Different genotypes of human polyomaviruses found in patients with autoimmune diseases in Taiwan

We have assayed for the presence of human polyomaviruses in urine of autoimmune disease patients, such as systemic lupus erythematosus (SLE), Sjogren's syndrome (SS), rheumatoid arthritis (RA), or dermatomyositis/polymositis (DM/PM), by PCR. The results indicate that approximately 40% of patients were JCV positive and 15% of the JCV positive patients were also infected by BKV at the same time according to Southern blot and DNA sequencing of the PCR products. Interestingly, the JCV present in autoimmune diseases patients were Taiwan-1, Taiwan-2, and Taiwan-3 strains with pentanucleotide-A (GGGAA) and/or -B (AAAGC) deletions within the regulatory region. In addition, BKV found in the examined samples were Taichung-1 and Taichung-2 strains. Taichung-1 had two nucleotide alterations and Taichung-2 had six nucleotide differences within the regulatory region when compared to WW BKV archetype. Although the examined autoimmune diseases patients included RA, SLE, PM, DM, and SS patients, there appears to be no correlation between disease and virus strains. However, Taiwan-2 strain JCV with two copies of pentanucleotide-A deletion was present in the patient with the longest period of immunosuppressive medication.