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H5N1 Recombination in Novosibirsk Russia

Recombinomics Commentary

June 10, 2006

A report from members of Vector Labs in Novosibirsk, Russia have described the initial detection of H5N1 bird flu in the region around Chany Lake in southern Siberia last summer (see dynamic map).  This outbreak indicated that the H5N1 Qinghai strain identified at Qinghai Lake in China in the spring of 2005 was migrating via wild waterfowl over long distances.

The movement into the Chany Lake region was important because it is located at the intersection of several flyways which link southern Siberia to Asia, including the Indian subcontinent as well as Europe, the Middle East, and Africa.  The outbreak at Chany Lake led to a major geographical expansion of H5N1

The characteristic Qinghai strain was subsequently identified in many countries that had never reported the Asia version of H5N1.  Some of these isolates can be seen in the phylogenetic tree, which shows the Qinghai branch including isolates from Astrakhan, Italy, Nigeria.

The isolates that were wildly spread are in the middle region of the Qinghai branch.  The extremes of the branch are represented by a goose from Krasnoozerskoye and a red head from Dovolonye.  Both of these isolates were from 2005 and these two locations are in southeastern Novosibirsk and are separated by 60 km.

The close geographical location of the two most divergent Qinghai isolates suggests the emergent strains, which were then dispersed from the region arose via recombination with the divergent strains which were co-circulating in this region.  The sequences of the two divergent isolates have not been made public, but these two isolates likely contain the polymorphisms required to generate the dominant strain that emerged in 2005,

Recent outbreaks of H5N1 in the region forecast more diversity in 2006 as H5N1 from Qinghai Province migrate into the region to mix with Qinghai strains flying in from Africa, the Middle East, and Europe.

The new recombinants will be significantly different from the H5N1 version seeded in Europe the Middle East, and Africa, and the early detection of H5N1 in the region around Chany Lake is cause for concern..

Predictions of these new recombinants can be made with a robust database, including the new H5N1 infections that are currently being reported in several provinces in southern Siberia.  Release of these sequences, including the divergent H5N1 sequences from the summer of 2005 would be useful.

H5N1 evolution is driven by recombination is predictable if the appropriate parental sequences are known.

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