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Will genomics help prevent the next pandemic?

The first outbreak of the new "swine flu" strain, now known as H1N1, earlier this year in Mexico caught the world by surprise. Public health officials around the world tried to stop the virus at the borders but were largely helpless. Shortly after, on the other side of the world from Mexico, I saw the health check posts in Cambodia at the airport and at a borderpost with Vietnam, right when the country found its first H1N1 cases which were flown in by US exchange students. The weapons used by the health officials to combat the spread of the virus were primarily paper survey forms and thermometers; the virus won, very quickly. Genomics is rapidly changing both the way diseases are diagnosed and the way medications and vaccines are developed - but will it give us the tools to prevent the next pandemic?

  • What if countries where emerging infections originate, from Cameroon to Cambodia, could rapidly sequence suspect samples and discover new pathogens when only a few people have become sick?
  • What if all such sequence data were immediately shared in a single global open access database?
  • What if you could search for a string of sequence data and all associated data, annotations or publications as easily and effectively as a Google search?
  • What if markers discovered for a new disease would quickly be incorporated into affordable hand held multi-pathogen diagnostic tests widely available at the point of care?
  • What if the results of those tests were uploaded to a database where surveillance tools like Google Flu Trends could discover outbreaks?
Today the Public Library of Science, a mission driven, non-profit and open access publisher, presents "The Genomics of Infectious Disease" a collection of essays, perspectives and reviews that explores how genomics—with all its associated tools and techniques—can provide insights into our understanding of emerging infectious disease. This collection was produced with financial support from with the editorial independence and rigor of PLoS and the expert opinion of leading researchers.

In one piece Rajesh Gupta, Mark Michalski (of Stanford, but at last year) and I provide’s perspective and vision for how systematic application of genomics, proteomics, and bioinformatics to infectious diseases could predict and prevent the next pandemic. To realize this vision, however, we feel that a focused, coordinated and scaled-up effort would be required. We urge the community to unite under an “Infectious Disease Genomics Project,” analogous to the Human Genome Project, to accelerate today's impressive progress as reviewed by this cross-journal open access collection.

You can read more in this blog from PLoS and listen to a fascinating audio interview debate with with Jonathan Eisen, Siv Andersson, and Raj Gupta, led by Kirsten Sanford.

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