Scientists have identified a likely culprit underlying the massive and mysterious plague that has killed off tens of millions of bees in the United States over the past year. By sequencing the DNA of every microbe inhabiting the bees, researchers have pinpointed a novel virus strongly linked to infected hives. The findings could help beekeepers protect their colonies. The research also suggests an effective new method for identifying infectious pathogens, be they from bees or humans.

"This is a very significant finding," says Dewey Caron, an entomologist at the University of Delaware, in Maryland, who was not involved in the study. "It's not yet a smoking gun, but it really helps narrow the search."

Over the past year, tens of millions of bees have mysteriously vanished from their hives, amounting to a loss of 50 to 90 percent of U.S. colonies. While honeybee populations have sustained several major hits to their numbers over the past century, this particular plague is unique in that adult bees seem to disappear from their hives without a trace. Because honeybees pollinate hundreds of species of fruits, vegetables, and nuts--commercial beekeepers truck their hives across the country during flowering season to pollinate crops--that loss is a major agricultural concern.

Scientists have been scrambling to find a source for the problem--known as colony collapse disorder--ever since the first case was reported in 2006. A host of possibilities have been suggested: genetically modified crops, pesticides, parasites, stress, cell phones, and even celestial intervention in the form of a honeybee rapture. But scientists now say that they are closing in on the root of the problem.

Using new, rapid gene-sequencing methods, scientists from Columbia University, Pennsylvania State University, and the U.S. Department of Agriculture (USDA) analyzed DNA from both healthy and infected bee colonies, along with the viruses, bacteria, and fungi that colonize them--an approach known as metagenomics. (See "Sequencing in a Flash" and "Our Microbial Menagerie.") After subtracting out bee DNA sequences--identified with the aid of the recently released honeybee genome--scientists were left with microbial DNA. They found that one particular virus, known as Israeli acute paralysis virus of bees, was found only in colonies that suffered significant losses. In a follow-up study of 51 bee colonies from across the country--30 diseased colonies and 21 healthy ones--all but one colony infected with Israeli acute paralysis virus also had colony collapse disorder. In other words, the virus could predict collapse 96 percent of the time. The findings are published today online in the journal Science.

While the results are exciting, scientists caution that it's too soon to say whether the virus truly triggers the disorder. "We still have a great deal of research to do to figure out why honeybees are dying in the U.S.," says Jeffery Pettis, an entomologist at the USDA, in Beltsville, MD, who was involved in the research.

Autopsies performed soon after the first reports of the problem revealed that bees from collapsed colonies had signs of multiple infections, suggesting that the virus may act in conjunction with other stressors, such as parasitic mites. "Mites are a major source of bee mortality," says Diana Cox-Foster, an entomologist at Pennsylvania State University who led the new study and has previously shown that the parasites can immunosuppress bees. "That might weaken the bee and cause amplification of other pathogens or the virus." To determine exactly how these different factors interact, Cox-Foster and her collaborators are now planning controlled studies in which they will expose bees to both the virus and a series of other stressors, such as mites and pesticides.