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Bird Flu Sequence Conservation in NA in Thailand in 2004

Recombinomics Commentary
May 23, 2005

Thirty-eight H5N1 2004 partial sequences of the NA gene just became publicly available at GenBank.  These partial sequences were from chickens, ducks, and a cuckoo-dove from over 10 provinces in Thailand isolated between July - September of 2004.  The sequences were most closely related to other Thai sequences from early 2004 isolates.  The  amount of genetic change during the 2003/2004 season was minor

The isolates formed two clades.  One was very closely related to the tiger isolates from the Sri Racha zoo and the mother of the cluster described in the New England Journal of Medicine showing human-to-human transmission.  The other clade was related to other early 2004 isolates from Thailand.

These data indicate that the clade associated with mammal-to-mammal transmission was widespread in Thailand last season, and it was relatively stable.  These sequences provide additional evidence against a polymerase that makes frequent errors, because the sequences at the end of the 2004 season were virtually identical to the sequences from the beginning of 2004.

As noted in the Manila report, the 2005 sequences in Thailand are closely related to the 2005 sequences from northern Vietnam, which show significant changes at the protein level.  Significantly more change would be expected at the nucleotide level.  These data add additional support to the notion that the new season brings news sequences via migrating birds and these new sequences represent recombination. 

Thus, while none of the 2004 Vietnam and Thailand isolates had dropped the arginine at the multi-basic cleavage site in HA, that alteration, which had been detected in 2003 and 2004 in Yunnan, Guangzhou, and Japan isolates, appeared in 2005 Vietnam / Thailand isolates via recombination.

These data also support concerns raised by detection of H5N1 in Qinghai in bar-headed geese.  These geese migrate from India, suggesting H5N1 in India in the same region of human meningitis / meningococcemia transmissions.  Moreover, H5N1 in the Qinghai Lake Nature Reserve allow for significant mixing of bird populations, creating the opportunity for more dual infections, recombination, and novel H5N1 sequences in the fall if 2005 when the geese migrate back to India.

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