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H5N1 Wild Bird Sequence From France

Recombinomics Commentary

February 24, 2006

Partial HA and NA sequences from the first H5N1 isolate in France, A/common pochard/France/06167/2006(H5N1), has been placed on deposit.  The French are to be commended for rapidly making these valuable sequences available.  It seems that these are the sequences described in the recent OIE report.  H5N1 was confirmed on Feb 17, the sequences were deposited Feb 21, and viewable by the public today.

The sequences are clearly the Qinghai strain.  The HA sequence was 241 BP and differed form the Qinghai consensus sequence at two positions.  Both polymorphisms were synonymous and were shared with H5N1's from eastern China.  The NA sequence was 688 BP and had three polymorphisms that differed from the consensus sequence.  One was shared with the Mongolian and Kurgan isolates and was synonymous.  The other two were non-synonymous.  One was found in H5N1 from China while the other appeared to be acquired from H5N1 PB2 sequences.

The isolate from Nigeria also had some polymorphisms share with the Kurgan and Mongolian isolates.  Sequences from additional genes would help determine the relationship between the French and Nigerian isolates as well as the relationship to the H5N1 on the turkey farm.  These regional polymorphisms are useful in tracing origins.

For the Astrakahn mute swan sequences, there were polymorphisms from North America as well as Hunan Province.

Since it is common for polymorphisms to be acquired by recombination, these rare polymorphism help trace the prior travel history of the various isolates.  Therefore deposit of full sequences from all eight genes are useful for determining origins and migration patterns of the various Qinghai isolates circulation in Europe, the Middle East, and Africa.


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