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More Swine H3N2v Match Failures
Recombinomics Commentary 23:15
February 9, 2012

The USDA released series of swine sequences from 24 isolates (6 H1N1, 15 H1N2v, 3 H3N2v). 23/24 were from 2011, including two H3N2v isolates from samples collected November 15, 2011 (see list here).  The sequences included M gene sequences from 11 isolates, including the three H3N2v.  Four of the M genes were from H1N1pdm09, but all four were from H1N2v isolates.  Thus, none of the 24 isolates matched the twelve 2011 human H3N2 cases.  However, this series followed a release of H3n2v sequences last week which included three with an H1N1pdm09 gene and one, A/swine/Iowa/A01202640/2011, matched the human cases.

Two of the H1N2v isolates released today matched the H1N2 parental isolate from Ohio, A/swine/Ohio/FAH10-1/2010 ,which is the most common swine H1N2 sequence.  However, even though this constellation has an H1N2M gene and an N2 and PB1 which matches the human cases, no matching H1N2v human case has been identified.  The only H1N2v human case since the 2009 pandemic is an isolate with a swine M gene.  Similarly, the H3N2v sequence released last week increased the number of isolates with an H1N1pdm09 M gene, but that constellation, which also has H1N1pdm09 NP and NS genes also has not been identified in humans.

These swine sequences have been from isolates identified under enhanced surveillance, yet only two swine isolates (A/swine/NY/A01104005//2011 and A/swine/Iowa/A01202640/2011) matching the 12 human 2011 H3N2v cases have been identified, and both were from September isolates, which followed the initial human cases in July and August.

Thus, the latest series of sequences released last week and today suggests that no matching sequences will be found in samples collected prior to the initial human cases, and the number of 2011 isolates will be limited, adding further support for the transmission of H3N2v in humans.
Neither of the matching swine isolates have been linked to human cases, and the five most recent confirmed cases were from clusters in Iowa and West Virginia which had no swine exposure.  The West Virginia index case was linked to 23 contacts with influenza like illness, and the sequences from the one tested case matched the index case.

Although the CDC issued an alert, no additional cases have been identified.  The detection is dependent on cross reactivity with seasonal H3N2 or H1N1pdmo MP genes, and most of the prior cases tested negative, inconclusive, or as seasonal H3N2, so detection of additional cases after seasonal H3N2 and H1N1pdm09 levels increase is limited.

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