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Acquisition of Asian Sequences by H5N2 in British Columbia
Recombinomics Commentary
March 5, 2006
Recent analysis of sequences in Astrakhan isolates has identified polymorphisms that are found in North America, raising the possibility that H5N1 has already migrated to North America. In 2005 Canada surveyed young ducks that were swabbed in August as part of a banding study. Although HPAI H5N1 was not identified, a surprisingly high number of H5 isolates were identified. In British Columbia 24% of the isolates were H5. However, H5 isolates were found throughout southern Canada. Although the bird flu sequences were said to have similarities with prior North America isolates, the sequences have not been deposited and therefore have not been analyzed fro H5N1 polymorphisms.
The only sequences deposited was an H5N2 isolated, A/duck/British Columbia/CN26-6/2005, from a farm duck. Only partial HA and NA sequences were deposited. The larger N2 sequences shared polymorphisms with a number of N2 isolates from Asia. A few of these polymorphisms were also found in H5N2 isolates from California or Texas, but the majority of the sequences were H9N2 isolates from Asia, as shown by one of the representative polymorphisms shown below.
Because the polymorphisms are acquired by recombination, these newly acquired polymorphism can be used to create a historical path for the polymorphisms. These past histories are most useful when applied to a robust sequence database. Moreover, a current database can be used to track recent and future movements of the virus as well as new recombinations base on the prevalent strains in the area.
Most of the recent isolates however, are not publicly available. They have been placed in a private database maintained by WHO. The WHO announcements on the sequences indicate that they are evolving via "random mutations" and future changes cannot be predicted. However, because the changes are primarily due to recombination, co-circulation of parental sequences can be used to predict recombinant.. Changes have been predicted for the receptor binding domain. As predicted, S227N appeared in the Middle East in the fall, and a Spring acquisition by H5N1of G228S in Europe has been predicted.
A robust and current database would allow for additional predictions. WHO should immediately release these sequences.
G179A
DQ309439 A/duck/BritishColumbia/CN26-6/05 2005 H5N2
AY790307 A/swine/Korea/S452/2004 2004 H9N2
AY790277 A/swine/Korea/S81/2004 2004 H9N2
AY800235 A/chicken/Korea/S1/2003 2003 H9N2
AY862633 A/chicken/Korea/S12/03 2003 H9N2
AY862637 A/chicken/Korea/S16/03 2003 H9N2
AY862638 A/chicken/Korea/S18/03 2003 H9N2
AY862631 A/chicken/Korea/S4/03 2003 H9N2
AY862632 A/chicken/Korea/S5/03 2003 H9N2
AY862635 A/dove/Korea/S14/03 2003 H9N2
AY862634 A/duck/Korea/S13/03 2003 H9N2
AY862630 A/silky chicken/Korea/S3/03 2003 H9N2
AY300945 A/turkey/CA/D0208652-C/02 2002 H5N2
AY262367 A/chicken/Hebei/1/01 2001 H9N2
DQ064412 A/chicken/Guangdong/4/00 2000 H9N2
DQ064419 A/chicken/Hebei/31/00 2000 H9N2
AY180813 A/Chicken/Nanchang/1-0016/2000 2000 H9N2
AY180815 A/Chicken/Nanchang/4-010/2000 2000 H9N2
AY180819 A/Duck/Nanchang/1-0070/2000 2000 H9N2
AY180825 A/Duck/Nanchang/7-092/2000 2000 H9N2
AY180828 A/Pigeon/Nanchang/7-058/2000 2000 H9N2
AY180829 A/Quail/Nanchang/2-0460/2000 2000 H9N2
AY180820 A/Quail/Nanchang/4-040/2000 2000 H9N2
AF222658 A/Chicken/Hong Kong/KC12/99 1999 H9N2
AF536717 A/Chicken/Liaoning/99 1999 H9N2
DQ064429 A/chicken/Ningxia/4/99 1999 H9N2
AF508583 A/Chicken/Beijing/8/98 1998 H9N2
DQ064434 A/chicken/Beijing/8/98 1998 H9N2
AF536714 A/Chicken/Hebei/2/98 1998 H9N2
AF536715 A/Chicken/Hebei/3/98 1998 H9N2
AF508586 A/Chicken/Hebei/4/98 1998 H9N2
DQ064424 A/chicken/Henan/5/98 1998 H9N2
AF536716 A/Chicken/Henan/98 1998 H9N2
AF536710 A/Chicken/Beijing/2/97 1997 H9N2
AF508595 A/Quail/Shanghai/8/96 1996 H9N2
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