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Worldwide Low Reactor H3N2 Sub-clade Emerges
Recombinomics Commentary 12:15
November 2, 2010

The CDC has released 9 new sets of sequences (at GISAID) from recent H3N2 isolates.  One of the nine, A/Wyoming/03/2010 was designated as a low reactor, raising the total of recently released H3N2 with that designation to five.  However, the HA sequence of WY/03 is identical to Hawaii/09/2010, which was not designated as a low reactor, highlighting the low sensitivity of the ferret assay used by the CDC to identify low reactors.

Phylogenetic analysis of recently released CDC H3N2 sequences demonstrates the clustering of 3 (WY/03, CA/16, Nonthaburi/342) of the 5 designated low reactors into the same sub-clade.

This sub-clade has two non-synonymous changes (T48A and K92R using H3 numbering).  Sequences with both polymorphisms include partial HA sequences released by NIID in Japan (see lists here and here).  The sub-clade also has a synonymous change, G1185A, which is present in the isolates with full HA sequences (see list here).

The H3N2 sequences with these acquisitions were largely collected between June and August in 2010 and include sequences from the United States, Japan, Australia, Singapore, Sri Lanka, Egypt, and Thailand.  The broad geographic reach of these recent isolates suggests that vaccine failures will be far reaching and will seriously impact the elderly population, who are preferentially targeted by fatal H3N2 infections.

These recent sequences indicate the P&I (pneumonia and influenza) deaths will rise significantly in the upcoming flu season.
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