Regulatory evaluation of antiviral drug resistance in the era of next-generation sequencing

Next-generation sequencing (NGS) is changing the landscape of antiviral drug resistance analysis, allowing for deeper sequencing of viral populations at greatly reduced costs compared with Sanger sequencing [1]. Sofosbuvir (Sovaldi, approved December 2013) was the first antiviral drug approved by the US FDA based on resistance data from pivotal Phase 2 and 3 clinical trials using NGS data [2,3]. Prior to that approval, nonpivotal Phase 2 NGS resistance data were analyzed for simeprevir (Olysio, approved November 2013) [4]. In October 2014, the FDA approved the combination of sofosbuvir and ledipasvir (Harvoni) based in part on resistance data generated using NGS [5]. Given the emerging nature of NGS technology and the steadily reduced sequencing costs, the FDA Division of Antiviral Products (DAVP) anticipates that most drug sponsors will switch to NGS for resistance analysis in the future. DAVP conducts independent analyses of resistance data in their review of new drug applications (NDAs) for antiviral drugs to determine if: treatment-emergent amino acid substitutions can be correlated with treatment failure (emergence of resistance), resistant variants persist after treatment failure, shifts in cell culture susceptibility can be associated with treatment failure, baseline polymorphisms lead to reduced efficacy and resistance-associated substitutions confer cross resistance to other antiviral drugs. Historically, genotypic antiviral resistance data generated by Sanger sequencing were submitted to the DAVP using standardized datasets. In these cases, raw sequence data were not requested or analyzed. In contrast to Sanger sequencing, NGS is an emerging technology that presents many data analysis and data integrity issues that must be considered when conducting a regulatory review [2]. Some of these issues include: