Development of a real-time quantitative PCR assay for detection of a stable genomic region of BK virus

Virology Journal

Volumn 7, Issue , 2010, Pages

  Iwaki, Kosuke K ^a   Qazi, Suhail H ^a   Garcia Gomez, Jean ^a   Zeng, Deanna ^a   Matsuda, Yasuhiro ^a   Matsuda, Kazuko ^a   Martinez, Monica E ^a   Toyoda, Mieko ^b   Kore, Arputharaj ^c   Stevens, Wesley T ^d   Smogorzewski, Miroslaw ^a   Iwaki, Daisuke D ^a   Qazi, Yasir ^a   Iwaki, Yuichi ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b CEDARS SINAI MEDICAL CENTER   (United States)

^c LOMA LINDA UNIVERSITY MEDICAL CENTER   (United States)

^d LOMA LINDA UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; GENOMIC DNA; VIRUS DNA;

ARTICLE; BK VIRUS; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; GENE AMPLIFICATION; GENETIC POLYMORPHISM; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; QUANTITATIVE ASSAY; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; VIRUS GENOME; VIRUS INFECTION; EVALUATION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; METHODOLOGY; POLYMERASE CHAIN REACTION; POLYOMAVIRUS INFECTION; SENSITIVITY AND SPECIFICITY; VIROLOGY;

BK POLYOMAVIRUS;

BK VIRUS; CONSERVED SEQUENCE; DNA, VIRAL; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; POLYOMAVIRUS INFECTIONS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; VIROLOGY;

EID: 77958537975     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-7-295     Document Type: Article

References (34)

1. Discovery and epidemiology of the human polyomaviruses BK virus (BKV) and JC virus (JCV). WA Knowles, Adv Exp Med Biol 2006 577 19 45 16626025
2. Serological diagnosis of human polyomavirus infection. A Lundstig J Dillner, Adv Exp Med Biol 2006 577 96 101 16626030
3. K Khalili GL Stoner, Human polyomaviruses: molecular and clinical perspectives New York: Wiley 1 2001
4. Pathogenesis and management of polyomavirus infection in transplant recipients. EJ Kwak RA Vilchez P Randhawa R Shapiro JS Butel S Kusne, Clin Infect Dis 2002 35 1081 1087 10.1086/344060 12384842 (Pubitemid 35239468)
5. Polyomavirus-associated nephropathy in renal transplantation: interdisciplinary analyses and recommendations. HH Hirsch DC Brennan CB Drachenberg F Ginevri J Gordon AP Limaye MJ Mihatsch V Nickeleit E Ramos P Randhawa,,et al Transplantation 2005 79 1277 1286 10.1097/01.TP.0000156165. 83160.09 15912088
6. Polyoma virus nephropathy in native kidneys after lung transplantation. A Schwarz M Mengel H Haller J Niedermeyer, Am J Transplant 2005 5 2582 2585 10.1111/j.1600-6143.2005.01043.x 16162212
7. Polyomavirus nephropathy in native kidneys of non-renal transplant recipients. AP Limaye KD Smith L Cook DA Groom NC Hunt KR Jerome M Boeckh, Am J Transplant 2005 5 614 620 10.1046/j.1600-6143.2003.00209.x 15707418
8. The pathobiology of polyomavirus infection in man. P Randhawa A Vats R Shapiro, Adv Exp Med Biol 2006 577 148 159 16626033
9. Prevalence of BK virus replication among recipients of solid organ transplants. P Munoz M Fogeda E Bouza E Verde J Palomo R Banares, Clin Infect Dis 2005 41 1720 1725 10.1086/498118 16288394 (Pubitemid 41759854)
10. Polyomavirus infection in lung transplant recipients [Abstract #633]. L Thomas R Vilchez A Milstone J Butel S Dummer, 42nd Meeting of the Infectious Diseases Society of America 2004 165
11. Human polyoma virus in renal allograft biopsies: morphological findings and correlation with urine cytology. CB Drachenberg CO Beskow CB Cangro PM Bourquin A Simsir J Fink MR Weir DK Klassen ST Bartlett JC Papadimitriou, Hum Pathol 1999 30 970 977 10.1016/S0046-8177(99)90252-6 10452511
12. Prospective study of polyomavirus type BK replication and nephropathy in renal-transplant recipients. HH Hirsch W Knowles M Dickenmann J Passweg T Klimkait MJ Mihatsch J Steiger, N Engl J Med 2002 347 488 496 10.1056/NEJMoa020439 12181403
13. Testing for polyomavirus type BK DNA in plasma to identify renal-allograft recipients with viral nephropathy. V Nickeleit T Klimkait IF Binet P Dalquen V Del Zenero G Thiel MJ Mihatsch HH Hirsch, N Engl J Med 2000 342 1309 1315 10.1056/NEJM200005043421802 10793163
14. Treatment of refractory BK virus-associated nephropathy with cidofovir. PV Kadambi MA Josephson J Williams L Corey KR Jerome SM Meehan AP Limaye, Am J Transplant 2003 3 186 191 10.1034/j.1600-6143.2003.30202.x 12614296
15. Quantitative viral load monitoring and cidofovir therapy for the management of BK virus-associated nephropathy in children and adults. A Vats R Shapiro P Singh Randhawa V Scantlebury A Tuzuner M Saxena ML Moritz TJ Beattie T Gonwa MD Green D Ellis, Transplantation 2003 75 105 112 10.1097/00007890- 200301150-00020 12544881
16. Clustal W and Clustal X version 2.0. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez,,et al Bioinformatics 2007 23 2947 2948 10.1093/bioinformatics/btm404 17846036
17. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147
18. Interaction of polyomavirus internal protein VP2 with the major capsid protein VP1 and implications for participation of VP2 in viral entry. XS Chen T Stehle SC Harrison, EMBO J 1998 17 3233 3240 10.1093/emboj/17.12.3233 9628860
19. The capacity of polyomavirus enhancer binding protein 2alphaB (AML1/Cbfa2) to stimulate polyomavirus DNA replication is related to its affinity for the nuclear matrix. LF Chen K Ito Y Murakami Y Ito, Mol Cell Biol 1998 18 4165 4176 9632801
20. Functional complementation of nuclear targeting-defective mutants of simian virus 40 structural proteins. N Ishii A Nakanishi M Yamada MH Macalalad H Kasamatsu, J Virol 1994 68 8209 8216 7966613
21. Identification of a nuclear localization sequence in the polyomavirus capsid protein VP2. D Chang JI Haynes JN Brady RA Consigli, Virology 1992 191 978 983 10.1016/0042-6822(92)90276-U 1333132
22. Major and minor capsid proteins of human polyomavirus JC cooperatively accumulate to nuclear domain 10 for assembly into virions. Y Shishido-Hara S Ichinose K Higuchi Y Hara K Yasui, J Virol 2004 78 9890 9903 10.1128/JVI.78.18.9890-9903.2004 15331723
23. Identification of a DNA binding domain in simian virus 40 capsid proteins Vp2 and Vp3. J Clever DA Dean H Kasamatsu, J Biol Chem 1993 268 20877 20883 8407920
24. The Universal Protein Resource (UniProt); Swiss-Prot Accession #P03094. The UniProt Consortium, 2010 http://www.uniprot.org/uniprot/P03094
25. The genome of human papovavirus BKV. I Seif G Khoury R Dhar, Cell 1979 18 963 977 10.1016/0092-8674(79)90209-5 229976
26. BK virus DNA: complete nucleotide sequence of a human tumor virus. RC Yang R Wu, Science 1979 206 456 462 10.1126/science.228391 228391
27. Marked variability of BK virus load measurement using quantitative real-time PCR among commonly used assays. NG Hoffman L Cook EE Atienza AP Limaye KR Jerome, J Clin Microbiol 2008 46 2671 2680 10.1128/JCM.00258-08 18562587
28. Quantitation of BK virus load in serum for the diagnosis of BK virus-associated nephropathy in renal transplant recipients. AP Limaye KR Jerome CS Kuhr J Ferrenberg ML Huang CL Davis L Corey CL Marsh, J Infect Dis 2001 183 1669 1672 10.1086/320711 11343217
29. OligoCalc: an online oligonucleotide properties calculator. WA Kibbe, Nucleic Acids Res 2007 35 43 46 10.1093/nar/gkm234 17452344
30. "Primer3 on the www for general users and for biologist programmers.". S Rozen H Skaletsky, Bioinformatics Methods and Protocols: Methods in Molecular Biology Totowa, NJ: Humana Press, Krawetz S, Misener S, 2000 365 386 http://fokker.wi.mit.edu/primer3/
31. Genomic Typing of BK Virus in Clinical Specimens by Direct Sequencing of Polymerase Chain Reaction Products. L Jin PE Gibson JC Booth JP Clewley, J Med Virol 1993 41 11 17 10.1002/jmv.1890410104 8228931
32. Genotying Schemes for Polyomavirus BK, Using Gene-Specific Phylogenetic Trees and Single Nucleotide Polymorphism Analysis. C Luo M Bueno J Kant J Martinson P Randhawa, J Virol 2009 83 2285 2297 10.1128/JVI.02180-08 19109389
33. Phylogenetic Analysis of Polyomavirus BK Sequences. PM Sharma G Gupta A Vats R Shapiro P Randhawa, J Virol 2006 80 8869 8879 10.1128/JVI.00510-06 16940499
34. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738