Accurate quantification of hepatitis C virus (HCV) RNA from all HCV genotypes by using branched-DNA technology

Journal of Clinical Microbiology

Volumn 34, Issue 4, 1996, Pages 901-907

  Detmer, Jill ^a   Lagier, Robert ^a   Flynn, Julie ^a   Zayati, Crystle ^a   Kolberg, Janice ^a   Collins, Mark ^a   Urdea, Mickey ^a   Sánchez Pescador, Ray ^a  

^a NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ACCURACY; ARTICLE; GENOTYPE; HEPATITIS C; HEPATITIS C VIRUS; HEPATITIS NON A NON B; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; SEQUENCE ANALYSIS; VIRUS GENE;

EID: 0029985468     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/jcm.34.4.901-907.1996     Document Type: Article

References (57)

1. Alter, H. J., R. Sánchez-Pescador, M. S. Urdea, J. C. Wilber, R. J. Lagier, A. M. Di Bisceglie, J. W. Shih, and P. D. Neuwald. 1995. Evaluation of branched DNA signal amplification for the detection of hepatitis C virus RNA. J. Viral Hepatitis. 2:121-132.
2. Alter, M. J. 1989. Chronic consequences of non-A non-B hepatitis, p. 83-97. In L B. Seeff and J. H. Lewis (ed.), Current perspectives in hepatology. Plenum Publishing Corporation, New York.
3. Bresters, D., H. T. M. Cuypers, H. W. Reesink, E. P. Mauser-Bunschoten, H. M. van den Berg, W. P. Schaasberg, J. C. Wilber, M. S. Urdea, P. Neuwald, and P. N. Lelie. 1994. Comparison of quantitative cDNA-PCR with the branched DNA hybridization assay for monitoring plasma hepatitis C virus RNA levels in hemophilia patients participating m a controlled interferon trial. J. Med. Virol. 43:262-268.
4. Bukh, J., R. H. Purcell, and R. H. Miller. 1992. Sequence analysis of the 5' noncoding region of hepatitis C virus Proc. Natl. Acad. Sci. USA 89:4942-4946.
5. Chan, C.-Y., S.-D. Lee, S.-J. Hwang, R.-H. Lu, C.-L. Lu, and K.-J. Lo. 1995. Quantitative branched DNA assay and genotyping for hepatitis C virus RNA in Chinese patients with acute and chronic hepatitis C J. Infect. Dis. 171:443-446.
6. Chazouilleres, O., M. Kim, C. Combs, L. Ferrell, P. Bacclietti, J. Roberts, N. L. Ascher, P. Neuwald, J. Wilber, M. Urdea, S. Quan, R. Sanchez-Pescador, and T. L. Wright. 1994. Quantitation of hepatitis C virus RNA in liver transplant recipients. Gastroenterology 106:994-999.
7. Chemello, L., A. Alberti, K. Rose, and P. Simmonds. 1994. Hepatitis C serotype and response to Interferon therapy. N. Engl J Med. 330:143.
8. Choo, Q.-L., G. Kuo, A. J. Weiner, L. R. Overby, D. W. Bradley, and M. Houghton. 1989. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244:359-364.
9. Choo, Q. L., K. H. Richman, J. H. Han, K. Berger, C. Lee, C. Dong, C. Gallegos, D. Coit, R. Medina-Selby, P. J. Barr, A. J. Weiner, D. W. Bradley, G. Kuo, and M. Houghton. 1991. Genetic organization and diversity of the hepatitis C virus. Proc. Natl. Acad Sci. USA 88:2451-2455.
10. Choo, Q. L., A. J. Weiner, L. R. Overby, G. Kuo, M. Houghton, and D. W. Bradley. 1990. Hepatitis C virus: the major causative agent of viral non-A, non-B hepatitis. Br. Med. Bull. 46:423-441.
11. Coelbo-Little, E., L. J. Jeffers, M. Bartholomew, K. R. Reddy, E. R. Schiff, and P. J. Dailey. 1995. Correlation of HCV-RNA levels in serum and liver of patients with chronic hepatitis C. J. Hepatol. 22:508.
12. Collins, M. L., C. Zayati, J. J. Detmer, B. Daly, J. A. Kolberg, T. A. Cha, B. D. Irvine, J. Tucker, and M. S. Urdea. 1995 Preparation and characterization of RNA standards for use in quantitative branched DNA hybridization assays. Anal. Biochem. 226:120-129.
13. Daly, J. A., and G. Ertingshausen. 1972. Direct method for determining inorganic phosphate in serum with the "CentnfiChem." Clin. Chem. 18:263-265.
14. Davis, G. L. 1994. Prediction of response to Interferon treatment of chronic hepatitis C. J. Hepatol. 21:1-3.
15. Davis, G. L., J. Y. N. Lau, M. S. Urdea, P. D. Neuwald, J. C. Wilber, K. Lindsay, R. P. Perrillo, and J. Albrecht. 1994. Quantitative detection of hepatitis C virus RNA with a solid-phase signal amplification method: definition of optimal conditions for specimen collection and clinical application in interferon-treated patients. Hepatology 19:1337-1341.
16. Diodati, G., P. Bonetti, F. Noventa, C. Casarin, M. Rugge, S. Scaccabarozzi, A. Tagger, L. Pollice, F. Tremolada, C. Davite, G. Realdi, and A. Ruol. 1994 Treatment of chronic hepatitis C with recombinant human interferon-α2a: results of a randomized controlled clinical trial. Hepatology 19:1-5.
17. Enomoto, N., A. Takada, T. Nakao, and T. Date. 1990 There are two majoi types of hepatitis C virus in Japan Biochem. Biophys. Res. Commun. 170:1021-1025.
18. Féray, C., M. Gigou, D. Samuel, V. Paradis, J. Wilber, M. F. David, M. Urdea, M. Reynes, C. Bréchot, and H. Bismuth. 1994. The course of hepatitis C virus infection after liver transplantation. Hepatology 20:1137-1143.
19. Gordon, S. C., V. P. Kodali, A. L. Silverman, C. F. Dmuchowski, M. S. Urdea, C. S. Chan, and J. C. Wilber. 1994. Levels of hepatitis C virus RNA and liver histology in chronic type C hepatitis. Am J. Gastroenterol 89:1458-1461.
20. Hayashi, J., M. Ohmiya, N. Kishihara, N. Kinukawa, H. Ikematsu, and S. Kashiwagi. 1994. A statistical analysis of predictive factors of response to human lymphoblastoid interferon in patients with chronic hepatitis C. Am. J. Gastroenterol. 89:2151-2156.
21. Horn, T., and M. S. Urdea. 1989. Forks and combs and DNA: the synthesis of branched oligodeoxyribonuclcotidcs. Nucleic Acids Res. 17:6959-6967.
22. Kanai, K., M. Kako, and H. Okamoto. 1992. HCV genotypes in chronichepatitis C. and response to interferon. Lancet 339:1543
23. Kendall, M., and A. Stewart. 1979. The advanced theory of statistics, vol 2. Charles Griffin and Company, Ltd., London.
24. Kirk, R. E. 1982. Experimental design. Brooks/Cole Publishing Company, Monterey, Calif.
25. Kolberg, J., R. Sánchez-Pescador, J. Detmer, M. Collins, P. Sheridan, P. Neuwald, J. Wilber, P. Dailey, and M. Urdea. 1994. Branched DNA (bDNA) quantitation of hepatitis C viral RNA in patient sera, p 57-69. In Hepatitis C virus: new diagnostic tools. John Libbey Eurotext, Paris.
26. Lau, J. Y. N., G. L. Davis, J. Kniffen, K.-P. Qian, M. S. Urdea, C. S. Chan, M. Mizokami, P. D. Neuwald, and J. C. Wilber. 1993. Significance of serum hepatitis C virus RNA levels in chronic hepatitis C. Lancet 341:1501-1504.
27. Lau, J. Y. N., M. Mizokami, J. A. Kolberg, G. L. Davis, L. E. Prescott, T. Ohno, R. P. Perrillo, K. L. Lindsay, R. G. Gish, K.-P. Qian, M. Kohara, P. Simmonds, and M. S. Urdea. 1995. Application of six hepatitis C virus genotyping systems to sera from chronic hepatitis C patients in the United States. J. Infect. Dis. 171:281-289.
28. Lau, J. Y. N., P. Simmonds, and M. S. Urdea. 1995. Implications of the variation of the conserved region of hepatitis C virus genome. Lancet 346:425-426.
29. Lin, L. L. 1989. A concordance correlation coefficient to evaluate reproducibility. Biometrics 45:255-268.
30. Magrin, S., A. Craxi, C. Fabiano, R. G. Simonetti, G. Fiorentino, L. Marino, O. Diquattro, V. Di Marco, O. Loiacono, R. Volpes, P. Almasio, M. S. Urdea, P. Neuwald, R. Sanchez-Pescador, J. Detmer, J. C. Wilber, and L. Pagliaro. 1994 Hepatitis C viremia in chronic liver disease: relationship to interferon-α or corticosteroid treatment. Hepatology 19:273-279.
31. Mahaney, K., V. Tedeschi, G. Maertens, A. M. Di Bisceglie, J. Vergalla, J. H. Hoofnagle, and R. Sallie. 1994. Genotypic analysis of hepatitis C virus in American patients. Hepatology 20:1405-1411.
32. Matsumoto, A, E. Tanaka, T. Suzuki, H. Ogata, and K. Kiyosawa. 1994. Viral and host factors that contribute to efficacy of interferon-α2a therapy in patients with chronic hepatitis C. Dig. Dis Sci. 39:1273-1230.
33. Mita, E., N. Hayashi, H. Hagiwara, K. Ueda, Y. Kanazawa, A. Kasahara, H. Fusamoto, and T. Kamada. 1994 Predicting interferon therapy efficacy from hepatitis C virus genotype and RNA titer. Dig. Dis Sci. 39:977-982.
34. National Committee for Clinical Laboratory Standards. 1986. Evaluation of quantitative analytical methods. Proposed guideline. NCCLS publication EP6-P. National Committee for Clinical Laboratory Standards, Villanova. Pa.
35. Nousbaum, J.-B., S. Pol, B. Nalpas, P. Landais, P. Berthelot, C. Bréchet, and The Collaborative Study Group. 1995. Hepatitis C virus type Ib (II) infection in France and Italy. Ann Intern. Mod. 122:161-168
36. Ogata, N., H. J. Alter, R. H. Miller, and R. H. Purcell. 1991. Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proc. Natl. Acad. Sci. USA 88:3391-3396.
37. Okamoto, H., M. Kojima, S.-I. Okada, H. Yoshizawa, H. lizuka, T. Tanaka, E. E. Muchmore, D. A. Peterson, Y. Ito, and S. Mishiro. 1992. Genetic drift of hepatitis C virus during an 8.2 year infection in a chimpanzee: variability and stability. Virology 190:894-899.
38. Orito, E., M. Mizokami, T. Nakano, H. Terashima, O. Nojiri, K. Sakakibara, M. Mizuno, M. Ogino, M. Nakamura, Y. Matsumoto, K.-L Miyata, and J. Y. N. Lau. 1994. Serum hepatitis C virus RNA level as a predictor of subsequent response to intcrferon-alpha therapy in Japanese patients with chronic hepatitis C J. Med Virol. 44:410-414.
39. Pozzato, G., M. Moretti, L. S. Croce, F. Sasso, S. Kaneko, M. Unoara, K. Kobayashi, M. Crovatto, G. Santini, and C. Tiribelli. 1995 Interferon therapy in chronic hepatitis C: evidence of different outcome with respect to different viral strains. J. Med. Virol. 45:445-450.
40. Rassam, S., A. Ridley-Dash, J. Wilber, M. Urdea, P. Neuwald, S. Sherlock, N, Thompson, N. McIntyre, and G. Dusheiko. 1994. Ribavirin or alpha Interferon treatment of chronic hepatitis C: assessment of antiviral efficacy, p. 642-646. In K. Nishioka, H. Suzuki, S. Mishiro, and T. Oda (ed.), Viral hepatitis and liver disease. Springer-Verlag, Tokyo.
41. Running, J. A., and M. S. Urdea. 1990 A procedure for productive coupling of synthetic oligonucleotides to polystyrene microtiter wells for hybridization capture. BioTechniques 8:276-277.
42. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
43. Schaap, A. P., M. D. Sandison, and R. S. Handley. 1987 Chemical and enzymatic triggering of 1,2-dioxetanes 3. Alkaline phosphatase-catalyzed chemiluminescence from an acryl phosphate-substituted dioxetane. Tetrahedron Lett. 28:1159-1162
44. Simmonds, P. 1995. Variability of hepatitis C virus Hepatology 21:570-583.
45. Simmonds, P., A. Albertt, H. J. Alter, F. Bonino, D. W. Bradley, C. Bréchet, J. T. Brouwer, S.-W. Chan, K. Chayama, D.-S. Chen, Q.-L. Choo, M. Colombo, H. T. M. Cuypers, T. Date, G. M. Dusheiko, J. I. Esteban, O. Fay, S. J. Hadziyannis, J. Han, A. Hatzakis, E. C. Holmes, H. Hotta, and M. Houghton. 1994. A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology 19:1321-1324.
46. Simmonds, P., E. C. Holmes, T.-A. Cha, S.-W. Chan, F. McOmish, B. Irvine, E. Beall, P. L. Yap, J. Kolberg, and M. S. Urdea. 1993. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J. Gen. Virol. 74:2391-2399.
47. Stuyver, L., R. Rossau, A. Wyseur, M. Duhamel, B. Vanderborght, H. Van Heuverswyn, and G. Maertens. 1993. Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. J Gen. Virol. 74:1093-1102.
48. Tokita, H., H. Okamoto, F. Tsuda, P. Song, S. Nakata, T. Chosa, H. lizuka, S. Mishiro, Y. Miyakawa, and M. Mayumi. 1994. Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups Proc. Natl Acad. Sci. USA 91:11022-11026.
49. Tsubota, A., K. Chayama, K. Ikeda, A. Yasuji, I. Koida, S. Saitoh, M. Hashimoto, S. Iwasaki, M. Kobayashi, and K. Hiromitsu. 1994. Factors predictive of response to interferon-alpha therapy m hepatitis C virus infection. Hepatology 19:1088-1094.
50. Urdea, M. 1993. Synthesis and characterization of branched DNA (bDNA) for the direct and quantitative detection of CMV, HBV, HCV and HIV. Clin. Chem. 39:725-726.
51. Urdea, M. S., T. Horn, T. Fultz, M. Andersoa, J. Running, S. Hamren, D. Ahle, and C.-A. Chang, 1991. Branched DNA amplification multimers for the sensitive, direct detection of human hepatitis viruses. Nucleic Acids Res. Symp. Ser. 24:197-200
52. Urdea, M. S., B. D. Warner, J. A. Running, M. Stempien, J. Clyne, and T. Horn. 1988 A comparison of non-radioisotopic hybridization assay methods using fluorescent, chemiluminescent and enzyme labeled synthetic oligodeoxyribonucleotide probes. Nucleic Acids Res. 16:4937-4956.
53. van Doorn, L. J., B. Kleter, L. Stuyver, G. Maertens, H. Brouwer, S. Schalm, R. Heijtink, and W. Quint. 1994. Analysis of hepatitis C virus genotypes by a line probe assay and correlation with antibody profiles. J. Hepatol. 21:122-129.
54. Warshaw, M. M., and I. Tinoco, Jr. 1966. Optical properties of sixteen dinucleoside phosphates. J Mol. Biol 20:29-38.
55. Wright, T. L., C. Combs, M. Kim, L. Ferrell, P. Bacchetti, N. Ascher, J. Roberts, J. Wilber, P. Sheridan, and M. Urdea. 1994. Interferon-α therapy for hepatitis C virus infection after liver transplantation. Hepatology 20:773-779.
56. Yamada, G., M. Takatani, F. Kishi, M. Takahashi, T. Doi, T. Tsuji, S. Shin, M. Tanno, M. Urdea, and J. A. Kolberg. 1995. Efficacy of alpha Interferon therapy in chronic hepatitis C patients depends primarily on HCV RNA level. Hepatology 22:1351-1354.
57. Yoshioka, K., S. Kakumu, T. Wakita, T. Ishikawa, Y. Itoh, M. Takayanagi, Y. Higashi, M. Shibata, and T. Morishima. 1992. Detection of hepatitis C virus by polymerase chain reaction and response to interfcron-α therapy: relationship to genotypes of hepatitis C virus. Hepatology 16:293-299.