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H5N1 In Missouri
Recombinomics Commentary
November 17, 2006

The number of H5N1 positive samples in the United States continue to grow, as H5N1 migrates to the south.  The latest samples are from hunter killed Northern Shoveler in Stodard County, MO, collected on November 4, 2006.  H5N1 was also detected in Stanley County, SD in hunter killed Northern Shoveler.  H5N1 Mallard duck samples from three locations in Grundy County, IL, two locations in Niagara County, NY, and two counties in MI signal the widespread distribution of H5N1 in the United States.

However, although H5N1 was isolated in August in MD, MI, and PA, subsequent isolation attempts have failed to isolate H5N1 from samples that are PCR positive for H5N1.  H5N3 was isolated in Montana and H6N2 was isolated in IL.  No virus was isolated from more recent samples from MI and IL.  These isolation failures are cause for concern.  The majority of the failures are from samples from hunter killed birds.  It is likely that improper handling has led to the failures.  These failures are cause for concern.

No sequence data has been released for the H5N1 or H5N3 isolates.  Although the samples are said to be low path North American strains, low path H5 can recombine with high path H5N1, and vice verse.  Isolation of the high path Qinghai strain from live (or hunter killed) wild birds is rare, but the presence of the high path can be determined by the sequences in the low path isolates.

The H5N1 isolated in Maryland in August were part of an Ohio State University monitoring program, which has also isolated avian influenza in Alaska last year.  These samples were fully sequenced under the NIAID sequencing project.  However, the H5N1 isolates from August are not listed in the table of OSU samples to be sequenced.

H5N2 sequence from Maryland in 2002 contain H5N1 sequences from Asia, as well as swine and human sequences.  The additional sequences that have been in the validation stage since June should be released, and all H5 isolates from this year should be sequenced and the sequences should be made public.

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