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CDC Comments On trH3N2 Match in IN and PA
Recombinomics Commentary 19:50
September 3, 2011

These viruses are genetically related, but different enough to suggest there was not a common source of infection. No epidemiologic link between these two cases has been identified.

The above comments from this week's FluView (week 34) on the sequence similarities between the confirmed cases in Indiana and Pennsylvania argues against extensive human transmission.  However, both isolates have an MP gene segment from the H1N1 pandemic clade, which has not been reported previously, in spite of increased swine surveillance.

A full set of sequences from the Indiana isolate, A/Indiana/08/2011 (IN/08), has been made public at GISAID.  That isolate is a reassortant in the MP and PB1 gene segments.  As noted, the MP gene segment is of pandemic H1N1 origin.  The PB1 gene segment is related to the PB1 from virus isolated from the Huron County fair outbreak of 2007, and is readily distinguished from other recent trH3N2 isolates, which are closely related to IN/08.  Thus, the IN/08 sequence may signal multiple sub-clades circulating in humans which have acquired an MP gene segment from pandemic H1N1.

A recent report on swine reassortants in the United States has found 7 different combinations. All had an MP from pandemic H1N1 on a tr background (H1N1, H1N2, and H3N2).  However, none of the swine isolates had a pandemic H1N1 acquisition limited to the MP segment (all had at least one additional gene segment from pandemic H1N1).

Thus, the constellation found in the two recent cases from IN and PA have not been reported in swine, and the finding of that constellation in two human cases argues for human transmission, as does the lack of swine contact for the Indiana case.  Media reports of symptomatic fair attendees in Washington County, Pennsylvania also increase concerns that the novel trH3N2 constellation is transmitting in humans.

Release of the Pennsylvania trH3N2 sequences, and status on the symptomatic fair attendees, would be useful

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