The classic signs of rotavirus infection are yellow diarrhea in fuzzy to hopper stage mice and rats, many times with drying of this material around the anal region and thus causing impactions. Some intestinal bloating may also be noticed. Another indication that this may be rotavirus is that the adults will never show symptoms, as they remain unaffected, but are carriers. I do not know of any treatment, as this is viral, and it is just usually left to run its course. You may lose some of the babies to this, but eventually it will move through the colony and the immune response of the survivors will cause these symptoms to eventually disappear after several weeks.
This is just my interpretation of your situation based on your observations. If the condition of your colony continues to deteriorate, I would definitely recommend a call to your vet.
Kelly