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CDC False Statements On Swine H3N2v Matches Raise Concerns
Recombinomics Commentary 05:30
August 13, 2012

Human infections with an influenza A (H3N2) variant (H3N2v) virus that contains the M gene from the influenza A(H1N1)pdm09 virus (2009 H1N1 pandemic virus) were first detected in 2011. Notably, a large increase in cases of H3N2v virus infection has been identified since July 2012. (This virus has been circulating among pigs in the U.S. since 2011, has been detected in pigs in many states, and appears to be circulating widely in swine in the U.S.)
The above comments from the CDC H3N2v August 10, 2012 update for physicians are false.  The H3N2v that has increased in humans since July 2012 has not been circulating in many states and data supporting wide circulation is clearly lacking.  The July 2012 H3N2v sequences from cases matches the earlier sequences from Utah in March, as well as the West Virginia cases in November and December, 2011.  The H3N2v detected in many states has not been reported in a human since November, 2011.

The CDC claims represent pseudoscience and raise serious concerns about the CDC’s abiity to analyze its own data.  Moreover, false statements, such as those in the physician’s update are accepted as evidence that the latest H3N2v cases are due to H3N2 jumping from swine to humans, even though the swine distribution supports the jumping of H3N2v from humans to swine.

The H3N2v detected in the initial human cases has not been identified in any swine isolate collected prior to the first human case in July 2011.  A recent Journal of Virology paper, "The evolution of novel reassortant A/H3N2v influenza virus in North American swine and humans, 2009-2011", described  674 MP sequences from swine collections from 2009-2010, as well as 388 HA and NA sequences from these isolates.  The extensive survey of USDA public sequences as well as a large series generated by the authors of the paper, identified one match with the H3N2v identified in the first 10 human cases in 2011.  This isolate, A/swine/NY/A01104005/2011, was from a September 17, 2011 and was initially noted in November, 2011

More recently released sequences identified additional matches.  However, the earliest matches, A/swine/Iowa/A01202529/2011 and A/swine/Iowa/A01202530/2011, were collected on August 22, 2011 which followed the first human case, A/Indiana/08/2011, which was from July, 2011. 

Thus, the extensive USDA surveillance failed to identify any examples of the matching H3N2v in swine prior to the first human case.

Subsequent sequences identified a total of 24 swine isolates from 6 states (Illinois, Indiana, Iowa, New York, Ohio, and Texas) which matched (based on HA, NA, MP sequences) the H3N2v from the first 10 human cases.  However none of the 2012 human H3N2v cases, including the sequences from July collections from four outbreaks in three states (Hawaii, Indiana, Ohio), matched the constellation in the 24 swine isolates above (or the first 10 reported human cases in 2011).  The July, 2012 H3N2v sequences matched a novel constellation (with an N2 from H3N2 swine), first identified in a large human cluster in at a West Virginia day care center, where the confirmed cases had no swine contact or exposure.

This novel sub-clade has only been identified in two swine isolates from samples collected prior to the July, 2012 cases.  These two isolates, A/swine/North Carolina/A01203272/2012 and A/swine/Indiana/A01203509/2012, were collected in 2012, well after the West Virginia cluster from November and December cases.

The absence of any human 2012 cases which match the swine sequences described by the CDC cast serious doubt on the CDC position of swine H3N2 jumps to humans are a major cause of human cases, and instead supports the jump of human H3N2v into swine, leading to widespread detections in swine that follow novel constellations or sequences in humans.

Thus, the false statements by the CDC to physicians and the media continues to raise pandemic concerns and highlights the need for an independent investigation into the ability of the CDC to analyze its sequence data and convey those results to decision makers and the public.

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