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First Novel Swine trH3N2 Raises Pandemic Concerns
Recombinomics Commentary 23:45
November 20, 2011

Today the USDA released a full set of sequences for a New York swine isolate, A/swine/NY/A01104005/2011 , which was collected on September 13, 2011 as expected.  In spite of enhanced surveillance, the FDA failed to find this novel trH3N2 in swine infections prior to the human cases in July and August.  The sequence of events has striking parallels with the 2009 pandemic.  Matches were not found in swine isolates prior to the pandemic, and after the virus spread in humans it was found in swine worldwide.

The swine isolate has the same constellation of flu genes, as well as the same linages.  Thus, all eight gene segments are closely related to the seven 2011 human trH3N2 isolates.  The swine isolate is more closely related to each sub-clade in one or more genes, indicating it is not a precursor for any of the human isolates.  It is likely that this novel sub-clade is widespread, and is clearly easily detected in humans.

The USDA has identified more than two dozen SOIV’s in 2011, and today’s isolate is the first match.  In contrast, only two human influenza isolates have been reported in Maine, and both are trH3N2.  Similarly, 2 of the 3 isolates in Indiana since July are trH3N2.  In Pennsylvania 3 of 5 influenza isolates are trH3N2.

Moreover, 6 of the 7 human trH3N2 are from adolescents, and there have only been 5 seasonal adolescent H3N2 reported for the entire country since late July.  Thus, most adolescent H3N2 cases are trH3N2.
The finding of the swine case in a collection from September continues to raise concerns that this trH3N2 is widespread in human populations and is now jumping to swine. 

The human surveillance of human influenza for the 2011/2012 season remains abysmal and the low level of serotyping remains alarming.

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