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CDC Updates Comments On H3N2pdm11 In Swine
Recombinomics Commentary 19:45
December 13, 2011

Prior to the three cases in Iowa, most human infections with this virus were associated with exposure to swine. In Iowa, however, no swine exposure has been identified. At this time, it appears that unsustained human-to-human transmission may have occurred. These viruses have been reported in swine in several states in the United States.

While the prevalence of the novel influenza A H3N2 virus with the 2009 H1N1 M gene in swine is unknown, the virus has been detected in U.S. swine through the United States Department of Agriculture’s swine influenza surveillance program.
The above comments (in blue) are from the November 23 “Have You Heard?” on the Iowa cluster, which claimed that the H3N2pdm11 found in the cluster, as well as the prior 7 cases in 2011 was reported in swine in several states.  However, there has only been one reported case,
A/swine/NY/A01104005/2011, which was identified through the USDA influenza surveillance program, although a media report quoted Nancy Cox as indicting the sub-clade was in pigs in the US Midwest. This isolate(s) has not been made public, suggesting that like the New York isolate, it was from a sample collected after the spread of the virus in humans as indicated by the cases in Indiana (A/Indiana/08/2011) and Pennsylvania (A/Pennsylvania/09/2011, A/Pennsylvania/10/2011, A/Pennsylvania/11/2011).

The second quote (in red) is from the December 9 “Have You Heard?”, which simply cites detection through the USDA, which would be the one public sequence.  Thus, the CDC is modifying its former position to reflect the failure to detect the sub-clade prior to spread in humans.
The two statements are from updates covering the five most recent confirmed cases, which have no swine exposure.  This lack of swine exposure is also consistent with the lack of widespread detection of the H3N2pdm11 in swine.  The USDA surveillance program readily found swine that matched the H1N2 parent for the human sequences.  A full sequence for an Ohio isolate, A/
swine/Ohio/FAH10-1/2010 contained all three genes (PB1, NA, MP) acquired by H3N2pdm11.  This 2010 isolate was sequences by Ohio State, but the USDA released matching HA, NA. MP sequences from swine collections from 2010 and 2011.

Thus, the absence of H3N2pdm11 in swine collections prior to the spread in humans, strongly suggests  that the “swine exposure” for the first seven cases led to PCR testing and sequencing, which identified the novel virus, which was spreading in humans, not swine.

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