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US H1N1pdm09 Tamiflu Resistance Increases
Recombinomics Commentary 17:30
November 22, 2013
Week 46 ILI

The above figure from the CDC week 46 FluView shows the highest US ILI in states flanking Louisiana.  In addition, the week 46 report indicates H1N1pdm09 is clearly the dominant influenza currently in circulation in the US.  For week 46 280/312 (89.7%) of typed samples were influenza A, and of the sub-typed influenza A samples 118/132 (89.4%) were H1N1pdm09.

Recently the CDC released the initial sequences from the 2013/2014 season, which included two sequences from Louisiana.  Both sequences contained H274Y, which led to the release of full sequences for both samples - the vast majority of CDC seasonal flu sequences include only three gene segments (HA, NA, and MP).  The 8 gene segments from A/Louisiana/07/2013 and A/Louisiana/08/2013 were virtually identical, signaling clonal expansion (samples were collected 2 days apart).  In week 44 the CDC cited the first 2 Tamiflu resistant sequences for the 2013/2014 season, which were almost certainly from the above two case (25F and 56F, respectively).

The week 45 FluView cited a third case, and in week 46 the number increased to four.  Although sequences from week 45 and 46 cases have not been released, it is likely that one or both of the newer cases are also from Louisiana due to concerns generated by the above matching sequences.

More information about the relationship between the first two sequences, as well as the locations for the two most recent examples of oseltamivir resistance would be useful, as well as the number of H1N1pdm09 cases in Louisiana being tested for H274Y.

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