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H1N1 US Sequences Maintain Dominance Polymorphisms
Recombinomics Commentary 15:52
December 23, 2008

The CDC has deposited HA and NA sequences at Genbank, which will be available shortly (see list below).  As expected, all are clade IIB (Brisbane) and have H274Y.  One sequence from August, A/Missouri/06/2008, was also released and it is the only oseltamivir sensitive isolate.  However, it is clade IIC, and like the clade IIC isolates in the US last season and over the summer, it is adamantidine resistant and oseltamivir sensitive.

The new sequences have evolved from the dominant sub-clade in circulation last season, and have changes that led to dominance last season and in the 2008 season for the southern hemisphere.  As noted earlier, one US sequence from the summer had the clustered changes near the position 190 receptor binding domain.  The current sequences have one of the polymorphisms in that cluster A193T.

Most of the new sequences formed a branch that included Memphis/03/2008 and Hawai/02/2008.  The new isolates on this branch were from Hawaii, Texas, and Pennsylvania, so more samples are required to see the full distribution of this sub-clade.

However, the sequences from these initial isolates indicate that the changes that initiated dominance last season, have been maintained over the summer and into the new season.  These dominance changes were acquired via recombination from clade IIC sequences.


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