Population genetic tests suggest that the epidemiologies of JCV and BKV are strikingly different

Infection, Genetics and Evolution

Volumn 10, Issue 3, 2010, Pages 397-403

  Mes, Ted H M ^a   van Doornum, Gerard J J ^a   Schutten, Martin ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Deleterious mutations; Demography; Fu and Li's D; Polyomavirus; Population expansion

Indexed keywords

ARTICLE; BK VIRUS; CONTROLLED STUDY; DEMOGRAPHY; GENETIC ANALYSIS; GENETIC MODEL; JC VIRUS; KIDNEY DISEASE; MOLECULAR EPIDEMIOLOGY; MUTATION RATE; POPULATION GENETICS; PRIORITY JOURNAL; PROGRESSIVE MULTIFOCAL LEUKOENCEPHALOPATHY; VIRUS GENOME; VIRUS MUTATION;

BK VIRUS; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GENOME, VIRAL; HUMANS; JC VIRUS; MUTATION; PHYLOGENY; POLYOMAVIRUS INFECTIONS; SEQUENCE ANALYSIS, DNA; TUMOR VIRUS INFECTIONS;

BK POLYOMAVIRUS; POLYOMAVIRUS;

EID: 77951090256     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2009.04.007     Document Type: Article

References (35)

1. Agostini H.T., Shishido-Hara Y., Baumhefner R.W., Singer E.J., Ryschkewitsch C.F., Stoner G.L. JC virus type 2: definition of subtypes based on DNA sequence analysis of ten complete genomes. J. Gen. Virol. 1998, 79:1143-1151.
2. Binggeli S., Egli A., Schaub S., Binet I., Mayr M., Steiger J., Hirsch H.H. Polyomavirus BK-specific cellular immune response to VP1 and large T-antigen in kidney transplant recipients. Am. J. Transplant. 2007, 7:1131-1139.
3. Chen Y., Sharp P.M., Fowkes M., Kocher O., Joseph J.T., Koralnik I.J. Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity. J. Gen. Virol. 2004, 85:2651-2663.
4. Fagundes N.J.R., Ray N., Beaumont M., Neuenschwander S., Salzano F.M., Bonatto S.L., Excoffier L. Statistical evaluation of alternative models of human evolution. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:17614-17619.
5. Fay J.C., Wu C.I. Hitchhiking under positive Darwinian selection. Genetics 2000, 155:1405-1413.
6. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 1981, 17:368-376.
7. Fu Y.X., Li W.H. Statistical tests of neutrality of mutations. Genetics 1993, 133:693-709.
8. Hahn M.W., Rausher M.D., Cunningham C.W. Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7. Genetics 2002, 161:11-20.
9. Ikegaya H., Zheng H.-Y., Saukko P.J., Varesmaa-Korhonen L., Hovi T., Vesikari T., Suganami H., Takasaka T., Sugimoto C., Ohasi Y., Kitamura T., Yogo Y. Genetic diversity of JC virus in the Saami and the Finns: implications for their population history. Am. J. Phys. Anthropol. 2005, 128:185-193.
10. Jobes D.V., Chima S.C., Ryschkewitsch C.F., Stoner G.L. Phylogenetic analysis of 22 complete genomes of the human polyomavirus JC virus. J. Gen. Virol. 1998, 79:2491-2498.
11. Kitchen A., Miyamoto M.M., Mulligan C.J. Utility of DNA viruses for studying human host history: case study of JC virus. Mol. Phylogenet. Evol. 2008, 46:673-682.
12. Knowles W.A. Discovery and epidemiology of the human polyomaviruses BK virus (BKV) and JC virus (JCV). Polyomaviruses and human diseases. Adv. Exp. Med. Biol. 2006, 577:19-45.
13. Krumbholz A., Bininda-Emonds O.R.P., Wutzler P., Zell R. Evolution of four BK virus subtypes. Infect., Genet., Evol. 2008, 8:632-643.
14. Kuhner M.K. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 2006, 22:768-770.
15. Martin D., Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 2000, 16:562-563.
16. McDaniel S.F., Shaw A.J. Selective sweeps and intercontinental migration in the cosmopolitan moss Ceratodon purpureus (Hedw.) Brid. Mol. Ecol. 2005, 14:1121-1132.
17. Moens U., van Ghelue M. Polymorphism in the genome of non-passaged human polyomavirus BK: implications for cell tropism and the pathological role of the virus. Virology 2005, 331:209-231.
18. Nagashima K., Yamaguchi K., Nakase H., Miyazaki J. Progressive multifocal leukoencephalopathy. A case report and review of the literature. Acta Pathol. Jpn. 1982, 32:333-343.
19. Nishimoto Y., Takasaka T., Hasegawa M., Zheng H.-Y., Chen Q., Sugimoto C., Kitamura T., Yogo Y. Evolution of BK virus based on complete genome data. J. Mol. Evol. 2006, 63:341-352.
20. Otto S.P. Detecting the form of selection from DNA sequence data. TIG 2000, 16:526-529.
21. Perez-Losada M., Christensen R.G., McClennan D.A., Adams B.J., Viscidi R.P., Demma J.C., Crandall K.A. Comparing phylogenetic codivergence between polyomaviruses and their hosts. J. Virol. 2006, 80:5663-5669.
22. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer.
23. Rinaldi A. Tiny travel companions. EMBO Rep. 2007, 8:121-125.
24. Rodrigues C., Pinto D., Medeiros R. Molecular epidemiology characterization of the urinary excretion of polyomavirus in healthy individuals from Portugal-a Southern European population. J. Med. Virol. 2007, 79:1194-1198.
25. Shackelton L.A., Rambaut A., Pybus O.G., Holmes E.C. JC virus evolution and its association with human populations. J. Virol. 2006, 80:9928-9933.
26. Stoner G.L., Jobes D.V., Cobo M.F., Agostini H.T., Chima S.C., Ryschkewitsch C.F. JC virus as a marker of human migration to the Americas. Microb. Infect. 2000, 2:1905-1911.
27. Sugimoto C., Kitamura T., Guo J., AlAhdal M.N., Shchelkunov S.N., Otova B., Ondrejka P., Chollet J.Y., ElSafi S., Ettayebi M., Gresenguet G., Kocagoz T., Chaiyarasamee S., Thant K.Z., Thein S., Moe K., Kobayashi N., Taguchi F., Yogo Y. Typing of urinary JC virus DNA offers a novel means of tracing human migrations. Proc. Natl. Acad. Sci. U.S.A. 1997, 94:9191-9196.
28. Sugimoto C., Hasegawa M., Kato A., Zheng H.-Y., Ebihara H., Taguchi F., Kitamura T., Yogo Y. Evolution of human polyomavirus JC: implications for the population history of humans. J. Mol. Evol. 2002, 54:285-297.
29. Swofford D.L. PAUP. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4 2003, Sinauer Associates, Sunderland, Massachusetts.
30. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
31. Takasaka T., Miranda J.J.C., Sugimoto C., Paraguison R., Zheng H.-Y., Kitamura T., Yogo Y. Genotypes of JC virus in Southeast Asia and the Western Pacific: implications for human migrations from Asia to the Pacific. Anthropol. Sci. 2004, 112:53-59.
32. Takasaka T., Goya N., Ishida H., Tanabe K., Toma H., Fujioka T., Omori S., Zheng H.Y., Chen Q., Nukuzuma S., Kitamura T., Yogo Y. Stability of the BK polyomavirus genome in renal-transplant patients without nephropathy. J. Gen. Virol. 2006, 87:303-306.
33. Yang Z.H. PAML4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.
34. Yogo Y., Zhong S., Suzuki M., Shibuya A., Kitamura T. Occurrence of the European subgroup I BK polyomavirus in Japanese-Americans suggests transmission outside the family. J. Virol. 2007, 81:13254-13258.
35. Zheng H.-Y., Kitamura T., Takasaka T., Chen Q., Yogo Y. Unambiguous identification of JC polyomavirus strains transmitted from parents to children. Arch. Virol. 2004, 149:261-273.