Is the government hiding something about the next flu pandemic?

Remember the flu pandemic? The one that swept the world just two years ago? You might be forgiven if this has slipped your mind - after all, it doesn't seem like such a big deal now. That's because we got lucky: despite many dire warnings about the danger of another 1918 "Spanish flu", when the 2009 pandemic arrived, it was far milder than previous pandemics. Hundreds of millions of people got the flu in 2009, but for most of them, it wasn't so bad. In fact, the new flu is less severe the old flu - the strain that was circulating before the new pandemic hit.

Now we have two flus circulating: the "old" H3N2, and the 2009 pandemic flu, called H1N1. (And the vaccine protects against both of them, so get your flu shot! Your friends, neighbors, and co-workers will all benefit.)

We really dodged a bullet in 2009. Despite our best efforts, it took 7 months (April to November) before a new vaccine was ready. Before we realized how mild it was, people were desperately snapping up stores of Tamiflu, an anti-viral medicine that only barely helps to treat the flu. If it had been like 1918, Tamiflu wouldn't have helped much, and tens of millions would have died.

The 2009 pandemic originated in pig farms in Mexico. We don't know precisely where it made the first leap into humans, but it appears that two different strains joined together in a pig somewhere to create the new H1N1. The flu has a nasty habit of jumping the species barrier, hopping to humans from both pigs and chickens.

So now that we know all this, next time will be different, right? The world's influenza scientists are monitoring pigs and chickens closely now, keeping a close eye on any new flu strains. Right? RIGHT???

Er, no. Not exactly. For one thing, surveillance in pigs appears to be nonexistent. I checked to see how many flu sequences from pigs in Mexican have been desposited in the public archive at GenBank since 2009 (using this terrific database). The result? One, in 2009. Nothing from 2010 or 2011. Hello, is anyone awake at the CDC and the WHO?

This despite the fact that scientists have serious concerns that the deadly H5N1 avian flu (the "bird flu") could combine its genes with H1N1 and create a really nasty new flu strain. And scientists have long had concerns that pigs could be the mixing vessels for new flu outbreaks - exactly what happened in 2009.

But wait… maybe they are monitoring the flu, but they're just not telling us. That would feed into all the fringe government conspiracy groups that claimed the 2009 pandemic was an intentionally engineered government-funded enterprise (see this BMJ article for more). I don't believe any of those conspiracy theories - most of them are just nuts - but read on.

Sharing data about flu viruses has been a touchy subject with the WHO and the CDC for years. As reported by the University of Minnesota's CIDRAP,
"In late 2006, virus sharing became an international flash point when Indonesia broke a long tradition of free international sharing of flu virus specimens by withholding its H5N1 virus samples as a protest against the high cost of commercial vaccines derived from such samples. The controversy has drawn attention to the problem of equitably distributing vaccines in the event of a pandemic."
A few months ago, the WHO finally agreed on a new set of principles on data sharing, which states that
"The WHO GISRS laboratories [which includes the CDC] will submit genetic sequences data to GISAID and Genbank or similar databases in a timely manner."
Excellent! If they do it.

As every biomedical scientist knows, GenBank is a free, public database of genetic sequence data that contains millions of sequences, from humans, bacteria, viruses, you name it. But GISAID is another database, in Switzerland - one that I initially supported - just for flu data. The original mission of GISAID was that data deposited there would go to GenBank as well, with little or no delay. But in a classic bait-and-switch move, the GISAID board changed that policy after the database was up and running, and now they can sit on data as long as they want.

OK, you say, but it's a private database, so they can do what they want. True enough. But here's the surprising bit: the CDC deposits most of its flu sequences ONLY in GISAID, where they can milk them for scientific results for years without sharing them with others. As one of GISAID's original supporters, I have an account there, and here's what I found.

So far, the CDC has deposited sequences from 6,801 flu isolates in GISAID, of which only a tiny handful are in GenBank. 3201 of these originated in the U.S., so there can't be any foreign government insisting that they be kept secret. These provide critical data that could help scientists predict what is coming in the next flu season. But you can't get these sequences without a GISAID account. And even if you have a GISAID account, as I do, you have to agree not to release the data as a condition of getting a look.

So why does the CDC deposit sequences in GISAID? I think it's precisely because of the restrictions. CDC's scientists don't want others to look at "their" data, because they're afraid someone else might discover something important and publish it before them.

The CDC, of course, is part of the U.S. government, and all its work is funded by the public. But it seems that the CDC flu scientists have forgotten their public health mission - or at least, they appear to be more concerned about their own careers (and the papers they might publish) than about making sure the world is ready for the next pandemic.

And by the way, even these sequences don't seem to include anything from pigs in Mexico. Hello, CDC? You are looking at swine flu now, aren't you?

Perhaps I'm being a bit harsh. I love the CDC: they do a terrific job most of the time, providing vital services to protect the public from infectious diseases. But their internal scientists sometimes seem to operate within a cocoon, and I'm afraid that's happening here. This culture of secrecy has got to stop, and I suspect that will only happen under pressure from the outside. The CDC Director, Thomas Frieden, needs to tell his flu people to start sharing what they know with the rest of the world. And they can start by putting their data in GenBank.


  1. The picture cracks me up :) I have to admit, I've been curious about exactly how the virus jumps species.

  2. Another instance of "gratuitous meanness," as my late friend Guy Davenport called it.

  3. Excellent piece - I really had no idea this was happening. I (maybe stupidly) believed the CDC a commitment to uploading the seqs into the public databases. If this is happening for influenza, what about the other viruses they keep an eye on? Like: Dengue, chikungunya, west nile, etc?

  4. I only know the flu people, through my own research on flu. And they always say (when asked) that they are completely committed to sharing data publicly and openly. But once the media attention moves on, they either keep their data private or they put it in this Swiss database where, for all intents, it is still private. I guess they really do consider it "their" data, not the public's.

  5. Scientists are an unusual bunch... It seems their life's purpose is to get as many papers 'published' as possible.

    From reading your post it seems the scientist want to keep the sequences to themselves so that no one 'publishes' a paper before them - even if it increases the risk of a new flu outbreak...
    Doesn't seem right.

  6. Also, there's, an NIAID project.....they are supposed to be in Genbank, too. But may go into this repository first.

  7. Don't get me started about That's a huge waste of money - basically it's an NIAID contract where they are paying Northrop Grumman to just copy data from GenBank and re-display with very similar tools. A complete waste of funds, which they should use to fund real research instead. And they've been funding it for years now.

  8. Once a Mom, always a Mom. The photo doesn't crack me up, it makes me want to leap up and snatch the kid!

  9. This comment has been removed by a blog administrator.

  10. jctong: Attacking me by calling me names is known as an ad hominem attack. This has nothing to do with my main points. (Not to mention that it is laughable for you to call me a "surrogate" of Yiming Bao.)

    I make no secret of the fact that David Lipman and I were the founders of the Influenza Genome Sequencing Project - I'm quite proud of what we did. As a result of that project, over 5000 complete flu sequences have been completed and made public. When we started, only a handful of such sequences were available.

    However, the CDC opposed our goals of free and unrestricted access to data from the beginning, and through GISAID they continue to undermine this goal. GISAID is not free, despite your claims - you can see the data only if you agree to their terms, which allow the depositors to keep the data from the public indefinitely.

    Finally, why the heck should influenza sequence data be any different from the hundreds of other pathogens? My group sequenced the genomes for anthrax, syphilis, tuberculosis, staph, cholera - and we didn't need a "special" restricted database for any of those. Neither do the flu people. It's an embarrassment.

    1. Note: I am leaving my reply, but the previous message was posted by someone who was pretending to be a known influenza researcher. The real person contacted me to point out the identity theft.


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