A novel diagnostic target in the hepatitis C virus genome

PLoS Medicine

Volumn 6, Issue 2, 2009, Pages 0210-0220

  Drexler, Jan Felix ^a,b,c   Kupfer, Bernd ^b   Petersen, Nadine ^a   Grotto, Rejane Maria Tommasini ^d   Rodrigues, Silvia Maria Corvino ^d   Grywna, Klaus ^a   Panning, Marcus ^a   Annan, Augustina ^a   Silva, Giovanni Faria ^d   Douglas, Jill ^e   Koay, Evelyns C ^f,g   Smuts, Heidi ^h   Netto, Eduardo M ^c   Simmonds, Peter ^e   De Moura Campos Pardini, Maria Inês ^d   Roth, W Kurt ⁱ   Drosten, Christian ^b  

^a BERNHARD NOCHT INSTITUTE FOR TROPICAL MEDICINE   (Germany)

^b UNIVERSITY OF BONN   (Germany)

^c FEDERAL UNIVERSITY OF BAHIA   (Brazil)

^d SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

^f NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^g NATIONAL UNIVERSITY HOSPITAL   (Singapore)

^h UNIVERSITY OF CAPE TOWN   (South Africa)

ⁱ GFE Blut mbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BLOOD DONOR; BLOOD SAMPLING; BRAZIL; CONTROLLED STUDY; COST BENEFIT ANALYSIS; GENE SEQUENCE; GENOTYPE; GERMANY; HEPATITIS C VIRUS; HUMAN; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; SCREENING TEST; SINGAPORE; SOUTH AFRICA; TURNAROUND TIME; UNITED KINGDOM; VIRUS DETECTION; VIRUS GENOME; VIRUS LOAD; 5' UNTRANSLATED REGION; BLOOD; GENETICS; HEPATITIS C; ISOLATION AND PURIFICATION; METHODOLOGY; MOLECULAR GENETICS; VIROLOGY;

VIRUS RNA;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; GENOME, VIRAL; GENOTYPE; HEPACIVIRUS; HEPATITIS C; HUMANS; MOLECULAR SEQUENCE DATA; RNA, VIRAL; VIRAL LOAD;

EID: 61449094626     PISSN: 15491277     EISSN: 15491676     Source Type: Journal    
DOI: 10.1371/journal.pmed.1000031     Document Type: Article

References (68)

1. Poynard T, Yuen MF, Ratziu V, Lai CL (2003) Viral hepatitis C. Lancet 362: 2095-2100.
2. Perz JF, Alter MJ (2006) The coming wave of HCV-related liver disease: dilemmas and challenges. J Hepatol 44: 441-443.
3. Anonymous (1999) Global surveillance and control of hepatitis C. Report of a WHO Consultation organized in collaboration with the Viral Hepatitis Prevention Board, Antwerp, Belgium. J Viral Hepat 6: 35-47.
4. Simmonds P, Bukh J, Combet C, Deleage G, Enomoto N, et al. (2005) Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42: 962-973.
5. Berg T, Sarrazin C, Herrmann E, Hinrichsen H, Gerlach T, et al. (2003) Prediction of treatment outcome in patients with chronic hepatitis C: significance of baseline parameters and viral dynamics during therapy. Hepatology 37: 600-609.
6. Terrault NA, Pawlotsky JM, McHutchison J, Anderson F, Krajden M, et al. (2005) Clinical utility of viral load measurements in individuals with chronic hepatitis C infection on antiviral therapy. J Viral Hepat 12: 465-472.
7. Beld M, Sentjens R, Rebers S, Weegink C, Weel J, et al. (2002) Performance of the New Bayer VERSANT HCV RNA 3.0 assay for quantitation of hepatitis C virus RNA in plasma and serum: conversion to international units and comparison with the Roche COBAS Amplicor HCV Monitor, Version 2.0, assay. J Clin Microbiol 40: 788-793.
8. Halfon P, Bourliere M, Penaranda G, Khiri H, Ouzan D (2006) Real-time PCR assays for hepatitis C virus (HCV) RNA quantitation are adequate for clinical management of patients with chronic HCV infection. J Clin Microbiol 44: 2507-2511.
9. Lee SC, Antony A, Lee N, Leibow J, Yang JQ, et al. (2000) Improved version 2.0 qualitative and quantitative AMPLICOR reverse transcription-PCR tests for hepatitis C virus RNA: calibration to international units, enhanced genotype reactivity, and performance characteristics. J Clin Microbiol 38: 4171-4179.
10. Sizmann D, Boeck C, Boelter J, Fischer D, Miethke M, et al. (2007) Fully automated quantification of hepatitis C virus (HCV) RNA in human plasma and human serum by the COBAS AmpliPrep/COBAS TaqMan system. J Clin Virol 38: 326-333.
11. Morishima C, Chung M, Ng KW, Brambilla DJ, Gretch DR (2004) Strengths and limitations of commercial tests for hepatitis C virus RNA quantification. J Clin Microbiol 42: 421-425.
12. Colson P, Motte A, Tamalet C (2006) Broad differences between the COBAS AmpliPrep total nucleic acid isolation-COBAS TaqMan 48 hepatitis C virus (HCV) and COBAS HCV monitor v2.0 assays for quantification of serum HCV RNA of non-1 genotypes. J Clin Microbiol 44: 1602-1603.
13. Gelderblom HC, Menting S, Beld MG (2006) Clinical performance of the new Roche COBAS TaqMan HCV Test and High Pure System for extraction, detection and quantitation of HCV RNA in plasma and serum. Antivir Ther 11: 95-103.
14. Mellor J, Hawkins A, Simmonds P (1999) Genotype dependence of hepatitis C virus load measurement in commercially available quantitative assays. J Clin Microbiol 37: 2525-2532.
15. Chevaliez S, Bouvier-Alias M, Brillet R, Pawlotsky JM (2007) Overestimation and underestimation of hepatitis C virus RNA levels in a widely used realtime polymerase chain reaction-based method. Hepatology 46: 22-31.
16. Tang YW, Sefers SE, Li H (2005) Primer sequence modification enhances hepatitis C virus genotype coverage. J Clin Microbiol 43: 3576-3577.
17. Colucci G, Ferguson J, Harkleroad C, Lee S, Romo D, et al. (2007) Improved COBAS TaqMan hepatitis C virus test (Version 2.0) for use with the High Pure system: enhanced genotype inclusivity and performance characteristics in a multisite study. J Clin Microbiol 45: 3595-3600.
18. Pittaluga F, Allice T, Abate ML, Ciancio A, Cerutti F, et al. (2008) Clinical evaluation of the COBAS Ampliprep/COBAS TaqMan for HCV RNA quantitation in comparison with the branched-DNA assay. J Med Virol 80: 254-260.
19. Sandres-Saune K, Abravanel F, Nicot F, Peron JM, Alric L, et al. (2007) Detection and quantitation of HCV RNA using real-time PCR after automated sample processing. J Med Virol 79: 1821-1826.
20. Sarrazin C, Dragan A, Gartner BC, Forman MS, Traver S, et al. (2008) Evaluation of an automated, highly sensitive, real-time PCR-based assay (COBAS Ampliprep/COBAS TaqMan) for quantification of HCV RNA. J Clin Virol 43: 162-168.
21. Vermehren J, Kau A, Gartner BC, Gobel R, Zeuzem S, et al. (2008) Differences between two real-time PCR-based hepatitis C virus (HCV) assays (RealTime HCV and Cobas AmpliPrep/Cobas TaqMan) and one signal amplification assay (Versant HCV RNA 3.0) for RNA detection and quantification. J Clin Microbiol 46: 3880-3891.
22. Pawlotsky JM (2003) Mechanisms of antiviral treatment efficacy and failure in chronic hepatitis C. Antiviral Res 59: 1-11.
23. Sarrazin C, Gartner BC, Sizmann D, Babiel R, Mihm U, et al. (2006) Comparison of conventional PCR with real-time PCR and branched DNA-based assays for hepatitis C virus RNA quantification and clinical significance for genotypes 1 to 5. J Clin Microbiol 44: 729-737.
24. de Lamballerie X, Colson P (2006) The battle against infectious diseases in developing countries: the inseparable twins of diagnosis and therapy. Clin Chem 52: 1217.
25. Fiscus SA, Cheng B, Crowe SM, Demeter L, Jennings C, et al. (2006) HIV-1 viral load assays for resource-limited settings. PLoS Med 3: e417. doi:10.1371/journal.pmed.0030417
26. Phillips AN, Pillay D, Miners AH, Bennett DE, Gilks CF, et al. (2008) Outcomes from monitoring of patients on antiretroviral therapy in resource-limited settings with viral load, CD4 cell count, or clinical observation alone: a computer simulation model. Lancet 371: 1443-1451.
27. Preiser W, Drexler JF, Drosten C (2006) HIV-1 viral load assays for resource-limited settings: clades matter. PLoS Med 3: e538; author reply e550. doi:10.1371/journal.pmed.0030538
28. Drosten C, Panning M, Drexler JF, Hansel F, Pedroso C, et al. (2006) Ultrasensitive monitoring of HIV-1 viral load by a low-cost real-time reverse transcription-PCR assay with internal control for the 5′ long terminal repeat domain. Clin Chem 52: 1258-1266.
29. Bukh J, Purcell RH, Miller RH (1992) Sequence analysis ofthe 5′ noncoding region of hepatitis C virus. Proc Natl Acad Sci U S A 89: 4942-4946.
30. Anonymous (2004) Verbot der Verwendung des HPS COBAS TaqMan HCV Test (Roche Diagnostics GmbH, 68298 Mannheim) bei der Herstellung von zellulären Blutkomponenten und gefrorenem Frischplasma.-Paul-Ehrlich-Institut, editor. Bundesanzeiger Nr 166: Paul-Ehrlich-Institut. pp. 19770.
31. Honda M, Brown EA, Lemon SM (1996) Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA. RNA 2: 955-968.
32. Simmonds P (2004) Genetic diversity and evolution of hepatitis C virus-15 years on. J Gen Virol 85: 3173-3188.
33. Kolykhalov AA, Feinstone SM, Rice CM (1996) Identification of a highly conserved sequence element at the 3′ terminus of hepatitis C virus genome RNA. J Virol 70: 3363-3371.
34. Tanaka T, Kato N, Cho MJ, Shimotohno K (1995) A novel sequence found at the 3′ terminus of hepatitis C virus genome. Biochim Biophysic Res Comm 215: 744-749.
35. Friebe P, Bartenschlager R (2002) Genetic analysis of sequences in the 3′ nontranslated region of hepatitis C virus that are important for RNA replication. J Virol 76: 5326-5338.
36. Ito T, Tahara SM, Lai MM (1998) The 3′-untranslated region of hepatitis C virus RNA enhances translation from an internal ribosomal entry site. J Virol 72: 8789-8796.
37. Tsuchihara K, Tanaka T, Hijikata M, Kuge S, Toyoda H, et al. (1997) Specific interaction of polypyrimidine tract-binding protein with the extreme 3′-terminal structure of the hepatitis C virus genome, the 3'X. J Virol 71: 6720-6726.
38. Wood J, Frederickson RM, Fields S, Patel AH (2001) Hepatitis C virus 3′X region interacts with human ribosomal proteins. J Virol 75: 1348-1358.
39. Saldanha J, Heath A, Aberham C, Albrecht J, Gentili G, et al. (2005) World Health Organization collaborative study to establish a replacement WHO international standard for hepatitis C virus RNA nucleic acid amplification technology assays. Vox Sang 88: 202-204.
40. McOmish F, Yap PL, Dow BC, Follett EA, Seed C, et al. (1994) Geographical distribution of hepatitis C virus genotypes in blood donors: an international collaborative survey. J Clin Microbiol 32: 884-892.
41. Davidson F, Simmonds P, Ferguson JC, Jarvis LM, Dow BC, et al. (1995) Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5′ non-coding region. J Gen Virol 76: 1197-1204.
42. Laperche S, Lunel F, Izopet J, Alain S, Deny P, et al. (2005) Comparison of hepatitis C virus NS5b and 5′ noncoding gene sequencing methods in a multicenter study. J Clin Microbiol 43: 733-739.
43. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
44. Christopherson C, Sninsky J, Kwok S (1997) The effects of internal primer-template mismatches on RT-PCR: HIV-1 model studies. Nucleic Acids Res 25: 654-658.
45. Kwok S, Kellogg DE, McKinney N, Spasic D, Goda L, et al. (1990) Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res 18: 999-1005.
46. Peyret N, Seneviratne PA, Allawi HT, SantaLucia J Jr. (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry 38: 3468-3477.
47. Holmes H, Davis C, Heath A (2008) Development of the 1st International Reference Panel for HIV-1 RNA genotypes for use in nucleic acid-based techniques. J Virol Methods 154: 86-91.
48. Pierre V, Drouet M, Deubel V (1994) Identification of mosquito-borne flavivirus sequences using universal primers and reverse transcription/ polymerase chain reaction. Res Virol 145: 93-104.
49. Caliendo AM, Valsamakis A, Zhou Y, Yen-Lieberman B, Andersen J, et al. (2006) Multilaboratory comparison of hepatitis C virus viral load assays. J Clin Microbiol 44: 1726-1732.
50. Elbeik T, Surtihadi J, Destree M, Gorlin J, Holodniy M, et al. (2004) Multicenter evaluation of the performance characteristics of the Bayer VERSANT HCV RNA 3.0 assay (bDNA). JClin Microbiol 42: 563-569.
51. Tuaillon E, Mondain AM, Ottomani L, Roudiere L, Perney P, et al. (2007) Impact of hepatitis C virus (HCV) genotypes on quantification of HCV RNA in serum by COBAS AmpliPrep/COBAS TaqMan HCV test, Abbott HCV realtime assay and VERSANT HCV RNA assay. J Clin Microbiol 45: 3077-3081.
52. You S, Rice CM (2008) 3′ RNA elements in hepatitis C virus replication: kissing partners and long poly(U). J Virol 82: 184-195.
53. Saito T, Owen DM, Jiang F, Marcotrigiano J, Gale M Jr. (2008) Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA. Nature 454: 523-527.
54. Germer JJ, Harmsen WS, Mandrekar JN, Mitchell PS, Yao JD (2005) Evaluation of the COBAS TaqMan HCV test with automated sample processing using the MagNA pure LC instrument. JClin Microbiol 43: 293-298.
55. Highbarger HC, Hu Z, Kottilil S, Metcalf JA, Polis MA, et al. (2007) Comparison of the Abbott 7000 and Bayer 340 systems for measurement of hepatitis C virus load. J Clin Microbiol 45: 2808-2812.
56. Sabato MF, Shiffman ML, Langley MR, Wilkinson DS, Ferreira-Gonzalez A (2007) Comparison of performance characteristics of three real-time reverse transcription-PCR test systems for detection and quantification of hepatitis C virus. J Clin Microbiol 45: 2529-2536.
57. Gelderblom HC, Beld MG (2007) Hepatitis C virus RNA quantification by the COBAS AmpliPrep/COBAS TaqMan System: averages do not tell the whole story. J Clin Virol 39: 326-327.
58. Konnick EQ, Williams SM, Ashwood ER, Hillyard DR (2005) Evaluation of the COBAS Hepatitis C Virus (HCV) TaqMan analyte-specific reagent assay and comparison to the COBAS Amplicor HCV Monitor V2.0 and Versant HCV bDNA 3.0 assays. J Clin Microbiol 43: 2133-2140.
59. Greco DB, Simao M (2007) Brazilian policy of universal access to AIDS treatment: sustainability challenges and perspectives. Aids 21 Suppl 4: S37-45.
60. Campiotto S, Pinho JR, Carrilho FJ, Da Silva LC, Souto FJ, et al. (2005) Geographic distribution of hepatitis C virus genotypes in Brazil. Braz J Med Biol Res 38: 41-49.
61. Anonymous (2003) Portaria no. 79, de 31 de janeiro de 2003.Saude Md editor. Portarias (Brazil): Ministerio da Saude.
62. Anonymous (2002): Brazilian Ministry of Health, National Viral Hepatitis Program. Available: http://sistemas.aids.gov.br/imprensa/Noticias.asp?NOTCod= 45078. Accessed 8 November 2008.
63. Roth WK, Weber M, Seifried E (1999) Feasibility and efficacy of routine PCR screening of blood donations for hepatitis C virus, hepatitis B virus, and HIV-1 in a blood-bank setting. Lancet 353: 359-363.
64. Stramer SL, Glynn SA, Kleinman SH, Strong DM, Caglioti S, et al. (2004) Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-amplification testing. N Engl J Med 351: 760-768.
65. Roth WK, Weber M, Buhr S, Drosten C, Weichert W, et al. (2002) Yield of HCV and HIV-1 NAT after screening of 3.6 million blood donations in central Europe. Transfusion 42: 862-868.
66. Hourfar MK, Jork C, Schottstedt V, Weber-Schehl M, Brixner V, et al. (2008) Experience of German Red Cross blood donor services with nucleic acid testing: results of screening more than 30 million blood donations for human immunodeficiency virus-1, hepatitis C virus, and hepatitis B virus. Transfusion 48: 1558-1566.
67. Grant PR, Busch MP (2002) Nucleic acid amplification technology methods used in blood donor screening. Transfus Med 12: 229-242.
68. Diario Oficial Poder Executivo (2006) Seção I, São Paulo, 116: 161, 16 February 2006.