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H3N2v Match In Iowa Swine
Recombinomics Commentary 16:45
January 31, 2012

The USDA has released another series of swine H3N2 sequences, which included an M gene sequence from 13 isolates (largely from 2010 and 2011).  Three of the 2011 isolates had a H1N1pdm09 M gene (A/swine/Illinois/A01201606/2011, A/swine/Iowa/A01202640/2011, A/swine/Iowa/A01202659/2011).  The sequences from Illinois had H3 and N2 sequences which were not closely related to the 2011 human H3N2v sequences and four additional gene segments (PB1, PA, NP, NS) also were from H1N1 pdm09.

CORRECTION: The third sequences with H1N1pdm09 M gene is A/swine/Iowa/A01202709/2011.  It does not have a matching HA or NA, and has three additional gene segments from H1N1pdm09 (PB2, PA, NP) so it is not a match.  The other swine isolate above,
A/swine/Iowa/A01202659/2011, has a swine M gene, so it only matches in 6 of 8 genes.  The discussion below has been edited to reflect this.

The isolate from Iowa, A/swine/Iowa/A01202640/2011, had the same constellation as the human H3N2v cases in 2011 (an H1N1pdm09 M gene with 7 gene segments from H3N2 or H1N2 swine isolates). This isolate (collected on Sep 30), A/swine/Iowa/A01202640/2011, is closely related to the new H3N2v vaccine target, A/Indiana/10/2011, in all eight gene segments. 

The second isolate (collected Oct 6), A/swine/Iowa/A01202659/2011, also was closely related to the vaccine target in 6 of the 8 gene segments.  However, the NS gene segment matched a lineage found in other H3N2 swine, and is most closely related to a human H1N1v isolate, A/Iowa/02/2009 and the M gene is swine.

Thus, there have been two different constellations of H3N2v which have an H1N1pdm09 M gene and 7 gene segments from H3N2 or H1N2 swine.  The most common constellation is a reassortant with five gene segments from 2010 human trH3N2 isolates (PB2, PA, HA, NP, NS) and three gene segments from H1N2 sequences similar to A/swine/Ohio/FAH10-1/2010 (PB1, NA, MP).  This constellation has now also been found in two swine isolates, A/swine/NY/A01104005//2011 and A/swine/Iowa/A01202640/2011, which were both collected in September, after the human cases in Indiana and Pennsylvania.  Another constellation exchanges  NA with an NA usually found in trH3N2 swine.  This constellation was found in the West Virginia cluster, and has not been reported in swine.

The latest sequences identify three more isolates with H1N1 pdm09 gene segments, and like all prior isolates, the H1N1pdm09 gene segments include the M gene.  The Iowa swine isolate was from a lung sample, suggesting the infection in swine was severe or fatal, and the collection date raises the strong possibility that the swine case was due to a jump to swine from humans, and the USDA surveillance will not find widespread matches in samples collected prior to the human cases from July and August.

The two different constellations in isolates with H1N1pdm09 M and 7 swine gene segments highlights the genetic instability associated with the H1N1pdm09 M gene in triple reassortants in the United States, and strongly suggest that the earlier cases with “swine exposure” were not infected by H3N2v from the swine identified in the exposure designation. 

Instead, these cases were identified because of increased testing of cases with a swine exposure in the off season.

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