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More 2012 Swine H3N2pM Matches With 2011 Human Cases
Recombinomics Commentary 16:00
September 12, 2012

Overall, 73 H3N2 positive submissions were detected in FY2011 (October 1, 2010 to September 30, 2011) and 138 in FY2012 from October 1, 2011 to July 31, 2012. 57 Of the 138 H3N2 cases identified in FY2012 and tested to date contain the pandemic M gene and were classified as H3N2pM.

The above summary of the H3N2v swine cases identified by the USDA is listed on the USDA and CDC websites.  The summaries note that in the current fiscal year (beginning on October 1), the surveillance program identified 138 H3N2v swine cases, and a small subset (57) had the H1N1pdm09 M gene (and such isolates are now designated as H3N2pM).  An earlier analysis noted that the USDA had deposited 67 sets of swine sequences which included HA, NA, and MP from samples collected during FY2012 and 45 sets were designated as H3N2pM.  Only 19 of these 45 sequences matched the 2011 and 2012 human cases and only two of those matches were the same sub-clade as the 2012 human cases.

In addition to the sequences which included HA, NA and MP, a series of 13 sets of sequences consisted of the 5 remaining genes (PB2, PB1, PA, NP, NS), but did not include HA, NA, or MP.  Those isolates are listed below and match other H3N2pM isolates.  Five of sequences also match the human cases, as well as swine isolates with a full set of sequences, and the five matches also match the 2011 human cases.  These additional matches are from Illinois and Iowa with collection dates between February 8 and March 1 and are closely related to two sets of Illinois swine identified earlier.

Thus, these 5 new matches increase the number of human matches to 24 out of the 57 H3N2pM isolates from FY2012, and keep the number matching the 2012 human cases at 2.

These updated numbers do not match CDC statements that matches of the 2012 H3N2v sequences are widespread.  22 out of 24 of the matches in FY2012 match the 2011 human cases, and these swine sequences have not produce a reported human case since the fall of 2011.

Moreover, the USDA recently released one of the 12 LaPorte swine sequences,
A/swine/Indiana/A00968380/2012, and although it increased the number of swine matches of the 2012 human cases to three, the swine sequence was easily distinguished from the human LaPorte sequences.

Matches with 2011 human H3N2v cases
A/swine/Illinois/A01241469/2012       02-08
A/swine/Iowa/A01241840/2012          02-27
A/swine/Illinois/A01241842/2012       02-27
A/swine/Illinois/A01241871/2012       02-29
A/swine/Illinois/A01241916/2012       03-01

Likely H3N2pM swine isolates which do not match human cases
A/swine/Illinois/A01240575/2011       12-20
A/swine/Illinois/A01240578/2011       12-20
A/swine/Nebraska/A01240867/2011 12-22
A/swine/Illinois/A01240774/2011        12-28 
A/swine/Illinois/A01240784/2011        12-28
A/swine/Nebraska/A01241114/2012  01-10
A/swine/Missouri/A01241610/2012     02-14
A/swine/Missouri/A01241619/2012     02-14

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