Conservation Patterns of HIV-1 RT Connection and RNase H Domains: Identification of New Mutations in NRTI-Treated Patients

Abstract

BackgroundAlthough extensive HIV drug resistance information is available for the first 400 amino acids of its reverse transcriptase, the impact of antiretroviral treatment in C-terminal domains of Pol (thumb, connection and RNase H) is poorly understood.Methods and FindingsWe wanted to characterize conserved regions in RT C-terminal domains among HIV-1 group M subtypes and CRF. Additionally, we wished to identify NRTI-related mutations in HIV-1 RT C-terminal domains. We sequenced 118 RNase H domains from clinical viral isolates in Brazil, and analyzed 510 thumb and connection domain and 450 RNase H domain sequences collected from public HIV sequence databases, together with their treatment status and histories. Drug-naïve and NRTI-treated datasets were compared for intra- and inter-group conservation, and differences were determined using Fisher's exact tests. One third of RT C-terminal residues were found to be conserved among group M variants. Three mutations were found exclusively in NRTI-treated isolates. Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B. Some of them lay in or close to amino acid residues which contact nucleic acid or near the RNase H active site. Several of the residues pointed out herein have been recently associated to NRTI exposure or increase drug resistance to NRTI.ConclusionsThis is the first comprehensive genotypic analysis of a large sequence dataset that describes NRTI-related mutations in HIV-1 RT C-terminal domains in vivo. The findings into the conservation of RT C-terminal domains may pave the way to more rational drug design initiatives targeting those regions.

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

“…Q509L has been first described during in vitro selection of HIV-1B in the presence of AZT, 45 but studies in vivo have failed to find this mutation. [48][49][50] The A371V mutation, rarely seen among viruses from drug-naive subjects, 14 was notably enriched in our study (23%), further confirming its role as an accessory mutation, positively correlated with the number of co-occurring TAMs. 34 The N348I mutation occurred in 11% of viruses in Southern Brazil and it is associated with major resistance to nevirapine, etravirine, and rilpivirine, and as an accessory mutation for thymidine analogs.…”

Connection Domain Mutations N348I and A360V in HIV-1 Reverse Transcriptase Enhance Resistance to 3′-Azido-3′-deoxythymidine through Both RNase H-dependent and -independent Mechanisms

“…Both mutations have been identified in clinical samples of treatment-experienced individuals (24 -26, 33). Clinical data obtained from Canadian (26) (this study) and Brazilian cohorts (25) suggest that N348I can appear early in therapy, independently of preselected TAMs, whereas A360V appears late following the emergence of TAMs. It has been proposed that connection domain mutations exert their effects on excision indirectly through alterations in RNase H cleavage (26,28,32,33).…”

“…Recent findings have suggested that mutations in the C-terminal connection and RNase H domains of RT can significantly amplify resistance to AZT (22)(23)(24)(25)(26)(27). Most importantly, many of these mutations, including mutations N348I, A360I/V, and A371V, in the connection domain of HIV-1 RT were identified in clinical samples of HIV-infected individuals.…”

Subtype-Specific Differences in the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Connection Subdomain of CRF01_AE Are Associated with Higher Levels of Resistance to 3′-Azido-3′-Deoxythymidine

“…Santos et al reported that a threonine at position 400 in subtype B HIV-1 is more frequent in NRTI-exposed patients (25,26). Sequence database analysis of the CN and RH domains in subtype B (26) showed that a threonine at position 400 was present in 43% of naïve and 69% of NRTI-experienced subtype B patients, and selection of the threonine at this position in subtype B appeared to be linked to the acquisition of NRTI resistance mutations in the POL domain.…”

“…Sequence database analysis of the CN and RH domains in subtype B (26) showed that a threonine at position 400 was present in 43% of naïve and 69% of NRTI-experienced subtype B patients, and selection of the threonine at this position in subtype B appeared to be linked to the acquisition of NRTI resistance mutations in the POL domain. Interestingly, analysis of 140 CRF01_AE genomes that were sequenced through the CN subdomain (Stanford University HIV Drug Resistance Database; http://hivdb.stanford.edu) showed that among both treatment-naïve (90%) and NRTI-experienced (96%) CRF01_AE patients, the threonine at position 400 is highly conserved.…”