Indonesia Pledges to Release H5N1 Bird Flu Sequences
Recombinomics Commentary
August 3, 2006
Indonesia's health minister, Siti Fadilah Supari, said the country will deposit avian flu virus data in GenBank, a public database of genetic sequences, according to today's Bloomberg report. She said data from the recent family case cluster in Sumatra involving person-to-person transmission would be included.
The journal Nature reported Jul 28 that until very recently, Indonesia had shared few, if any, H5N1 virus samples from birds over the past year.
The above comments indicate Indonesia has pledge to release the H5N1 sequences in the private WHO database at Los Alamos. These sequences can be released by simply removing the password protection. This was recently done for the human H5N1 sequences from Turkey, which were sumitted by the WHO H5 group and have the characteristic ISDN numbers assigned at Los Alamos.. Earlier, this was also done for H5N1 from the first human case in Indonesia. Although that sequence was deposited in the WHO data base on August 1, 2005, it was not released until March 25, 2006.
The phylogenetic tree from the H5N1 meeting in Jakarta has 37 human HA sequences. Only one is public, which is A/Indonesia/5/05(H5N1), the index case for the country. The only other gene segment from that patient is the NA sequences. The other six sequences from this patient as well as all eight sequences from the 37 patients described above have been sequestered at the WHO database. These human sequences do not match public avian sequences from Indonesia (or any other location). 91 recent avian samples have been sent to Australia for sequencing. The human and recent avian sequences will be useful in the interpretation of the evolution of H5N1 in Indonesia as well as predictions of future vaccine target sequences..
Similarly, there are about 100 sets of sequences from Europe that also remain sequestered although Weybridge has promised to release these sequences, which represent many of the isolates from Europe and the Middle East. Examples of reassortment in Israel and India have already been identified in the limited number of public Qinghai sequences.
Release of all eight gene segments from these isolates would be useful.
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