JC Virus causes a fatal disease in the brain called progressive multifocal leukoencephalopathy (PML) that occurs in many patients with immunocompromised conditions. The finding of JCV DNA in the patients with neurological symptoms of PML is a diagnostic criterion and is needed to confirm the diagnosis of PML to rule out other neurological conditions. Certain JC virus variants are known to have a greater association with PML. For example, "Prototype" JC virus is far more pathogenic than "Archetype" JC virus.

This invention claims novel assays for identifying Archetype and/or Prototype JC virus by detecting the presence or absence of the unique Archetype nucleic acid sequence in the non-coding regulatory region of JC virus. While the sequences of Archetype and Prototype JC virus are known, these are the first assays that allow discrimination between Prototype and Archetype JC virus in a simple assay without the need for DNA sequencing. The identification of a JC virus as a prototype can lead to early treatment of infected individuals.