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New H5N1 Sequences Confirm Recombination in China
October 5, 2006
New H5N1 bird flu sequences have been deposited at Genbank and Los Alamos (see list here and here). These sequences were deposited by the Beijing Genome Institute and represent complete sequences of all eight gene segments of H5N1 isolates from poultry and wild birds in China from 1997 to 2004. Some of these sequences are updated versions of a series of sequences released earlier this year 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 sequence contained a number of examples of clear-cut recombination.
Recently additional sequences from the 1970’s were released and these sequences from Hong Kong are well conserved in the above 2004 sequences, which again raise questions about the central dogma of influenza genetics which maintains that season variation is due to random mutations. In addition to the sequences from the 1970’s, the new sequences from 1997 also show a high level of sequence conservation. In the PB2 gene the 2004 tree sparrow sequence, A/tree sparrow/Henan/2/2004(H5N1) between positions 685 and 2146 has only three differences with the 1997 chicken sequence, A/chicken/Hubei/wi/1997(H5N1). This sequence conservation is inconsistent with an error prone polymerase lacking a proof reader function as the source of seasonal variation in human flu, or rapid evolution in pandemic flu.
Instead, the data clearly shows that both season flu and pandemic flu evolve via homologous recombination. The confirmation of the earlier data demonstrates that the clear examples of recombination are not due to lab error, but reflects the primary mechanism of influenza evolution.