Poland303 19M similar to Sapporo1, NJ01, Almati01 and Changsha78

The National Influenza Center in Warsaw deposited two NA sequences today. The second deposit, A/Poland/303/2009, is exceptional. Poland303 from a 19 year old male sampled on 2009-07-10 varies significantly with the first deposit from a 71 year old female sampled in the same week.  Mixed peaks or dropouts may be involved in each sequence at multiple locations.

Further study is required due to several potential anomalies. However, the preliminary inspection shows that Poland303 is most similar to Sapporo1, NewJersey01, Almati01 and Changsha78. The nucleotide similarity is 99% (>1401 of 1407), but the few dissimilarities are curious.

Poland303 demonstrates 8 NA SNPs and is inconclusive at residues 79, 166 and 216 with additional distinguishable amino acid polymorphisms:

N2I
N200K
G201W
N209T
D392N

The KW at 200:201 appears to be unique within ΣPF11 during our initial enquiries.

Poland282 demonstrates 12 NA SNPs and is inconclusive at 79, 190, 195, 205, 220, 322 and 335 with the following distinguishable polymorphisms:

N2B
V177F
191L synonymous
T192Q
N221H

The variability between these two sequences and secondly among this group and the others in their geography may signal the presence of a genetic acquisition stimulator or, the more likely explanation, a lab contamination.

Outside of a multi-stage lab contamination (unlikely after reviewing the full set of Poland sequences), these two specimens follow a trend indicative of SNP recombinations with Avian H1N1 from Europe AND Swine H3N2 from Europe.  That capitalised word in the previous sentence is an "AND".  Until we find intermediate forms bearing Neuraminidase hybridisations of European swine H3N2, European avian H1N1 and PF11, the estimation presented here is my most logical explanation for a very unlikely set of sequences.

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Almaty, Kazakhstan - Unique Cross-Segment Quadruple Combination (QC1)

A sequence from Kazakhstan's largest city, the capital Almaty, was deposited at GenBank on 2009-08-18 by the Russian Vector lab using the nomenklatura's nomenclature of A/Almati/01/2009 with no collection date. Elevation and population density of the host geography raised our interest in this particular specimen and the signal was correlated upon inspection.

At the amino acid level, Almati01 matches the HA of NewJersey01 and Sapporo1, the NA of Amagasaki1, Amagasaki2 and Hyogo1.  Bear in mind that NewJersey01 is closely related to the Tamiflu-resistant HongKong2369 specimen.

Of a more compelling interest is the first deposited emergence of a particular Cross-Segment Quadruple Combination (QC1) that may prepare the virus for additional human-fitness acquisitions. This Almati01 sequence appears to be the singular ΣPF11 sequence on file that carries the quadruple set of amino acids:

     QC1 

• HA 206T
• HA 225E
• NA 106I
• NA 248N

The introduction appears to be NA 248N, but the collection date is absent on Almati01 so conclusions may not be drawn. Comparison data is sparse because the neuraminidase segment is unavailable or unpublished on many of the 13 candidate ΣPF11 dual HA combinations of 206T and 225E. Plainly stated, the database coverage to investigate this quadruple combination is far from broad. However, in this case, scarcity breeds clarity, sharpening a focus for future monitoring in anticipation of a more robust dataset. 

Movement within and around the Receptor Binding Domain (RBD) always draws focus on a new specimen.  The genetic acquisition path of ΣPF11, including this profiled specimen, suggests a non-random pattern of polymorphisms.

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