Indonesia Allows Release of Human H5N1 Sequences
Recombinomics Commentary
June 1, 2006
The sequences of virus from the victims of the Indonesia cluster have not been made public. Why not? In the article, there is much buck passing among the three actors involved.
1.”Malik Peiris, a virologist, doing a great honest job at the University of Hong Kong who sequenced the virus, declined to comment on any mutations, saying that making sequences public is not his call. “Our job as a WHO reference lab is to report back to the originating country and the WHO,” he says.”
2.”The WHO also declined to give any details. “We will leave that to the government of Indonesia, the owner of the data,” says Bjorge.”
3. In an email received from the Indonesian government after my deadline, it states with respect to making data public: “We are fully aware of the threat of the next influenza pandemic. And Indonesia is fully supporting whatever measures are considered necessary to prevent, control and contain a potential pandemic.
The above comments from Declan Butler's personal blog expand on issues raised by him in today’s Nature news article on the large familial cluster in Sumatra. The cluster is the largest reported to date from Indonesia and is a clear example of H5N1 transmission from the index case to family members to an additional family member (H2H2H).
Although WHO provided a description of the sequences of H5N1 from family members, the description had more information what was not said than what was said. One interpretation of the statements indicated the H5N1 was amantadine resistant with M2 polymorphism S31N, and was virulent with PB2 polymorphism, E627K, and had a wild type H5N1 HA cleavage site, RERRRKKR. None of these issues were spelled out in the update and Malik Peiris declined to comment on specific questions about these changes. The WHO statement indicated that there was no reassortment with human or swine sequences and no “significant mutations”.
Many would consider the above data “significant” because it would indicate that the H5N1 was resistant to treatment with amantadanes, and as more virulent and transmissible because of the acquisition of the human polymorphism, which allows the polymerase to be more active at lower temperatures found in the nose and throat, thereby make the H5N1 more transmissible to those in close contact to a coughing infected patient as described in the earlier WHO update.
Additional questions on H5N1 sequences in Indonesia have been raised by Andrew Jerimijenko, former head in ifluenza surveillence - US Naval Medical Research Unit 2 in Jaklarta, because the only human sequence made public had a novel cleavage site, RESRRRKKR, and reports indicate that all but one of the human sequences from the West Java region have the novel site, but no published poultry sequences have that change, raising concerns that the human infections are from a source other than poultry. If so, testing would produce a serious undercount human cases because testing is largely limited to patients with links to dead or dying poultry.
The one human sequence that has been made public is from the first reported H5N1 case in Indonesia. Although the CDC deposited the sequence at Los Alamos on August 1, 2005, it was not released to the public until March 25, 2006, after it was selected as a new target for a pandemic vaccine being developed in the United States.
Only two of the eight gene segments (HA and NA) have been released from this isolate, A/Indonesia/5/2005, and no sequences of the other human isolates, including those from the Sumatra cluster, have been released.
Instead, there has been a great deal of buck passing, but in reality the labs that generate the sequences control the release of the data and several have just tried passing the buck to the WHO and/or the governments of the countries of origin, such as Indonesia.
As noted above, Indonesia has indicated that the data can be released, and those sequences, as well as those deposited in the WHO private data base from Weybridge and other agencies, should be released immediately.
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