Viruses could be involved in a number of autoimmune conditions. A recent study links the ubiquitous (i.e. found almost anywhere) Epstein Barr Virus with Multiple Sclerosis: http://www.sciencedaily.com/releases/2009/09/090914111535.htm.
Dr. Clark has said that parasites are involved in causing MS. She has also said that parasites quite frequently bring along viruses, and that in fact persistent viral infections usually have an underlying parasite infection. Certainly interesting information when one tries to get rid of a viral infection.
It is also interesting to note that bio feedback testers have reported for many years that they frequently find high viral loads in persons with MS. Borrelia (the bacteria causing Lyme disease) have also often been reported to be connected to MS.
So, the overall picture is still blurry, but it seems some progress is made in finding out what really causes this autoimmune condition.