Saturday, March 04, 2006

Let's see the sequences

Good for Ilaria Capua of the Istituto Zooprofilattico Sperimentale delle Venezie in Italy. She is asking her scientific colleagues to make all their H5N1 sequence data public immediately. No hoarding while they write papers. No holding back so others can't write papers using their data. No time for that kind of nonsense now. Brava!

Capua made good by depositing her own data from Nigeria and Italy into the publicly accessible GenBank database and refused to join a small group of labs that share sequences on a protected site at Los Alamos National Laboratory. The LANL scheme is supported by WHO, but the UN's Food and Agriculture Organization (FAO) and the World Organisation for Animal Health (OIE) support Capua, whose own lab is an FAO reference lab.

Here is the LANL argument:
WHO, FAO, and OIE encourage countries to send virus samples to specialized reference labs that can confirm the outbreak and study the virus further. Some have been reluctant to do so because they worry about intellectual-property rights or not receiving a fair share of the scientific credit; China, for instance, has not shared any avian samples for a year, a WHO spokesperson says. But even when reference labs do get their hands on a virus, they don't always release the data immediately.

For instance, in the past few months, H5N1 samples from about 15 European countries have been sent to the Veterinary Laboratories Agency (VLA) in Weybridge, U.K., a reference lab for OIE and the European Union. Lab director Ian Brown says he's sharing sequence and other data with governments and the international agencies; to show support for Capua's campaign, he also submitted the sequence of a virus from an outbreak in Turkey that he says is a "progenitor to the European epidemic" into GenBank last week. However, until a paper about the European outbreaks--which he says could be submitted in a matter of weeks--has been accepted, Brown says he needs to hold on to the European sequences. "The staff in this institute is working 24/7 to provide this service," he says. "I don't think it's unreasonable to expect … for their endeavors." It also takes time to negotiate the conditions of release with dozens of individual governments, Brown says. (Martin Enserink in Science)
This is not a new problem. We have posted on it frequently. But we are in a new situation and the old ways don't make it anymore. These days if you don't want to share your influenza data, then study something else. I am a scientist and I know what it means to spend months and -- in the case of my field, chronic disease epidemiology -- years collecting data. Many of my colleagues have been similarly reluctant to provide raw data (confidentiality issues aside) because they don't want someone else to scarf up the cream of their hard work.

That was then. This is now. Capua's got it exactly right:
Capua counters that just isolating and sequencing a virus that comes in the mail does not give researchers the right to sit on the data--especially not at a government lab. "Most of us are paid to protect human and animal health," she says. "If publishing one more paper becomes more important, we have our priorities messed up." Governments can often be persuaded to release the sequences, adds Capua, who repeated her call at an OIE meeting in Paris on Monday and also plans to submit it to ProMED, an e-mail list about emerging infectious diseases.
Frankly, the whole business stinks to high heaven. Scientific data, especially data collected at public expense, should be public from the outset. Journals shouldn't be requiring copyright, either. No one should need permission to see and use data and research done at public expense. Scientists and government agencies in China, Turkey, UK, the US and elsewhere who are not sharing their flu sequences should be held up to ridicule and censure.

I am a long time academic (and journal editor) who understands and is even sympathetic to the usual way scientists behave. Publication, priority and credit are the coin of the realm in our world. They have real implications for people's careers and motivations. But at this moment in time the blogger and public health professional in me has another reaction to those concerns: too fucking bad. Scientists, agencies and governments who sit on the their flu sequences should be pilloried, reputations impugned and careers should suffer. Let's reverse the incentives.

Make your sequences available in GenBank. All of them. Now.