Abstract
Since the identification of hepatitis C virus (HCV), viral sequencing has been important in understanding HCV classification, epidemiology, evolution, transmission clustering, treatment response and natural history. The length and diversity of the HCV genome has resulted in analysis of certain regions of the virus, however there has been little standardisation of protocols. This systematic review was undertaken to map the location and frequency of sequencing on the HCV genome in peer reviewed publications, with the aim to produce a database of sequencing primers and amplicons to inform future research. Medline and Scopus databases were searched for English language publications based on keyword/MeSH terms related to sequence analysis (9 terms) or HCV (3 terms), plus “primer” as a general search term. Exclusion criteria included non-HCV research, review articles, duplicate records, and incomplete description of HCV sequencing methods. The PCR primer locations of accepted publications were noted, and purpose of sequencing was determined. A total of 450 studies were accepted from the 2099 identified, with 629 HCV sequencing amplicons identified and mapped on the HCV genome. The most commonly sequenced region was the HVR-1 region, often utilised for studies of natural history, clustering/transmission, evolution and treatment response. Studies related to genotyping/classification or epidemiology of HCV genotype generally targeted the 5′UTR, Core and NS5B regions, while treatment response/resistance was assessed mainly in the NS3–NS5B region with emphasis on the Interferon sensitivity determining region (ISDR) region of NS5A. While the sequencing of HCV is generally constricted to certain regions of the HCV genome there is little consistency in the positioning of sequencing primers, with the exception of a few highly referenced manuscripts. This study demonstrates the heterogeneity of HCV sequencing, providing a comprehensive database of previously published primer sets to be utilised in future sequencing studies.
Highlights
Given the difficulty in producing a continuous culture of the hepatitis C virus (HCV), investigations of HCV have been conducted mainly through the isolation and sequencing of the virus from infected patients
Systematic reviews are commonly used in biomedical, epidemiology, public health and clinical research to provide an exhaustive summary of literature relevant to a specific research question, but are less common in the field of virology
Systematic and general reviews of published data related to sequencing of HCV have reported on genetic diversity [4], viral evolution [5], transmission of HCV [6] and predictors of treatment response or resistance [7], but there has been no review of the sequencing methodologies used for HCV
Summary
Given the difficulty in producing a continuous culture of the hepatitis C virus (HCV), investigations of HCV have been conducted mainly through the isolation and sequencing of the virus from infected patients. From this sequence data, a great deal has been learnt about the evolution of the virus within individuals, variability across geographic locations, and correlations between viral variation and clinical treatment response and disease progression. Systematic and general reviews of published data related to sequencing of HCV have reported on genetic diversity [4], viral evolution [5], transmission of HCV [6] and predictors of treatment response or resistance [7], but there has been no review of the sequencing methodologies used for HCV
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