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July 14, 2006

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this story is clearly mutating and evolving too. the earlier strains of it focused on "arrogant scientists in it for the glory" which always gave me a chuckle. (quick, name a glorified scientist.) it seems to be settling down into the issue of who owns gene sequences -- the people of the country where they're found, the researchers who discover them, or the world.

I'm still not clear what solution there is to advocate here. "Fuck Indonesia and publish 'em anyway"? Seems like a good way to get even LESS access in the region. Should the human-adpated virus be treated like a natural resource or a WMD?

That last is a real question, but pushing Indonesia through the UN in return for aid is different than what to expect from CDC, which has fewer excuses about soveriegnity. WHO will release whatever indonesia askes them to. But there's many countries besides Indonesia whoich have flu sequences including Turkey, China and Azerbaijan. We have leverage with some. Use it.

They treat flu as a WMD, part of their misguided approach to bioterror. NIH and NAMRU (US Navy) do not.

I'm with you on most of that, but didn't follow the part about CDC having fewer excuses about sovereignty. Do you mean that CDC is holding secret some sequences that have no nations-rights issues attached to them, or that the CDC is holding sequences that do have sovereignty issues attached but CDC hasn't signed any treaties and doesn't have to worry about those things?

Actually CDC is holding thousands of sequences and we don't know how many and we don't know why.

Nature 437, 458-459 (22 September 2005) | doi: 10.1038/437458a Flu researchers slam US agency for hoarding data

Better sharing of information would help vaccine design.

Influenza researchers are complaining that the poor sharing of data by the US disease-control agency is hindering their work.

Still reeling from accusations that his administration was unprepared for the hurricane that hit New Orleans last month, President George W. Bush called last week for an international partnership on influenza that would require countries facing an outbreak to share immediately information and samples with the World Health Organization (WHO).

But investigations by Nature have revealed widespread concern that too few of the flu data collected by the US Centers for Disease Control and Prevention (CDC) in Atlanta are made generally available. Experts say research would speed up if the CDC's influenza branch threw open its databases of virus sequences and immunological and epidemiological data.

"Many in the influenza field are displeased with the CDC's practice of refusing to deposit sequences of most of the strains that they sequence," says Michael Deem, a physicist at Rice University in Houston, who works on predicting flu vaccine efficiency.

Policy decisions, such as which vaccine to produce ahead of each flu season, are being made without the full data being available to the scientific community, he says. "The quality of their decisions, which can affect millions of people, cannot be checked."

Deem's criticisms are echoed widely, although most scientists are reluctant to speak on the record. "This is a very delicate issue. It is important to keep a positive working relationship with the CDC, and they do lots of things well," says one evolutionary ecologist. "But getting data from them has been somewhere between extremely difficult and impossible."

Researchers say they have no idea what or even how many flu sequences the CDC processes, but it is thought to be up to thousands each year. Apart from occasional large deposits accompanying published papers, required by journals, data are "coming through an eye dropper", says one bioinformatician at the US National Institutes of Health (NIH) in Bethesda, Maryland.

see also what should be done

The debate gets nasty. From the FluWiki link: "Anyone who blocks H5N1 sequences from the public databases is guilty of crimes against humanity." The complaints against the CDC may be legitimate, but as you point out when there is no information on how many sequences are being held, where they came from, or why they're being held, and the anti-CDC rhetoric gets that hyperbolic, I can't seem to address the problem thoughtfully.

I take exception to the "crimes against humanity" comment as well, though passions run high (that's filed in the Opinion section of the wiki, btw). As an analogy, I happen to disagree with the war in iraq, but I don't change that POV because there are vociforous anti-war protestors who use hyperbole at times.

But one doesn't need to know exact numbers... "thousands" will do, thank you. That's not in dispute.

As an analogy, I happen to disagree with the war in iraq, but I don't change that POV because there are vociforous anti-war protestors who use hyperbole at times. Right, but they didn't help bring you to your opinion either.

It seems to me that the first call should be for the CDC to come clean with how many sequences they're withholding under what classifications for secrecy. This piece from last year (which borrows verbatim much of the Nature article) says "The CDC's manual, issued on July 22, lists 19 different categories where information can be withheld from the public." One category, for example, is "Contractor Access Restricted Information" which may refer to deals they've brokered with vaccine developers.

I am not really trying to be difficult, and I'm certainly not comfortable getting in the position of defending the CDC keeping results secret. But I'm also not comfortable just assuming the CDC is out to kill us all. I can imagine some good reason for the secrecy -- say, if it's part of a deal that's going to make a vaccine ten times cheaper, that ought to be weighed. I just don't know what's going on, and it seems like no one else does either.

I am surprised not to find any defense of this policy on the CDC website. It seems that they should be ordered by Congress to reveal how many sequences they're withholding, and for what reason. And then we can all talk in an informed way about whether they should release everything at once.

I appreciate that that sounds slow and there is urgency here. On the other hand, at least some of these demands to release everything immediately date back to last September, and there doesn't seem to be much movement, except maybe heightened tension on both sides.

Actually, sequences have been begun appearing in GenBank regularly, so the pressure has had some saluatory effect. The letters from scientists like Steven Salzberg and Ilaria Capua have been appearing in Science and Nature, the letter from Kucinich and Gilchrest et al, didn't happen out of thin air, and other scientists publicly and privately are having their say.

I would be fine with your approach, and i think a good case could be made for some withholding (Webster, for example, says he's got some sequences that officially don't exist from places where bird flu is not reported). If the end result is more transparency, great.

But don't forget it's CDC and WHO (different agencies, different rules of engagement) that issue the pronouncements about 'significant/no significant mutations' that they may well have gotten wrong in Indonesia. Their obligation is quite high to ensure that the best scientists in the world get to study the data. The current system fails in that regard. and change comes slowly and painfully, or, left to their own devices, not at all.

Still, with all the emphasis that's been placed on the importance of openness when it comes to fighting avian flu, it seems a tad hypocritical for such vital data to be kept confidential. As soon as possible, the sequences should made public.
TIME got it right and so did Nature, Salzberg, Capua and the rest.

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