Two distinct genotypes (MY-x and MX) of JC virus previously identified in Hokkaido Ainu

Anthropological Science

Volumn 113, Issue 2, 2005, Pages 225-231

  Zheng, Huai Ying ^a,b   Ikegaya, Hiroshi ^c   Nakajima, Makoto ^c   Sakurada, Koichi ^d   Takasaka, Tomokazu ^a   Kitamura, Tadaichi ^a   Yogo, Yoshiaki ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b Japanese Foundation of AIDS Prevention   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d NATIONAL RESEARCH INSTITUTE OF POLICE SCIENCE   (Japan)

Author keywords

Ainu; Genotype; JC virus; MX; MY x

Indexed keywords

EID: 25644451872     PISSN: 09187960     EISSN: 13488570     Source Type: Journal    
DOI: 10.1537/ase.040716     Document Type: Article

References (39)

1. Agostini H.T., Ryschkewitsch C.F., and Stoner G.L. (1996) Genotype profile of human polyomavirus JC excreted in urine of immunocompetent individuals. Journal of Clinical Microbiology, 34: 159-164.
2. Agostini H.T., Ryschkewitsch C.F., Brubaker G.R., Shao J., and Stoner G.I. (1997) Five complete genomes of JC virus type 3 from Africans and African Americans. Archives of Virology, 142: 637-655.
3. Agostini H.T., Ryschkewitsch C.F., and Stoner G.L. (1998a) JC virus Type 1 has multiple subtypes: three new complete genomes. Journal of General Virology, 79: 801-805.
4. Agostini H.T., Shishido-Hara Y., Baumhefner R.W., Singer E.J., Ryschkewitsch C.F., and Stoner G.L. (1998b) JC virus Type 2: definition of subtypes based on DNA sequence analysis of ten complete genomes. Journal of General Virology, 79: 1143-1151.
5. Agostini H.T., Ryschkewitsch C.F., and Stoner G.L. (1998c) Complete genome of a JC virus genotype type 6 from the brain of an African American with progressive multifocal leukoencephalopathy. Journal of Human Virology, 1: 267-272.
6. Chesters P.M., Heritage J., and McCance D.J. (1983) Persistence of DNA sequences of BK virus and JC virus in normal human tissues and in diseased tissues. The Journal of Infectious Diseases, 147: 676-684.
7. Cole C.N. and Conzen S.D. (2001) Polyomaviridae: the viruses and their replication. In: Knipe D.M., Howley P.M., Griffin D.E., Lamb R.A., Martin M.A., Roizman B., and Straus S.E. (eds.), Fields Virology. Lippincott Williams & Wilkins, Philadelphia, pp. 2141-2173.
8. Cui X., Wang J.C., Deckhut A., Joseph B.C., Eberwein P., Cubitt C.L., Ryschkewitsch C.F., Agostini H.T., and Stoner G.L. (2004) Chinese strains (Type 7) of JC virus are Afro-Asiatic in origin but are phylogenetically distinct from the Mongolian and Indian strains (Type 2D) and the Korean and Japanese strain (Type 2A). Journal of Molecular Evolution, 58: 568-583.
9. Felsenstein J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783-791.
10. Frisque R.J., Bream G.L., and Cannella M.T. (1984) Human polyomavirus JC virus genome. Journal of Virology, 51: 458-469.
11. Guo Z, Zheng S.P., Sugimoto C., Wang Y.L., Zheng H.Y., Takassaka T., Kitamura T., Guo J., and Yogo Y. (2001) JC virus genotypes in northwestern China: implications for its population history. Anthropological Science, 109: 203-212.
12. Hillis D.M. and Bull, J.J. (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology, 42: 182-192.
13. Jobes D.V, Friedlaender J.S., Mgone C.S., Agostini H.T., Koki G., Yanagihara R., Ng T.C.N., Chima S.C., Ryschkewitsch C.F., and Stoner G.L. (2001) New JC virus (JCV) genotypes from Papua New Guinea and Micronesia (Type 8 and Type 2E) and evolutionary analysis of 32 complete JCV genomes. Archives of Virology, 146: 2097-2113.
14. Kato A., Sugimoto C., Zheng H.-Y., Kitamura T., and Yogo Y. (2000) Lack of disease-specific amino acid changes in the viral proteins of JC virus isolates from the brain with progressive multifocal leukoencephalopathy. Archives of Virology, 145: 2173-2182.
15. Kimura M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16: 111-120.
16. Kitamura T., Aso Y., Kuniyoshi N., Hara K., and Yogo Y. (1990) High incidence of urinary JC virus excretion in nonimmunosuppressed older patients. The Journal of Infectious Diseases, 161: 1128-1133.
17. Kitamura T., Kunitake T., Guo J., Tominaga T., Kawabe K., and Yogo Y. (1994) Transmission of the human polyomavirus JC virus occurs both within the family and outside the family. Journal of Clinical Microbiology, 32: 2359-2363.
18. Kitamura T., Sugimoto C., Kato A., Ebihara H., Suzuki M., Taguchi F., Kawabe K., and Yogo Y. (1997) Persistent JC virus (JCV) infection is demonstrated by continuous shedding of the same JCV strains. Journal of Clinical Microbiology, 35: 1255-1257.
19. Kitamura T., Sugimoto C., Ebihara H., Kato A., Guo J., Taguchi F., Tominaga T., Ogawa Y., Ohta N., Kizu N., Imamura K., Funaki H., Kurosawa T., Yasumoto S., and Yogo Y. (1998) People of Japan as revealed by genotypingof urinary JC virus DNA. Anthropological Science, 106: 311-325.
20. Kunitake T., Kitamura T., Guo J., Taguchi F., Kawabe K., and Yogo Y. (1995) Parent-to-child transmission is relatively common in the spread of the human polyomavirus JC virus. Journal of Clinical Microbiology, 33: 1448-1451.
21. Loeber G. and Dörries K. (1988) DNA rearrangements in organ-specific variants of polyomavirus JC strain GS. Journal of Virology 62: 1730-1735.
22. Miranda J.J., Takasaka T., Zheng H.-Y., Kitamura T., and Yogo Y. (2004) JC virus genotype profile in the Mamanwa, a Philippine Negrito tribe, and implications for its population history. Anthropological Science, 112: 161-172.
23. Padgett B.L. and Walker D.L. (1973) Prevalence of antibodies in human sera against JC virus, an isolate from a case of progressive multifocal leukoencephalopathy. The Journal of Infectious Diseases, 127: 467-470.
24. Page R.D.M. (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12: 357-358.
25. Pavesi A. (2003) African origin of polyomavirus JC and implications for prehistoric human migrations. Journal of Molecular Evolution, 56: 564-572.
26. Saitou N. and Nei M. (1987) The neighbor-joining method: a new method for reconstructing phylogentic trees. Molecular Biology and Evolution, 4: 406-425.
27. Saruwatari R., Zheng H.Y., Takasaka T., Sugimoto C., Sakai E., Bo B., Aung N.N., Kitamura T., Yogo Y., and Ohno N. (2002) People of Myanmar as demonstrated by genotyping of urinary JC virus DNA. Anthropological Science, 110: 235-249.
28. Sugimoto C., Kitamura T., Guo J., Al-Ahdal M.N., Shchelkunov S.N., Otova B., Ondrejka P., Chollet J.-Y., El-Safi S., Ettayebi M., Grésenguet G., Kocagöz T., Chaiyarasamee S., Thant K.Z., Thein S., Moe K., Kobayashi N., Taguchi F., and Yogo Y. (1997) Typing of urinary JC virus DNA offers a novel means of tracing human migrations. Proceedings of the National Academy of Sciences of the United States of America, 94: 9191-9196.
29. Sugimoto C., Hasegawa M., Kato A., Zheng H.-Y., Ebihara H., Taguchi F., Kitamura T., and Yogo Y. (2002a) Evolution of human polyomavirus JC: implications for the population history of humans. Journal of Molecular Evolution, 54: 285-297.
30. Sugimoto C., Hasegawa M., Zheng H.-Y., Demenev V., Sekino Y., Kojima K., Honjo T., Kida H., Hovi T., Vesikari T., Schalken J.A., Tomita K., Mitsunobu Y., Ikegaya H., Kobayashi N., Kitamura T., and Yogo Y. (2002b) JC virus strains indigenous to northeastern Siberians and Canadian Inuits are unique but evolutionally related to those distributed throughout Europe and Mediterranean areas. Journal of Molecular Evolution, 55: 322-335.
31. Takasaka T., Miranda J.J., Sugimoto C., Paraguison R., Zheng H.-Y., Kitamura T., and Yogo Y. (2004) Genotypes of JC virus in Southeast Asia and the western Pacific: implications for human migrations from Asia to the Pacific. Anthropological Science, 112: 53-59.
32. Thompson J.D., Higgins D.G., and Gibson T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680.
33. Tominaga T., Yogo Y., Kitamura T., and Aso Y. (1992) Persistence of archetypal JC virus DNA in normal renal tissue derived from tumor-bearing patients. Virology, 186: 736-741.
34. Walker D.L. (1985) Progressive multifocal leukoencephalopathy. In: Vinken P.J., Bruyn G.W., Klawans H.L., and Koetsier J.C. (eds.), Handbook of Clinical Neurology, Volume 47(3), Demyelinating Diseases. Elsevier, Amsterdam, pp. 503-524.
35. Yogo Y. and Sugimoto C. (2001) The archetype concept and regulatory region rearrangement. In: Khalili K. and Stoner G.L. (eds.), Human Polyomaviruses: Molecular and Clinical Perspectives. John Wiley & Sons, New York, pp. 127-148.
36. Yogo Y., Iida T., Taguchi F., Kitamura T., and Aso Y. (1991) Typing of human polyomavirus JC virus on the basis of restriction fragment length polymorphisms. Journal of Clinical Microbiology, 29: 2130-2138.
37. Yogo Y., Zheng H.-Y., Hasegawa M., Sugimoto C., Tanaka S., Honjo T., Kobayashi N., Ohta N., and Kitamura T. (2003) Phylogenetic analysis of JC virus DNAs detected in Ainus: an attempt to elucidate the origin and diversity of the Ainu. Anthropological Science (Japanese Series), 111: 19-34.
38. Yogo Y., Sugimoto C., Zheng H.-Y., Ikegaya H., Takasaka T., and Kitamura T. (2004) JC virus genotyping offers a new paradigm in the study of human populations. Reviews in Medical Virology, 14: 179-191.
39. Zheng H.-Y., Sugimoto C., Hasegawa M., Kobayashi N., Kanayama A., Rodas A., Mejia M., Nakamichi J., Guo J., Kitamura T., and Yogo Y. (2003) Phylogenetic relationships among JC virus strains in Japanese/Koreans and Native Americans speaking Amerind or Na-Dene. Journal of Molecular Evolution, 56: 18-27.