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2005 H5N1 Sequences At GenBank

Recombinomics Commentary
May 20, 2005
>>  CDC has only one isolate and sequence for H5N1 from North Vietnam cases reported in 2005," said Ruben O'Donis, US Centers of Disease Control and Prevention's Chief of the Molecular Genetics Section, Influenza Branch <<

The lack of sequences from 2005 isolates is cause for concern.  There are no publicly available 2005 H5N1 sequences at GenBank at this time, although some of the restricted sequences may be publicly available shortly,  The CDC has data from only one case in northern Vietnam, but the number of infected birds is high and more isolates should be forthcoming.  Use of appropriate primers can also generate PCR sequence data from the many samples collected.  The Institute for Hygiene and Epidemiology in Hanoi has collected 1000 serum samples, which were analyzed by the CDC prior to the urgent meeting in Manila.

The analysis of these sequences will demonstrate additional recombination between earlier isolates to generate new 2005 sequences.  The 2005 sequences can be used to predict the sequences of the H5N1 bird flu that will emerge in southeast Asia in the fall.

It is likely that the new isolates will have evolved away from the 2004 isolates being used for a pandemic vaccine, so preparing for 2005 isolates now, rather waiting for them to emerge in the fall would be useful.

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