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Kansas Swine trH3N2 With H1N1pdm09 M Gene
Recombinomics Commentary 14:00
December 01, 2011

An informal analysis by the USDA's Agricultural Research Service has found that 8 of about 30 swine H3N2 viruses in the GenBank database have the pandemic H1N1 matrix gene so far, said the USDA official, who requested anonymity. "More detailed analyses of these and other samples continue," the official added.
The above comments from a CIDRAP update describe the eight sets of public Genbank sequences with the H1N1pdm09 M gene.  However, only one of those swine isolates match the 10 human cases, H3N2pdm11,

Today, the College of Veterinary Medicine at Kansas State University released seven sets of swine trH3N2 sequences (collected between Dec 30, 2010 and April 08, 2011) from Kansas (as well as swine H1N1 and H1N2 sequences from Illinois).  All seven isolates had the H1N1pdm11 M gene (see list below).  However, none of the HA genes matched H3N2pdm11 HA sequences found in all ten 2011 trH3N2 cases, as well as the swine from New York.

Six of the HA sequences are closely related to the Texas and Iowa swine H3N2 isolates with the H1N1pdm09 M gene. 

Full sets of genes from the Kansas series are still being analyzed.  However, one, A/swine/Kansas/11-109700/2011, has been analyzed and it matches the HA, NA, and MP of the Texas and Iowa isolates.  Analysis of the remaining five genes indicates NP and NS gene segments also match H1N1pdm09.  Constellations with multiple H1N1pdm09 genes, including M have been reported previously for swine H1N2 and H3N2 isolates.

Thus, the number of public swine sequences with H1N1pdm09 has now increased to 15, but the only swine isolate with H3N2pdm11 is the recently released New York sequence.

HA related to TX and IA Swine trH3N2 with H1N1pdm09 M gene


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