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More US H1N1 Chihuahua Sequences Raise Concerns

Recombinomics Commentary 21:20
May 4, 2011

The CDC released a series of 35 H1N1 HA sequences at GISAID which were largely from 2011 isolates in the United States.  Included were three US sequences (A/Pennsylvania/04/2011, A/Texas/08/2011, A/New Jersey/05/2011) which were collected in March and were closely related to the Chihuahua sub-clade sequences from Mexico.  The three US sequences were identical to each other, as well as three sequences released earlier (A/Maryland/04/2011, A/Oregon/03/2011, A/Texas/07/2011) providing further evidence for the spread of this sub-clade in the United States.  Two other closely related US sequences (A/Utah/08/2011 and A/Pennsylvania/02/2011) represent the eight US sequences which are closely related to the sequences from Mexico including the presence of K149N. 

Two of the sequences from severe or fatal cases in Mexico have D225N, raising concerns that the US patients also have D225N, which is not found in the viral isolates from their samples due to collection or isolation issues.

The sequences from Mexico were generated by direct sequencing of the clinical samples, while the US sequences come from virus isolated in culture.  Unreleased sequences from Mexico, as well as other countries in North and South America have D225N on a Chihuahua sub-clade genetic background, raising concerns that this receptor binding domain change is widespread and in samples represented by the CDC sequences.

This emerging sub-clade with D225N has led to a pandemic alert, and recent comments from the Air Force as well as sequences from vaccinated Air Force dependents has raised concerns that massive vaccination campaigns will have limited success.

The time for a new H1N1 vaccine targeting the Chihuahua sub-clade is long overdue.

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