When a particularly deadly pathogen appears, any delay in identifying it can slow the development of treatments and diagnostic tests. But until recently, identifying a pathogen usually required some advance knowledge of its genetic makeup. Now a team led by W. Ian Lipkin, director of the Center for Infection and Immunity at Columbia University’s Mailman School of Public Health, has shown how to use advanced gene-sequencing technology to identify even the most mysterious pathogen. Lipkin starts by partly isolating a pathogen’s genetic material from that of its human host. Then he sequences the sample using technology developed by 454 Life Sciences of Branford, CT; unlike other systems, 454’s doesn’t require prior information about the sequence you are looking for. Finally, Lipkin searches a database to see if any known sequences match the ones he’s identified.
The team’s first feat: identifying the virus that killed three Australian transplant patients who had received organs from a single donor. Lipkin has since used the technique to identify more than 20 viruses.
1. To identify an unknown pathogen, researchers begin by extracting a tissue sample from an infected patient.
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