Human dispersals based on a global phylogenetic analysis of JC virus isolates of genotype B1-b

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  • ZHENG HUAI-YING
    Department of Urology, Faculty of Medicine, The University of Tokyo
  • TAKASAKA TOMOKAZU
    Department of Urology, Faculty of Medicine, The University of Tokyo
  • OHNO NORIKAZU
    Department of First Anatomy, School of Dentistry, Aichi-Gakuin University
  • SUGIMOTO CHIE
    AIDS Research Center, National Institute of Infectious Diseases, Tokyo Tsukuba Primate Research Center, National Institute of Biomedical Innovation
  • KITAMURA TADAICHI
    Department of Urology, Faculty of Medicine, The University of Tokyo
  • YOGO YOSHIAKI
    Department of Urology, Faculty of Medicine, The University of Tokyo

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Abstract

JC virus (JCV) is a useful marker for tracing human dispersal. Four genotypes of JCV (CY, SC, B1-b, and MY) are mainly distributed in Asia. The population history of humans carrying CY, SC, or MY has been studied in some detail, but that of humans carrying B1-b remains poorly understood. The objective of this study was to gain insights into the population history of Asians carrying B1-b. A neighbor-joining phylogenetic tree was reconstructed from 26 complete B1-b DNA sequences from various regions of Asia. On the tree, the B1-b DNA sequences diverged into two clades, designated B1-b1 and B1-b2, each clustered with a high bootstrap probability. The split into B1-b1 and B1-b2 was estimated to have occurred about 20000 years ago, based on Ks values (synonymous substitutions per synonymous site) and the suggested rate of synonymous nucleotide substitutions. Comparison of the complete B1-b1 and B1-b2 sequences revealed that two single nucleotide polymorphisms (SNPs) between B1-b1 and B1-b2 occurred in a 610 bp region (the IG region) of the viral genome. Based on these SNPs, 145 B1-b isolates previously identified in the Old World were classified into B1-b1 or B1-b2. B1-b1 was widespread on the Asian continent, spreading from Northeast Siberia to West Asia. In contrast, B1-b2 was localized to part of South Asia, including South India and Sri Lanka. On the basis of the present findings, we inferred the dispersals of Asians carrying B1-b.<br>

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