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Migrating Russian Bird Flu Recombinants

Recombinomics Commentary
January 9, 2005

>>We have subsequently learned that on several occasions H5N1 avian influenza viruses have been isolated from migrating birds in the Novosibirsk region of Russia during the past 4 years. In 2003, an H5 avian influenza virus was isolated and sequenced by the Laboratory to Investigate and Monitor Emerging Zoonotic Diseases (Novosibirsk, Russia) from a wild mallard duck on Lake Chany in the south of Western Siberia. The A/mallard/Chany/9/03 avian influenza virus was related, but not identical, to H5N1 avian influenza viruses currently circulating in domestic poultry in Asia. The virus's hemagglutinin sequence showed 90-95% similarity to the current Asian H5N1, which is in turn similar to Eurasian H5 avian influenza viruses A/duck/Potsdam/1402-6/86 (H5N2) and A/turkey/England/50-92/91 (H5N1).<<

The sequences of the two 2001 H5 isolates released by GenBank have sequences that are similar to the 2003 isolate, A/mallard/Chany/9/03, described above.  At Genbank the 1047 bp of A/duck/Primorie/2621/01(H5N2) is virtually identical to the corresponding sequences in A/duck/Primorie/2633/01(H5N3).  Thus, it would seem that H5 isolates from southwestern Russia have similar H5 regardless of whether the N is N1, N2, or N3.  The H5 has is a recombinant with polymorphisms found in European isolates including the first H5N1 isolate in 1959 as well as polymorphisms found in 2004 isolates from Vietnam and Thailand. Two of the other genes at Genbank, NS and NP also have polymorphisms found in Asia.

The presence of these polymorphisms in migrating birds, including ducks and mallards strongly suggests that these new polymorphisms are brought into regions of Asia hard hit by H5N1 infections last season, and increases the likelihood that new sequences will be found in H5N1 this season.

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