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Novosibirsk H5N1 Wild Bird Flu Evolving Via Recombination
Recombinomics Commentary
August 13, 2005
The supplemental information provided to the OIE by Dr Evgueny A. Nepoklonov, Head of the Main Veterinary Department, Ministry of Agriculture and Food, Moscow is extremely detailed. Data is provided for H5N1 isolates from birds collected in Novosibirsk Included is an electropherogram of five extracts from five sites in two villages. The samples are from domestic ducks, a chicken, a goose, and a wild duck. All are N1 based on amplified products, although the wild duck extract produced the most complex pattern. This data was provided by the All-Russia State Scientific Research Institute for Monitoring, Standardisation and Certification of Veterinary Preparations (FGU VGNKI).
Sequencing of the HA cleavage site indicated that it was an exact match with the sequences from the 16 isolates from Qinghai Lake. In addition, Vector, the State Scientific Centre for Virology and Biotechnology, provided data from a turkey isolate which included a 124 amino acid sequence encompassing the HA cleavage site, as well as phylogenetic analysis of a 640 BP amplicon from NA, which was virtually identical to sequences from bar headed geese form Qinghai Lake.
Providing that level of detail within days of the outbreak is commendable and should set a standard for investigators trying to control the looming pandemic.
The detailed data provides a good deal of useful information. The exact match with the Qinghai isolates is significant. Although the HA cleavage site is multibasic and is clearly HPAI, there is one polymorphism that is rare. It was in all 16 isolates from Qinghai Lake, but had rarely been reported previously. It was in two ducks from Hong Kong in 2000, A/Duck/Hong Kong/ww487/2000 and A/Duck/Hong Kong/ww461/2000, as well as a chicken from Macheng in 2004, A/chick/Macheng/2004. Finding the identical change in all of the reported isolates from Novosibirsk (a turkey, two ducks, a goose, a chicken, and a wild bird), clearly links the two outbreaks. This linkage was further supported by the phylogenetic analysis on the NA fragment, which was virtually identical to the bar headed geese sequences from Qinghai Lake.
However, one of the polymorphisms, N325S, in the turkey sequence was not found in the bar headed geese sequences, but was found in several isolates from South Korea and Japan, as well as two isolates from China. This polymorphism indicates the Novosibirsk sequence is a recombinant. Recombination with H5N1 linked to Japan and Korea is not surprising because a prior H5 sequence from Chany Lake was very similar to H5 from Primorie, which is close to Japan and South Korea.
Thus, the Novosibirsk isolates are most closely related to Qinghai Lake isolates, but there are some differences. The HA sequence has 3 additional polymorphisms not seen in other H5N1 isolates, providing more evidence of evolution away from the pandemic vaccine under development worldwide.
Thus, the data from Novosibirsk indicate two closely related H5N1s are rapidly spreading throughout Asia. The version in Russia and Kazakhstan is rapidly advancing on Europe (see map) and will likely spread significantly in the upcoming months. In addition, the outbreaks in Mongolia and Tibet signal more spread in Asia, including areas such as India where H5N1 has not previously been reported, although poultry workers have H5N1 antibodies and the bar headed geese winter in India and may have already had H5N1 when they arrived at Qinghai Lake in early May.
The sequence data demonstrate that H5N1 wild bird flu did not burn out at Qinghai Lake, but instead is spreading and evolving in natural reserves in China and Russia.
As the weather turns colder, these birds are migrating to warmer regions of Europe, Asia, and beyond. The transport and transmission of wild bird flu will be a major challenge as they arrive in new areas and recombine with H5N1 in endemic regions such as Vietnam, Thailand, and Indonesia.
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