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Ohio H3N2v Swine With PB1 E618D and H1N1pdm09 M Gene
Recombinomics Commentary 19:45
October 1, 2012

The USDA has released addition recent H3N2v swine sequences.  Included were sequences for the internal genes (PB2, PB1, PA, NP, NS) for 3 June, 2012 isolates from Ohio.  Earlier sequences for the other three genes (HA, NA, MP) were released ((A/swine/Ohio/1/2012,  A/swine/Ohio/6/2012 ,  A/swine/Ohio/7/2012) and the sequences matched the initial 10 human cases in 2011.  The H3N2v was created though reassortment which had 5 genes from the 2010 human cases (PB2, PA, HA, NP, NS), as represented by A/Wisconsin/12/2010 and A/Pennsylvania/40/2010, and 3 genes (PB1, NA, MP) from swine H1N2 isolates which had an H1N1pdm09 M gene.  The new PB1 did not have E618D, which is in all H1N1pdm09 isolates and was also in the first US H3N2v case, A/Kansas/13/2009, as well as all six 2010 human cases.

The release of the sequences from the three Ohio swine (A/swine/Ohio/1/2012, A/swine/Ohio/6/2012, A/swine/Ohio/7/2012), identified a PB1 sequence in all three isolates which was closely related to the sequences from the human 2010 case and had E618D.  All human variant sequences since 2010 have had a PB1 with E618D or an H1N1pdm09 M gene, but none had both changes (which are present in all human and swine H1N1pdm09 isolates).

Therefore, the presence of both changes in the June Ohio swine raises concerns that this combination will increase the potential for human adaptation and transmission.  However, these isolates, like the first 10 human cases in 2011, have an NA lineage found in H1N2v swine, but all 2012 human cases (58 public sets of sequences) have had an N2 lineage found in H3N2v swine and first seen in human cases in the sequences from the 2011 West Virginia day care outbreak in Mineral county (
A/West Virginia/06/2011 and A/West Virginia/07/2011).

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