Design of a genotyping assay for identifying and monitoring HIV-2 drug resistance

Introduction: Human immunodeficiency virus type 2 (HIV-2) is a causative agent of acquired immunodeficiency syndrome (AIDS) but is distinct from the more prevalent HIV-1. HIV-1 and HIV-2 can rapidly acquire mutations which confer drug resistance (DR). HIV-2 can be treated with some HIV-1 antiretrovirals, but is intrinsically resistant to others. Genotyping assays for HIV-1 are used to identify DR mutations and guide treatment. No clinically approved genotyping assays exist for HIV-2, making treatment difficult. Objectives: Our overall objective is to develop and validate an HIV-2 DR genotyping assay for clinical use. The goal of this project was to develop a set of pol region amplification and sequencing primers and to collect and organize DR mutation information by genomic region with appropriate evidence. Methods: HIV-2 information was gathered from literature and public databases. Amplification and sequencing primers were aligned for compatibility with reference sequences from HIV-2 group A and B using sequence analysis software and tools available from the Los Alamos HIV databases (http://www.hiv.lanl.gov). Results: Primers were developed that successfully amplified and sequenced the pol region of HIV-2 group A viruses. An annotated pol region gene map was created using HIV-2 group A and B reference sequences, which will allow for sequence analysis at positions known to confer DR and for comparison with closely related viruses. Conclusion: We have made significant progress in developing the HIV-2 DR genotyping assay. Our future goals are to optimize the assay, validate it for clinical use and create an HIV-2 rules-based DR interpretation tool.