A fungus and a virus.
Take it from this professional entomologist - the jury is still out on this.
Talk to 10 bee biologists, you’ll get 15 different reasons for CCD. They are probably all correct. CCD is a syndrome, and likely lots of things, either singular or in combination, can cause it. There are some data to suggest that bee colonies have gone through this periodically for a long time.
Do viruses and fungi contribute? Probably. Probably also pesticides, climate, breeding methods and movement of hives.
There is a lot of research still to be done here. Not to take away from this study - its a good one - but more info is needed.
Poor bees.
Is it just in the U.S. that this syndrome is being observed or does it extend further, even beyond North and South America?
So there really is a fungus among us…
As I understand it, India is having very severe problems.
According to Wikipedia:
European beekeepers observed similar phenomena in Belgium, France, the Netherlands, Greece, Italy, Portugal, and Spain, and initial reports have also come in from Switzerland and Germany, albeit to a lesser degree while the Northern Ireland Assembly received reports of a decline greater than 50%. Possible cases of CCD have also been reported in Taiwan since April 2007
but the good news is
As of 2009, the number of reported cases of CCD in the U.S. had dropped considerably; over the 2008/2009 winter, a total loss of 28.6% of managed honey bee colonies was recorded in the U.S., and only 15% of that subset (equal to only 4.3% of the national total) died with symptoms of CCD.

So there really is a fungus among us…
Well, people have called me funguy …