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CDC Retraction of H3N2v / H3N2pM Pseudolinkage Overdue
Recombinomics Commentary 10:45
August 22, 2012

According Dr. Joseph Bresee, “We expect the number of H3N2v cases to rise since this virus has been found in pigs in a number of U.S. states per the USDA and there is so much interaction between people and pigs in fair settings at this time of year.”

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 CDC comments (in blue) were in the August 17 H3N2v update, which claims that “this virus has been found in a number of U.S. states per the USDA……”  However, the USDA update (in red) cites 57 H3N2pM cases in FY2012 which are representing by the 45 public H3N2pM cases.  The 12 unpublished are likely from the 12 swine at the LaPorte County fair which were cited in media reports and the CDC note that the H3N2pM matched the human cases.

The 12 examples of H3N2pM at the LaPorte County Fair in Indiana don’t address the growing list of H3N2v cases because the CDC has acknowledged the ability of H3N2v to transmit from humans to swine, and at least 5 attendees at the fair were H3n2v confirmed, and many more were symptomatic.

The 45 public H3N2pM sequences generated by the USDA have 19 matches with the human H3N2v cases in 2011 and 2012, but only two of these H3N2pM match the 2012 H3N2v cases.  The two cases were in North Carolina (
A/swine/North Carolina/A01203272/2012) and Indiana ( A/swine/Indiana/A01203509/2012 and the LaPorte swine were also in Indiana), so the CDC comment that “this virus” had been found “in a number of U.S. states per the USDA” is misleading at best, because a match of the US cases has only been found in 2 states, and the 17 matches with the 2011 H3N2v sub-clade that was found in 10 human cases has not been reported in any 2012 cases.

Thus, the USDA data does not support widespread transmission of H3N2v from swine to humans, and the CDC should issue a clarification and retraction of its claim that the USDA data supports swine to human transmission of the H3N2 sub-clade detected in in multiple states in 2012.  Instead the USDA data refutes the CDC data since the dominant H3N2pM sub-clade has not cause any reported human cases in 2012, while the rare H3N2pM sub-clade has been nconfirmed in the West Virginia H3N2v cluster in 2011, as well as 2012 H3N2v cases from Utah, Hawaii, Indiana, and Ohio.

Although the CDC is now suggesting testing of ILI cases without swine exposure, which has already been implemented by the California Department of Public Health, the damage done by statements such as the one in the latest CDC update, as well as focus of testing on cases with swine contact, have created a pseudo-inkage that has been widely cited in the media and is the basis of UK screening of arrivals from the United States with ILI and swine exposure.

The CDC should unwind the misconceptions created by the pseudolinkage created by biased sampling.  The need for a scientific approach to address the human to human spread of the H3N2v sub-clade seen in the 20 most recent H3N2v sequences is long overdue.

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