Short Communication Compilation and Prevalence of Mutations Associated with Resistance to Non-Nucleoside Reverse Transcriptase Inhibitors
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Antiviral Therapy 14:103–109 Short communication Compilation and prevalence of mutations associated with resistance to non-nucleoside reverse transcriptase inhibitors Lotke Tambuyzer1*, Hilde Azijn1, Laurence T Rimsky1, Johan Vingerhoets1, Pierre Lecocq2, Guenter Kraus1, Gaston Picchio3 and Marie-Pierre de Béthune1 1Tibotec BVBA, Mechelen, Belgium 2Virco BVBA, Mechelen, Belgium 3Tibotec Inc., Yardley, PA, USA *Corresponding author: E-mail: [email protected] Background: Non-nucleoside reverse transcriptase inhibi- Results: In total, 44 NNRTI RAMs were identified. These tors (NNRTIs) are an important component of antiretroviral included V90I, A98G, L100I, K101E/P/Q, K103H/N/S/T, therapy for HIV type-1 (HIV-1)-infected patients. Develop- V106A/I/M, V108I, E138G/K/Q, V179D/E/F/G/I, Y181C/ ment of NNRTI resistance can lead to treatment failure I/V, Y188C/H/L, V189I, G190A/C/E/Q/S, H221Y, P225H, and is conferred by the presence of specific resistance- F227C/L, M230I/L, P236L, K238N/T and Y318F. These associated mutations (RAMs) in the reverse transcriptase. NNRTI RAMs were observed, either alone or in combi- In addition to the widely used list of NNRTI RAMs provided nation with others, ranging in frequency from 0.02% to by the International AIDS Society-USA HIV-1 Drug Resist- 56.96% in a panel of 101,679 NNRTI-resistant isolates ance Mutation Group, which were identified on the basis submitted to Virco BVBA (Mechelen, Belgium) for routine of clinical experience with the approved NNRTIs, a more clinical resistance testing. Phenotypical data from site- comprehensive list of NNRTI RAMs is needed to guide the directed mutants helped to establish the contribution of study of baseline and emerging resistance to new NNRTIs. each mutation to NNRTI resistance. Methods: We conducted an extensive review of the exist- Conclusions: The list of 44 NNRTI RAMs compiled in this ing literature on NNRTI resistance, together with several study provides a comprehensive overview of mutations in vitro and in vivo studies on the mechanism of HIV-1 that play a role in HIV-1 NNRTI resistance and can be resistance to approved NNRTIs and to NNRTIs formerly or used to guide further in vitro and in vivo research on the currently in clinical development. mechanisms of HIV-1 NNRTI resistance. Introduction Non-nucleoside reverse transcriptase inhibitors first-line antiretroviral (ARV) therapy for patients (NNRTIs) target the viral reverse transcriptase (RT) infected by HIV type-1 (HIV-1), mainly because of responsible for the conversion of the single-stranded their proven efficacy and favourable safety and tol- RNA genome into double-stranded DNA, which is erability profiles. However, EFV, NVP and the other subsequently integrated into the host genomic DNA first-generation NNRTI, delavirdine (DLV), are char- [1,2]. NNRTIs are non-competitive inhibitors of acterized by a low genetic barrier to the development the RT enzyme and bind into a hydrophobic pocket of resistance and extensive cross-resistance, prevent- located in the p66 subunit domain, at 10 Å from ing sequential treatment with these NNRTIs [3,4]. the active site, and overlapping with the p66/p51 Recently, a next-generation NNRTI, etravirine (ETR; heterodimer interface [3]. Specific mutations in the TMC125), was approved in the United States [5] and NNRTI binding pocket cause resistance to NNRTIs the European Union [6] for the treatment of ARV and might lead to treatment failure. therapy- experienced adult patients. ETR exhibits a The first-generation NNRTIs, efavirenz (EFV) high genetic barrier to the development of resistance and nevirapine (NVP), are recommended as part of [7] and is an important new option for constructing © 2009 International Medical Press 1359-6535 103 Tambuyzer.indd 103 5/2/09 14:23:38 L Tambuyzer et al. an active ARV regimen because the prevalence of effective concentration [FC]) for the HIV-1/HXB2 site- NNRTI resistance in ARV-treated patients appears to directed mutant harbouring the single mutation in the be substantial [8] and the transmission of NNRTI-re- RT [7] and genotypical and phenotypical resistance sistant HIV-1 (primary resistance) has been reported information of HIV-1 isolates from patients who par- with an overall prevalence of 10–15% [9,10]. ticipated in the Tibotec clinical trials and were on an NNRTI resistance involves specific mutations, NNRTI-containing treatment regimen. either alone or in multiple and complex patterns. The The prevalence of each NNRTI RAM was determined International AIDS Society (IAS)-USA HIV-1 drug in a panel of 237,958 recombinant HIV-1 isolates sub- resistance mutations update provides a list of NNRTI mitted to Virco BVBA for routine clinical resistance resistance-associated mutations (RAMs), which were testing between January 1999 and June 2007 and in two identified on the basis of clinical experience with the subsets of this panel. The first subset included 101,679 approved NNRTIs [11,12]. In addition, several in NNRTI-resistant isolates for which the predicted FC vitro studies have identified RAMs that are directly for any first- generation NNRTI (EFV, NVP or DLV) associated with NNRTI resistance [13–15]. There is was greater than the respective virco®TYPE biological expanding evidence on new mutations that play a cutoff and the second subset contained the remaining role in NNRTI resistance; therefore, the present study 136,279 isolates that were not NNRTI resistant. aimed to compile a comprehensive list of RAMs to aid the study of resistance to new NNRTIs. Results Methods At the time of the analysis, 44 amino acid changes at 20 different positions along the RT were identified An extensive review of the existing literature on based on an extensive review of the existing literature in vitro and in vivo NNRTI resistance data was on NNRTI resistance data together with several in conducted in early to mid 2007. Bibliographical vitro and in vivo studies on the mechanism of HIV-1 searches on the mechanism of HIV-1 resistance to the resistance to approved NNRTIs and to NNRTIs for- approved NNRTIs (DLV, EFV, NVP and ETR) and to merly or currently in clinical development. The 44 the NNRTIs currently (TMC278 [rilpivirine], RDEA NNRTI RAMs included in the list were V90I, A98G, 806 and BILR 355 BS) or formerly (HEPT-, TIBO- L100I, K101E, K101P, K101Q, K103H, K103N, and BHAP derivatives, capravirine, emivirine and K103S, K103T, V106A, V106I, V106M, V108I, loviride) in clinical development, were included. E138G, E138K, E138Q, V179D, V179E, V179F, Several listings of NNRTI RAMs are available V179G, V179I, Y181C, Y181I, Y181V, Y188C, today. The IAS-USA 2007 drug resistance mutations Y188H, Y188L, V189I, G190A, G190C, G190E, update outlines 21 NNRTI RAMs at 12 different G190Q, G190S, H221Y, P225H, F227C, F227L, positions in the RT that might contribute to a reduced M230I, M230L, P236L, K238N, K238T and Y318F. virological response to DLV, EFV, NVP and ETR [11]. Results for each NNRTI RAM appear in Table 1 The NNRTI resistance matrix from the Stanford Uni- [7,11,14–16,18–53] and Figure 1. The prevalence of versity HIV Drug Resistance Database comprises 29 the NNRTI RAM in the total panel of 237,958 HIV-1 NNRTI RAMs at 16 different positions in the RT clinical isolates is shown. K103N had the highest prev- [16]. Mutational patterns including RT mutations at alence (24.34%) followed by Y181C (10.66%), V179I different positions have been described for the gener- (8.55%), G190A (8.16%) and V108I (4.81%). The ation of a quantitative phenotypical prediction (fold lowest prevalence was observed for F227C (0.01%). change) by the virco®TYPE (Virco BVBA, Mechelen, Table 1 also shows the prevalence of the NNRTI Belgium) analysis [17]. In the HIV Sequence Compen- RAM in the subset of 101,679 NNRTI-resistant HIV-1 dium 2006/2007 published by Los Alamos National clinical isolates. The five most prevalent NNRTI Laboratory (Los Alamos, NM, USA), 57 mutations at RAMs in this subset were K103N (56.96%), Y181C 28 different positions in the RT gene were considered (24.95%), G190A (19.09%), V179I (11.82%) and to be associated with NNRTI resistance [18]. V108I (10.68%) and were the same as in the whole In addition to this literature study and the com- panel. F227C also showed the lowest prevalence parison of different mutation listings, mutations were (0.02%) in this subset. included in the list of NNRTI RAMs on the basis of The five most prevalent NNRTI RAMs in the phenotypical evidence of NNRTI resistance using one remaining 136,279 HIV-1 clinical isolates that were or more of the following criteria: the selection of the not NNRTI resistant were V179I (6.11%), V90I mutation in vitro in selection experiments starting (3.06%), V106I (1.98%), V189I (0.93%) and K101Q from wild-type or mutant HIV-1 strains [7], a decrease (0.84%). Twenty-four NNRTI RAMs were not in phenotypical susceptibility (fold change in 50% present in this subset. 104 © 2009 International Medical Press Tambuyzer.indd 104 5/2/09 14:23:38 Extended list of NNRTI RAMs Table 1 shows the number of nucleotide substitutions B subtypes (91%). This number could give an indication needed for the HIV-1/HXB2 wild-type amino acid to of the genetic barrier to develop a particular RAM. switch to the mutant amino acid, using the most preva- The FC values for EFV, NVP and ETR obtained lent codon in a genotype database including mainly clade using HIV-1/HXB2 site-directed mutants harbouring Table 1. Mutations associated with resistance to NNRTIs Prevalence in samples for RCRT, % NNRTI- Not NNRTI- Number of NNRTI