Peopling of Japan as revealed by genotyping of urinary JC Virus DNA

It has been shown that the typing of urinary JC polyomavirus (JCV) DNA offe rs a novel means of tracing human migrations. We used this approach to eluc idate the colonization of the Japanese Archipelago. Approximately 1,000 JCV DNA-positive urine samples were collected throughout the Japanese Archipel ago, and used to amplify a 610-base-pair JCV DNA region (IG region). We det ermined about 100 IG sequences, from which a phylogenetic tree was construc ted to classify them into distinct genotypes. The rest of the amplified fra gments were classified into genotypes on the basis of the results of a rest riction fragment length polymorphism analysis. Two major (CY and MY) and th ree minor JCV genotypes (SC, Bl;a, and EU) were identified. There was marke d variation in the frequency of these JCV genotypes among the sites of samp le collection. For example, MY was more frequently detected in northeastern areas and CY was predominant in southwestern areas. The possibility that t he detection of EU in Japan is a result of recent Caucasian immigration was excluded by a phylogenetic comparison of Japanese and European EU isolates . These findings suggest that not only two major groups carrying CY or MY b ut also three minor groups carrying SC, B1-a or EU migrated to the Japanese Archipelago and that all contributed to founding modern Japan.