H5N1 Poultry Matches in Indonesia
Recombinomics Commentary
February 12, 2007
Recent poultry H5N1 sequences from Indonesia match sequences from human cases. Eighteen HA sequences from H5N1 isolates in Indonesia were made public via the Los Alamos flu database. These sequences were collected in 2006 and most were collected between May and September. In contrast to earlier collections from poultry, most of these sequences (see 12 isolates below), had the novel HA cleavage site RESRRKKR.
Previously, the vast majority of poultry sequences from Indonesia had the common HPAI cleavage site, RERRRKKR. Only one poultry sequence from Java had the novel cleavage site, yet every human H5N1 sequence from Java since August 2005 had the novel cleavage site, including sequences from isolates collected this year.
The matches from the more recent isolates indicates the version found in patients is more common in poultry isolates from West Java and Jakarta, the location of most reported cases in Indonesia.
These data suggest infections from poultry will be more common, unless the latest sequence represent a significant difference in sampling. 12 of the 14 samples from Jakarta or West Java have the novel cleavage site, which is cause for concern.
Media reports of H5N1 positive birds throughout Indonesia are common, and the number of confirmed human cases has risen this year. Submission of sequences from the most recent cases has been suspended, pending the creation of a materials transfer agreement preserving commercial rights in association with the samples.
The increase in the sequences from poultry and patients with the novel cleavage site indicates the H5N1 continues to evolve, and current sequences are required to make the most effective vaccines.
A/Chicken/West Java/PWT-WIJ/2006
A/Chicken/West Java/SMI-CSLK-EB/2006
A/Chicken/West Java/SMI-CSLK-EC/2006
A/Chicken/West Java/SMI-ENDRI1/2006
A/Chicken/West Java/SMI-ENDRI2/2006
A/Chicken/West Java/SMI-PAT/2006
A/Chicken/West Java/TASIK1/2006
A/Chicken/West Java/TASIK2/2006
A/Chicken/West Java/TASIKSOB/2006
A/Chicken/West Java/TASIKSOL/2006
A/Muscovy Duck/Jakarta/HABWIN/2006
A/Quail/Jakarta/JU1/2006
Media sources
Phylogenetic Trees