Analysis of resistance-associated substitutions in acute hepatitis C virus infection by deep sequencing across six genotypes and three continents

Abstract

Several direct-acting antivirals (DAAs) have been approved for the treatment of chronic hepatitis C virus (HCV) infections, opening the door to highly effective interferon-free treatment regimens. Resistance-associated substitutions (RASs) have been reported both in treatment-naïve patients and following treatment with protease (NS3), phosphoprotein (NS5A) and polymerase (NS5B) inhibitors. The prevalence of naturally occurring RASs in untreated HCV-infected individuals has mostly been analysed in those infected with genotype 1 (GT1), in the late phase of infection, and only within limited regions of the genome. Furthermore, the geographic distribution of RASs remains poorly characterized. In this study, we used next-generation sequencing to analyse full-length HCV genomes for the prevalence of RASs in acute HCV infections identified in nine international prospective cohorts. RASs were analysed in 179 participants infected with all six major HCV genotypes (GT1-GT6), and the geographic distribution of RASs was assessed in 107 GT1a and GT3a samples. While RASs were detected at varied frequencies across the three genomic regions, and between genotypes, RASs relevant to multiple DAAs in the leading IFN-free regimens were rarely detected in combination. Low-frequency RASs (<10% of the viral population) were also shown to have a GT-specific distribution. The main RASs with geographic associations were NS3 Q80K in GT1a samples and NS5B N142T in GT3a. These data provide the backdrop for prospective surveillance of RASs during DAA treatment scale-up.

Keywords: DAA; antiviral; hepatitis C virus; inhibitors; resistance.

Figure 1.. A summary of the resistance-associated variants (RAVs) detected by deep-sequencing across the HCV genome.

RAVs detected by deep-sequencing of the HCV genome are shown together with their frequency of occurrence as a heat map. Rows represent individual samples and columns indicate a position within NS3, NS5A and NS5B which is known to confer resistance to DAAs. A neighbour-joining phylogenetic tree based on the NS5B consensus sequences is also shown. Tree branches are coloured according to the sample origin, where North American samples are shown in red, Australian samples in green and European samples in yellow. The genotype of the sample is indicated by the bracket on the right. The frequency of RAVs is indicated by the color according to the scale bar, and positions where RAVs were not analysed are shown in grey. RAVs associated with new IFN-free DAA combination regimens are highlighted at the top of the figure; ombitasvir, paritaprevir and dasabuvir (red spheres), daclatasvir, asunaprevir, and beclabuvir (blue spheres), grazoprevir and elbasvir (green spheres).