Reevaluating and optimizing polyomavirus BK and JC real-time PCR assays to detect rare sequence polymorphisms

Journal of Clinical Microbiology

Volumn 49, Issue 4, 2011, Pages 1382-1388

  Dumoulin, A ^a   Hirsch, H H ^a,b  

^a UNIVERSITY OF BASEL   (Switzerland)

^b UNIVERSITY HOSPITAL BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; VIRUS DNA;

ADULT; ARTICLE; BK VIRUS; BLOOD ANALYSIS; CONTROLLED STUDY; CROSS REACTION; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; DNA DETERMINATION; DNA POLYMORPHISM; DNA SEQUENCE; EVALUATION RESEARCH; FEMALE; GENE TARGETING; GENETIC VARIABILITY; HUMAN; INTERMETHOD COMPARISON; JC VIRUS; MAJOR CLINICAL STUDY; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REPEAT PROCEDURE; SENSITIVITY AND SPECIFICITY; SEQUENCE DATABASE; URINALYSIS; VIRUS DETECTION; VIRUS GENOME; VIRUS INFECTION;

ADULT; BK VIRUS; DNA PRIMERS; FEMALE; HUMANS; JC VIRUS; MALE; MIDDLE AGED; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; POLYOMAVIRUS INFECTIONS; SENSITIVITY AND SPECIFICITY; VIROLOGY;

BK POLYOMAVIRUS; POLYOMAVIRUS;

EID: 79953874291     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.02008-10     Document Type: Article

References (34)

1. Baksh, F. K., et al. 2001. Molecular genotyping of BK and JC viruses in human polyomavirus-associated interstitial nephritis after renal transplantation. Am. J. Kidney Dis. 38:354-365.
2. Bland, J. M., and D. G. Altman. 1986. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet i:307-310. (Pubitemid 16134762)
3. Bodaghi, S., et al. 2009. Antibody responses to recombinant polyomavirus BK large T and VP1 proteins in pediatric kidney transplant patients. J. Clin. Microbiol. 47:2577-2585.
4. Chen, Y., et al. 2004. Analysis of 15 novel full-length BK virus sequences from three individuals: Evidence of a high intra-strain genetic diversity. J. Gen. Virol. 85:2651-2663. (Pubitemid 39214361)
5. Cinque, P., A. Dumoulin, and H. H. Hirsch. 2009. Diagnosis of polyomavirus infection, replication and disease, p. 401-424. In K. Jerome (ed.), Laboratory diagnosis of viral infections. Informa Healthcare, New York, NY.
6. Cinque, P., P. Scarpellini, L. Vago, A. Linde, and A. Lazzarin. 1997. Diagnosis of central nervous system complications in HIV-infected patients: Cerebrospinal fluid analysis by the polymerase chain reaction. AIDS 11:1-17. (Pubitemid 27023207)
7. Dalianis, T., T. Ramqvist, K. Andreasson, J. M. Kean, and R. L. Garcea. 2009. KI, WU, and Merkel cell polyomaviruses: A new era for human polyomavirus research. Semin. Cancer Biol. 19:270-275.
8. Drachenberg, C. B., et al. 2007. Polyomavirus BK versus JC replication and nephropathy in renal transplant recipients: A prospective evaluation. Transplantation 84:323-330. (Pubitemid 47258319)
9. Egli, A., A. Dumoulin, S. Köhli, and H. H. Hirsch. 2009. Polyomavirus BK after kidney transplantation: Role of molecular and immunological markers. Trends Transplant. 3:85-102.
10. Egli, A., et al. 2009. Prevalence of polyomavirus BK and JC infection and replication in 400 healthy blood donors. J. Infect. Dis. 199:837-846.
11. Egli, A., et al. 2007. Cytomegalovirus and polyomavirus BK posttransplant. Nephrol. Dial. Transplant. 22(Suppl. 8):viii72-viii82.
12. Funk, G. A., R. Gosert, P. Comoli, F. Ginevri, and H. H. Hirsch. 2008. Polyomavirus BK replication dynamics in vivo and in silico to predict cytopathology and viral clearance in kidney transplants. Am. J. Transplant. 8:2368-2377.
13. Gosert, R., P. Kardas, E. O. Major, and H. H. Hirsch. 2010. Rearranged JC virus noncoding control regions found in progressive multifocal leukoencephalopathy patient samples increase virus early gene expression and replication rate. J. Virol. 84:10448-10456.
14. Gosert, R., et al. 2008. Polyomavirus BK with rearranged noncoding control region emerge in vivo in renal transplant patients and increase viral replication and cytopathology. J. Exp. Med. 205:841-852. (Pubitemid 351549882)
15. Gunson, R. N., T. C. Collins, and W. F. Carman. 2006. Practical experience of high throughput real-time PCR in the routine diagnostic virology setting. J. Clin. Virol. 35:355-367. (Pubitemid 43324830)
16. Hirsch, H. H., et al. 2005. Polyomavirus-associated nephropathy in renal transplantation: Interdisciplinary analyses and recommendations. Transplantation 79:1277-1286. (Pubitemid 40734783)
17. Hirsch, H. H., et al. 2002. Prospective study of polyomavirus type BK rep-lication and nephropathy in renal-transplant recipients. N. Engl. J. Med. 347:488-496. (Pubitemid 34879336)
18. Hirsch, H. H., et al. 1998. HIV-1-infected patients with focal neurologic signs: Diagnostic role of PCR for Toxoplasma gondii, Epstein-Barr virus, and JC virus. Clin. Microbiol. Infect. 4:577-584. (Pubitemid 28498022)
19. Hirsch, H. H., M. Mohaupt, and T. Klimkait. 2001. Prospective monitoring of BK virus load after discontinuing sirolimus treatment in a renal transplant patient with BK virus nephropathy. J. Infect. Dis. 184:1494-1496. (Pubitemid 33108869)
20. Hirsch, H. H., and P. Randhawa. 2009. BK virus in solid organ transplant recipients. Am. J. Transplant. 9(Suppl. 4):S136-S146.
21. Hoffman, N. G., L. Cook, E. E. Atienza, A. P. Limaye, and K. R. Jerome. 2008. Marked variability of BK virus load measurement using quantitative real-time PCR among commonly used assays. J. Clin. Microbiol. 46:2671-2680.
22. Jin, L., P. E. Gibson, W. A. Knowles, and J. P. Clewley. 1993. BK virus antigenic variants: Sequence analysis within the capsid VP1 epitope. J. Med. Virol. 39:50-56. (Pubitemid 23030416)
23. Kasiske, B. L., et al. 2009. KDIGO clinical practice guideline for the care of kidney transplant recipients. Am. J. Transplant 9(Suppl. 3):S1-S155.
24. Khanna, N., et al. 2009. JC virus-specific immune responses in human immunodeficiency virus type 1 patients with progressive multifocal leukoencephalopathy. J. Virol. 83:4404-4411.
25. Landry, M. L., T. Eid, S. Bannykh, and E. Major. 2008. False-negative PCR despite high levels of JC virus DNA in spinal fluid: Implications for diagnostic testing. J. Clin. Virol. 43:247-249.
26. Nickeleit, V., et al. 1999. Polyomavirus infection of renal allograft recipients: From latent infection to manifest disease. J. Am. Soc. Nephrol. 10:1080-1089. (Pubitemid 29203096)
27. Nickeleit, V., et al. 2000. Testing for polyomavirus type BK DNA in plasma to identify renal-allograft recipients with viral nephropathy. N. Engl. J. Med. 342:1309-1315. (Pubitemid 30408715)
28. Olsen, G. H., et al. 2006. Genetic variability in BK Virus regulatory regions in urine and kidney biopsies from renal-transplant patients. J. Med. Virol. 78:384-393.
29. Olsen, G. H., H. H. Hirsch, and C. H. Rinaldo. 2009. Functional analysis of polyomavirus BK noncoding control region quasispecies from kidney transplant recipients. J. Med. Virol. 81:1959-1967.
30. Schowalter, R. M., D. V. Pastrana, K. A. Pumphrey, A. L. Moyer, and C. B. Buck. 2010. Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin. Cell Host Microbe 7:509-515.
31. Sunyaev, S. R., A. Lugovskoy, K. Simon, and L. Gorelik. 2009. Adaptive mutations in the JC virus protein capsid are associated with progressive multifocal leukoencephalopathy (PML). PLoS Genet. 5:e1000368.
32. Tremolada, S., et al. 2010. Polymorphisms of the BK virus subtypes and their influence on viral in vitro growth efficiency. Virus Res. 149:190-196.
33. van der Meijden, E., et al. 2010. Discovery of a new human polyomavirus associated with trichodysplasia spinulosa in an immunocompromised patient. PLoS Pathog. 6:e1001024.
34. Viscount, H. B., et al. 2007. Polyomavirus polymerase chain reaction as a surrogate marker of polyomavirus-associated nephropathy. Transplantation 84:340-345. (Pubitemid 47258321)