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Additional Swine H3N2v Match Failures
Recombinomics Commentary 17:00
March 20, 2012

The latest update of Genbank sequences includes 10 sets of US H3N2v swine sequences, including 6 which have an H1N1pdm09 M gene (A/swine/Minnesota/239105/2009,  A/swine/Iowa/A01049036/2010, A/swine/Missouri/A01047968/2010, A/swine/Missouri/A01047969/2010, A/swine/Minnesota/A01047396/2011, A/swine/NE/A01101010/2011).  However, none of the 10 sets have an H3 gene that matches the H3 lineage found in all 12 human H3N2v cases from 2011. 

Thus, in spite of enhanced surveillance by the USDA since the 2009 pandemic and the detection of H1N1pdm09 M genes in H3N2v isolates from 2009, 2010, and 2011, only two matches of the human lineage have been identified and both isolates (
A/swine/NY/A01104005//2011 and A/swine/Iowa/A01202640/2011) were from collections made in September, after the human cases in July and August from Indiana and Pennsylvania.

Although the first 7 cases in 2011 were identified via a CDC program that targets cases with swine exposure, none of the 7 cases have been linked to H3N2v identied in epidemiologically linked swine, and only one case was linked to symptomatic swine, which tested negative for influenza.

The two swine matched were from samples collected through an FDA anonymous testing program and both isolates were from lung samples, signaling severe or fatal swine infections.  The only confirmed examples of H3N2v in contacts of index cases have been other humans.  In Iowa neither the index case nor the two confirmed contacts had a history of recent swine exposure, which was also true for two symptomatic family members, who were not tested.  The same absence of swine exposure was reported for the West Virginia cluster, where H3N2v was confirmed in a daycare center classmate, and 23 contacts had influenza like illness but were not tested.  In the Iowa and West Virginia clusters the sequences from the H3N2v positive contacts matched the sequences of the index case.

In contrast, the recently released swine sequence from Nebraska matches swine sequences from Kansas, Iowa, and Texas.  Although this lineage is the largest series of confirmed H3N2v swine sequences with an H1N1pdm11 M gene, no corresponding sequence has been found in humans.  Instead the human cases in 2011 evolved from the most dominant 2010 human H3N2v sequences for five genes (PB2, PA, HA, NP, NS) while the other three genes in the first 10 human cases was from sequences found in an Ohio H1N2 isolate (
A/swine/Ohio/FAH10-1/2010), and the two most recent sequences (from West Virginia) have the same genes except the N2 is from H3N2v circulating in swine.

Thus, the epidemiological and sequence data supports human transmission of H3N2v in 2011 and the two matches from September collections are due to this constellation jumping from humans to swine.

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