Effect Measure

The momentum is building to release the sequestered flu sequence data. The prestigious scientific journal Nature today published a strongly worded editorial, excerpts of which you can read Nature senior correspondent Declan Butler’s blog:

Indonesia has become the hot spot of avian flu, with the virus spreading quickly in animal populations, and human cases occurring more often there than elsewhere. Yet from 51 reported human cases so far — 39 of them fatal — the genetic sequence of only one flu virus strain has been deposited in GenBank, the publicly accessible database for such information.

Yet scientists outside the WHO networks have no access to these data. The problem last year spurred the US National Institutes of Health (NIH) to create a consortium to sequence and make public thousands of flu strains from humans and birds. Very quickly, this more open approach led to the useful discovery that viruses swap genes with each other more frequently than had been previously thought. (Nature; subscription required)

A Democrat (Dennis Kucinich) and a Republican (Wayne Gilchrest) are circulating a letter (.pdf) asking House and Human Services Secretary Michael Leavitt to require sequences obtained with DHHS funding to be deposited in GenBank, the publicly available respository of genetic sequences. Currently many sequences are being kept private by US agencies like CDC or deposited in a password protected database at Los Alamos National Laboratory for use by a Gang of Fifteen flu laboratories. Unacceptable behavior for scientists, and Nature is unequivocal about it:

When samples are sequenced, the results are usually either restricted by governments or kept private to an old-boy network of researchers linked to the WHO, the US Centers for Disease Control and Prevention, and the FAO. This is a far cry from the Human Genome Project, in which all the data were placed in the public domain 24 hours after sequencing. Many scientists and organizations are also hoarding sequence data, often for years, so they can be the first to publish in academic journals. With the world facing a possible pandemic, such practices are wholly unacceptable. Nature and its associated journals are not alone in supporting the rapid prior exposure of data when there are acute public-health necessities.

[snip]

Nature and its associated journals are not alone in supporting the rapid prior exposure of data when there are acute public-health necessities.

Declan Butler is a good reporter with good sources. He gives the opinion WHO will exert pressure to allow release of hoarded flu sequences by the end of the summer. Not fast enough for some, but a big step forward if it happens. We’ll see.

Meanwhile, my scientific colleagues need to get the message: if you hoard flu sequence data your reputation will suffer. Many of us will consider it a form of scientific misconduct in the context of “acute public-health necessities,” as Nature so delicately put it. Scientists I have admired and respected are now guilty parties, as are national health agencies like CDC and international ones like WHO. Flushing reputations down the toilet like this is a tragedy. I urge them in the strongest possible terms to make their flu data public. They can do so with a public statement of principle that includes all the accession numbers and appropriate requests to their colleagues to assign the proper credit in publications for use of the sequence data.

It’s past time.

Comments

#1 slovenia
June 30, 2006

I posted this comment on crofsblog. I’ll simply repeat it.

Is there a downside to naming and shaming individual scientists and institutions that refuse to make genetic information available? Could Nature and other like-minded journals simply refuse to publish ANY work on ANY subject submitted by those named and shamed entities?
I’m out of my depth here.
#2 Andy
June 30, 2006

Probably a silly question, but are governments worried that terrorists could use the public sequences to manufacture “designer” viruses of high virulence and H2H transmissibility? Should one be worried about such a scenario?
#3 revere
June 30, 2006

Andy: Not a silly question but it would be a silly thing to do. This is an uncontrollable virus so the only purpose would be if you were some kind of apocalyptic end times nut and wanted to wipe everyone out. It would serve no political purpose. On the more micro level, we don’t understand the virulence factors well enough to do this anyway. You’d have to be one smart nutcase to turn this info to account and even then you aren’t likely to succeed. This is very difficult science, now occupying some of the most experienced scientists on earth in this area. You couldn’t do it in garage in Hamburg or a ranch in Montana or even a lab in Iran.

Bottom line: we don’t know how to do it, the blowback would be horrific and the benefits of putting more minds and hands to work figuring out how to predict and control a pandemic weighs overwhelmingly in favor of having the sequences public. We have been looking at molecular determinants of Tamiflu resistance with molecular modeling techniques. We can’t do this without the sequences and the protein structures.
#4 Andy
June 30, 2006

Revere: Thanks for the answer; it makes a lot of sense. However, my question really was about the _perception_ on the part of (some?) governments that keeping the sequences out of public hands would be _seen_ as part of the GWOT, similar to the other (silly) things that these governments are doing. Could that be a rationale, albeit a _very_ bad one, for the secrecy?
#5 revere
June 30, 2006

Andy: Of course what you suggest is possible. But governments are not people, they are made up of people. The decision to release sequences would have to involve people with technical knowledge. It’s not like a City Council deciding whether to put the tax assessments up on the internet.

What has happened, I think, is government agencies (or people within them) using the GWOT as an excuse. I believe CDC did this at one point regarding these sequences, although nobody takes them seriously and they know it’s bullshit. NIH automatically deposits there sequences immediately in GenBank. So I think it’s not as much perception as a convenient excuse. It is inexcusable, therefore, in two senses.
#6 Dizzy
June 30, 2006

Today’s BF report on the BBC website is headlined Bird flu vaccine ’10 years away’. What difference will it make to release sequences?

Dr Fedson, at one time a director of medical affairs at Aventis Pasteur, who is quoted in the report, says
“Why can’t governments be driving the boat on this? Especially in the UK. Your experience of developing the meningitis vaccine is a role model of how to do it. The Department of Health said they would be in control, be in charge of data; they said here’s the schedule and we have the money – from A to Z, the process worked like a charm.”

He goes on to say there’s no point blaming the vaccine manufacturing companies who make hard-nosed decisions about where they are going to make their profits.

Aha. So no responsibility lies with those who shelved their vaccine manufacturing capabilities for more profitable ventures, only with those who still have them. But could it be that now we don’t have the money, having pissed it away on assaulting Iraq? Will we see an influx of international investment to address an international problem, or just more finger-pointing and tutting at a few small countries?
#7 Name
June 30, 2006

A poster over on Crofsblog notes that clinical data on human cases are also not being released, that this info could be vitally important in guiding treatment protocols and that this failure is even more inexcusable. What are your thoughts on this, Revere.
#8 revere
June 30, 2006

Name: Was just “penning” a post on this subject (more or less). Probably the crofsblog post was a result of the CP article on age distributions which is my take off point. Tomorrow a.m., likely.
#9 Jun
June 30, 2006

Petition to release H5N1 sequences:

http://www.petitiononline.com/h5n12006/petition.html
#10 Thinlina
June 30, 2006

Give us the names! Give us the heads!

Or is this just another a fraud of the Bush administration? What if there is no such REAL thing than H5N1? Just another way to keep peoples in leash of fear… Not my thought but a thought widely held in Europe.

Why would anyone keep the knowledge to themselves in a situation like this?
#11 another
July 1, 2006

Time to name names. If they want to flush their reputations, may as well give them some help. Or at least jiggle the handle and publish initials.
#12 Dr.C
July 2, 2006

I think if releasing the sequences was a “threat to security” of the US for the GWOT, the US Navy wouldn’t have released their sequences, which they have already done. The CDC really has no excuse.
#13 Anon
July 4, 2006

“They can do so with a public statement of principle that includes all the accession numbers and appropriate requests to their colleagues to assign the proper credit in publications for use of the sequence data.”

Even better, why not just stipulate that the sequences can only be used for public health or disease control purposes and are not available for publication or commercial gain?

If this was the case then the scientist working in the field would have their interests protected and anyone that is asking for the release of the sequences for disease control also has nothing to complain about.

Except that I think this would not satisfy as there are people out there (the loudest ones) who would like to use the seuqence data for their own promotion (either through publication or commercial gain) and who use the “public health” reason as a smoke screen.
#14 revere
July 4, 2006

anon: Because we want them published. That’s how the scientific community gains access to them. Publication is a stronger motivator than money for most scientists and that’s as it should be. I have no problem with that. But journals could refuse to publlish articles whose sequences weren’t already deposited in GenBank at the time of submittal of the paper, at least. This doesn’t solve the problem completely but it would help a great deal.
#15 Dizi ozetleri
December 5, 2007

thanks