Routine drug resistance testing in HIV-1 proviral DNA, using an automated next-generation sequencing assay

Background: HIV-1 DNA genotypic drug resistance testing is increasingly performed to guide treatment switching or simplification in controlled patients. The Sentosa NGS platform is a fully automated system marketed for drug resistance testing on HIV-1 RNA samples. Objectives: The aim of this study was to evaluate this automated NGS solution for routine resistance genotypic resistance testing in proviral HIV-1 DNA. Study design: Sanger sequencing (SS) of the reverse transcriptase (RT), protease (PR) and integrase (IN) genes was performed using the French ANRS protocol. NGS was performed retrospectively on frozen samples, using the Sentosa platform combined with the Sentosa SQ HIV genotyping Assay. Results: A total of 77 samples were run once using NGS. A successful sequencing of the three HIV-1 genes (RT, PR, IN) was obtained for 45 samples. The number of cumulated RAMs was 179, 185 and 219 with SS, NGS 20% and NGS 10% respectively; however most of them were minor mutations in the PR region. The mutation detection rate was similar between SS and NGS 20%. Several discordances were observed between both methods in the RT and PR regions, mainly due to the use of different DNA extracts, and hypermutation. Conclusions: HIV-1 DNA genotypic resistance testing can be performed with the Sentosa platform. Few technical optimizations are still needed to include the extraction step and to improve the sequencing efficiency.