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H1N1 In United States Identical to United Kingdom
Recombinomics Commentary 17:10
February 4, 2011

The CDC has released a series of sequences (at GISAID) from recently collected isolates, which extends the trend generated by the prior sets of sequences from October and November.  Most of the latest sequences were collected in December 2010 or January 2011, and all sequences collected after December 10 had either S188T or S186P, with the vast majority carrying S188T.  The emergence was similar to the H1N1 seen in the UK, which had an unusually high frequency of severe and fatal cases.

In fact many of the H1N1 sequences in the United States were identical to the sequences from the United Kingdom.  Sequences from A/Kansas/08/2010, A/Kentucky/08/2010, A/Delaware/05/2010, A/Indiana/09/2010, and A/Oregon/04/2010 were identical to each other and sequences from A/England/4920303/2010, A/England/119/2010, and A/England/142/2010. Moreover, sequences from A/Connecticut/0/2010, A/Wisconsin/09/2010, A/Maine/03/2010, A/Missouri/01/2010, A/Alaska/02/2011, A/Kentucky/16/2010, and A/Rhode Island/03/2010 were all closely related to the identical sequences above.

These sequences represent infections covering a large portion of the United States, from Alaska to Missouri to Maine.  Other sequences had similar relationships with sequences in the United Kingdom, suggesting that the problems in December and January in the UK would soon develop into similar problems in the US. 

Recent state reports in the US indicated H1N1 had become the dominant serotype, and the week four pneumonia and influenza deaths for week 4 spike to 8.45% nationally, which is well above the epidemic threshold.  Similarly, the number of pediatric deaths jumped to six, even though this is a lagging indicator.

The national week 4 report is likely to extend the above observations and signal increases in serious cases across the country.  The dominance of S188T and S186P is likely due to immunological escape and vaccine breakthrough.  The WHO regional center in Australia also released recent sequences which were also dominated by S188T and S186P, even though the 2010 flu season has ended for the southern hemisphere.  Two of the sequences were from young adults (20M and 21M) who had received the 2010 vaccine and were part of a cluster.  Both sequences (which had S186P) from this cluster were identical and provided additional evidence for vaccine escape.

Such escapes are not unexpected.  However, the vaccine used in 2010 in the southern and northern hemisphere targeted California/7/2009, which was isolated in April 2009, so escape in 2010 and 2011 was not unexpected.  Most remarkably, this outdated target is being used for the 2011 vaccine for the southern hemisphere, which is scandalous.

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