Drug Resistance Pathways and Impact of Protease Mutation L10I/V in HIV-1 Non-B Subtypes

Abstract

Background: Molecular pathways to drug resistance have yet to be fully characterized in HIV-1 non-B subtypes. Furthermore, polymorphisms such as protease L10I/V are ubiquitous in non-B subtypes, but their biological implications are still unknown. We evaluated resistance pathways emerging at treatment failure in a cohort of HIV infected individuals in Mali, and characterized in vitro the role of L10I/V. Methods: Genotypic resistance testing was performed on plasma obtained from 132 HIV-infected individuals from Mali before and after 9 months of treatment using population sequencing. CRF02_AG chimeric viruses containing 10I/V mutants CRF02_AG were constructed using site directed mutagenesis and susceptibility to protease inhibitors (PI) as well as replicative capacity were determined in a PBMC culture assay. Results: At treatment initiation, 11/132 (8.3%; 95% CI 3.6-13.0%) patients harboured resistance mutations to NRTI (D67N, T69N, L210W, K219E and T215A) or NNRTI (K103N, V108I and V179E). Among these 11 patients, 5 with NNRTI mutations were in virological failure after 9 months of treatment. Six others with one Thymidine Analog Mutations (TAM) did not show complete resistance. Overall, 18/132 (14.0%; 95% CI 8.1-19.9%) patients failed at 9 months and resistance mutations to NRTI or NNRTI could be identified in 8 (6.10%; 95% CI 2.0-10.2%). NRTI mutation M184V was the most commonly observed, followed by NNRTI mutations Y181C and K103N. Polymorphisms in protease such as L10I/V were observed frequently. Their role was evaluated in vitro. CRF02_AGwt_10L showed a slight increase in IC50 for darunavir, lopinavir and nelfinavir compared to subtype BHXB2_10L with 1.2, 1.3 and 1.5 Fold-Changes (FC) respectively. Mutant’s viruses CRF02_AGL10I and CRF02_AGL10V showed a slight increase in IC50 for indinavir with 1.30 and 1.20 FC and a slight decrease in IC50 for lopinavir with 0.78 FC and 0.75 FC respectively compared to CRF02_AGwt_10L. We did not observe any difference in replicative capacity between CRF02_AGwt_10L and HXB2. However, compared to CRF02_AGwt_10L, mutants, viruses CRF02_AGL10I, and CRF02_AGL10V showed a significant reduction in replication capacity by 10% (p<0.03) and 12% (p<0.02) respectively. Conclusion: Primary resistance to NRTI and NNRTI impacts response to treatment. The presence of a single TAM mutation may have limited impact on first line treatment in CRF02_AG. A common polymorphism in non-B subtypes, L10V, may affect susceptibility of certain PIs. In the context of large-scale use of antiretroviral, monitoring the emergence of resistance in non-B subtypes is important to preserve treatment options.