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Novosibirsk H5N1 Wild Bird Flu Recombinants from Europe

Recombinomics Commentary

September 30, 2005

Five partial HA sequences from the summer outbreak of H5N1 wild bird flu were deposited at GenBank.  Included was a sequence from a health great crested grebe (Podiceps cristatus), A/grebe/Novosibirsk/29/05(H5N1), a sick domestic duck, A/duck/Novosibirsk/56/05(H5N1), and three dead chickens (A/chicken/Novosibirsk/64/05(H5N1), A/chicken/Novosibirsk/65/05(H5N1), A/chicken/Novosibirsk/66/05(H5N1)).  All five sequences were very similar to each other and the sixteen H5N1 wild bird isolates from dead waterfowl at Qinghai Lake.  The deposited sequences cover the highly pathogenic HA cleavage site and all sequences in this area were identical. 

The highly pathogenic sequence in the healthy great crested grebe demonstrates that highly pathogenic H5N1 is present in asymptomatic wild waterfowl.  This is similar to the asymptomatic waterfowl in Vietnam, which harbor high concentrations of highly pathogenic virus that is lethal to humans and chickens, yet produces mild or no ill effects in the waterfowl.

The ability of these wild birds to transport H5N1 over long distances was also support by sequence analysis.  Two the polymorphism found in all five Novosibirsk H5N1 isolates, C934T and T940C were not found in other H5N1 isolates, including the H5N1 isolates from Qinghai lake.  Instead, the polymorphisms were restricted to H5N2 sequences isolated in chickens and guinea fowl in Italy in 1997 and 1998.  The polymorphisms were acquired by recombination, just as the PB2 polymorphisms in the Qinghai lake isolates were acquired from European swine.

The acquisition of these polymorphisms is cited because each acquisition involves more than one polymorphism in a small area.  However many of the polymorphism in the wild bird sequences are from Europe, even though the H5N1 sequences, including the highly pathogenic HA cleavage site, and the 20 amino acid deletion of NA are exclusively found in Asia.

The recombinant sequences from Europe provide more evidence showing that the polymorphism are carried by wild birds.  Dual infections by flu from Europe and flu from Asia lead to these recombinants with mixtures of polymorphisms.  The European sequences also indicate the H5N1 will be migrating to Europe this season due to the widespread infections of H5N1 waterfowl in Russia, Mongolia, and Kazakhstan

These birds are now migrating to warmer climates, and transporting highly pathogenic H5N1 into areas where it has not previously been repotted.


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