . . syn216I (ATt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . SwitzerlandGeneva4201955_xF_2011_01_06 (
. . . . . . . . GISAID HA EPI309651
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . 157N mix wt,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . SwitzerlandGeneva4201955_xF_2011_01_06 (
. . . . . . . . GISAID NA EPI309652
. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)
. . . . . . . . 81A,
. . . . . . . . syn138A (GCt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . syn271A (GCt),
. . . . . . . . syn298G (GGa),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn449N (AAt))

. . . . FranceLyon3_58x_2010_12_31 (
. . . . . . . . GISAID HA EPI319497
. . . . . . . . 11 Polymorphisms (5 Amino and 6 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa),
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . syn221P (CCt),
. . . . . . . . 252L,
. . . . . . . . syn319T (ACg),
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . FranceLyon3_58x_2010_12_31 (
. . . . . . . . GISAID NA EPI319498
. . . . . . . . 9 Polymorphisms (3 Amino and 6 Silent)
. . . . . . . . syn60T (ACc),
. . . . . . . . 81A,
. . . . . . . . syn124C (TGt),
. . . . . . . . syn138A (GCt),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn382G (GGa))

. . . . Iowa04_2009_04_24 (
. . . . . . . . GISAID HA EPI179262
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . 206S,
. . . . . . . . syn221P (CCt),
. . . . . . . . syn498L (TTg))

. . . . Iowa04_2009_04_24 (
. . . . . . . . GISAID NA EPI186289
. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)
. . . . . . . . syn306F (TTt),
. . . . . . . . syn307N (AAt))

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