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In late 2006, something strange began to happen to America's honeybees. Colonies that were once thriving suddenly went still, almost overnight. The worker bees that make hives run simply disappeared, their bodies never to be found. Over the past couple of years, nearly one-third of all honeybee colonies have collapsed this way, which led to a straightforward name for the phenomenon: colony collapse disorder (CCD).

This might seem like little more than a tantalizing mystery for entomologists, except for one fact: honeybees provide $15 billion worth of value to U.S. farmers, pollinating crops that range from apples to avocados to almonds. Any number of possible causes for CCD have been put forward, from bee viruses to parasites to environmental triggers like pesticides or even cell-phone transmissions. Despite the Department of Agriculture's allotment of $20 million a year for the next five years to study CCD, it's still a mystery — and the bees keep dying.

A new study in the Proceedings of the National Academy of Sciences (PNAS) shows that the causes of CCD may be more varied than scientists expect. The bees may be dying not from a single toxin or disease but rather from an assault directed by a collection of pathogens. A research team led by entomologist May Berenbaum at the University of Illinois compared the whole genome of honeybees that came from hives that had suffered from CCD with hives that were healthy. The sick bees exhibited genetic damage that could account for the die-off, and that damage indicated that they might be afflicted with multiple viruses simultaneously. This could weaken them enough to trigger CCD. "It's like a perfect storm," says Berenbaum.

The PNAS team's work was possible only because the honeybee's genome is one of the few animal genomes that scientists have decoded in full. The researchers looked at the genes that were switched on in the guts of sick and healthy bees — the gut being both the place pesticides are detoxified and the main region for immune defense. The technique they used is what's known as a whole-genome microarray, and it's ideal for this kind of sweeping analysis. "It's a really powerful tool that lets us look at all 10,000 honeybee genes at the same time," says Berenbaum. "The causative agents [for CCD] might just leap out."

In the guts of CCD-afflicted bees, the microarray analysis showed unusual fragments of ribosomal RNA. Ribosomes are essentially the protein factories inside cells — they're vital to the health of the cell itself and the larger organism. Berenbaum believes that the presence of those genetic fragments inside the CCD-afflicted bees indicates that they may be under attack by a number of insect viruses — including deformed wing virus and Israeli acute paralysis virus — that damage the ribosomes. "It was the one factor that remained consistently associated with the CCD bees we tested, no matter where they came from or how severe the disorder was," says Berenbaum. "It doesn't have to be a specific virus, just an overload." Once the bees' systems get burdened this way, they are less capable of fighting off any other threat, from pesticides to other environmental causes.

Berenbaum is quick to point out that the microarray analysis is only correlative, meaning that while it can show evidence that certain viruses are present in CCD-afflicted bees, it doesn't reveal exactly what role the viruses play, nor how best to battle them. One approach might be to control infestations by varroa mites, which carry multiple viruses into the hives they attack. The good news is that the disorder may be on the wane, with the Apiary Inspectors of America reporting that deaths from CCD are below 30% for the first time since the crisis began. "The phenomenon seems to be in decline," says Berenbaum. "The most vulnerable populations might have already crashed." American farmers should be thankful; just think of trying to pollinate all those crops by hand.

• Bryan Walsh
• Why do beehives suddenly collapse? The explanation may be a perfect storm of viruses