Japan Demonstrates 2011 pH1N1 Multi-Segment Hypermorphism
On 2011-10-19, the Japanese Influenza Collaborative Study Group based at Niigata University released a group of human pH1N1 sequences at GenBank and GISAID including 46 HA fragments and 46 full NA segments. The sample dates span 2011-01-04 to 2011-03-08. Seven geographic areas of Japan are covered with no specification of subject age, subject gender, treatment protocol, clinical progression or clinical outcome notated. Clade2: 188T is represented on 44 sequences crossing all geographic divisions and Clade3: 186P is found once each in Niigata and Osaka.
HA 320 Polymorphisms Averaging ~7.0 per Segment Fragment
NA 352 Polymorphisms Averaging ~7.6 per Segment
HA and NA 672 Total Polymorphisms Averaging ~14.6 per Sequence (HA Fragments)
The HA superset producing 77 distinct values includes 4 polymorphisms (syn31H, syn42G, 189T, syn287G) that appear on the High CFR Clade1.Upsilon revision set. Polymorphic sets shared across pH1N1 clades suggest cross-clade compatibility. H5N1 involvement is notated on JapanOsaka10K362_2011_02_15. JapanNiigata10F202_2011_01_31 represents hypermorphic behaviour with 10 revisions on an HA fragment. Notably absent are Receptor Binding Site changes at aa225.
Several of the NA segments are hypermorphic including JapanNiigata10F306_2011_02_05 and JapanHyogo10K283_2011_02_04. Two TamiFlu Resistant sequences (NA 275Y) each feature on Clade2: 188T backgrounds having significant HA and NA homology with Avian H1N1.
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