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 offers a novel means of tracing human migrations. We used this approach to elucidate the colonization of the Japanese Archipelago. Approximately 1,000 JCV DNA-positive urine samples were collected throughout the Japanese Archipelago, and used to amplify a 610-base-pair JCV DNA region (IG region). We determined about 100 IG sequences, from which a phylogenetic tree was constructed to classify them into distinct genotypes. The rest of the amplified fragments were classified into genotypes on the basis of the results of a restriction fragment length polymorphism analysis. Two major (CY and MY) and three minor JCV genotypes (SC, Bl;a, and EU) were identified. There was marked variation in the frequency of these JCV genotypes among the sites of sample collection. For example, MY was more frequently detected in northeastern areas and CY was predominant in southwestern areas. The possibility that the 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 but also three minor groups carrying SC, B1-a or EU migrated to the Japanese Archipelago and that all contributed to founding modern Japan.