Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients

Laure Ngono,Marie Nicole Ngoufack,Richard Njouom,Robert Banai,Simon Frédéric Lissock,Sebastien Kenmoe,Paul Alain Tagnouokam-Ngoupo,Marie Amougou-Atsama

doi:10.1186/s12985-019-1214-9

Abstract

BackgroundCurrent HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients.MethodsAll plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences.ResultsA total of 369 samples were received during the study period with high viral load values (median: 930,952 IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p = 0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region.ConclusionsWe found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1–4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.

Highlights

Current Hepatitis C virus (HCV) treatments are genotype specific potential pan-genotype treatments have recently been described
Three hundred and forty six (93.8%) samples were positive in the core region while 338 (91.6%) were positive in the Non-structural protein 5B (NS5B) region
Three hundred and fifteen samples were positive in both regions (85.4%), 31 (8.4%) samples positive in core region only and 23 (6.2%) samples positive in the NS5B region only (Table 2)

Summary

Introduction

Current HCV treatments are genotype specific potential pan-genotype treatments have recently been described. Restriction fragment length polymorphism (RFLP) analysis has been developed for some HCV genomic regions: the 5′ non-coding and the contiguous core regions. The choice of these genomic sequences was based on their relative nucleotide homology among different genotypes and the presence of polymorphic sites [10]. RFLP is performed using endonucleases that will break down the DNA amplicons at specific sites, different HCV genotypes and subtypes will be illustrated by RFLP digestion patterns on agarose gel. A mutation occurring in one of the polymorphic sites recognized by the restriction endonuclease could be could be limiting for HCV genotyping and subtyping [10]

Methods

Results

Conclusion