Rostov Chicken and Starling H5N1 Sequences Match
Recombinomics Commentary 17:04
February 25, 2008
Wild bird H5N1 sequences associated with a poultry outbreak in Rostov on December 14, 2007 are being released at Genbank. Complete sequences for all eight gene segments were generated, and the starling sequences, A/starling/Rostov-on-Don/37/2007 are virtually identical to the chicken H5N1 sequences, A/chicken/Rostov-on-Don/35/2007. Five of the gene segments (PB1, PA, HA, NP, NS) are exact matches, while the other three gene segments (PB2, NA, MP, differ by one nucleotide each.
This high level of identity parallels results from an outbreak in Krasnodar, where chicken and whooper swan sequences were over 99.95% identical (6 differences in over 12,000 positions). These examples demonstrate the level of identity in isolates from a common source and provide additional compelling data linking poultry outbreaks to H5N1 circulating in wild birds in the region of the outbreak. The above sequences were clade 2.2.3. As noted previously, the Krasnodar sequences trace back to the Uvs Lake wild bird outbreak in the summer of 2006 as do most of the recent sequences from Europe, as well as 2007 isolates in Kuwait and Saudi Arabia. However, although all of these sequences trace back to Uvs Lake, they are readily distinguished from each other (but these recent sequences also have NA G743A)..
The recent outbreak in mute swans in England are also closely related, although the percent identity is well below the 99.9% which is characteristic of a common as seen above or seen in chicken, duck, and cat isolates from Romania, which had identical HA sequences.
Thus, sequence analysis can be used to trace origins and readily distinguish between infections by a common source, or independent introductions, as seen in the mute swan population in Dorset, England.
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