Phylogenetic comparison between archetypal and disease-associated JC virus isolates in Japan.

We examined the phylogenetical correlation between two types of JC virus (JCV) isolates, archetypes derived from the urine of nonimmunocompromised individuals and PML-types derived from the brain of patients with progressive multifocal leukoencephalopathy (PML) in Japan. A phylogenetic tree was constructed for eight JCV isolates, five PML-types obtained in this and previous studies and three representative archetypes, from DNA sequence data on the VP1 (major capsid protein) gene. The eight isolates were divided into two major groups, named subtypes MY and CY after the representative archetypal isolates. Four of five PML-type isolates belonged to subtype MY, and the other one to subtype CY. Isolates belonging to subtype MY were further divided into two groups; one group containing archetype MY and three PML-types and the other one containing archetype YI and a PML-type. These findings, together with those in our previous study that correlated various JCV isolates in the world provide evidence for the hypothesis that JCVs associated with PML may have been generated from archetypal JCVs persisting in the patients.