Antigenic Diversity Increases with 7 Novel H1 SNPs from Chengdu and Jiangyin

On 2009-10-06 China deposited 22 Hemagglutinin sequences and 23 matching partial Neuraminidase sequences from the areas of Chengdu and Jiangyin sampled respectively on 2009-07-26 and 2009-08-16. The two sets of sequences are from patients that were students at boarding schools during an outbreak.  The Neuraminidase segments are far too limited in data for evaluation. The HA segments are remarkable due to the fact that 100% of the distinguishable SNPs are, on first inspection, novel introductions to ΣPF11.  These wild type changes directly upstream and downstream of the Receptor Binding Domain may increase the velocity of vaccine escape.

HA Amino Acid Codings to 7 Novel Polymorphisms and 1 Mixed Signal

•   76T
• 131P
• 191R
• 238K
• 259V
• 264X
• 286N
• 502K

All 22 HA sequences carry 206T.  As we have discussed previously, the polymorphism from the mixed signal coding for residue 264 will likely match one of the variations in Seasonal H1N1 2006, 2007, 2008 and 2009, in 1918, in WSN33 or the two appearances on the PF11 background, CatS1161 and NY3012.  That domain is among the most active since late May.

76T
Novel to ΣPF11.
All Jiangyin (10 sequences).
Progenitors may include:
Korea swine 2006 H1N2 (2 Entries)
Iowa human swine worker 2005 H1N1 (IA/CEID23/2005)

131P
Novel to ΣPF11.
All Chengdu (12 sequences).
Progenitor unknown.

191R
Novel to ΣPF11.
Chengdu18
Progenitor unknown.
Further inspection required:
Quail/Nanchang/12-340/2000 H1N1
Beijing/262/95 H1N1 (FluMist Vaccine Virus)

With the 3 residue deletion producing E130del (similar to S129del in several human H5N1 sub-clade 2.2.1.2), a conformational proximity may exist at 192R for alignment and / or transposition onto Chengdu18 residue 191.  These two donor candidates also carry M230I, though the Chinese Quail is the only Avian H1N1 sequence on file with this human-fit RBD change.  Chengdu is approximately 1,100 miles west of Lake Poyang (Nanchang) with a series of inland lakes and rivers on the flightpath.


238K
Novel to ΣPF11.
Chengdu04
Progenitors may include:
Seasonal 2008 H1N1 (1 Entry)
Seasonal 2005 H1N1 (2 Entries)
Guangdong swine 2009 H1N1
NC swine 2008 H1N1 (8 Entries)
PR8_34
LabVir_hvPR8_34
H5N1 Sub-clade 2.2

259V
Novel to ΣPF11.
Jiangyin01
Jiangyin15
Jiangyin16
Jiangyin17
Progenitors may include:
Seasonal 2006 H1N1 (South Carolina/2)

264X
Indistinguishable amino acid.
Jiangyin68

286N
Novel to ΣPF11.
Chengdu40
Progenitors may include:
Swine H1N1 2003-2007 (NC, Ohio, Kansas)

502K
Novel to ΣPF11.
Jiangyin34
Progenitors may include:
red-winged tinamou/Argentina/MP1/2008 H1N1
     with HA 225G, 277N, 286H, 298V / NA 106I, 248N, 286G
Seasonal 2009 H1N1
Seasonal 2007 H1N1
WSN33

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