Minority variants associated with resistance to HIV-1 nonnucleoside reverse transcriptase inhibitors during primary infection

Abstract Background Recent data suggest that subjects harbouring low-frequency variants of HIV that are resistant to non-nucleoside reverse-transcriptase inhibitors (NNRTI) could suffer virological failure when treated with NNRTI-based therapy. Rilpivirine, a second-generation NNRTI, will be used in first-line regimen therapy, but the prevalence of minority variants that are resistant to rilpivirine is unknown. Objectives We evaluated the presence of low-frequency NNRTI resistance associated mutations (RAMs) in 27 patients with a primary HIV-1 infection. Study design We performed genotypic resistance test at baseline and used ultradeep pyrosequencing (UDPS) to detect minority RAMs. Results Bulk genotyping identified NNRTI-resistant RAMs in 3/27 (11%) patients while UDPS identified NNRTI-resistant RAMs in 10/27 (37%) patients. The 11 RAMs not detected by bulk sequencing were A98G ( n = 2), L100I ( n = 3), K101E ( n = 2), V106I ( n = 3) and E138G ( n = 1). The prevalence of these minority variants was 0.34–18.26%. The absolute copy numbers of minority resistant variants were 3.21–5.53 log copies/mL. CRF02 harboured more minority resistant variants than subtypes B ( P < 0.05). Four samples (15%) had a major rilpivirine resistant mutation (E138G, K101E and E138A), 3 of which were detected by UDPS. Conclusion In these primary HIV infected patients, as regards to the detection of RAMs at the cut-off level > 15–25% of the virus population, the concordance between bulk genotypic and UDPS was perfect. UDPS detected additional major NNRTI-resistant mutations, including rilpivirine resistant variants. Further studies are needed to assess the impact of these minority variants on treatment efficacy.