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S199A Emergence and Spread in H3N2 Variants
Recombinomics Commentary 22:40
September 23, 2010

In August the US CDC issued an H3N2 health alert linked to two small outbreaks in eastern Iowa.  The level of H3N2 in the US last season was very low, due largely to the spread of pandemic H1N1.  However, H3N2 began to rebound in several Asian countries, and labs worldwide have been releasing H3N2 sequences. 

The CDC released the sequence from Iowa.  It was the Perth/16 strain, but like most of the H3N2 circulating in late 2009, early 2010 it had evolved away from the Perth target, which had been isolated in April, 2009.

However, in addition to these isolates, two of the CDC sequences, A/Pennsylvania/02/2010 and A/Kansas/06/2010, had evolved beyond these Perth-like sequences, raising concerns that a more evolved strain was emerging.  This concern was confirmed by another series of sequences released by the CDC, which showed that these more evolved sequences had spread worldwide.

Today the CDC released 21 more H3N2 sequences from recent isolates, collected between June and August, 2010.  10 of those sequences, had evolved further, and all 10 had S199A (see list here).  Earlier (mostly 2004-2005), a small subset of H3N2 sequences had S199A (see list here).

The rapid spread of S199A on an emerging variant which also has receptor binding domain change I230V raises concerns that the virus will have limited reactivity with antibodies directed against prior H3N2, including the Perth/16 vaccine.  One of the recent sequences with S199A, A/Colombia/6722/2010, has been designated a “low reactor” by the CDC.

This emerging strain may cause widespread H3N2.  In contrast to pandemic H1N1, the elderly population is most vulnerable to an emerging H3N2.

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