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Recombination in M Gene of H5N1 Guangdong Wild Bird
Recombinomics Commentary
March 3, 2006
Researchers in Beijing have recently submitted sequences from H5N1 isolates in China under the title "A cohort of AIV H5N1 subtypes isolated from wild aquatic birds and domestic poultry revealed rapid transmission, frequent reassortment, and identifiable recombination events." The sequences from A/wild bird/Guangdong/314/2004(H5N1) showed evidence of both reassortment and recombination. The eight genes were derived from isolates related to tree sparrow sequences from Henan, a duck smuggled onto Quemoy Island in 2003, and a series isolates from of Hong Kong ducks in the late 1970's
PB2 shows evidence of extensive recombination with a variety of parents that have clustered polymorphisms. Recombination is also seen in the M gene. The 2004 wild bird sequence was closely related to a series of Hong Kong waterfowl such as A/duck/Hong Kong/365/1978(H4N6) isolated in the late 1970's. However, there wee also several polymorphisms that were shared with the H5N1 Qinghai isolates. Most of these polymorphisms were clustered in two regions (C306T, C315T, A318G) and (G580A, T604G, G610A, T640C, G645A, G670A). The clusters represent "identifiable recombination events".
These extensive regions of recombination highlight the need for a current and robust database of flu sequences. Many of these sequences were recently deposited at Genbank, although the samples were collected in the 1970's. H5N1 sequences have been deposited in a more timely manner, but there are still significant delays. These delays were highlighted in today's Science which described a private WHO database with recent important sequences such has human sequences from Indonesia and bird sequences from many countries in Europe. In the past, H5N1 sequences have been delayed for 6-12 months, pending publication.
H5N1 is evolving and migrating at a record pace. Recent sequences from Russia, Nigeria, France, and Italy identifies formation of new clades related to the Qinghai strain. In addition there are human and American sequences that are being acquired.
Immediate deposit of the valuable H5N1 sequences and all recent sero-types identified in recent expanded surveillance worldwide would facilitate tracking of H5N1 sequences and development of effective vaccines.
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