Nucleoside reverse transcriptase inhibitors-associated mutations in the RNase H region of HIV-1 isolates in South African adults and children failing highly active antiretroviral therapy.

Abstract

Background: The South African national treatment program includes NRTIs in both first and second line highly active antiretroviral therapy regimens. Recently, mutations in the RNase H domain have been associated with resistance to NRTIs. Here we investigated the prevalence and association of RNase H mutations with NRTI resistance in isolates of HIV-1 subtype C infected individuals. Methods: RNase H sequences from 134 NRTI treated (104 adults and 30 children) and 134 drug-naïve sequences (30 KZN isolates and 104 downloaded from the Los Alamos Database) were analyzed. Spearman’s rank correlation and a Bayesian network were used to explore the relationship between mutations occurring within the RNase H domain and NRTI treatment. Results: 130 of 134 samples clustered phylogenetically with HIV-1 subtype C, with one subtype A, two subtype B and two subtype D. All 30 sequences from HAART-naїve patients were classified as subtype C. Five mutations in the RNase H region had significantly higher frequency when comparing ART-naïve and NRTI-experienced patients. These were: (E438GKR, L517ISV, K527GENQR, E529DK and Q547HKR) (Table 1). Three mutations (E432D, A446SVY and Q507HK) showed decreased proportions in treatment-experienced isolates when compared to ART- naїve isolates. E438GKR was seen in 6.72% of treated versus only 0% of naїve isolates (p= 0.0034), L517IV was found in 17.16% of treated isolates versus 7.46% of naїve isolates (p= 0.0245). Similarly, K527GENQRS was found in 41.04% of treated isolates versus 26.12% of naїve isolates (p= 0.0138), and E529DK was more prevalent in treated (17.91%) when compared to 2.99% of naїve subtype isolates (p <0.001). Finally, Q547HKR was seen in 5.22% of treated versus 0% of naïve subtype C patients (p= 0.0144). Interestingly, samples of twenty treatment experienced individuals that did not show of the classical NRTI mutations in the RT domain harbored E438GKR, L517ISV, K527GENQR, E529DK and Q547HKR. Conclusion: Results obtained from this study suggested that drug resistance could be caused by mutations in the RNase H domain either alone (T470S), or in combination with mutations in the pol region (D67N and L491P). Phenotypic studies are required to understand the prevalence and impact of RNase H mutations, particularly E438GKR, T470S, L517ISV, K527GENQR, E529DK and Q547HKR on NRTI resistance in HIV-1 subtype C as suggested by our data. Further studies using site-directed mutagenesis may also reveal the impact of these mutations on viral fitness.