Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges

Abstract

Therapy for hepatitis C is currently undergoing a revolution. The arrival of new antiviral agents targeting viral proteins reinforces the need for a better knowledge of the viral strains infecting each patient. Hepatitis C virus (HCV) whole genome sequencing provides essential information for precise typing, study of the viral natural history or identification of resistance-associated variants. First performed with Sanger sequencing, the arrival of next-generation sequencing (NGS) has simplified the technical process and provided more detailed data on the nature and evolution of viral quasi-species. We will review the different techniques used for HCV complete genome sequencing and their applications, both before and after the apparition of NGS. The progress brought by new and future technologies will also be discussed, as well as the remaining difficulties, largely due to the genomic variability.

• Sanger sequencing
• next-generation sequencing
• genotyping
• resistance-associated variants

Acknowledgements

The authors wish to thank Emma Beale who assisted in the proof-reading of the article.

Declaration of interest

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.