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Curious CIDRAP Comments On Swine H3N2pdm11 Matches
Recombinomics Commentary 19:00
November 30, 2011

An informal analysis by the USDA's Agricultural Research Service has found that 8 of about 30 swine H3N2 viruses in the GenBank database have the pandemic H1N1 matrix gene so far, said the USDA official, who requested anonymity. "More detailed analyses of these and other samples continue," the official added.

The significance of the above comment from a CIDRAP update is unclear. 

All eight isolates with H1N1pdm09 M gene identified.  Details here.

Most sequences “in the Genbank database” are public and can be accessed by anyone with internet access.  The public sequences have been analyzed and report weeks or months ago.

As noted in the Sept 2 MMWR early release describing the first two H3N2pdm11 cases, none of the sequences at Genbank matched the novel constellation of genes in H3N2pdm11, which had 7 gene segments from trH3N2, as well as an M gene from H1N1pdm09.

Several sets of swine sequences have been deposited since that released, and those sequences have been analyzed with a few days of release.  On Oct 1, 2010 one such series of sequences was released, and the sequences could be accessed a few days later.  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.

The five sequences were listed and each was linked to its HA sequence.  The CDC has been depositing the 2011 H3N2pdm11 sequences at GISAID and Genbank, so the lack of a match could be confirmed in less than a minute using three mouse clicks.

That analysis was followed by an Oct 26 analysis, which listed the 30 trH3N2 swine sequences from US collections from samples collected in the prior 12 months.  19 of the sequences were collected in the final 3 months of 2010, and 11 more were from 2011.  Five of the thirty sets of sequences had H1N1pdm09, and they were the same five sequences listed above.

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.

Since the CIDRAP report cites 8 sequences with the H1N1pdm09 M gene, the 2 additional sequences may represent deposits that have not been released.  As was seen by the five swine sequences described above, there can be a 3-4 week lag between deposit and released, based on release instructions accompanying the deposits.

In the November 22 “Have You Heard?", the CDC cited reported matches in swine from several states, which was repeated by CIDRAP, which was incorrect because the sequence from New York was the only reported match.  However, the CDC comments on several states was followed by a Nancy Cox quote in a Helen Branswell piece claiming matches in pigs in the US Midwest, which may be related to the comment on several states, since New York is not in the Midwest and would be distinct from the cited unpublished sequences.

Thus, a clarification by CIDRAP on the definition of “in Genbank” would be useful.  If that is in reference to sequences that are released, the eight mention above is likely to be in error, since there are only 6 trH3N2 swine isolates with the H1N1pdm09 M gene. 

If the additional two examples refer to sequences deposited but not released, a released date would be useful.

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