Skip to main content

Advertisement

SpringerLink
Log in

Hepatitis C Assays: The Pitfalls of Polymerase Chain Reaction and Genotyping

  • Published:
Current Hepatitis Reports Aims and scope Submit manuscript

Abstract

Hepatitis C virus (HCV) continues to represent a worldwide threat to the lives of millions of people chronically infected with the virus. Accurately identifying the virus in terms of genetic characteristics, as well as quantifying its replicative equilibrium both during steady state and in the presence of antiviral therapy, is critically important for providing optimal care and prognoses. Genotype testing continues to evolve; however, it is important to recognize its limitations, particularly as we enter the world of direct-acting antivirals, in which the precise subtyping of HCV may play an even more important role in guiding therapy. Polymerase chain reaction (PCR) has revolutionized the management of chronic viral illnesses, and the advent of real-time PCR has broadened the awareness of the hepatology community to the tenacity of HCV in the face of potent antiviral therapy. With new technology, however, comes the responsibility of learning how to harness the techniques and to avoid common pitfalls of improper use or interpretation.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Choo QL, Kuo G, Weiner AJ, et al.: Isolation of a cDNA derived from a blood-borne non-A, non-B hepatitis genome. Science 1989, 244:359–362.

    Article  CAS  PubMed  Google Scholar 

  2. Simmonds P, Bukh J, Combet C et al.: Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 2005, 42:962–973.

    Article  CAS  PubMed  Google Scholar 

  3. Los Alamos National Laboratory: HCV Sequence Database. Available at http://hcv.lanl.gov/content/sequence/HCV/ToolsOutline.html. Accessed December 2009.

  4. Kuiken C, Yusim K, Boykin L, Richardson R: HCV sequence database: the Los Alamos HCV Sequence Database. Bioinformatics 2005, 21:379–384.

    Article  CAS  PubMed  Google Scholar 

  5. Zheng X, Pang M, Chan A, et al.: Direct comparison of hepatitis C virus genotypes tested by INNO-LiPA HCV II and TRUGENE HCV genotyping methods. J Clin Virol 2003, 28:214–216.

    Article  CAS  PubMed  Google Scholar 

  6. Zekri AR, El-Din HM, Bahnassy AA, et al.: TRUGENE sequencing versus INNO-LiPA for sub-genotyping of HCV genotype-4. J Med Virol 2005, 75:412–420.

    Article  CAS  PubMed  Google Scholar 

  7. Haushofer AC, Berg J, Hauer R, et al.: Genotyping of hepatitis C virus—comparison of three assays. J Clin Virol 2003, 27:276–285.

    Article  CAS  PubMed  Google Scholar 

  8. Nolte FS, Green AM, Fiebelkorn KR, et al.: Clinical evaluation of two methods for genotyping hepatitis C virus based on analysis of the 5' noncoding region. J Clin Microbiol 2003, 41:1558–1564.

    Article  CAS  PubMed  Google Scholar 

  9. Stelzl E, van der Meer C, Gouw R, et al.: Determination of the hepatitis C virus subtype: comparison of sequencing and reverse hybridization assays. Clin Chem Lab Med 2007, 45:167–170.

    Article  CAS  PubMed  Google Scholar 

  10. Verbeeck J, Stanley M, Shieh J et al.: Evaluation of versant hepatitis C virus genotype assay (LiPA) 2.0. J Clin Microbiol 2008, 46:1901–1906.

    Article  CAS  PubMed  Google Scholar 

  11. Bouchardeau F, Cantaloube JF, Chevaliez S, et al.: Improvement of hepatitis C virus (HCV) genotype determination with the new version of the INNO-LiPA HCV assay. J Clin Microbiol 2007, 45:1140–1145.

    Article  CAS  PubMed  Google Scholar 

  12. Noppornpanth S, Sablon E, De Nys K, et al.: Genotyping hepatitis C viruses from Southeast Asia by a novel line probe assay that simultaneously detects core and 5' untranslated regions. J Clin Microbiol 2006, 44:3969–3974.

    Article  CAS  PubMed  Google Scholar 

  13. Legrand-Abravanel F, Colson P, Leguillou-Guillemette H, et al.: Influence of the HCV subtype on the virological response to pegylated interferon and ribavirin therapy. J Med Virol. 2009 Dec;81(12):2029–35.

    Article  CAS  PubMed  Google Scholar 

  14. Sarrazin C, Hong J, Lim S, et al.: Incidence of virologic escape observed during ITMN-191 (R7227) monotherapy is genotype dependent, associated with a specific NS3 substitution, and suppressed upon combination with Peginterferon alfa-2a/Ribavirin [abstract 964]. Presented at the European Association for the Study of the Liver 44th Annual Meeting. Copenhagen, Denmark; April 22–26, 2009.

  15. Qian KP, Natov SN, Pereira BJ, et al.: Hepatitis C virus mixed genotype infection in patients on haemodialysis. J Viral Hepat 2000, 7:153–160.

    Article  CAS  PubMed  Google Scholar 

  16. Parodi C, Culasso A, Aloisi N, et al.: Evidence of occult HCV genotypes in haemophilic individuals with unapparent HCV mixed infections. Haemophilia 2008, 14:816–822.

    Article  CAS  PubMed  Google Scholar 

  17. Hu YW, Balaskas E, Furione M, et al.: Comparison and application of a novel genotyping method, semiautomated primer-specific and mispair extension analysis, and four other genotyping assays for detection of hepatitis C virus mixed-genotype infections. J Clin Microbiol 2000, 38:2807–2813.

    CAS  PubMed  Google Scholar 

  18. Kalinina O, Norder H, Mukomolov S, Magnius LO: A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg. J Virol 2002, 76:4034–4043.

    CAS  Google Scholar 

  19. Baylis S, Heath A, and the Collaborative Study Group: WHO Collaborative Study to Establish a Replacement WHO International Standard for Hepatitis C Virus RNA Nucleic Acid Amplification Technology (NAT)–Based Assays. Expert Committee on Biological Standardization. Geneva: World Health Organization; October 8–12, 2007.

  20. Halfon P, Bourlière M, Pénaranda G, et al.: 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 2006, 44:2507–2511.

    Article  CAS  PubMed  Google Scholar 

  21. National Institutes of Health: National Institutes of Health Consensus Development Conference statement: management of hepatitis C: 2002—June 10–12, 2002. Hepatology 2002, 36:S3–S20.

    Google Scholar 

  22. COBAS AmpliPrep/COBAS TaqMan HCV Test [package insert]. Branchburg, NJ: Roche Molecular Systems; 2008. Available at http://www.accessdata.fda.gov/cdrh_docs/pdf6/P060030c.pdf. Accessed December 2009.

  23. McHutchison JG, Everson GT, Gordon SC, et al.: Telaprevir with peginterferon and ribavirin for chronic HCV genotype 1 infection. N Engl J Med 2009, 360:1827–1838.

    Article  CAS  PubMed  Google Scholar 

  24. Matsuura K, Tanaka Y, Hasegawa I, et al.: Abbott realtime hepatitis C virus (HCV) and Roche Cobas AmpliPrep/Cobas TaqMan HCV assays for prediction of sustained virological response to pegylated interferon and ribavirin in chronic hepatitis C patients. J Clin Microbiol 2009, 47:385–389.

    Article  CAS  PubMed  Google Scholar 

  25. Gerotto M, Dal Pero F, Bortoletto G, et al.: Hepatitis C minimal residual viremia (MRV) detected by TMA at the end of Peg-IFN plus ribavirin therapy predicts post-treatment relapse. J Hepatol 2006, 44:83–87.

    Article  CAS  PubMed  Google Scholar 

  26. Berg T, Weich V, Teuber G, et al.: Individualized treatment strategy according to early viral kinetics in hepatitis C virus type 1-infected patients. Hepatology 2009, 50:369–377.

    Article  CAS  PubMed  Google Scholar 

  27. Martinot-Peignoux M, Khiri H, Leclere L, et al.: Clinical performances of two real-time PCR assays and bDNA/TMA to early monitor treatment outcome in patients with chronic hepatitis C. J Clin Virol 2009, 46:216–221.

    Article  CAS  PubMed  Google Scholar 

Download references

Disclosure

No potential conflict of interest relevant to this article was reported.

Author information

Authors and Affiliations

  1. California Pacific Medical Center, 2340 Clay Street, Third Floor, San Francisco, CA, 94115, USA

    R. Todd Frederick

Authors
  1. R. Todd Frederick
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. Todd Frederick.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Frederick, R.T. Hepatitis C Assays: The Pitfalls of Polymerase Chain Reaction and Genotyping. Curr Hepatitis Rep 9, 9–14 (2010). https://doi.org/10.1007/s11901-010-0031-9

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11901-010-0031-9

Keywords

Search

Navigation