Characterization of Nucleoside Reverse Transcriptase Inhibitor-Associated Mutations in the RNase H Region of HIV-1 Subtype C Infected Individuals

Abstract

The South African national treatment programme includes nucleoside reverse transcriptase inhibitors (NRTIs) in both first and second line highly active antiretroviral therapy regimens. Mutations in the RNase H domain have been associated with resistance to NRTIs but primarily in HIV-1 subtype B studies. Here, we investigated the prevalence and association of RNase H mutations with NRTI resistance in sequences from HIV-1 subtype C infected individuals. RNase H sequences from 112 NRTI treated but virologically failing individuals and 28 antiretroviral therapy (ART)-naive individuals were generated and analysed. In addition, sequences from 359 subtype C ART-naive sequences were downloaded from Los Alamos database to give a total of 387 sequences from ART-naive individuals for the analysis. Fisher's exact test was used to identify mutations and Bayesian network learning was applied to identify novel NRTI resistance mutation pathways in RNase H domain. The mutations A435L, S468A, T470S, L484I, A508S, Q509L, L517I, Q524E and E529D were more prevalent in sequences from treatment-experienced compared to antiretroviral treatment naive individuals, however, only the E529D mutation remained significant after correction for multiple comparison. Our findings suggest a potential interaction between E529D and NRTI-treatment; however, site-directed mutagenesis is needed to understand the impact of this RNase H mutation.

Keywords: HIV-1; NRTIs; RNase H; mutations; resistance.

Figure 1

Natural variability in 387 RNAse H subtype C sequences and in 1782 RNAse H subtype B sequences from ART-naive patients. The consensus amino acid at each position is coloured according to frequency.

Figure 2

The frequency (%) of treatment-associated mutations in antiretroviral therapy (ART)-naive patients and ART-experienced patients.

Figure 3

Annotated Bayesian network, based on 500 bootstraps, showing graphically the learned associations between nodes denoting amino acids or treatment experience. An arc (arrows) represents a direct dependency between corresponding nodes and arc thickness is proportional to bootstrap support. An antagonistic arc with a wild type was treated the same as a synergistic arc with mutations at this position. Arc direction has no causal meaning, but may indicate a non-additive multivariate effect.