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Friday, July 11, 2008

Why public health requires open data

Brandon Keim, Crowdsourcing the Flu Vaccine, Wired Science, July 10, 2008.  (Thanks to Glyn Moody.)  Excerpt:

A bit of data sharing and networking could prevent a repeat of last winter's catastrophic flu vaccine failure.

Selected six months before each flu season by an expert World Health Organization panel, the influenza vaccine is made from three common strains of the virus....For the last half-century, the system worked. But last season was different: By the time the vaccine went public, a real-world strain had already mutated. People who received the vaccine were no better protected than those who didn't. Influenza and pneumonia mortality in the United States reached epidemic levels and stayed there for five months.

It's unknown whether the disaster could have been averted. But according to University of Maryland bioinformaticist Steven Salzberg, it was enabled by the WHO's old-fashioned approach: The meeting was open only to select invitees, depriving them of the expertise of other virologists and geneticists. Data used to justify their decision was released only afterward, in limited form. The genomes of circulating flu strains weren't shared with the scientific community.

"I can't be sure that a more open process would have prevented the epidemic, but it's possible, maybe even likely," said Salzberg, who argued his case in a commentary published yesterday in Nature....

"I wouldn't change the people responsible for the final decision, but had the process been more open, it's possible that other voices would have spoken up and said, 'You can't leave the strain the same,'" said Salzberg. "That's how science works. The process works better when everyone gets to contribute." ...

"What if there was an open process, and there were 100 scientists trying to grow it in eggs? It's not a secret technology," said Salzberg. "Someone else might have stepped forward and said, 'I've got a good match and this one grows in eggs.'" But the WHO and Centers for Disease Control and Prevention don't share up-to-date flu genome sequences. Nobody else could help.

"Sequence data is very easy to share if you're willing to share it. It's just data," said Salzberg, who cites as relevant examples the GISAID bird flu database and the Influenza Genome Sequencing Project, started by Salzberg and NIH biologist David Lipman.

"The architecture is there. It's already been scaled up. All they have to do is put the sequences in there...," he said.

From Salzberg's paper in Nature:

...The WHO and the CDC have stated publicly that they support placing sequence data in the public domain. Unfortunately, the WHO’s own centres do not release all their influenza sequences, and when they do, they often use the Los Alamos National Laboratory influenza database. This database is, as reported on its own website, “a private database for collaborators” — access is restricted to a private group of subscribers. A closed database limits the free exchange that is so important to scientific research, and it sets the wrong example....

Nature's editorial in the same issue calls for redoubled efforts to prepare for an avian flu pandemic, but doesn't comment on Salzberg's call for open data.

Related:  See my past posts on OA to avian flu data.