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Maine trH3N2 Evolution Raises Detection Concerns
Recombinomics Commentary 13:30
October 20, 2011

The CDC recently released partial sequences for all 8 gene segments of a new trH3N2 cases (8M), A/Maine/06/2011, seven days after collection on October 10, 2011.  Hours later, the CDC released complete or nearly complete sequences for all eight gene segments.  The CDC is commended for the rapid release of these important sequences.

The partial sequences clearly demonstrated the relatedness between this isolate and the four 2011 trH3N2 isolates from Indiana (A/Indiana/08/2011) and Pennsylvania (A/Pennsylvania/09/2011, A/Pennsylvania/10/2011, A/Pennsylvania/11/2011), which had acquired a pandemic H1N1 M gene.  The full sequences allowed for phylogenetic analysis, which confirmed the identity between the Maine isolate and the earlier 2011 trH3N2 isolates.  However, most of the Maine gene segments began to evolve from the 2010 human trH3N2 cases at an earlier date.

Consequently, some of these Maine segments, including H3, are more closely related to the 2010 sequences, than the earlier 2011 isolates from Indiana and Pennsylvania, which signals additional diversity in these emerging human trH3N2 sequences, and has implications for the detection of trH3N2 in 2011.

trH3N2 in the United States first appeared in the 1990’s and was associated with a seasonal H3N2 in swine, which were double reassortants that were the precursors to triple reassortants.  Previously, these H3 sequences have been positive for human typing reagents.  However, two of the 2011 isolates from Pennsylvania, were reported as “unsubtypable” in the CDC Fluview due to additional evolution away from the 2010 sequences.  This designation would aid in detection by state labs because these unsubtyple would be flagged by a designation of influenza A positive, H1/H3 negative, which could be confirmed as trH3N2 by PCR testing.

However, the Maine H3 sequence is more closely related to the 2010 sequences raising the possibility that these sequences will type as seasonal H3, limiting detection.  Moreover, the trH3N2 case is not reported in the week 41 MMWR.

Therefore the CDC should distribute swine H3 PCR detection reagents to state labs to aid in the detection of the emerging human contagion.

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