Do you mean the tomatoes as fruits rotted? If so, you are experiencing Blossom End Rot and it's not a virus. It's caused, as you've suggested, by the overly wet conditions. The plant experiences a large fluctuation of calcium. Ironically, the problem can be caused by drought or over watering. Be sure to provide adequate drainage next year and they should be fine.
If, however, you've seen the plant's stems rot, or become limp an unable to hold themselves, you may have experienced damping off... again, not a virus or mildew, but caused by over watering (and often, over fertilization). Especially notable in diagnosing this malady is the soil line around the base of the plant may be discolored in yellows, browns or blacks.
Lastly, the various blights such as Early, Late, Fusarium and Verticillium are caused by any number virus' or fungi.
Be sure to thoroughly clean the garden this fall and treat the soil with an anti-fungal compound. I use an Ortho product called Dormant Oil. It's a sulphur based product (don't get any on your shoe or clothes... it stinks) which one sprays on the soil either after garden clean up in the fall or very early in the spring. Others are available... best of luck!