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Maine CDC Detects trH3N2 With Newly Approved PCR Test
Recombinomics Commentary 20:00
November 16, 2011

Testing performed at Maine’s Health and Environmental Testing Laboratory on October 14, 2011 indicated a likely swine origin influenza A (H3N2) virus and this result was confirmed at CDC on October 16, 2011.

The above comments from the CDC’s week 41 FluView describes the detection of the first trH3N2 case in Maine (8M, A/Maine/06/2011) using the newly approved CDC PCR kit.  The kit includes assays for H1N1pdm09 H1 and NP, in addition to seasonal H3.  These specific sub-typing tests are used on influenza A positive samples.  Although the test does not directly test for trH3, the pdm NP test detects triple reassortants (see list here), including the first trH3N2 case in Maine.

The H3 from trH3N2 traces back to a seasonal H3N2 infection of swine in the early 1990’s.  The H3 has been evolving in swine, leading to reduced activity with reagents targeting human H3, but positive results for H3 can lead to a seasonal H3N2 designation of trH3N2 as was seen in the first trH3N2 confirmed in 2011.  This was a 2010 case, A/Pennsylvania/40/2010, which was initially designated as seasonal H3N2, and was not reported as trH3N2 until week 4 in 2011, 5 months after collection.

The Maine case also tested positive for H3, in part because the cases from Maine (A/Maine/06/2011 and A/Maine/07/2011) as well as the second case from Indiana (A/Indiana/10/2011) are closely related to the dominant human H3 in 2010 (A/Pennsylvania/30/2011, A/Wisconsin/12/2011, A/Minnesota/11/2011).  However, it also tested positive for pdm NP (pandemic swine NP) indicating it was not seasonal H3N2 and was a likely trH3N2, which was confirmed by the CDC, as noted above.

Thus, the newly approved CDC PCR test should lead to increased precision in sub-typing tests, which are critical for the determination of true extent of trH3N2 cases.  However, many samples are not sub-typed, as seen in the week 44 FluView or 31/32 influenza A positive samples in Region 4.

More widespread and aggressive use of this PCR test is long overdue, and the CDC should issue an early release MMWR noting the low frequency of testing and sub-typing.

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