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For more than a year now, a mysterious plague has been ravaging honeybee populations all over the United States. Beekeepers who've lost hives by the thousands call it colony collapse disorder. Now, a group of scientists says they may have figured out what's causing it.

NPR's John Nielsen has the story.

JOHN NIELSEN: Honeybees trucked back and forth across the country pollinate roughly $15 billion worth of crops every year. And when the current pollination season started late last winter, beekeepers, like Dave Hackenberg of Lewisburg, Pennsylvania, were ready for a banner year.

Then, the mysterious bee plague hit and nearly drove Hackenberg out of business. He spoke to us on a cell phone while examining hives containing bees that had managed to survive.

Mr. DAVE HACKENBERG (Beekeeper): What we lost was probably about - over 2,000 hives of bees, a little less than 3,000 and that's (unintelligible). So, you know, that cuts into your income pretty hard when you got to rent these things and - because it's been a real long, hard year, to put it bluntly.

NIELSEN: Hackenberg says he's never seen anything like what's now known as colony collapse disorder or CCD. When it hits a hive, adult worker bees suddenly fly off, never to return.

Bee researcher Jeff Pettis at the U.S. Department of Agriculture says queen bees and undeveloped bees called brood are left behind to die.

Mr. JEFF PETTIS (Researcher, U.S. Department of Agriculture): So something is killing or those bees are leaving, abandoning the hive or whatever, in a very short time window, and that particular characteristic symptom is what we're defining as CCD.

NIELSEN: The first cases of colony collapse disorder turned up in Southern California in 2004. When tests for well-known bee diseases came up negative, Pettis and his colleagues asked experts on infectious diseases in humans for help. One of those experts, Ian Lipkin, from Columbia University, began by collecting bees from diseased and undiseased hives, and then grinding them up, and then collecting their DNA.

Dr. IAN LIPKIN (Epidemiology, Neurology, and Pathology, Columbia University): And this gives us not only bee material but also everything that might be associated with bees, such as bacteria, viruses, fungi, parasites of different types.

NIELSEN: Lipkin says he set aside the bits and pieces of DNA from the bees and started searching for what was left over, looking for material found only in beehives infected by CCD. What he found, eventually, was a bee-killing virus first identified in Israel. These findings have now been published online by the journal, Science, but both Pettis and Lipkin are quick to note that they have yet to prove conclusively that the Middle Eastern virus they have discovered is the sole cause of CCD.

Pettis puts it this way.

Mr. PETTIS: Right now, we're claiming it's a marker in colony collapse disorder. We have shown that is present when colonies are collapsing, but we haven't shown cause and effect.

NIELSEN: One big unanswered question here is why this virus is having such dramatic effects in the United States and not elsewhere. Pettis says a hunch that the bees in this country are already overstressed because they have to deal with a host of other problems, ranging from killer fungi to parasitic mites. He thinks beekeepers should take special care to make sure their hives are free of those older problems. Beekeepers can also irradiate infective hives since that kills the virus.

Beekeeper Dave Hackenberg of Pennsylvania says he's already doing all of these things. But he's not sure it's going to be enough.

Mr. HACKENBERG: And unfortunately, there are beekeepers already starting to see problems. There are beekeepers across the country that they're colonies are dwindling and disappearing and it didn't happen this early last year.

NIELSEN: Hackenberg says some of his beekeeper friends lost 90 percent of their bee colonies to CCD in the pollination season that has just ended. If they lose the same amount next year, some of the farmers that rent those bees may not be able to get them.

John Nielsen, NPR News, Washington.

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