Performance of three common hepatitis c virus (HCV) genotyping assays for identification of HCV genotype 2/1 chimeras

Kai Henrik Peiffer, Lisa Kuhnhenn, Evelyn Stelzl, Julia Dietz, Simone Susser, Andrea Oliver Tal, Fabian Finkelmeier, Eli Zuckerman, Marcus Cornberg, Mira Barak, Valeria Piazzolla, Alessandra Mangia, Stefan Zeuzem, Harald H. Kessler, Johannes Vermehren, Christoph Sarrazin

Research output: Contribution to journalArticle

Abstract

Besides seven major hepatitis C virus (HCV) genotypes (GT), a number of intergenotypic recombinant strains have been described. These so-called chimeras combine genetic characteristics of different HCV genotypes. However, correct genotype classification is important, as choice and duration of direct-acting antiviral (DAA) treatment is mainly based on the viral genotype. Therefore, misclassification of chimeras might lead to suboptimal treatment of patients infected with these strains. For example, 2k/1b chimeras are typically described as HCV genotype 2 strains by commercially available hybridization assays, but real-time PCR-based tests recognizing another HCV region might be more suitable for correct chimera detection. In this study, the analytic capacity of the hybridization-assay Versant HCV Genotype 2.0 (LiPA 2.0) and the real-time PCR-based-assays cobas HCV GT and Abbott RealTime HCV Genotype II were tested in a selected cohort of 230 patients infected with HCV genotype 1 (n = 53) and 2 (n = 177) and 48 patients infected with HCV 2/1 chimeric strains. While the Versant HCV Genotype 2.0 (LiPA 2.0) assay failed to identify chimeras in all of the patients (48/48, 100%), cobas HCV GT and Abbott HCV Genotype II assays identified chimeras correctly in 90% (43/48) and 65% (31/48) of the cases, respectively. In conclusion, while the hybridization-based Versant HCV Genotype 2.0 (LiPA 2.0) assay seems to be unsuitable for detection of HCV 2/1 chimeras, use of the real-time PCR-based assays cobas HCV GT and Abbott RealTime HCV Genotype II led to a higher rate of chimera detection.

Original languageEnglish
Article numbere00060-19
JournalJournal of Clinical Microbiology
Volume57
Issue number7
DOIs
Publication statusPublished - Jan 1 2019

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Hepatitis Viruses
Genotype
Real-Time Polymerase Chain Reaction
Hepacivirus

Keywords

  • 2k/1b
  • Assay
  • Chimera
  • Hepatitis C virus
  • Recombinant

ASJC Scopus subject areas

  • Microbiology (medical)

Cite this

Peiffer, K. H., Kuhnhenn, L., Stelzl, E., Dietz, J., Susser, S., Tal, A. O., ... Sarrazin, C. (2019). Performance of three common hepatitis c virus (HCV) genotyping assays for identification of HCV genotype 2/1 chimeras. Journal of Clinical Microbiology, 57(7), [e00060-19]. https://doi.org/10.1128/JCM.00060-19

Performance of three common hepatitis c virus (HCV) genotyping assays for identification of HCV genotype 2/1 chimeras. / Peiffer, Kai Henrik; Kuhnhenn, Lisa; Stelzl, Evelyn; Dietz, Julia; Susser, Simone; Tal, Andrea Oliver; Finkelmeier, Fabian; Zuckerman, Eli; Cornberg, Marcus; Barak, Mira; Piazzolla, Valeria; Mangia, Alessandra; Zeuzem, Stefan; Kessler, Harald H.; Vermehren, Johannes; Sarrazin, Christoph.

In: Journal of Clinical Microbiology, Vol. 57, No. 7, e00060-19, 01.01.2019.

Research output: Contribution to journalArticle

Peiffer, KH, Kuhnhenn, L, Stelzl, E, Dietz, J, Susser, S, Tal, AO, Finkelmeier, F, Zuckerman, E, Cornberg, M, Barak, M, Piazzolla, V, Mangia, A, Zeuzem, S, Kessler, HH, Vermehren, J & Sarrazin, C 2019, 'Performance of three common hepatitis c virus (HCV) genotyping assays for identification of HCV genotype 2/1 chimeras', Journal of Clinical Microbiology, vol. 57, no. 7, e00060-19. https://doi.org/10.1128/JCM.00060-19
Peiffer, Kai Henrik ; Kuhnhenn, Lisa ; Stelzl, Evelyn ; Dietz, Julia ; Susser, Simone ; Tal, Andrea Oliver ; Finkelmeier, Fabian ; Zuckerman, Eli ; Cornberg, Marcus ; Barak, Mira ; Piazzolla, Valeria ; Mangia, Alessandra ; Zeuzem, Stefan ; Kessler, Harald H. ; Vermehren, Johannes ; Sarrazin, Christoph. / Performance of three common hepatitis c virus (HCV) genotyping assays for identification of HCV genotype 2/1 chimeras. In: Journal of Clinical Microbiology. 2019 ; Vol. 57, No. 7.
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abstract = "Besides seven major hepatitis C virus (HCV) genotypes (GT), a number of intergenotypic recombinant strains have been described. These so-called chimeras combine genetic characteristics of different HCV genotypes. However, correct genotype classification is important, as choice and duration of direct-acting antiviral (DAA) treatment is mainly based on the viral genotype. Therefore, misclassification of chimeras might lead to suboptimal treatment of patients infected with these strains. For example, 2k/1b chimeras are typically described as HCV genotype 2 strains by commercially available hybridization assays, but real-time PCR-based tests recognizing another HCV region might be more suitable for correct chimera detection. In this study, the analytic capacity of the hybridization-assay Versant HCV Genotype 2.0 (LiPA 2.0) and the real-time PCR-based-assays cobas HCV GT and Abbott RealTime HCV Genotype II were tested in a selected cohort of 230 patients infected with HCV genotype 1 (n = 53) and 2 (n = 177) and 48 patients infected with HCV 2/1 chimeric strains. While the Versant HCV Genotype 2.0 (LiPA 2.0) assay failed to identify chimeras in all of the patients (48/48, 100{\%}), cobas HCV GT and Abbott HCV Genotype II assays identified chimeras correctly in 90{\%} (43/48) and 65{\%} (31/48) of the cases, respectively. In conclusion, while the hybridization-based Versant HCV Genotype 2.0 (LiPA 2.0) assay seems to be unsuitable for detection of HCV 2/1 chimeras, use of the real-time PCR-based assays cobas HCV GT and Abbott RealTime HCV Genotype II led to a higher rate of chimera detection.",
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