The co-morbidity of Fibromyalgia and several autoimmune diseases is well documented in medical literature. It was accepted for a time that FM CFS/ME were autoimmune disease as well. It leads me to theorize that many autoimmune diseases are not autoimmune diseases, but rather a consequence of an XMRV-mediated immunodeficiency syndrome. The finding that the human genome contains many endogenous viral genes that cannot be expressed under normal physiological mechanisms, but can be turned on by certain viruses like EBV, and most likely XMRV makes this a distinct possibility. So how could this happen?
Many viral proteins are membrane proteins - they embed in the lipid membrane of the virion. Conceivably, our cells could start expressing these proteins at their surfaces, triggering an immune response. Many retroviruses contain transcriptional transactivators which there is a strong possibility could accomplish this very event. It is also conceivable that herpesviruses could work in concert with XMRV to amplify this effect. An XMRV ravaged immune system in theory can't mount an effective enough response to keep EBV, HHV-6 levels below the "Noise floor".
Ultimately, the significance could be that one viral gene could mean Rheumatoid Artthritis, another could mean Ankylosing Spondylitis, and another could mean Multiple Sclerosis. This hypothesis could also help explain why what we call autoimmune diseases follow a relapsing-remitting pattern. It could also help prove/disprove the concept of molecular mimicry.