Just from that link it seems rather alarmist conclusions. Words like, could be connected, CCD, possibly,etc., rather than is, or has been found to, directly linked etc.
Any virus that an organism has been exposed to and overcome, can be found to have parts of that viral DNA left behind. That does not indicate the bearer is infective. I dont think it necessarily means that it was harmful to the bearer at the time of its exposure.
I would want to know much more about this before I got excited: I sense a bit of tabloid style reporting. We sure know we cant believe every insinuation we see in print.
Below is a clip from another source about the original research; I dont think it warrants all the conclusions derived in the a lot of reports about the study.
"The US-China team screened six strong and four weak colonies over a year for tobacco ringspot and other viruses, deformed wing bee virus, black queen cell virus and Israel acute paralysis virus and found that higher concentrations presaged colony collapse, although no apparent disease symptoms were spotted in individual bees. The four weak colonies studied had collapsed by February."
What remains unclear is whether the viruses are causing the decline, contributing to it or just taking advantage of it."