Overall, 73 H3N2 positive submissions were detected in FY2011 (October 1, 2010 to September 30, 2011) and 138 in FY2012 from October 1, 2011 to July 31, 2012. 57 Of the 138 H3N2 cases identified in FY2012 and tested to date contain the pandemic M gene and were classified as H3N2pM.
The above USDA update from the CDC website confirms that the bulk of the USDA data has already been made public at Genbank and the discordance between the human and swine sub-clades in circulation in FY2012 does not support swine to human transmission.
As seen in the above numbers, as well as larger collections described at the CDC site, most swine influenza is not H3N2 and most H3N2 does not have the H1N1pdm09 M gene. However, of greater significance is the number of isolates (57) with H1N1pdm09 M gene in recent collections (FY2012). In this collection period the CDC has released 45 sets of sequences with the H1N1pdm09 M gene (which is heavily weighted with H3N2pM isolates).
Thus, sequences from only 12 H3N2pM have not been made public, and these sequences are likely either non-matches or recent, and therefore of little significance in the analysis since the number of reported human cases exploded in July, and swine isolates from that time period may have been due to human to swine transmission.
Although there are 45 H3N2pM sequences collected in FY2012, only 19 of these sequences have HA and NA sequences that match the human cases from 2011/2012 and only 2 of the 19 match the 2012 human cases (see list below). Thus, the widespread H3N2v in swine cited by the CDC per USDA are largely matches with the human sub-clade from 2011 and none of the 2012 human cases match this sub-clade.
In contrast, the 20 most recent human sequences, which were all collected in FY2012, match the 2 cases with N2 from a swine H3N2 lineage. This discordance is even more dramatic for the most recent isolates from Indiana and Ohio. Since March 2012 there have been 9 swine isolates and 8 of the 9 match the sub-clade in last year’s human cases. Moreover 8 of these 9 collections were from Indiana or Ohio.
Thus, of the 8 most recent isolates from Indiana and Ohio, only one matches the human 2012 cases, while the seven that match the 2011 cases, but have not produced any reported human cases in 2012.
Therefore, the CDC claim of USDA support for swine to human transmission is refuted by the public data, which represents the key data generated by the USDA.
The only real support for the CDC position is their heavily biased sample collection which creates a link with swine because testing is largely limited to samples collected from patients with swine exposure.