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Nine H5N1 Bird Flu Isolates Sequenced at Novosibirsk

Recombinomics Commentary

August 4, 2005

In an interview on NPR Radio, researchers at the Vector Laboratories in Novosibirsk, Russia indicated that they had sequenced nine separate isolates and they were all H5N1 and somewhat related to H5N1 in Vietnam.  The data should remove doubts about the Russian OIE report which indicated the outbreak was H5, but the N sequencing was ongoing.  There was initial confusion because Russian officials indicated it was H5N2 and Kazakhstan officials indicated it was not H5N1.  Neither statements were credible, because geese were dying, matching the pathological profile of H5N1 positive outbreaks at Qinghai Lake and two areas in adjacent Xinjiang province.  The Tacheng outbreak was just a few miles from the Kazakhstan border.  Moreover, geese from Qinghai Lake summer at Chany Lake, which was surrounded by outbreaks of geese dying, including those just across the border in the Irtysh district of the Pavlodar region .

The outbreak at Qinghai lake was without precedent and involved at least 5 species of migratory birds.  In June there were poultry deaths linked to migratory birds and the outbreak in Novosibirsk killed geese and other birds.  The death toll on domestic and migratory birds was extensive with reports of deaths in all six southern regions of Siberia as well as Tomsk to the north and Pavlodar to the south.

The description of the sequences sounds like the Qinghai sequences.  They were unique, bit clearly related to the deadly sequences in Vietnam and Thailand.  However, they also has European markers and were Amantadine sensitive.  It seems almost certain that the H5N1 in Russia and Kazakhstan is related toi the Qinghai sequences, although additional sequence data would be useful because the virus has probably recombined more because of the large number of migratory birds from southeast Asia, eastern China, the Indian subcontinent, and Europe.  These recombinant will soon be heading south to recombine with local endemic populations in southeast Asia and China

The Vector lab is supported in part by an NIAID grant to Robert Webster at St Jude, so sequence data should be available soon.  It will be important to see how much additional recombination has happened since Qinghai lake. 16 sets of sequences are at GenBank, but all were from dead birds and 12 of the sixteen are from bar headed geese.

The birds should be entering Europe and then heading for the Caspian and Black Seas.  H5N1 will have opportunities to extend its host range to birds and people in Europe and beyond.

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