Journal of Molecular Evolution

, Volume 55, Issue 3, pp 322-335

JC Virus Strains Indigenous to Northeastern Siberians and Canadian Inuits Are Unique But Evolutionally Related to Those Distributed Throughout Europe and Mediterranean Areas

  • Chie SugimotoAffiliated withLaboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
  • , Masami  HasegawaAffiliated withDepartment of Prediction and Control, The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan
  • , Huai-Ying  ZhengAffiliated withLaboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
  • , Vladimir  DemenevAffiliated withDepartment of Public Health, Administration of Khabarovsk Territory, Khabarovsk, Russia
  • , Yoshiharu  SekinoAffiliated withThe Great Journey, 1-6 Wakaba, Shinjuku-ku, Tokyo 160-0011, Japan
  • , Kazuo  KojimaAffiliated withThe Last Great Expedition on the Earth, 2-454 Kurashiki, Higashiyamato, Tokyo 207-0032, Japan
  • , Takeo  HonjoAffiliated withHimalayan Veterinary Hospital, 2-43-11 Mitsuhuji, Musashimurayama, Tokyo 208-0021, Japan
  • , Hiroshi  KidaAffiliated withLaboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo 060-0818, Japan
  • , Tapani  HoviAffiliated withDepartment of Virology, National Public Health Institute, Mannerheimintie, 166, 00300 Helsinki, Finland
    • , Timo  VesikariAffiliated withDepartment of Virology and Vaccine Research, University of Tampere Medical School, 33101 Tampere, Finland
    • , Jack A. SchalkenAffiliated withUrological Research Laboratory, University Hospital Nijmegen, Nijmegen, The Netherlands
    • , Kyoichi  TomitaAffiliated withDepartment of Urology, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
    • , Yukari  MitsunobuAffiliated withLaboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
    • , Hiroshi  IkegayaAffiliated withDepartment of Forensic Medicine, The Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
    • , Nobuyoshi  KobayashiAffiliated withLaboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
    • , Tadaichi  KitamuraAffiliated withDepartment of Urology, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
    • , Yoshiaki  YogoAffiliated withLaboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

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Human polyomavirus JC virus (JCV) isolates around the world are classified into more than 10 geographically distinct genotypes (designated as subtypes). Evolutionary relationships among JCV subtypes were recently examined, and the following pattern of JCV evolution was indicated. The ancestral JCV first divided into three superclusters, designated Types A, B, and C. A split in Type A generated two subtypes, EU-a and -b, containing mainly European and Mediterranean isolates. The split in Type B generated Af 2 (the major African subtype), Bl-c (a minor European subtype), and various Asian subtypes. Type C generated a single subtype (Afl), consisting of isolates derived from western Africa. In this study, JCV isolates prevalent among northeastern Siberians and Canadian Inuits were evaluated in the context of the above-described pattern of JCV evolution. The Siberian/Arctic JCV isolates were classified as belonging mainly to Type A, based on the result of a preliminary phylogenetic analysis. We then examined, using the whole-genome approach, the phylogenetic relationships among worldwide Type A isolates. In neighbor-joining and maximum-likelihood analyses, Type A JCVs worldwide consistently diverged into three subtypes, EU-a, -b, and -c, with high bootstrap probabilities. EU-c was constructed only by northeastern Siberian isolates, derived mainly from Nanais living in the lower Amur River region, and was shown to have been generated by the first split in Type A. Most Siberian/Arctic isolates derived from Chukchis, Koryaks, and Canadian Inuits formed a distinct cluster within the EU-a subtype, with a high bootstrap probability. Based on the present findings, we discuss ancient human migrations, accompanied by Type A JCVs, across Asia and to Arctic areas of North America.