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Maine trH3N2 Not In Week 41 MMWR
Recombinomics Commentary 16:00
October 20, 2011

Novel influenza A infection virus *** - 6 0 4 43,774 2 4 NN  

As seen above, tomorrow’s (week 41) MMWR page on Notifiable Diseases does not include the trH3N2 case from Maine, which is curious.  The page covers reports through October 15, and the A/Maine/06/2011 sample was collected on October 10, which is in week 41.  The CDC released partial sequences from all eight gene segments on October 17, which was updated with complete or nearly complete sequences for all eight gene segments later that day.  Thus, the CDC was well aware of the fact that another trH3N2 cases had been identified and lab confirmed, but did not include this case in the week 41 MMWR report, which was available this morning.

The criteria for making these cases public remain obscure.  Although four earlier trH3N2 cases have been acknowledged, the representation in the FluView table of influenza sub-types has been both bizarre and incomplete.  Two of the Pennsylvania cases (isolated in weeks 33 and 34) have been listed as unsubtypable, which would facilitate detection by state labs.  However, these cases were in week 35 and 36 tables/figures, absent in week 37 and 38, present in week 39, and absent in week 40, raising concern that criteria for classifying / reporting these cases was under constant flux, which is supported by the absence of the Maine, trH3N2 cases in the week 41 MMWR.  Moreover, the other two earlier cases (collected in weeks 30 and 34) were not included in the sub-type table or figures in FluView.

The sequence of the H3 from the Maine case raises concerns that the sample will sub-type as seasonal H3, leading to a serious undercount since state labs do not have PCR testing kits for the identification of swine H3, and must rely on a positive influenza A test coupled with a negative H3 test, which may not apply to a subset of trH3N2 cases.  A more reliable approach would include distribution to state labs of appropriate PCR kits for detection of swine H3 as was done for the detection of swine H1, when the CDC was overwhelmed with unsubtypable samples in 2009.

Thus, the absence of the Maine case in tomorrow’s MMWR, coupled with the inability of state labs to direct test for swine H3, continues to increase pandemic concerns.

Distribution of swine H3 detection kits to state labs is long overdue.

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