Brasil Shows 94% Avian Zoonotic Potential on Diverse Early Pandemic Sequences

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 Update
2011-10-18

On 2011-08-30, a group of researchers from Instituto Adolfo Lutz Sao Paulo in Brasil, including Santos,C.L.S.; Oliveira,M.I.; Borborema,S.E.T.; Ferreira,J.L.P. and Paiva,T.M., deposited a large group of early Pandemic H1N1 sequences at GenBank and GISAID.  For this analysis, 7 HA sequences were selected for review due to their high affinity for polymorphisms homologous to Avian sequences.

The set of HA polymorphisms spans the gene segment.  23 distinct values are demonstrated.  Of the 35 total HA polymorphisms found across the 7 selected sequences, 33 trace to Avian Influenza A serotypes (H1N1, H3N8, H5N1 & H9N2).  The remaining 2 changes (HA 225N) are from mixed traces that resulted in HA 225G & 225N.  These non-Avian, Receptor Binding Site 225N values are wild-type, Human H3N2 homologies.  This early, large scale acquisition (94%) of disparate Avian polymorphisms across multiple backgrounds is suggestive that the basic Pandemic H1N1 background is related to Avian progenitors or is highly attractant to Avian genetic data upon co-infection.

Co-infection is known to produce mixed peaks on sequencing traces.  The mixed trace sequences in this selection carry H5N1 homology.  100% of the polymorphisms on BrasilSaoPaulo64519_2009_08_18 are mixed, as are the early changes on BrasilMatoGrossoDoSul64045_2009_08_13.  Each sequence carries recognised fatality markers.  Evidence supports the probability of H5N1 influence on the human carriers of the mixed trace sequences or on a progenitor animal that subsequently transported the H5N1 genetic material into proximity with the human subjects from Brasil.

. . . . BrasilSaoPaulo2227_2010_01_13 (
. . . . . . . . GISAID HA EPI335469
. . . . . . . . 6 Polymorphisms (1 Amino and 5 Silent)
. . . . . . . . HA Truncated before aa92,
. . . . . . . . syn301I (ATt) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn338G (GGc) [H3N2 Avian, Canine, Feline],
. . . . . . . . . . . . . . . . . . [H3N8, H4, H5N1 Avian 2010, H6, sw],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn346G],
. . . . . . . . syn346G (GGa) [H3N2 Human & Avian wt],
. . . . . . . . . . . . . . . . . . [H3N8],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Preschool 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . . . . . . . . . . . [H6N2, H6N4],
. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . [H1N1 Avian Farm with syn338G],
. . . . . . . . . . . . . . . . . . [S8, 1918], [swBelgium1_1998],
. . . . . . . . syn366A (GCt) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 377K [H9N2 Avian and Human],
. . . . . . . . syn548C (TGc) [H1N1 Avian wt])

. . . . BrasilSaoPaulo91656_2009_10_23 (
. . . . . . . . GISAID HA EPI335471
. . . . . . . . 4 Polymorphisms (0 Amino and 4 Silent)
. . . . . . . . syn354Y (TAc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn486T (ACc) [H3N8 Avian])

. . . . BrasilSaoPaulo89876_2009_10_19 (
. . . . . . . . GISAID HA EPI335473
. . . . . . . . 5 Polymorphisms (0 Amino and 5 Silent)
. . . . . . . . syn68P (CCg) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn202V (GTc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn446K (AAa) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilSaoPaulo83218_2009_09_27 (
. . . . . . . . GISAID HA EPI335474
. . . . . . . . 6 Polymorphisms (0 Amino and 6 Silent)
. . . . . . . . syn41N (AAt) [H5N1 Egypt Human 2007],
. . . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2008],
. . . . . . . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn140P (CCc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn356H (CAc) [H5N1 Human Egypt 2009],
. . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . with #1V, 87N, syn94Y, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . . . . . . . . . . . [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn375I (ATc) [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn461K (AAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilSaoPaulo64519_2009_08_18 (
. . . . . . . . GISAID HA EPI335504
. . . . . . . . GenBank HA HQ595254
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 34D mix wt [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . syn53L (TTa) mix wt [H5N1 Human, Avian, Civet],
. . . . . . . . . . . . . . . . . . . . . . [H6N1 Avian],
. . . . . . . . . . . . . . . . . . . . . . [H2 Avian]
. . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms],
. . . . . . . . 225G mix wt [pH1N1 Fatality Marker],
. . . . . . . . . . . . . . . . . [H5N1 Avian wt],
. . . . . . . . . . . . . . . . . [1918],
. . . . . . . . 225N mix wt [pH1N1 Fatality Marker],
. . . . . . . . syn413K (AAg) mix wt [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) mix wt [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 523A mix wt [H1N1 Avian Farm
. . . . . . . . . . . . . . . . . . . . with extensive pH1N1_υ polymorphisms])

. . . . BrasilMatoGrossoDoSul64045_2009_08_13 (
. . . . . . . . GISAID HA EPI335505
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 34D mix wt [H5N1 Egypt Human 2009-2010],
. . . . . . . . . . . . . . . . [H5N1 Egypt Human Gharbiyah, 80% CFR],
. . . . . . . . . . . . . . . . [H5N1 Egypt Equine 2009],
. . . . . . . . . . . . . . . . [H5N1 Egypt Avian 2007-2010],
. . . . . . . . 225G mix wt [pH1N1 Fatality Marker],
. . . . . . . . . . . . . . . . . [H5N1 Avian wt],
. . . . . . . . . . . . . . . . . [1918],
. . . . . . . . 225N mix wt [pH1N1 Fatality Marker],
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . [H1N1 Avian])

. . . . BrasilSaoPaulo52142_2009_07_30 (
. . . . . . . . GISAID HA EPI335518
. . . . . . . . 2 Polymorphisms (0 Amino and 2 Silent)
. . . . . . . . syn413K (AAg) [H1N1 Avian, H2, H5N1, H9N2],
. . . . . . . . syn419L (CTa) [H5N1 Human, Equine, Avian],
. . . . . . . . . . . . . . . . . . [H1N1 Avian])

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