Long story short: there's a plant virus which bees can contract by consuming it. This may not be the healthiest thing for the bees as the virus shows up all over their tiny bee bodies. The bees also have to deal with parasitic mites which may be unaffected carriers of the virus. The spread of this virus may contribute to colony collapse disorder, though it's likely not the only factor.
Update (Feb 18, 2014): Listened to an episode of This Week in Virology in which this paper was discussed. They were critical of it for a number of fully justified reasons, most notably that the authors don't show that the plant virus actually infects bees, just that some of the viral RNA can be found in bees and these bees may be less healthy as a result. The link to colony collapse disorder is the conclusion I found hardest to swallow. The TWiV guys suggested that the plant virus (if it is, in fact, even capable of infecting bees) may be one of many opportunistic infections of already weakened bees. This is true for many viral and bacterial infections of immunocompromised animals; without a sturdy immune system's protection, all kinds of otherwise benign life can become pathogens.