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H5N1 Swan Sequence From Italy
Recombinomics Commentary
February 25, 2006
The H5N1 sequence, A/swan/Italy/179/06, was made available at Genbank today. The swan was described in the OIE report of February 14. The H5N1 was isolated February 10, submitted to Genbank on February 24, and made available today. Like the recent deposits from Astrakhan, Nigeria, and France the sequences are closely related to the H5N1 Qinghai consensus sequence. The Italian swan 1247 BP sequence of HA had nine polymorphisms that differed from the consensus sequence. One was found in the Novosibirsk sequence, A/duck/Novosibirsk/56/2005. The remaining polymorphisms were unique and most were present in recent H5N1 isolates from eastern or southeastern Asia. However, most could also be identified in older isolates from North America.
These data further support the acquisition of polymorphisms via multiple recombinations. These acquisitions require dual infections and the sharing of the polymorphisms indicates extensive exchange of polymorphisms between North America and Europe, Asia, and Africa. Astrakhan sequences that are shared only with North American isolates have also been described, suggesting H5N1 has recently migrated to North America. Similarly American sequences have been described in H5N2 isolates from South Korea, Taiwan, A/chicken/Taiwan/1209/03 and Japan. Although HPAI H5N1 has not been reported in North America, the shared polymorphisms strongly suggest that H5N1 has previously migrated to North America.
Canada did an extensive study of young ducks banded in the fall of 2005. These ducks were swabbed and H5 was found in a surprisingly high percentage of ducks. The isolates included sero-types H5N1, H5N2, H5N3, and H5N9 and all were reported to be LPAI. However, the only sequence deposited at GenBank was an H5N2 isolate, A/duck/BritishColumbia/CN26-6/05 from a farm duck in British Columbia. The other isolates were described as "North American" sequences, but have not been made public.
The withholding of this data is cause for concern. The tracing of shared polymorphisms can determine origins of sequences and identity recombination frequencies. The presence of the large number of H5 sequences in southern Canada and the failure to subsequently identify additional H5 sequences in Canada or the United States raises significant question about surveillance methods and reporting. H5N1 in north Canada in the summer of 2005 would have been expected to migrate south in the fall and winter, as would the H5 sequences in the banded ducks.
H5N1 is clearly expanding its geographical reach. First time reports of the Qinghai strain have been recorded throughout Europe, the Middle East, and Africa. It is likely that the H5N1 in India is also the Qinghai strain and it is many neighboring countries that have not reported the virus. As H5N1 expands, it encounters hosts infected by other influenza isolates, offering new opportunities for recombination and creation of new genes.
Italy, France, and Russia are to be commended for the rapid isolation of H5N1 and the availability of sequence data. Similar deposits by other countries as well as expansion of sequences to include all eight genes would be useful in tracing the path and evolution of H5N1.
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