Computers decipher H1N1 genetic secrets

June 14, 2009 12:00:00 AM PDT
New research, updated this week, indicates that the H1N1 virus is not likely to become as devastating as the Spanish flu and other pandemics before it.

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The reason? It's just not in its DNA. A look at how computers are uncovering the genetic secrets of the virus.

More than ever before, computers are being enlisted in the battle against a virus. At labs like San Francisco's Public Health Laboratory they are used to analyze samples more quickly, using genetics instead of cultures. At Google, they are used to spot outbreaks. At Lawrence Livermore Lab, they are being used to determine how dangerous H1N1 really is.

"I look at this as the opening salvo," says bioinformatics scientist Jonathan Allan.

He and Tom Slezak, working with colleagues at the national laboratory, analyzed the genes of thousands of deadly viral strains going back to the Spanish Flu. They identified 34 markers for genes that contribute to a pandemic -- all shared by those strains.

"What we really looked at," Allen explains, "was the mutations that allow the virus to replicate efficiently both in the upper respiratory track and the lower respiratory track that are persistent and associated with past pandemics."

Less than a week after H1N1 flu hit the headlines, his team compared its genes with the rest of the flues, thanks to an advanced network of hundreds of widely distributed computers. They discovered that H1N1 possessed fewer than half the 34 markers of historic pandemics. That indicates it is only half as virulent.

Meanwhile, Google's computers don't use genetics; they use searches for the word "flu". The company believes that when and where people conduct such a search is a good indicator for outbreaks.

Google is cautious about selling this as a public health tool. They wouldn't talk on camera about it. But outside experts tell us that Google Flu could be a good way to spot outbreaks -- just not a good way to track them.

The markers being tracked by Livermore computers, on the other hand, go beyond statistics, with the potential to make a vaccine more effective. As Jonathan Allen likes to say, "You can always do more with more computer power."

Much of this high tech is a spin-off of Homeland Security. Equipment being used to study H1N1 was bought with federal funds originally intended to spot anthrax and other bioterror threats.

------- Links -------

  • Lawrence Livermore Laboratory Report on the virulence of the H1N1 virus
    http://www.biomedcentral.com/1471-2180/9/77

  • San Francisco Department of Health
    http://www.sfdph.org/

  • San Francisco's Public Health Laboratory
    http://www.cdc.gov/h1n1flu/

  • Updates on the H1N1 flu pandemic
    WorldHealth Organization Swine flu page http://www.who.int/csr/disease/swineflu/en/index.html

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