Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure

David A Smith,Rory Bowden,Nimisha Chaturvedi,Eleanor Barnes,Peter Simmonds,John Mclauchlan,Graham Foster ,William L Irving,Santseharay Ramírez ,Jacques Fellay,Carlota Fernandez-Antunez,Vincent Pedergnana,Jens Bukh,Andrea Magrì ,M Azim Ansari

doi:10.1038/s41467-021-25649-6

Abstract

Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. With the development of direct-acting antivirals, treatment of chronically infected patients has become highly effective, although a subset of patients responds less well to therapy. Sofosbuvir is a common component of current de novo or salvage combination therapies, that targets the HCV NS5B polymerase. We use pre-treatment whole-genome sequences of HCV from 507 patients infected with HCV subtype 3a and treated with sofosbuvir containing regimens to detect viral polymorphisms associated with response to treatment. We find three common polymorphisms in non-targeted HCV NS2 and NS3 proteins are associated with reduced treatment response. These polymorphisms are enriched in post-treatment HCV sequences of patients unresponsive to treatment. They are also associated with lower reductions in viral load in the first week of therapy. Using in vitro short-term dose-response assays, these polymorphisms do not cause any reduction in sofosbuvir potency, suggesting an indirect mechanism of action in decreasing sofosbuvir efficacy. The identification of polymorphisms in NS2 and NS3 proteins associated with poor treatment outcomes emphasises the value of systematic genome-wide analyses of viruses in uncovering clinically relevant polymorphisms that impact treatment.

Highlights

Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide
To account for non-viral factors associated with SVR, we used logistic regression to test for association between treatment outcome and patient’s cirrhosis status, gender, baseline viral load, prior IFN-based treatment and IFNL4 SNP rs12979860 genotypes (CC vs non-CC) in a multivariate model
Using viral genome-wide association study (V-GWAS) we performed a systematic assessment of the impact of HCV amino acids across all proteins on sofosbuvir treatment outcome

Summary

Introduction

Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. In multiple clinical trials using sofosbuvir, NS5B substitutions L159F, S282T, C316H/N, L320F and V321A are reported as RAS and have been detected post-treatment in patients who do not achieve SVR14, only in a small subset The acquisition of these RAS has been shown to have a large fitness cost for the virus in vitro[11] and they rarely persist for long after treatment failure[15]. We recently reported the NS5B A150V polymorphism as conferring resistance to sofosbuvir[17] using patient data and in vitro assays, others have shown no effect on sofosbuvir resistance in other in vitro assays[18] This polymorphism unlike previously reported substitutions is common in pre-treatment HCV subtype

Methods

Results

Conclusion