FORT COLLINS, COLORADO--Scientists have finally agreed on the identity of a virus that caused an epidemic of brain inflammation in and around New York City this summer, sickening 60 mostly older people and killing seven. A group of public health researchers announced at a workshop held here last week that the virus's DNA sequence shows conclusively that it is the West Nile virus--an identification that was under debate until recently. They also reported that the virus's genome suggests it originated in the Middle East.
Shortly after the first encephalitis cases emerged, a team from the Centers for Disease Control and Prevention (CDC) lab in Fort Collins concluded from antibody tests that the culprit was St. Louis encephalitis, a disease that is endemic in the southern United States. Alarmed by odd observations--most notably a die-off of crows and zoo birds in New York City--CDC changed its mind on 24 September. Genetic data had shown that another virus was involved, which the agency cautiously referred to as "West Nile-like." But a team led by molecular biologist Ian Lipkin at the University of California, Irvine, challenged the classification, saying the new virus most closely resembled another, related agent, the Australian Kunjin virus. In a Lancet paper, Lipkin dubbed it "Kunjin/West Nile-like" (Science, 8 October, p. 206).
The conflicting analyses, however, were based on small snippets of the genome. The full sequence resolves the issue, says the CDC team, which has submitted its results for publication. Indeed, the viral DNA is 99% identical to a West Nile strain found in a dead goose in Israel in 1998, which was partly sequenced by virologist Vincent Deubel of the Pasteur Institute in Paris. "It's essentially the same virus," says CDC's Robert Lanciotti, who presented the work. Lipkin now agrees, adding that the sequence also closely resembles a West Nile strain found earlier in Egypt.
The findings give researchers the first clear clues about where the virus came from, but they do not explain how it crossed the Atlantic. The most likely way was by hitching a ride in a natural host, researchers said--in an infected bird or mosquito, or a human traveler. "There's a lot of traffic between the Middle East and the New York area," says John Roehrig, who led the CDC study. "We may never know exactly what happened."