Emergence of resistance-associated variants during sofosbuvir treatment in chronically infected hepatitis E patients

Abstract

Background and Aims: Chronic HEV infections remain a serious problem in immunocompromised patients, as specifically approved antiviral drugs are unavailable. In 2020, a 24-week multicenter phase II pilot trial was carried out, evaluating the nucleotide analog sofosbuvir by treating nine chronically HEV-infected patients with sofosbuvir (Trial Number NCT03282474). During the study, antiviral therapy reduced virus RNA levels initially but did not lead to a sustained virologic response. Here, we characterize the changes in HEV intrahost populations during sofosbuvir treatment to identify the emergence of treatment-associated variants. Approach and Results: We performed high-throughput sequencing on RNA-dependent RNA polymerase sequences to characterize viral population dynamics in study participants. Subsequently, we used an HEV-based reporter replicon system to investigate sofosbuvir sensitivity in high-frequency variants. Most patients had heterogenous HEV populations, suggesting high adaptability to treatment-related selection pressures. We identified numerous amino acid alterations emerging during treatment and found that the EC50 of patient-derived replicon constructs was up to ~12-fold higher than the wild-type control, suggesting that variants associated with lower drug sensitivity were selected during sofosbuvir treatment. In particular, a single amino acid substitution (A1343V) in the finger domain of ORF1 could reduce susceptibility to sofosbuvir significantly in 8 of 9 patients. Conclusions: In conclusion, viral population dynamics played a critical role during antiviral treatment. High population diversity during sofosbuvir treatment led to the selection of variants (especially A1343V) with lower sensitivity to the drug, uncovering a novel mechanism of resistance-associated variants during sofosbuvir treatment.

Monitoring of hepatitis E virus in wastewater can identify clinically relevant variants

“…In addition, HEV variants with mutations in the viral polymerase have been found to be associated with RBV or SOF treatment failure. 6,8 However, for both HEV clades and variants, little is known about their distribution in the population. In this study, HEV-3c was the most prevalent variant.…”

“…7 Similarly, several variants correlating with treatment failure have been identified. 6,8 The prevalence of these subtypes and variants in the general population remains unknown, but their discovery could significantly impact the treatment of individuals with persistent infection. We therefore selected eight samples from eight different sampling sites to geographically cover most of North Rhine-Westphalia, highlighted in Figure 1B, for next-generation sequencing to gain insights into variant distribution.…”

“…Increased heterogeneity was present at Position 1479, which had also been detected in chronically infected patients who did not respond to RBV or SOF treatment. 8 We then reconstructed haplotypes from short reads and performed a multiple sequence alignment with subclones and references. Phylogenetic analysis revealed that all wastewater sequences (red) cluster with HEV-3 reference strains (Figure 2B; Figure S3) and were closely related to HEV-3c (FJ705359).…”

Toward antivirals against hepatitis E: In the steps of hepatitis C

“…In a study published in this issue of HEPATOLOGY, Gömer and colleagues analyzed in a systematic way the intrahost longitudinal viral genome evolution during sofosbuvir monotherapy in the 9 patients enrolled in the HepNet SofE pilot study. [7] High throughput sequencing of the viral RdRp region of samples collected during the clinical study was performed. Although a high variability was observed between patients, the analysis revealed that amino acid variation, A1343V, arose quasi-systematically (in 8 of 9 patients) following sofosbuvir treatment.…”

“…In a study published in this issue of H epatology , Gömer and colleagues analyzed in a systematic way the intrahost longitudinal viral genome evolution during sofosbuvir monotherapy in the 9 patients enrolled in the HepNet SofE pilot study 7 . High throughput sequencing of the viral RdRp region of samples collected during the clinical study was performed.…”