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H3N2v Acquisitions In United States Seasonal H3N2 
Recombinomics Commentary 22:15
March 2, 2012

The CDC has recently released 22 sets of 2012 seasonal H3N2 sequences from cases in the United States.  Several of the isolates have recenty acquired polymorphisms which are shared with 2011 H3N2v human cases.  12 such cases were from 2011 infections, including clusters in Iowa and West Virginia.  However, no cases have been reported in 2012, raising sensitivity concerns for the current PCR test, which relies on cross reactivates with seasonal H3N2 and H1N1pdm09 NP.  Although a sub-set of the 12 confirmed cases were H3 and NP positive, most cases were identified via sequence analysis of samples from patients who had exposure to swine or confirmed H3N2v cases.

Sequence analysis of seasonal H3N2 provides an alternative approach for the identification of H3N2v acquisitions, which occur in hosts infected with seasonal H3N2 and H3N2v
(via recombination).  Several of the seasonal H3N2 cases have such acquisitions, but the profile of a case (40F) from South Carolina (A/South Carolina/01/2012) is striking.  The HA sequence had 5 recent acquisitions (G138T, A246G, A335T, T351C, C379T), and 3 (A246G, T351C, C379T) were also in H3N2v isolates (see list here here here).  Similarly, the MP sequence had 3 recent acquisitions (A48G, G324A, C857A), and 2 (A48G, G324A) were also in H3N2v isolates (see lists here here).

Thus, there is little doubt that H3N2v is circulating in the United States, in spite of a lack of CDC reports on such cases.

However, today’s week 8 CDC FluView reports a dramatic spike in low reactors (62.8% of the newly reported H3N2 cases were low reactors).  In the past H3N2v sequences have been identified in routine surveillance, including a low reactor result in antigen characterization tests (which is expected for H3N2v since the H3 has evolved in swine and has evolved from seasonal H3 circulating in the 1990’s).  The current FluView is silent on the sequences associated with the 88 H3N2low reactors cited in the week 8 FluView.

Release of sequences from these low reactors would be useful.  None of the 22 2012 H3N2 sequences at GISAID are designated as low reactors (although only 7 have listed antigen characterization data indicated and all are designated as Perth/16-like).

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