Characterisation of single nucleotide polymorphisms in the genome of JC polyomavirus using MALDI TOF mass spectrometry

Journal of Virological Methods

Volumn 164, Issue 1-2, 2010, Pages 63-67

  Bayliss, Julianne ^a   Moser, Ralf ^b   Bowden, Scott ^a,c   McLean, Catriona A ^a,d  

^a MONASH UNIVERSITY   (Australia)

^b Sequenom Inc   (Australia)

^c VICTORIAN INFECTIOUS DISEASES REFERENCE LABORATORY   (Australia)

^d ALFRED HOSPITAL   (Australia)

Author keywords

JC virus; Mass spectrometry; Progressive multifocal leukoencephalopathy; Single nucleotide polymorphism; Viral genotyping

Indexed keywords

PROTEIN VP1;

ADOLESCENT; ADULT; AGED; AMPLICON; ARTICLE; CHILD; CLINICAL ARTICLE; FEMALE; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOTYPE; HUMAN; JC VIRUS; MALE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS LOAD; VIRUS REPLICATION; VIRUS STRAIN;

ADOLESCENT; ADULT; AGED; CAPSID PROTEINS; CHILD; CHILD, PRESCHOOL; FEMALE; HUMANS; JC VIRUS; MALE; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYOMAVIRUS INFECTIONS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; URINE; VIROLOGY; YOUNG ADULT;

JC POLYOMAVIRUS;

EID: 77249174730     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2009.11.029     Document Type: Article

References (26)

1. Agostini H.T., Ryschkewitsch C.F., Mory R., Singer E.J., and Stoner G.L. JC virus (JCV) genotypes in brain tissue from patients with progressive multifocal leukoencephalopathy (PML) and in urine from controls without PML: increased frequency of JCV type 2 in PML. J. Infect. Dis. 176 (1997) 1-8
2. Atwood W.J. Genotypes, archetypes, and tandem repeats in the molecular epidemiology and pathogenesis of JC virus induced disease. J. Neurovirol. 9 (2003) 519-521
3. Bofill-Mas S., and Girones R. Role of the environment in the transmission of JC virus. J. Neurovirol. 9 Suppl. 1 (2003) 54-58
4. Caldarelli-Stefano R., Vago L., Omodeo-Zorini E., Mediati M., Losciale L., Nebuloni M., Costanzi G., and Ferrante P. Detection and typing of JC virus in autopsy brains and extraneural organs of AIDS patients and non-immunocompromised individuals. J. Neurovirol. 5 (1999) 125-133
5. Dang X., and Koralnik I.J. A granule cell neuron-associated JC virus variant has a unique deletion in the VP1 gene. J. Gen. Virol. 87 (2006) 2533-2537
6. Delbue S., Branchetti E., Bertolacci S., Tavazzi E., Marchioni E., Maserati R., Minnucci G., Tremolada S., Vago G., and Ferrante P. JC virus VP1 loop-specific polymorphisms are associated with favorable prognosis for progressive multifocal leukoencephalopathy. J. Neurovirol. 15 (2009) 51-56
7. Eash S., Manley K., Gasparovic M., Querbes W., and Atwood W.J. The human polyomaviruses. Cell. Mol. Life Sci. 63 (2006) 865-876
8. Ferrante P., Mediati M., Caldarelli-Stefano R., Losciale L., Mancuso R., Cagni A.E., and Maserati R. Increased frequency of JC virus type 2 and of dual infection with JC virus type 1 and 2 in Italian progressive multifocal leukoencephalopathy patients. J. Neurovirol. 7 (2001) 35-42
9. Glass A.J., and Venter M. Improved detection of JC virus in AIDS patients with progressive multifocal leukoencephalopathy by T-antigen specific fluorescence resonance energy transfer hybridization probe real-time PCR: evidence of diverse JC virus genotypes associated with progressive multifocal leukoencephalopathy in Southern Africa. J. Med. Virol. 81 (2009) 1929-1937
10. Hartung H.-P. New cases of progressive multifocal leukoencephalopathy after treatment with natalizumab. Lancet Neurol. 8 (2009) 28-31
11. Honisch C., Chen Y., Mortimer C., Arnold C., Schmidt O., van den Boom D., Cantor C.R., Shah H.N., and Gharbia S.E. Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 10649-10654
12. Jobe 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. New JC virus (JCV) genotypes from papua new guinea and micronesia (type 8 and type 2E) and evolutionary analysis of 32 complete JCV genomes. Arch. Virol. 146 (2001) 2097-2113
13. Khalili K., White M.K., Lublin F., Ferrante P., and Berger J.R. Reactivation of JC virus and development of PML in patients with multiple sclerosis. Neurology 68 (2007) 985-990
14. Lai N.-S., Lu M.-C., Lee M.-C., Lin T.-Y., and Yin W.-Y. Detection of polyomavirus JC genotype from transplant patients by capillary electrophoresis: comparison to fragment length polymorphism analysis. J. Formos. Med. Assoc. 107 (2008) 239-244
15. Lefmann M., Honisch C., Bocker S., Storm N., von Wintzingerode F., Schlotelburg C., Moter A., van den Boom D., and Gobel U.B. Novel mass spectrometry-based tool for genotypic identification of mycobacteria. J. Clin. Microbiol. 42 (2004) 339-346
16. Luan J., Yuan J., Li X., Jin S., Yu L., Liao M., Zhang H., Xu C., He Q., Wen B., Zhong X., Chen X., Chan H.L.Y., Sung J.J.Y., Zhou B., and Ding C. Multiplex detection of 60 Hepatitis B virus variants by MALDI-TOF mass spectrometry. Clin. Chem. 55 (2009) 1503-1509
17. Marzocchetti A., Sanguinetti M., Giambenedetto S.D., Cingolani A., Fadda G., Cauda R., and De Luca A. Characterization of JC virus in cerebrospinal fluid from HIV-1 infected patients with progressive multifocal leukoencephalopathy: insights into viral pathogenesis and disease prognosis. J. Neurovirol. 13 (2007) 338-346
18. Monaco M.C., Atwood W.J., Gravell M., Tornatore C.S., and Major E.O. JC virus infection of hematopoietic progenitor cells, primary B lymphocytes, and tonsillar stromal cells: implications for viral latency. J. Virol. 70 (1996) 7004-7012
19. Pelosini M., Focosi D., Rita F., Galimberti S., Caracciolo F., Benedetti E., Papineschi F., and Petrini M. Progressive multifocal leukoencephalopathy: report of three cases in HIV-negative hematological patients and review of literature. Ann. Hematol. 87 (2008) 405-412
20. Roberts M.T.M. AIDS-associated progressive multifocal leukoencephalopathy: current management strategies. CNS Drugs 19 (2005) 671-682
21. Ryschkewitsch C., Jensen P., Hou J., Fahle G., Fischer S., and Major E.O. Comparison of PCR-southern hybridization and quantitative real-time PCR for the detection of JC and BK viral nucleotide sequences in urine and cerebrospinal fluid. J. Virol. Methods 121 (2004) 217-221
22. Sunyaev S.R., Lugovskoy A., Simon K., and Gorelik L. Adaptive mutations in the JC virus protein capsid are associated with progressive multifocal leukoencephalopathy (PML). PLoS Genet. 5 (2009) e1000368
23. Tan C.S., Dezube Bruce J., Bhargava P., Autissier P., Wuthrich C., Miller J., and Koralnik Igor J. Detection of JC virus DNA and proteins in the bone marrow of HIV positive and HIV negative patients: implications for viral latency and neurotropic transformation. J. Infect. Dis. 199 (2009) 881-888
24. Wang Y., Kirby J.E., and Qian Q. Effective use of JC virus PCR for diagnosis of progressive multifocal leukoencephalopathy. J. Med. Microbiol. 58 (2009) 253-255
25. Whiley D.M., Arden K.E., Mackay I.M., Syrmis M.W., and Sloots T.P. Simultaneous detection and differentiation of human polyomaviruses JC and BK by a rapid and sensitive PCR-ELAHA assay and a survey of the JCV subtypes within an Australian population. J. Med. Virol. 72 (2004) 467-472
26. Yanagihara R., Nerurkar V.R., Scheirich I., Agostini H.T., Mgone C.S., Cui X., Jobes D.V., Cubitt C.L., Ryschkewitsch C.F., Hrdy D.B., Friedlaender J.S., and Stoner G.L. JC virus genotypes in the western Pacific suggest Asian mainland relationships and virus association with early population movements. Hum. Biol. 74 (2002) 473-488