Open Access News

A leading scientist in the field of genetic sequencing is calling on publicly funded U.S. researchers and research organizations to throw open their collections of H5N1 avian flu viruses to allow others to work toward lessening the pandemic threat the virus poses. Steven Salzberg wants the U.S. Centers for Disease Control as well as researchers funded by the National Institutes of Health to place their virus sequence data in open-access databanks on an as-processed basis. He hopes such a move would entice scientists elsewhere, as well as governments in H5N1-afflicted countries, to end a pattern of virus hoarding many believe is undermining the world's ability to battle H5N1. "I think what ought to happen is that the U.S., starting with people funded by NIH and the CDC itself ought to start releasing all of their data and all of their samples — and lead by example," says Salzberg, director of the Center for Bioinformatics and Computational Biology at the University of Maryland. "Because one complaint I've heard from other scientists in other countries is: 'Hey, the CDC in the U.S. doesn't release all their data. So why should we?' And that's a very legitimate complaint."...Salzberg was involved in the historic human genome sequencing effort as well as the teams which sequenced the first plant genome, Arabidopsis (mustard weed) and the parasite that causes malaria. Most recently, he has been working on an NIH-funded project that is sequencing vast numbers of human flu viruses.

He is adding his voice to a campaign started by Dr. Ilaria Capua. An Italian influenza researcher, Capua is challenging the current system which gives a small network of prominent flu labs preferential access to data by virtue of the fact they do testing and surveillance for the World Health Organization. These labs register their findings in a secure database so that they and the WHO can track changes in H5N1 viruses. But those virus sequences are slow to trickle out to the rest of the research world. (Typically, scientists only post data publicly when they publish findings in a journal, a process that can take months or more.) Capua was offered a chance to join the 15 labs with access to the WHO's secure database after she sequenced H5N1 bird viruses from Nigeria and Italy, according to a recent article in the journal Science. She turned down the offer, choosing instead to place her sequence data in the open access database Genbank. Limiting who can work on the WHO data isn't just hindering science's ability to crack the mysteries of H5N1's incredible virulence, critics say. It also hampers efforts by countries outside the WHO network to keep their H5N1 diagnostic tests up to date....The WHO is hearing the growing chorus of complaints. But to some degree its hands are tied. The viruses belong to the countries where they were collected. WHO cannot force them to share. And it doesn't own — or pay — its collaborating labs, which are doing huge amounts of science for the global good.

Update. The Daily Kos is collecting links to related calls for OA to flu genome data. (Thanks to Scott Burns.) Excerpt:

We need your help to make sure scientists in the US and abroad working on this issue have access to all the data they need. The next effective vaccine may require sequences from Indonesia, China, or who knows where....The US should be leading the way in transparency and open access. Don't let politics get in the way of science. Support Dr. Capua and the other renowned scientists here and abroad in liberating the H5N1 sequences and let them be deposited in GenBank and the other Open Access repositories.

Update. Recombinomics, Inc., a for-profit company working (inter alia) on H4N1, supports the call for OA to sequence data collected by WHO. From its 3/10/06 press release:

Recombinomics fully supports the appeal by Dr. Llaria Capua of the OIE/FAO Reference Laboratory for Avian Influenza at the Istituto Zooprofilattica Sperimentale delle Venezie in Padova, Italy to allow influenza researchers worldwide open access to H5N1 sequences collected by the WHO. Currently, most of the recently collected H5N1 gene sequences are sequestered in a private, WHO controlled database, which can only be accessed by 15 laboratories. These sequences should be made available immediately to the general scientific community. The sequences are essential in pandemic vaccine development and should be accessible to all. This week the United States government announced a new pandemic vaccine target, the H5N1 sequence from a patient in Indonesia. Although available sequences indicate several pandemic vaccine targets would be desirable, the utility of the chosen sequence cannot be independently evaluated because none of the H5N1 sequences from human patients in Indonesia are publicly available.

PS: Does Recombinomics provide OA to its own flu virus sequence data? The press release doesn't say.