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Commentary
Curious CIDRAP
Comments On Swine
H3N2pdm11 Matches NOT
Recombinomics Commentary 21:30
November 30, 2011
The significance of the above comment from a CIDRAP update is clear.
A re-analysis of the 30 trH3N2 sequences listed in the Oct 26 analysis identified two 2010 isolates that were inadvertantly absent from the retest, and these two isolates, A/swine/Iowa/A01049035/2010 and A/swine/Iowa/A01049034/2010, increased the number of public H3N2 sequences at Genbank with H1N1pdm09 M gene to eight.
Recombinomics apologizes for the confusion created by the prior commentary.
The two 2010 sequences were virtually identical to each other, and the HA and NA genes did not match the human H3N2pdm11 sequences. Recently, sequences for the other five genes were released and all were H3N2 swine related but only the NP matched H3N2pdm11. Thus, the two isolates had a constellation of seven trH3N2 genes with H1N1 pdm09, but only one of the seven was the same lineage as H3N2pdm09.
An Oct 4 analysis identified five trH3N2 isolates with the H1N1pdm09 M gene, (A/swine/Texas/A01049555/2011, A/swine/Texas/A01049556/2011, A/swine/Iowa/A01049750/2011, A/swine/Texas/A01049914/2011, A/swine/Texas/A01049915/2011) but all five sets of sequences (HA, NA, MP) were virtually identical to each other, but neither the HA nor the NA sequences were closely related to the human H3N2pdm11 sequences.
Last week a single set of sequences from New York, A/swine/NY/A01104005/2011, was released. The release was unusual because it was not part of a larger release, and sequences from all eight gene segments were included. That sequence had the H1N1pdm09 M gene, and all seven of the other genes matched the 10 human H3N2pdm11 sequences.
Thus, the public portion of Genbank has 31 sets of swine trH3N2 sequences from samples collected since October 24, 2010, and one of those sequences matches the 10 human H3N2pdm11 sequences.
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