Identification of Novel Resistance-Related Polymorphisms in HIV-1 Subtype C RT Connection and RNase H Domains from Patients Under Virological Failure in Brazil

Abstract

Mutations in the connection and RNase H C-terminal reverse transcriptase (RT) domains of HIV-1 have been shown to impact drug resistance to RT inhibitors. However, their impact in the context of non-B subtypes has been poorly assessed. This study aimed to characterize resistance-related mutations in the C-terminal portions of RT in treatment-failing patients from southern Brazil, a region with endemic HIV-1 subtype C (HIV-1C). Viral RNA was isolated and reverse transcribed from 280 infected subjects, and genomic regions were analyzed by polymerase chain reaction, DNA sequencing, and phylogenetic analysis. Two novel mutations, M357R and E529D, were evidenced in Brazilian HIV-1C strains from treatment-failing patients. In global viral isolates of subjects on treatment, M357R was selected in HIV-1C and CRF01_AE and E529D was selected in HIV-1 subtype B (HIV-1B). While most C-terminal RT mutations described for HIV-1B also occur in HIV-1C, this work pinpointed novel mutations that display subtype-specific predominance or occurrence.

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

“…The presence of RNase H mutation E529D was directly dependent on whether or not the patient received an NRTI, supporting its role in the development of NRTI resistance. Recent work by Barral et al (2016) also observed a prevalence increase of E529D following treatment administration in subtype C patients in Brazil [ 8 ], further supporting our findings. Other RNase H mutations were also connected to treatment experience, although the support for these connections was low.…”

“…Here, treatment-related mutations were identified by comparing mutation frequencies in subtype C NRTI treatment-experienced sequences to those in subtype C ART naive sequences. Our findings indicate that several previously identified NRTI drug resistance mutations (435, 483, 491, 519, 530, and 554) of subtype B [ 7 , 8 , 9 , 11 , 12 ] represent the wild-type in subtype C, thereby warranting further characterization of their role. In our cohort, the E529D mutation was significantly more prevalent in sequences from NRTI treated patients, suggesting that it is a treatment related mutation in South African subtype C viruses.…”

“…The Fisher’s exact test was used to detect mutations significantly more prevalent in ART-experienced patients, with a level of significance of 0.05. p -Values were adjusted using a False discovery rate step-down procedure to reduce false positive results [ 21 ]. Known and novel mutations were identified by comparing with NRTI-associated RNase H mutations previously identified from subtype B drug-resistance studies: K451R, D460N, L469F, T470N, T473A, N474A, Q475A, K476A/N, D488E, L491S, Q500A, Y501A/F, I505A, I506L, Q509L, K512Q, K527N, K530R, H539N, V518I, E529D, Q547K, D549N, A554S and K558E/R [ 7 , 8 , 9 , 11 , 12 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ].…”

“…To date, for any subtype, most of the mutations identified to be associated with decreased treatment response have been described for the N-terminal half that corresponds to the polymerase region, up to the first 334 amino acids [ 7 ]. In contrast, the C-terminal RT region, encompassing the connection and RNase H domains, has historically been less well characterized in the context of drug resistance [ 7 , 8 ]; however, studies on subtype B-infected individuals suggested that mutations in the RNase H domain can increase NRTI resistance [ 9 , 10 , 11 , 12 , 13 ].…”

“…Data indicating whether similar mutations develop under NRTI drug selection pressure in the RNase H domain of HIV-1 non-B subtype viruses is limited [ 7 , 8 ]. Given the increasing accessibility of ART in South Africa, where subtype C prevails, we investigated the emergence of mutations in the RNase H domain of the subtype C virus in the context of during NRTI treatment.…”