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LaPorte H3N2v Swine Match 2011 West Virginia Sub-Clade
Recombinomics Commentary 12:00
September 5, 2012

The USDA has released the first swine H3N2v sequences (HA, NA, MP) from July isolates in Indiana, A/swine/Indiana/A00968380/2012, at Genbank.  The sequence was from a swine lung sample collected July 18, two days after the collection date for the four LaPorte cases, A/Indiana/06/2012, A/Indiana/07/2012, A/Indiana/08/2012, A/Indiana/09/2012, strongly suggesting the released sequences represent the 12 swine sequences described in the CDC MMWR on the LaPorte cases.

The NA gene, A/swine/Indiana/A00968380/2012, is the same H3N2 swine lineage found in the 2011 West Virginia day care center.  The NA and MP sequences are also from the same lineage, confirming the above sequence as the third swine match of novel sub-clade found in all 44 2012 human H3N2v sequences.  The two prior matches, A/swine/North Carolina/A01203272/2012 – collected February 13 and A/swine/Indiana/A01203509/2012 – collected May 9) were also from 2012 collections and were relatively rare (in 2012 13 of the 15 of the swine matches with human cases with H1N1pdm09 M gene were with the first 10 cases from 2011).  None of the 2012 human cases match this dominant swine sub-clade which match the 2011 human sequences.

Similarly, the above set of swine sequences are not identical to the LaPorte human sequences (all of the LaPorte human sequences exactly match each other), and do not have NA N234D, which is present in all LaPorte County, Indiana, and Butler County, Ohio human sequences.

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