Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Rapid sequencer puts virus in the frame for deaths

But researchers warn speed needs to be matched with certainty.

Transplanted organs can carry viruses. Credit: AJ PHOTO/SPL

The discovery of a virus that may have killed three transplant recipients in Australia could mark a dramatic acceleration in the speed at which new pathogens can be identified. But it raises concerns that the ease with which such suspects can now be found could lead to researchers overlooking the need to firmly establish them as the cause of the disease in question. Fingering the wrong microbe could lead to inappropriate treatment or divert attention away from the real cause.

The three patients received organs from a single donor in Melbourne in December 2006. By January all three were dead. Ian Lipkin of Columbia University's Mailman School of Public Health in New York, who specializes in identifying new pathogens, heard about the case and collaborated with the Australian researchers who first took it on. After looking for thousands of telltale signs of known pathogens without success, Lipkin, who sits on the advisory board of 454 Life Sciences in Branford, Connecticut, decided to use the company's technology to sequence genes from samples that had been filtered to enrich their non-human DNA component.

Roughly one month and 144,000 fragments of sequence later, a homemade algorithm in Lipkin's lab had pulled out 14 gene fragments that looked viral. Preliminary, unpublished analyses suggest they come from a new member of the family Arenaviridae. Although this sort of sequencing has been used to identify viruses in the past, the 454 technology cuts down on time and effort, says Anthony Fauci, director of the US National Institute of Allergy and Infectious Diseases, which funded part of Lipkin's work. Lipkin estimates that the technique could be used to process samples in a matter of days.

But simply finding a virus is not enough, cautions microbiologist David Wang of Washington University in St Louis. Establishing that the virus actually caused the deaths is also critical, and is a lot harder. At present, the virus has been found in tissue from all three patients, and not in tissue from 60 controls. The virus's closest relative seems to be the lymphocytic choriomeningitis virus, which is believed to have killed organ-transplant patients in the past. But the team does not know whether the virus was also present in the donor. Lipkin says donor tissue samples have not been supplied to him by his Australian collaborators.

The guilt-by-association approach to pathogens can be misleading, warns microbiologist David Relman of Stanford University. Viruses do not necessarily behave in the same way as their closest known relatives. And the very fact that these new techniques work with raw sequence, rather than entities that could be grown and studied in the lab, makes follow-up experiments more challenging.

“It's not hard to find somebody you can implicate,” says Relman, in police-procedural mode. “What's really hard is to nail the conviction.”

Authors

Related links

Related links

Related links in Nature Research

Sequencers step up to the speed challenge

Powerful new database pins down emerging infections

Omics Gateway

Nature Medicine blog

Related external links

CDC Arenavirus

454

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ledford, H. Rapid sequencer puts virus in the frame for deaths. Nature 447, 12–13 (2007). https://doi.org/10.1038/447012b

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing