1887

Abstract

The polyomavirus JC (JCV) establishes a persistent infection in the kidneys, and is the virus agent that causes the demyelinating disease progressive multifocal leukoencephalopathy. PCRand DNA sequence analyses of partial JCV genomes have shown that there are at least four main JCV types, each associated with a specific geographical region. Type 1 is of European origin, Type 2 is Asian, Type 3 is found in individuals of African decent and Type 4 is a potential recombinant of Types 1 and 3, and is widely distributed throughout the population of the United States. A comprehensive phylogenetic analysis of 22 complete JCV genomes excluding part of the regulatory region was accomplished using neighbour-joining, UPGMA and maximum parsimony methods. The resulting UPGMA and parsimony phylogenies suggest that the European Type 1 strains diverged from the other types during the evolution of JCV and that each of the other genotypes (and subtypes) falls into well-supported clades. This is the first whole genome approach to phylogeny reconstruction for JCV and represents a significant improvement over earlier studies that were limited to partial JCV sequences and the neighbour-joining method.

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1998-10-01
2022-05-28
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References

  1. Agostini H. T., Ryschkewitsch C. F., Stoner G. L. 1996; Genotype profile of human polyomavirus JC excreted in urine of immunocompetent individuals. Journal of Clinical Microbiology 34:159–164
    [Google Scholar]
  2. Agostini H. T., Ryschkewitsch C. F., Brubaker G. R., Shao J., Stoner G. L. 1997a; Five complete genomes of JC virus Type 3 from Africans and African Americans. Archives of Virology 142:637–655
    [Google Scholar]
  3. Agostini H. T., Ryschkewitsch C. F., Singer E. J., Stoner G. L. 1997b; JC virus regulatory region rearrangements and genotypes in progressive multifocal leukoencephalopathy: two independent aspects of virus variation. Journal of General Virology 78:659–664
    [Google Scholar]
  4. Agostini H. T., Ryschkewitsch C. F., Singer E. J., Baumhefner R. W., Stoner G. L. 1998a; JC virus Type 2B is found more frequently in brain tissue of progressive multifocal leukoencephalopathy (PML) patients than in control urines. Journal of Human Virology 1:200–206
    [Google Scholar]
  5. Agostini H. T., Ryschkewitsch C. F., Stoner G. L. 1998b; JC virus Type 1 has multiple subtypes : three new complete genomes. Journal of General Virology 79:801–805
    [Google Scholar]
  6. Agostini H. T., Shishido-Hara Y., Baumhefner R. W., Singer E. J., Ryschkewitsch C. F., Stoner G. L. 1998c; JC virus Type 2 : definition of subtypes based on DNA sequence analysis of ten complete genomes. Journal of General Virology 79:1143–1151
    [Google Scholar]
  7. Ault G. S., Stoner G. L. 1992; Two major types of JC virus defined in progressive multifocal leukoencephalopathy brain by early and late coding region DNA sequences. Journal of General Virology 73:2669–2678
    [Google Scholar]
  8. Ault G. S., Stoner G. L. 1993; Human polyomavirus JC promoter/ enhancer rearrangement patterns from progressive multifocal leuko- encephalopathy brain are unique derivatives of a single archetypal structure. Journal of General Virology 74:1499–1507
    [Google Scholar]
  9. Berger J. R., Concha M. 1995; Progressive multifocal leuko- encephalopathy: the evolution of a disease once considered rare. Journal of Neurovirology 1:5–18
    [Google Scholar]
  10. Berger J. R., Levy R. M. 1993; The neurologic complications of human immunodeficiency virus infection. Medical Clinics ofNorth America 77:1–23
    [Google Scholar]
  11. Brady J. N., Salzman N. P. 1986; The papovaviruses. General properties of polyoma and SV40. In The Papovaviridae 1 The Polyomaviruses pp 1–26 Salzman N. P. Edited by New York: Plenum Press;
    [Google Scholar]
  12. Cann R. L., Stoneking M., Wilson A. C. 1987; Mitochondrial DNA and human evolution. Nature 325:31–36
    [Google Scholar]
  13. Chase M. W., Soltis D. E., Olmstead R. G., Morgan D., Les D. H., Mishler B. D., Duval R. R., Price R., Hillis H. G., Qui Y.-L., Kron K. A., Rettig J. H., Conti E., Palmer J. D., Manhart J. R., Sytsma K. J., Michaels H. J., Kress W. J., Karol K. G., Clark W. D., Hedren M., Gaut B. S., Jansen R. K., Kim K.-J., Wimpee C. F., Smith J. F., Furnier G. R., Strauss S. H., Xiang Q.-Y., Plunkett G. M., Soltis P. S., Williams S. E., Gadek P. A., Quinn C. J., Eguiarte L. E., Golenberg E., Learn G. H., Graham S., Barrett S. C. H., Dayanandan S., Albert V. A. 1993; Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden 80:528–580
    [Google Scholar]
  14. Cole C. N. 1996; Polyomavirinae: the viruses and their replication. In Fields Virology, 3rd edn. pp 1997–2025 Fields B. N., Knipe D. M., Howley P. M. Edited by Philadelphia: Lippincott-Raven;
    [Google Scholar]
  15. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
    [Google Scholar]
  16. Field K. 1988; Molecular phylogeny of the animal kingdom. Science 239:748–753
    [Google Scholar]
  17. Frisque R. J., Bream G. L., Cannella M. T. 1984; Human polyomavirus JC virus genome. Journal of Virology 51:458–469
    [Google Scholar]
  18. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism pp 21–132 Munro H. N. Edited by New York: Academic Press;
    [Google Scholar]
  19. Kimura M. 1980; A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 47:471–486
    [Google Scholar]
  20. Li W.-H., Graur D. 1991 Fundamentals of Molecular Evolution Sunderland, MA, USA: Sinauer Associates;
    [Google Scholar]
  21. Loeber G., Dörries K. 1988; DNA rearrangement in organ-specific variants ofpolyomavirusJC strain GS. Journal of Virology 62:1730–1735
    [Google Scholar]
  22. Major E. O., Amemiya K., Tornatore C. S., Houff S. A., Berger J. R. 1992; Pathog enesis and molecular biology of progressive multifocal leukoencephalopathy, the JC virus-induced demyelinating disease of the human brain. Clinical Microbiology Reviews 5:49–73
    [Google Scholar]
  23. Ou W.-C., Tsai R.-T., Wang M., Fung C.-Y., Hseu T.-H., Chang D. 1997; Genomic cloning and sequence analysis of Taiwan-3 human polyomavirus JC virus. Journal of the Formosan Medical Association 96:511–516
    [Google Scholar]
  24. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406–425
    [Google Scholar]
  25. Shishido Y., Nukuzuma S., Mukaigawa J., Morikawa S., Yasui K., Nagashima K. 1997; Assembly of JC virus-like particles in COS7 cells. Journal of Medical Virology 51:265–272
    [Google Scholar]
  26. Sokal R. R., Michener C. D. 1958; A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin 38:1409–1438
    [Google Scholar]
  27. 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., Yogo Y. 1997; Typing of urinary JC virus DNA offers a novel means of tracing human migrations. Proceedings of the National Academy of Sciences, USA 94:9191–9196
    [Google Scholar]
  28. Swofford D. L. 1993; PAUP : phylogenetic analysis using parsimony, version 3.1.1. Champaign, IL, USA: Illinois Natural History Survey;
    [Google Scholar]
  29. Walker D. L. 1985; Progressive multifocal leukoencephalopathy. In Handbook of Clinical Neurology 47 Demyelinating Diseases pp 503–524 Vinken P. J., Bruyn G. W., Klawans H. L., Koetsier J. C. Edited by Amsterdam: Elsevier;
    [Google Scholar]
  30. Walker D. L., Frisque R. J. 1986; The biology and molecular biology of JC virus. In The Papovaviridae 1 The Polyomaviruses pp 327–377 Salzman N. P. Edited by New York: Plenum Press;
    [Google Scholar]
  31. Woese C. R. 1987; Bacterial evolution. Microbiological Reviews 51:221–271
    [Google Scholar]
  32. Woese C. R., Kandler O., Wheelis M. L. 1990; Towards a natural system of organisms : proposal for the domains Archaea, Bacteria, and Eukarya. Proceedings of the National Academy of Sciences, USA 87:4576–4579
    [Google Scholar]
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