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Iowa Swine trH3N2 Constellation Matches H3N2pdm11
Recombinomics Commentary 19:00
December 01, 2011

The recently released trH3N2 sequences from Kansas increased the number of public trH3N2 sequences with an H1N1pdm09 M gene to 15.  All seven NA sequence matched the NA sequences in 5 of the 7 prior trH3N2 isolates with H1N1pdm09 M gene, which was also true for six of the HA sequences (A/swine/Kansas/10-91088/2010, A/swine/Kansas/11-101926/2011, A/swine/Kansas/11-104465/2011, A/swine/Kansas/11-104467/2011, A/swine/Kansas/11-109700/2011
A/swine/Kansas/11-110529/2011).  Only A/swine/Kansas/11-107824/2011 failed to match the 5 earlier sequences from Texas and Iowa (A/swine/Texas/A01049555/2011, A/swine/Texas/A01049556/2011, A/swine/Iowa/A01049750/2011, A/swine/Texas/A01049914/2011, A/swine/Texas/A01049915/2011).  This isolate also had H1N1pdm09 PB2 and PA genes.  Moreover, all seven of the isolates from Kansas had H1N1 NP and NS genes in addition to MP.  Thus, the Kansas sequences had 3-5 H1N1pdm09 genes, suggesting that the five isolates from Texas and Iowa had similar frequencies of H1N1pdm09 genes.

In addition to the Kansas trH3N2 sequences from Kansas State University, the USDA released the missing genes (PB2, PB1, PA, NP, NS) from the two 2010 Iowa trH3N2 isolates, A/swine/Iowa/A01049035/2010 and A/swine/Iowa/A01049034/2010, and all five gene segments were of trH3N2 swine origin. Thus, the two Iowa isolates have the same constellation of genes as H3N2pdm11, which is in all 10 of the human cases as well as the swine isolate from New York, A/swine/NY/A01104005/2011. 

The Iowa sequences are easily distinguished from H3N2pdm11 because only the NP gene segment matches.  These data indicate that the constellation H3N2pdm11 alone does not generate a high frequency of human cases because all H3N2pdm11 isolates not only share the same constellation, but the lineage of all 8 gene segments match.

Thus, the latest series of newly released sequences highlight the low frequency of H3N2pdm11 in swine, which remains limited to New York isolate identified from a Sept 13 collection. The failure to find any matches in swine isolates prior to the first human cases continues to support H3N2pdm11 sustained spread in humans, leading to matches in 10 of 10 human cases and only one match in a collection after the spread in humans.

The November 22 “Have You Heard?" cites matches in “multiple states” and Nancy Cox is reported to have said there was a match in pigs in the “US Midwest”, which may represent as little as one unreported outbreak, which would represent “multiple states” since the New York match was not in the Midwest.  This match has not been reported, but the number of cases appears to be limited and increasingly likely to have happened after H3N2pdm11 accelerated spread in people. 

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