Variations in Reverse Transcriptase and RNase H Domain Mutations in Human Immunodeficiency Virus Type 1 Clinical Isolates Are Associated with Divergent Phenotypic Resistance to Zidovudine

Abstract

Mutations in the RNase H domain of human immunodeficiency virus type 1 RT have been reported to cause resistance to zidovudine (ZDV) in vitro. However, very limited data on the in vivo relevance of these mutations in patients exist to date. This study was designed to determine the relationship between mutations in the RNase H domain and viral susceptibility to nucleoside analogues. Viruses harboring complex thymidine analogue mutation (TAM) and nucleoside analogue mutation (NAM) profiles were evaluated for their phenotypic susceptibilities to ZDV, tenofovir (TNF), and the nonapproved nucleoside reverse transcriptase inhibitors (NRTIs) ␤-2,3-didehydro-2,3-dideoxy-5-fluorocytidine (Reverset), ␤-D-5-fluorodioxolane-cytosine, and apricitabine. As controls, viruses from NRTI-naïve patients were also studied. The pol RT region (codons 21 to 250) of the viruses were sequenced and evaluated for mutations in the RNase H domain (codons 441 to 560) and the connection domain (codons 289 to 400). The results showed that viruses from patients failing multiple NRTI-containing regimens had distinct TAM and NAM profiles that conferred various degrees of resistance to ZDV (0.9-to >300-fold). Sequencing of the RNase H domain identified five positions (positions 460,468, 483, 512, and 519) at which extensive amino acid polymorphisms common in both wild-type viruses and viruses from treated patients were identified. No mutations were observed at positions 539 and 549, which have previously been associated with ZDV resistance. Mutations in the RNase H domain did not appear to correlate with the levels of phenotypic resistance to ZDV. Although some mutations were also observed in the connection domain, the simultaneous presence of the L74V and M184V mutations was the most significant determinant of phenotypic resistance to ZDV in patients infected with viruses with TAMs.

Combinations of Mutations in the Connection Domain of Human Immunodeficiency Virus Type 1 Reverse Transcriptase: Assessing the Impact on Nucleoside and Nonnucleoside Reverse Transcriptase Inhibitor Resistance

“…It is noteworthy that in our survey of subtype B viruses, substitutions at positions 369 and 348 were more prevalent in viruses from treatment-experienced patients than in viruses from treatment-naïve individuals. This observation is in agreement with recent publications reporting a higher prevalence of N348I in RTI-experienced patients, the association of N348I with NRTI (M184V/I [TAMs]) and NNRTI (K103N, Y181C) resistance mutations, and the selection of N348I during NVP and ZDV treatment (20,36 (5,19). In our survey, mutations at 369 and 348 were not observed in non-subtype B viruses.…”

Anti-Human Immunodeficiency Virus Type 1 Activity of Novel 6-Substituted 1-Benzyl-3-(3,5-Dimethylbenzyl)Uracil Derivatives

“…A limitation of our study relates to the use of laboratory strains. However, the mutations that we identified have been reported in clinical isolates (38,45,54). Another limitation of our study relates to the lack of information on the mutations in the RNase H domain of NNRTI-treated patients, since these mutations have been reported mostly in NRTI-treated patients.…”

“…A comparison of RNase H sequences in naive versus NRTI-experienced patients in a French cohort showed that mutations L469T/I/M/H, T470P/S/E/K, A554T/L/K, and K558R/ G/E were more prevalent among treatment-experienced patients (44). However, Ntemgwa et al analyzed RNase H mutations in NRTI-experienced patients from a Canadian and an Italian cohort and found positions D460, P468, H483, K512, and S519 to be extensively polymorphic in both naive and experienced patients (38). Recently, an analysis of patient sequences from databases showed that several mutations in the connection subdomain were significantly higher for sequences that contained one or more RTI resistance mutations compared to sequences without RTI resistance mutations (16).…”

Clinical relevance of substitutions in the connection subdomain and RNase H domain of HIV-1 reverse transcriptase from a cohort of antiretroviral treatment-naïve patients

“…Certain mutations in the connection subdomain (codons 322 to 440) of the polymerase domain or in the RNase H domain (codons 441 to 560)of HIV-1 RT have been recently shown to be associated with resistance to AZT (Brehm et al, 2007; Hachiya et al, 2008; Kemp et al, 1998; Nikolenko et al, 2007; Ntemgwa et al, 2007; Yap et al, 2007). In some cases it appears that mutations that affect AZT resistance have different phenotypes, depending on the presence or absence of other resistance mutations.…”