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Acquired HIV drug resistance mutations on first-line antiretroviral therapy in Southern Africa: Systematic review and Bayesian evidence synthesis. J Clin Epidemiol 2022; 148:135-145. [PMID: 35192922 PMCID: PMC9388696 DOI: 10.1016/j.jclinepi.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/11/2022] [Accepted: 02/16/2022] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To estimate the prevalence of NRTI and NNRTI drug resistance mutations in patients failing NNRTI-based ART in Southern Africa. STUDY DESIGN We conducted a systematic review to identify studies reporting drug resistance mutations among adult people living with HIV (PLWH) who experienced virological failure on first-line NNRTI-based ART in Southern Africa. We used a Bayesian hierarchical meta-regression model to synthesize the evidence on the frequency of eight NRTI- and seven NNRTI-DRMs across different ART regimens, accounting for ART duration and study characteristics. RESULTS We included 19 study populations, including 2,690 PLWH. Patients failing first-line ART including emtricitabine or lamivudine showed high levels of the M184V/I mutation after 2 years: 75.7% (95% Credibility Interval [CrI] 61.9%-88.9%) if combined with tenofovir, and 72.1% (95% CrI 56.8%-85.9%) with zidovudine. With tenofovir disoproxil fumarate, the prevalence of the K65R mutation was 52.0% (95% CrI 32.5%-76.8%) at 2 years. On efavirenz, K103 was the most prevalent NNRTI resistance mutation (57.2%, 95% CrI 40.9%-80.1%), followed by V106 (46.8%, 95% CrI 31.3%-70.4%). CONCLUSIONS NRTI/NNRTI drug resistance mutations are common in patients failing first-line ART in Southern Africa. These patients might switch to dolutegravir-based regimen with compromised NRTIs, which could impair the long-term efficacy of ART.
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Rhee SY, Kassaye SG, Barrow G, Sundaramurthi JC, Jordan MR, Shafer RW. HIV-1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates. J Int AIDS Soc 2021; 23:e25611. [PMID: 32936523 PMCID: PMC7507012 DOI: 10.1002/jia2.25611] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/01/2020] [Accepted: 08/02/2020] [Indexed: 11/10/2022] Open
Abstract
Introduction HIV‐1 transmitted drug resistance (TDR) prevalence increased during the initial years of the antiretroviral therapy (ART) global scale‐up. Few studies have examined recent trends in TDR prevalence using published genetic sequences and described the characteristics of ART‐naïve persons from whom these published sequences have been obtained. Methods We identified 125 studies published between 2014 and 2019 for which HIV‐1 reverse transcriptase (RT) with or without protease from ≥50 ART‐naïve adult persons were submitted to the GenBank sequence database. The population characteristics and TDR prevalence were compared to those in 122 studies published in the preceding five years between 2009 and 2013. TDR prevalence was analysed using median study‐level and person‐level data. Results and discussion The 2009 to 2013 and 2014 to 2019 studies reported sequence data from 32,866 and 41,724 ART‐naïve persons respectively. Studies from the low‐ and middle‐income country (LMIC) regions in sub‐Saharan Africa, South/Southeast Asia and Latin America/Caribbean accounted for approximately two‐thirds of the studies during each period. Between the two periods, the proportion of studies from sub‐Saharan Africa and from South/Southeast Asia countries other than China decreased from 43% to 32% and the proportion of studies performed at sentinel sites for recent HIV‐1 infection decreased from 33% to 22%. Between 2014 and 2019, median study‐level TDR prevalence was 4.1% in South/Southeast Asia, 6.0% in sub‐Saharan Africa, 9.1% in Latin America/Caribbean, 8.5% in Europe and 14.2% in North America. In the person‐level analysis, there was an increase in overall, NNRTI and two‐class NRTI/NNRTI resistance in sub‐Saharan Africa; an increase in NNRTI resistance in Latin America/Caribbean, and an increase in overall, NNRTI and PI resistance in North America. Conclusions Overall, NNRTI and dual NRTI/NNRTI‐associated TDR prevalence was significantly higher in sub‐Saharan Africa studies published between 2014 and 2019 compared with those published between 2009 and 2013. The decreasing proportion of studies from the hardest hit LMIC regions and the shift away from sentinel sites for recent infection suggests that global TDR surveillance efforts and publication of findings require renewed emphasis.
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Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Seble G Kassaye
- Department of Medicine, Georgetown University, Washington, DC, USA
| | - Geoffrey Barrow
- Department of Medicine, Faculty of Medical Science, University of the West Indies, Mona, Jamaica
| | | | - Michael R Jordan
- Division of Geographic Medicine, Tufts Medical Center, Boston, MA, USA.,Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA.,Tufts Center for Integrated Management of Antimicrobial Resistance (CIMAR), Boston, MA, USA
| | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, CA, USA
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Njenda DT, Aralaguppe SG, Singh K, Rao R, Sönnerborg A, Sarafianos SG, Neogi U. Antiretroviral potency of 4'-ethnyl-2'-fluoro-2'-deoxyadenosine, tenofovir alafenamide and second-generation NNRTIs across diverse HIV-1 subtypes. J Antimicrob Chemother 2019; 73:2721-2728. [PMID: 30053052 DOI: 10.1093/jac/dky256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023] Open
Abstract
Objectives 4'-Ethnyl-2'-fluoro-2'-deoxyadenosine (EFdA) is a novel translocation-defective reverse transcriptase inhibitor. We investigated the virological and biochemical inhibitory potentials of EFdA against a broad spectrum of subtype-specific chimeric viruses and compared it with tenofovir alafenamide, nevirapine, efavirenz, rilpivirine and etravirine. Methods pNL4.3 chimeric viruses encoding gag-pol from treatment-naive patients (n = 24) and therapy-failure patients (n = 3) and a panel of reverse transcriptase inhibitor-resistant strains (n = 7) were used to compare the potency of reverse transcriptase inhibitor drugs. The phenotypic drug susceptibility assay was performed using TZM-bl cells. In vitro inhibition assays were done using patient-derived reverse transcriptase. IC50 values of NNRTIs were calculated using a PicoGreen-based spectrophotometric assay. Steady-state kinetics were used to determine the apparent binding affinity (Km.dNTP) of triphosphate form of EFdA (EFdA-TP) and dATP. Results Among the chimeric treatment-naive viruses, EFdA had an ex vivo antiretroviral activity [median (IQR) EC50 = 1.4 nM (0.6-2.1 nM)] comparable to that of tenofovir alafenamide [1.6 nM (0.5-3.6 nM)]. Subtype-specific differences were found for etravirine (P = 0.004) and rilpivirine (P = 0.017), where HIV-1C had the highest EC50 values. EFdA had a greater comparative efficiency [calculated by dividing the efficiency of monophosphate form of EFdA (EFdA-MP) incorporation (kcat.EFdA-TP/Km.EFdA-TP) over the efficiency of dATP incorporation (kcat.dATP/Km.dATP)] compared with the natural substrate dATP, with a fold change of between 1.6 and 3.2. Ex vivo analysis on reverse transcriptase inhibitor-resistant strains showed EFdA to have a higher potency. Despite the presence of rilpivirine DRMs, some non-B strains showed hypersusceptibility to rilpivirine. Conclusions Our combined virological and biochemical data suggest that EFdA inhibits both WT and reverse transcriptase inhibitor-resistant viruses efficiently in a subtype-independent manner. In contrast, HIV-1C is least susceptible to etravirine and rilpivirine.
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Affiliation(s)
- Duncan T Njenda
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kamalendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Rohit Rao
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
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Major drug resistance mutations to HIV-1 protease inhibitors (PI) among patients exposed to PI class failing antiretroviral therapy in São Paulo State, Brazil. PLoS One 2019; 14:e0223210. [PMID: 31574109 PMCID: PMC6772045 DOI: 10.1371/journal.pone.0223210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/15/2019] [Indexed: 11/21/2022] Open
Abstract
Background Protease inhibitors (PI) are especially important in salvage therapy. Previous treatment failure with a PI containing regimen may elicit resistance mutations, reducing PI susceptibility and limiting treatment options. The aim of this study was to describe major PI mutations among patients exposed to at least one PI to evaluate predictors of mutation emergence and the impact of subtypes on resistance. Methodology Partial HIV-1 pol sequences (Sanger Sequencing) from patients exposed to PI with virological failure were genotyped from January 2014 to December 2017. Drug resistance mutations (DRM), antiretroviral susceptibility (GSS) and subtypes, along clinical and laboratory parameters, were evaluated using logistic regression to access the predictors of mutation emergence. Results In 27.5% (466/1696) of the cases at least one major PI mutations was identified, most commonly M46 (14.7%), V82 (13.8%) and I54 (13.3%). Mutations to NRTI and NNRTI were observed in 69.6% and 59.9%, respectively, of the 1696 sequences. Full activity to darunavir was predicted in 88% (1496/1696), but was only 57% among those with at least one PI-DRM. Subtype C sequences had less major PI-DRMs (10%, 9/87) compared to B (28%, 338/1216) or F (35%, 58/168) (p <0.001) but adjusted analysis suggested that this association is not independent from a shorter treatment time and fewer regimens (OR 0.59, Confidence Interval 95: 0.2–2.5, p = 0.48). Subtype F, together with NRTI mutations and longer time on treatment was associated to presence of PI-DRM, to a lower darunavir GSS and to mutations at codon I50. Conclusions Among patients with PI-DRM, full activity to darunavir was compromised in almost half of the cases and efforts to detect failure at earlier time are warranted, particularly for HIV-1 subtype F that showed association to the emergence of resistance, with potential impact in protease inhibitors sequencing. Furthermore, NRTI mutations may serve as an indicative of sufficient adherence to allow PI-DRM emergence.
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HIV-1 Subtype C with PYxE Insertion Has Enhanced Binding of Gag-p6 to Host Cell Protein ALIX and Increased Replication Fitness. J Virol 2019; 93:JVI.00077-19. [PMID: 30760577 DOI: 10.1128/jvi.00077-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/07/2019] [Indexed: 02/02/2023] Open
Abstract
Human immunodeficiency virus type 1 subtype C (HIV-1C) has a natural deletion of a YPxL motif in its Gag-p6 late domain. This domain mediates the binding of Gag to host cell protein ALIX and subsequently facilitates viral budding. In a subset of HIV-1C-infected individuals, the tetrapeptide insertion PYxE has been identified at the deleted YPxL motif site. Here, we report the consequences of PYxE insertion on the interaction with ALIX and the relevance regarding replication fitness and drug sensitivity. In our three HIV-1C cohorts, PYKE and PYQE were most prevalent among PYxE variants. Through in silico predictions and in vitro experiments, we showed that HIV-1C Gag has an increased binding to ALIX when the PYxE motif is present. To go more into the clinical relevance of the PYxE insertion, we obtained patient-derived gag-pol sequences from HIV-1CPYxEi viruses and inserted them in a reference HIV-1 sequence. Viral growth was increased, and the sensitivity to the protease inhibitor (PI) lopinavir (LPV) and nucleoside reverse transcriptase inhibitor tenofovir alafenamide (TAF) was decreased for some of the HIV-1C PYxE variants compared to that of wild-type variants. Our data suggest that PYxE insertion in Gag restores the ability of Gag to bind ALIX and correlates with enhanced viral fitness in the absence or presence of LPV and TAF. The high prevalence and increased replication fitness of the HIV-1C virus with PYxE insertion indicates the clinical importance of these viral variants.IMPORTANCE Genomic differences within HIV-1 subtypes is associated with various degrees of viral spread, disease progression, and clinical outcome. Viral budding is essential in the HIV-1 life cycle and mainly mediated through the interaction of Gag with host proteins. Two motifs within Gag-p6 mediate binding of host cell proteins and facilitate budding. HIV-1C has a natural deletion of one of these two motifs, resulting in an inability to bind to host cell protein ALIX. Previously, we have identified a tetrapeptide (PYxE) insertion at this deleted motif site in a subset of HIV-1C patients. Here, we report the incidence of PYxE insertions in three different HIV-1C cohorts, and the insertion restores the binding of Gag to ALIX. It also increases viral growth even in the presence of the antiretroviral drugs lopinavir and tenofovir alafenamide. Hence, PYxE insertion in HIV-1C might be biologically relevant for viruses and clinically significant among patients.
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Inzaule SC, Hamers RL, Doherty M, Shafer RW, Bertagnolio S, Rinke de Wit TF. Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens. THE LANCET. INFECTIOUS DISEASES 2019; 19:e246-e252. [PMID: 30902440 DOI: 10.1016/s1473-3099(18)30710-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 10/08/2018] [Accepted: 11/13/2018] [Indexed: 12/17/2022]
Abstract
To improve virological suppression and address the emerging threat of HIV drug resistance, many low-income and middle-income countries are moving away from non-nucleoside reverse transcriptase inhibitors (NNRTI) and transitioning to dolutegravir as part of a more affordable and standardised antiretroviral therapy (ART). Although this transition could decrease the effect of rising NNRTI resistance and yield improved ART outcomes, it also presents new challenges. First, current safety concerns for dolutegravir use in women of childbearing potential require alternative solutions. Second, pre-existing resistance to the co-administered nucleoside reverse transcriptase inhibitors might reduce effectiveness and durability of dolutegravir, particularly if there is scarce access to viral load tests to monitor treatment outcomes. Third, there is inadequate information on the genetic correlates of resistance to dolutegravir, particularly in patients infected with HIV-1 non-B subtypes. Finally, clinical management of patients with confirmed virological failure on a dolutegravir-based regimen can pose challenges because of uncertainty around whether dolutegravir resistance has actually developed and switching is needed, or whether only interventions to improve adherence without switching are sufficient. These considerations should be addressed to consolidate expected gains from widespread introduction of dolutegravir in low-income and middle-income countries.
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Affiliation(s)
- Seth C Inzaule
- Amsterdam Institute for Global Health and Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Joep Lange Institute, Amsterdam, Netherlands
| | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Eijkman-Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Meg Doherty
- Department of HIV and Global Hepatitis Programme, WHO, Geneva, Switzerland
| | - Robert W Shafer
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Silvia Bertagnolio
- Department of HIV and Global Hepatitis Programme, WHO, Geneva, Switzerland
| | - Tobias F Rinke de Wit
- Amsterdam Institute for Global Health and Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Joep Lange Institute, Amsterdam, Netherlands
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Kinloch NN, Lee GQ, Carlson JM, Jin SW, Brumme CJ, Byakwaga H, Muzoora C, Bwana MB, Cobarrubias KD, Hunt PW, Martin JN, Carrington M, Bangsberg DR, Harrigan PR, Brockman MA, Brumme ZL. Genotypic and Mechanistic Characterization of Subtype-Specific HIV Adaptation to Host Cellular Immunity. J Virol 2019; 93:e01502-18. [PMID: 30305354 PMCID: PMC6288327 DOI: 10.1128/jvi.01502-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/28/2018] [Indexed: 11/20/2022] Open
Abstract
The extent to which viral genetic context influences HIV adaptation to human leukocyte antigen (HLA) class I-restricted immune pressures remains incompletely understood. The Ugandan HIV epidemic, where major pandemic group M subtypes A1 and D cocirculate in a single host population, provides an opportunity to investigate this question. We characterized plasma HIV RNA gag, pol, and nef sequences, along with host HLA genotypes, in 464 antiretroviral-naive individuals chronically infected with HIV subtype A1 or D. Using phylogenetically informed statistical approaches, we identified HLA-associated polymorphisms and formally compared their strengths of selection between viral subtypes. A substantial number (32%) of HLA-associated polymorphisms identified in subtype A1 and/or D had previously been reported in subtype B, C, and/or circulating recombinant form 01_AE (CRF01_AE), confirming the shared nature of many HLA-driven escape pathways regardless of viral genetic context. Nevertheless, 34% of the identified HLA-associated polymorphisms were significantly differentially selected between subtypes A1 and D. Experimental investigation of select examples of subtype-specific escape revealed distinct underlying mechanisms with important implications for vaccine design: whereas some were attributable to subtype-specific sequence variation that influenced epitope-HLA binding, others were attributable to differential mutational barriers to immune escape. Overall, our results confirm that HIV genetic context is a key modulator of viral adaptation to host cellular immunity and highlight the power of combined bioinformatic and mechanistic studies, paired with knowledge of epitope immunogenicity, to identify appropriate viral regions for inclusion in subtype-specific and universal HIV vaccine strategies.IMPORTANCE The identification of HIV polymorphisms reproducibly selected under pressure by specific HLA alleles and the elucidation of their impact on viral function can help identify immunogenic viral regions where immune escape incurs a fitness cost. However, our knowledge of HLA-driven escape pathways and their functional costs is largely limited to HIV subtype B and, to a lesser extent, subtype C. Our study represents the first characterization of HLA-driven adaptation pathways in HIV subtypes A1 and D, which dominate in East Africa, and the first statistically rigorous characterization of differential HLA-driven escape across viral subtypes. The results support a considerable impact of viral genetic context on HIV adaptation to host HLA, where HIV subtype-specific sequence variation influences both epitope-HLA binding and the fitness costs of escape. Integrated bioinformatic and mechanistic characterization of these and other instances of differential escape could aid rational cytotoxic T-lymphocyte-based vaccine immunogen selection for both subtype-specific and universal HIV vaccines.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Guinevere Q Lee
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachusetts, USA
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Helen Byakwaga
- Mbarara University of Science and Technology, Mbarara, Uganda
- University of California, San Francisco, San Francisco, California, USA
| | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Mwebesa B Bwana
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Kyle D Cobarrubias
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter W Hunt
- University of California, San Francisco, San Francisco, California, USA
| | - Jeff N Martin
- University of California, San Francisco, San Francisco, California, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David R Bangsberg
- Oregon Health and Science University-Portland State University School of Public Health, Portland, Oregon, USA
| | - P Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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Hamers RL, Rinke de Wit TF, Holmes CB. HIV drug resistance in low-income and middle-income countries. Lancet HIV 2018; 5:e588-e596. [PMID: 30193863 DOI: 10.1016/s2352-3018(18)30173-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/02/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
Abstract
After 15 years of global scale-up of antiretroviral therapy (ART), rising prevalence of HIV drug resistance in many low-income and middle-income countries (LMICs) poses a growing threat to the HIV response, with the potential to drive an increase in mortality, HIV incidence, and costs. To achieve UNAIDS global targets, enhanced strategies are needed to improve quality of ART services and durability of available ART regimens, and to curb resistance. These strategies include roll out of drugs with greater efficacy and higher genetic barriers to resistance than those that are currently widely used, universal access to and improved effectiveness of viral load monitoring, patient-centred care delivery models, and reliable drug supply chains, in conjunction with frameworks for resistance monitoring and prevention. In this Review, we assess contemporary data on HIV drug resistance in LMICs and their implications for the HIV response, highlighting the potential impact and resistance risks of novel ART strategies and knowledge gaps.
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Affiliation(s)
- Raph L Hamers
- Eijkman-Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Global Health, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands.
| | - Tobias F Rinke de Wit
- Department of Global Health, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands; Joep Lange Institute, Amsterdam, Netherlands
| | - Charles B Holmes
- Centre for Infectious Diseases Research Zambia, Lusaka, Zambia; Center for Global Health and Quality, Georgetown University Medical Center, Washington, DC, USA; Johns Hopkins University School of Medicine and Bloomberg School of Public Health, Baltimore, MD, USA
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Zhou Z, Tang K, Zhang G, Wadonda-Kabondo N, Moyo K, Rowe LA, DeVos JR, Wagar N, Zheng DP, Guo H, Nkengasong J, Frace M, Sammons S, Yang C. Detection of minority drug resistant mutations in Malawian HIV-1 subtype C-positive patients initiating and on first-line antiretroviral therapy. Afr J Lab Med 2018; 7:708. [PMID: 29977795 PMCID: PMC6018132 DOI: 10.4102/ajlm.v7i1.708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Minority drug resistance mutations (DRMs) that are often missed by Sanger sequencing are clinically significant, as they can cause virologic failure in individuals treated with antiretroviral therapy (ART) drugs. Objective This study aimed to estimate the prevalence of minor DRMs among patients enrolled in a Malawi HIV drug resistance monitoring survey at baseline and at one year after initiation of ART. Methods Forty-one plasma specimens collected from HIV-1 subtype C-positive patients and seven clonal control samples were analysed using ultra-deep sequencing technology. Results Deep sequencing identified all 72 DRMs detected by Sanger sequencing at the level of ≥20% and 79 additional minority DRMs at the level of < 20% from the 41 Malawian clinical specimens. Overall, DRMs were detected in 85% of pre-ART and 90.5% of virologic failure patients by deep sequencing. Among pre-ART patients, deep sequencing identified a statistically significant higher prevalence of DRMs to nucleoside reverse transcriptase inhibitors (NRTIs) compared with Sanger sequencing. The difference was mainly due to the high prevalence of minority K65R and M184I mutations. Most virologic failure patients harboured DRMs against both NRTIs and non-nucleoside reverse transcriptase inhibitors (NNRTIs). These minority DRMs contributed to the increased or enhanced virologic failures in these patients. Conclusion The results revealed the presence of minority DRMs to NRTIs and NNRTIs in specimens collected at baseline and virologic failure time points. These minority DRMs not only increased resistance levels to NRTIs and NNRTIs for the prescribed ART, but also expanded resistance to additional major first-line ART drugs. This study suggested that drug resistance testing that uses more sensitive technologies, is needed in this setting.
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Affiliation(s)
- Zhiyong Zhou
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Kevin Tang
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Guoqing Zhang
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | | | - Kundai Moyo
- Department of Preventive Health, Ministry of Health, Lilongwe, Malawi
| | - Lori A Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Joshua R DeVos
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Nick Wagar
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Du-Ping Zheng
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Hongxiong Guo
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - John Nkengasong
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Mike Frace
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Scott Sammons
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
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Cox S, Margot N, Miller M, Callebaut C. Antiviral Activity of Tenofovir Alafenamide Against HIV-1 Subtypes and Emergence of K65R. AIDS Res Hum Retroviruses 2018; 34:456-458. [PMID: 29620930 DOI: 10.1089/aid.2017.0248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Differences in emergence of HIV resistance between subtypes B and C in vitro and potential implications on tenofovir alafenamide efficacy in vivo were evaluated. Dose escalation resistance selections showed K65R emerging earlier for subtype C viruses in vitro, as previously reported. Viral breakthrough experiments at therapeutic drug concentrations, however, showed no difference in time to breakthrough between these subtypes. Finally, clinical trial data found no evidence of greater K65R emergence in patients harboring subtype C HIV.
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Affiliation(s)
- Stephanie Cox
- Clinical Virology, Gilead Sciences, Inc., Foster City, California
| | - Nicolas Margot
- Clinical Virology, Gilead Sciences, Inc., Foster City, California
| | - Michael Miller
- Clinical Virology, Gilead Sciences, Inc., Foster City, California
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Smit E, White E, Clark D, Churchill D, Zhang H, Collins S, Pillay D, Sabin C, Nelson M, Winston A, Jose S, Tostevin A, Dunn DT. An association between K65R and HIV-1 subtype C viruses in patients treated with multiple NRTIs. J Antimicrob Chemother 2018; 72:2075-2082. [PMID: 28379449 PMCID: PMC5890671 DOI: 10.1093/jac/dkx091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/28/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives: HIV-1 subtype C might have a greater propensity to develop K65R mutations in patients with virological failure compared with other subtypes. However, the strong association between viral subtype and confounding factors such as exposure groups and ethnicity affects the calculation of this propensity. We exploited the diversity of viral subtypes within the UK to undertake a direct comparative analysis. Patients and methods: We analysed only sequences with major IAS-defined mutations from patients with virological failure. Prevalence of K65R was related to subtype and exposure to the NRTIs that primarily select for this mutation (tenofovir, abacavir, didanosine and stavudine). A multivariate logistic regression model quantified the effect of subtype on the prevalence of K65R, adjusting for previous and current exposure to all four specified drugs. Results: Subtype B patients (n = 3410) were mostly MSM (78%) and those with subtype C (n = 810) were mostly heterosexual (82%). K65R was detected in 7.8% of subtype B patients compared with 14.2% of subtype C patients. The subtype difference in K65R prevalence was observed irrespective of NRTI exposure and K65R was frequently selected by abacavir, didanosine and stavudine in patients with no previous exposure to tenofovir. Multivariate logistic regression confirmed that K65R was significantly more common in subtype C viruses (adjusted OR = 2.02, 95% CI = 1.55–2.62, P < 0.001). Conclusions: Patients with subtype C HIV-1 have approximately double the frequency of K65R in our database compared with other subtypes. The exact clinical implications of this finding need to be further elucidated.
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Affiliation(s)
- Erasmus Smit
- Public Health Laboratory Birmingham, Public Health England, Heartlands Hospital, Birmingham, UK
| | - Ellen White
- MRC CTU at UCL, University College London, London, UK
| | | | - Duncan Churchill
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Hongyi Zhang
- Public Health Laboratory Cambridge, Public Health England, Addenbrooke's Hospital, Cambridge, UK
| | | | - Deenan Pillay
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK.,Wellcome Trust Africa Centre for Health and Population Sciences, University of KwaZulu Natal, Mtubatuba, South Africa
| | - Caroline Sabin
- Research Department of Infection and Population Health London, University College London, London, UK
| | - Mark Nelson
- Chelsea and Westminster Hospital, London, UK
| | - Alan Winston
- Section of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Sophie Jose
- Research Department of Infection and Population Health London, University College London, London, UK
| | - Anna Tostevin
- Research Department of Infection and Population Health London, University College London, London, UK
| | - David T Dunn
- Research Department of Infection and Population Health London, University College London, London, UK
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Karade S, Chaturbhuj DN, Sen S, Joshi RK, Kulkarni SS, Shankar S, Gangakhedkar RR. HIV drug resistance following a decade of the free antiretroviral therapy programme in India: A review. Int J Infect Dis 2017; 66:33-41. [PMID: 29128646 DOI: 10.1016/j.ijid.2017.10.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/12/2017] [Accepted: 10/27/2017] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE The objective of this review was to assess the burden of HIV drug resistance mutations (DRM) in Indian adults exposed to first-line antiretroviral therapy (ART) as per national guidelines. METHODS An advanced search of the published literature on HIV drug resistance in India was performed in the PubMed and Scopus databases. Data pertaining to age, sex, CD4 count, viral load, and prevalence of nucleoside reverse transcriptase inhibitor (NRTI)/non-nucleoside reverse transcriptase inhibitor (NNRTI) DRM were extracted from each publication. Year-wise Indian HIV-1 reverse transcriptase (RT) sequences were retrieved from the Los Alamos HIV database and mutation analyses were performed. A time trend analysis of the proportion of sequences showing NRTI resistance mutations among individuals exposed to first-line ART was conducted. RESULTS Overall, 23 studies (1046 unique RT sequences) were identified indicating a prevalence of drug resistance to NRTI and NNRTI. The proportion of RT sequences with any DRM, any NRTI DRM, and any NNRTI DRM was 78.39%, 68.83%, and 73.13%, respectively. The temporal trend analysis of individual DRM from sequences retrieved during 2004-2014 indicated a rising trend in K65R mutations (p=0.013). CONCLUSIONS Although the overall burden of resistance against first-line ART agents remained steady over the study decade, periodic monitoring is essential. There is the need to develop an HIV-1 subtype C-specific resistance database in India.
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Affiliation(s)
- Santosh Karade
- HIV Drug Resistance Laboratory, National AIDS Research Institute (ICMR), Pune, India; Department of Microbiology, Armed Forces Medical College, Pune, India
| | - Devidas N Chaturbhuj
- HIV Drug Resistance Laboratory, National AIDS Research Institute (ICMR), Pune, India; Symbiosis International University, Lavale, Pune, India
| | - Sourav Sen
- Department of Microbiology, Armed Forces Medical College, Pune, India
| | - Rajneesh K Joshi
- Department of Epidemiology and Biostatistics, National AIDS Research Institute, Pune, India; Department of Community Medicine, Armed Forces Medical College, Pune, India
| | - Smita S Kulkarni
- Department of Molecular Virology, National AIDS Research Institute, Pune, India
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HIV-1 Drug Resistance by Ultra-Deep Sequencing Following Short Course Zidovudine, Single-Dose Nevirapine, and Single-Dose Tenofovir with Emtricitabine for Prevention of Mother-to-Child Transmission. J Acquir Immune Defic Syndr 2017; 73:384-389. [PMID: 27327263 PMCID: PMC5172515 DOI: 10.1097/qai.0000000000001116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Supplemental Digital Content is Available in the Text. Antiretroviral drug resistance following pMTCT strategies remains a significant problem. With rapid advancements in next generation sequencing technologies, there is more focus on HIV drug-resistant variants of low frequency, or the so-called minority variants. In South Africa, AZT monotherapy for pMTCT, similar to World Health Organization option A, has been used since 2008. In 2010, a single dose of co-formulated TDF/FTC was included in the strategy for prevention of resistance conferred by single-dose nevirapine (sd NVP). The study was conducted in KwaZulu-Natal, South Africa, among pMTCT participants who received AZT monotherapy from 14 weeks of gestation, intrapartum AZT and sd NVP, and postpartum sd TDF/FTC. Twenty-six specimens collected at 6 weeks post-delivery were successfully sequenced using 454 ultra-deep sequencing. Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance was detected in 17 of 26 (65%) patients, 2 (7%) had Thymidine analogue mutations, and 3 (11%) had K65R. Of the 17 patients with NNRTI resistance, 11 (65%) had high-level NNRTI resistance, whereas 6 (35%) had intermediate NNRTI resistance. The levels of NNRTI resistance are much higher than would be expected, given the inclusion of antepartum AZT and postpartum TDF/FTC. This high level of NNRTI resistance could impact future NNRTI-containing treatment for a large proportion of pMTCT-exposed women. The detection of Thymidine analogue mutations highlights the need to understand the clinical impact of these on AZT-containing antiretroviral treatment in women exposed to AZT monotherapy.
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HIV-1 drug resistance and resistance testing. INFECTION GENETICS AND EVOLUTION 2016; 46:292-307. [PMID: 27587334 DOI: 10.1016/j.meegid.2016.08.031] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
The global scale-up of antiretroviral (ARV) therapy (ART) has led to dramatic reductions in HIV-1 mortality and incidence. However, HIV drug resistance (HIVDR) poses a potential threat to the long-term success of ART and is emerging as a threat to the elimination of AIDS as a public health problem by 2030. In this review we describe the genetic mechanisms, epidemiology, and management of HIVDR at both individual and population levels across diverse economic and geographic settings. To describe the genetic mechanisms of HIVDR, we review the genetic barriers to resistance for the most commonly used ARVs and describe the extent of cross-resistance between them. To describe the epidemiology of HIVDR, we summarize the prevalence and patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in both high-income and low- and middle-income countries (LMICs). We also review to two categories of HIVDR with important public health relevance: (i) pre-treatment drug resistance (PDR), a World Health Organization-recommended HIVDR surveillance metric and (ii) and pre-exposure prophylaxis (PrEP)-related drug resistance, a type of ADR that can impact clinical outcomes if present at the time of treatment initiation. To summarize the implications of HIVDR for patient management, we review the role of genotypic resistance testing and treatment practices in both high-income and LMIC settings. In high-income countries where drug resistance testing is part of routine care, such an understanding can help clinicians prevent virological failure and accumulation of further HIVDR on an individual level by selecting the most efficacious regimens for their patients. Although there is reduced access to diagnostic testing and to many ARVs in LMIC, understanding the scientific basis and clinical implications of HIVDR is useful in all regions in order to shape appropriate surveillance, inform treatment algorithms, and manage difficult cases.
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Inzaule SC, Weidle PJ, Yang C, Ndiege K, Hamers RL, Rinke de Wit TF, Thomas T, Zeh C. Prevalence and dynamics of the K65R drug resistance mutation in HIV-1-infected infants exposed to maternal therapy with lamivudine, zidovudine and either nevirapine or nelfinavir in breast milk. J Antimicrob Chemother 2016; 71:1619-26. [PMID: 26953333 DOI: 10.1093/jac/dkw039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/29/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND K65R is a relatively rare drug resistance mutation (DRM) selected by the NRTIs tenofovir, didanosine, abacavir and stavudine and confers cross-resistance to all NRTIs except zidovudine. Selection by other NRTIs is uncommon. OBJECTIVES In this study we investigated the frequency of emergence of the K65R mutation and factors associated with it in HIV-1-infected infants exposed to low doses of maternal lamivudine, zidovudine and either nevirapine or nelfinavir ingested through breast milk, using specimens collected from the Kisumu Breastfeeding Study. METHODS Plasma specimens with viral load ≥1000 copies/mL collected from HIV-infected infants at 0-1, 2, 6, 14, 24 and 36 weeks of age and maternal samples at delivery were tested for HIV drug resistance using Sanger sequencing of the polymerase gene. Factors associated with K65R emergence were assessed using Fisher's exact test and the Wilcoxon rank-sum test. RESULTS K65R was detected in samples from 6 of the 24 infants (25%) who acquired HIV-1 infection by the age of 6 months. K65R emerged in half of the infants by 6 weeks and in the rest by 14 weeks of age. None of the mothers at delivery or the infants with a positive genotype at first time of positivity had the K65R mutation. Infants with K65R had low baseline CD4 cell counts (P = 0.014), were more likely to have DRMs earlier (≤6 weeks versus ≥14 weeks, P = 0.007) and were more likely to have multiclass drug resistance (P = 0.035). M184V was the most common mutation associated with K65R emergence. K65R had reverted by 3 months after cessation of breastfeeding. CONCLUSIONS A high rate of K65R emergence may suggest that ingesting low doses of lamivudine via breast milk could select for this mutation. The presence of this mutation may have a negative impact on future responses to NRTI-based ART. More in vitro studies are, however, needed to establish the molecular mechanism for this selection.
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Affiliation(s)
- Seth C Inzaule
- Kenya Medical Research Institute, Kisumu, Kenya Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Paul J Weidle
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chunfu Yang
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Raph L Hamers
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Tobias F Rinke de Wit
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Timothy Thomas
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clement Zeh
- Centers for Disease Control and Prevention, Kisumu, Kenya
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16
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Cunha RD, Abreu CM, Sousa AK, Mabombo VC, Nijhuis M, de Jong D, Tanuri A. Short Communication: In Vitro Accumulation of Drug Resistance Mutations in Chimeric Infectious Clones Containing Subtype B or C Reverse Transcriptase and Selected with Tenofovir or Didanosine. AIDS Res Hum Retroviruses 2015; 31:851-8. [PMID: 26075306 DOI: 10.1089/aid.2014.0324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Highly active antiretroviral therapy (HAART) contributed to the improvement in the life expectancy of HIV-infected patients. However, the emergence of drug-resistant mutations (DRM) is a major viral factor impacting therapeutic failure. Differences in DRM can occur among HIV-1 subtypes. We evaluate the kinetics of the selection of resistance mutations in vitro analyzing two chimeric clones that contain the reverse transcriptases of subtypes B or C (RTB' and RTC') in cells treated with increasing concentrations of tenofovir disoproxil fumarate (TDF) and didanosine (ddI). The mutation K65R is selected more quickly in RTC' than in RTB' viruses with TDF and ddI, and additional mutations (positions 45, 62, and 68) were selected after K65R fixation. Other primary mutations (M184V and Q151M) were selected with ddI treatment in conjunction with K65R only in RTC' viruses. Both patterns, M184V+K65R and Q151M+K65R, have a significant impact on NRTI resistance. Our data suggest that selection of TDF and ddI DRMs can occur earlier in subtype C HIV in patients when compared to subtype B.
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Affiliation(s)
- Rodrigo D. Cunha
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Celina M. Abreu
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Arielly K.P. Sousa
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviana C.J. Mabombo
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Monique Nijhuis
- Department of Virology, Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dorien de Jong
- Department of Virology, Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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17
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Subtype-specific analysis of the K65R substitution in HIV-1 that confers hypersusceptibility to a novel nucleotide-competing reverse transcriptase inhibitor. Antimicrob Agents Chemother 2015; 59:3189-96. [PMID: 25779585 DOI: 10.1128/aac.00315-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/11/2015] [Indexed: 12/20/2022] Open
Abstract
Compound A is a novel nucleotide-competing HIV-1 reverse transcriptase (RT) inhibitor (NcRTI) that selects for a unique W153L substitution that confers hypersusceptibility to tenofovir, while the K65R substitution in RT confers resistance against tenofovir and enhances susceptibility to NcRTIs. Although the K65R substitution is more common in subtype C viruses, the impact of subtype variability on NcRTI susceptibility has not been studied. In the present study, we performed experiments with compound A by using purified recombinant RT enzymes and viruses of subtypes B and C and circulating recombinant form CRF_A/G. We confirmed the hypersusceptibility of K65R substitution-containing RTs to compound A for subtype C, CRF_A/G, and subtype B. Steady-state kinetic analysis showed that K65R RTs enhanced the susceptibility to compound A by increasing binding of the inhibitor to the nucleotide binding site of RT in a subtype-independent manner, without significantly discriminating against the natural nucleotide substrate. These data highlight the potential utility of NcRTIs, such as compound A, for treatment of infections with K65R substitution-containing viruses, regardless of HIV-1 subtype.
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18
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Telwatte S, Hearps AC, Johnson A, Latham CF, Moore K, Agius P, Tachedjian M, Sonza S, Sluis-Cremer N, Harrigan PR, Tachedjian G. Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations. Nucleic Acids Res 2015; 43:3256-71. [PMID: 25765644 PMCID: PMC4381058 DOI: 10.1093/nar/gkv128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/06/2015] [Indexed: 01/03/2023] Open
Abstract
Resistance to combined antiretroviral therapy (cART) in HIV-1-infected individuals is typically due to nonsynonymous mutations that change the protein sequence; however, the selection of synonymous or ‘silent’ mutations in the HIV-1 genome with cART has been reported. These silent K65K and K66K mutations in the HIV-1 reverse transcriptase (RT) occur in over 35% of drug-experienced individuals and are highly associated with the thymidine analog mutations D67N and K70R, which confer decreased susceptibility to most nucleoside and nucleotide RT inhibitors. However, the basis for selection of these silent mutations under selective drug pressure is unknown. Using Illumina next-generation sequencing, we demonstrate that the D67N/K70R substitutions in HIV-1 RT increase indel frequency by 100-fold at RT codons 65–67, consequently impairing viral fitness. Introduction of either K65K or K66K into HIV-1 containing D67N/K70R reversed the error-prone DNA synthesis at codons 65–67 in RT and improved viral replication fitness, but did not impact RT inhibitor drug susceptibility. These data provide new mechanistic insights into the role of silent mutations selected during antiretroviral therapy and have broader implications for the relevance of silent mutations in the evolution and fitness of RNA viruses.
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Affiliation(s)
- Sushama Telwatte
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Anna C Hearps
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia Department of Infectious Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Adam Johnson
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Catherine F Latham
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Katie Moore
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Paul Agius
- Centre for Population Health, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Mary Tachedjian
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria 3220, Australia
| | - Secondo Sonza
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicolas Sluis-Cremer
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z1Y6, Canada
| | - Gilda Tachedjian
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia Department of Infectious Diseases, Monash University, Melbourne, Victoria 3004, Australia Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
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Emerging antiretroviral drug resistance in sub-Saharan Africa: novel affordable technologies are needed to provide resistance testing for individual and public health benefits. AIDS 2014; 28:2643-8. [PMID: 25493592 DOI: 10.1097/qad.0000000000000502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. AIDS 2014; 28:F1-8. [PMID: 25259833 DOI: 10.1097/qad.0000000000000485] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The subtype A variant in the Former Soviet Union (A(FSU)) causes most of Russia's HIV-1 infections. However, the spectrum of drug-resistance mutations (DRMs) in antiretroviral experienced patients with this variant has not been studied. METHODS Between 2010 and 2013, genotypic resistance testing was performed on plasma samples from 366 antiretroviral-experienced patients in Siberia. RESULTS Three-hundred patients (82%) had subtype A(FSU) and 55 (15%) had CRF02_AG viruses. The pattern of DRMs was consistent with patient antiretroviral history with one exception. G190S was the most common nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, occurring in 55 (33%) subtype A(FSU) viruses from 167 NNRTI-experienced patients compared with none of 37 CRF02_AG viruses from NNRTI-experienced patients (P < 0.001). The next most common subtype A(FSU) NNRTI-resistance mutation, K103N, occurred in 25 (15%) viruses. Wild-type glycine (G) at position 190 is encoded by GGC in more than 99% of published A(FSU) strains. By contrast, G190 is encoded by GGA or GGG in 97% of other subtypes and in subtype A strains outside of the FSU. Therefore, G190S results from a single G→A transition: G (GGC) → S (AGC) almost exclusively in subtype A(FSU) viruses. CONCLUSION The predisposition of subtype A(FSU) to G190S is concerning because G→A is the most common HIV-1 mutation and because G190S causes higher levels of nevirapine and efavirenz resistance than K103N. This study exemplifies the need for characterizing the genetic mechanisms of resistance in diverse populations and warrants studies to verify that NRTI/NNRTI regimens are as efficacious in treating subtype A(FSU) as viruses belonging to other subtypes.
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Impact of human immunodeficiency virus type-1 sequence diversity on antiretroviral therapy outcomes. Viruses 2014; 6:3855-72. [PMID: 25333465 PMCID: PMC4213566 DOI: 10.3390/v6103855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 12/04/2022] Open
Abstract
Worldwide circulating HIV-1 genomes show extensive variation represented by different subtypes, polymorphisms and drug-resistant strains. Reports on the impact of sequence variation on antiretroviral therapy (ART) outcomes are mixed. In this review, we summarize relevant published data from both resource-rich and resource-limited countries in the last 10 years on the impact of HIV-1 sequence diversity on treatment outcomes. The prevalence of transmission of drug resistant mutations (DRMs) varies considerably, ranging from 0% to 27% worldwide. Factors such as geographic location, access and availability to ART, duration since inception of treatment programs, quality of care, risk-taking behaviors, mode of transmission, and viral subtype all dictate the prevalence in a particular geographical region. Although HIV-1 subtype may not be a good predictor of treatment outcome, review of emerging evidence supports the fact that HIV-1 genome sequence-resulting from natural polymorphisms or drug-associated mutations-matters when it comes to treatment outcomes. Therefore, continued surveillance of drug resistant variants in both treatment-naïve and treatment-experienced populations is needed to reduce the transmission of DRMs and to optimize the efficacy of the current ART armamentarium.
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Singh K, Flores JA, Kirby KA, Neogi U, Sonnerborg A, Hachiya A, Das K, Arnold E, McArthur C, Parniak M, Sarafianos SG. Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors. Viruses 2014; 6:3535-62. [PMID: 25254383 PMCID: PMC4189038 DOI: 10.3390/v6093535] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
Human immunodeficiency virus (HIV) causes approximately 2.5 million new infections every year, and nearly 1.6 million patients succumb to HIV each year. Several factors, including cross-species transmission and error-prone replication have resulted in extraordinary genetic diversity of HIV groups. One of these groups, known as group M (main) contains nine subtypes (A-D, F-H and J-K) and causes ~95% of all HIV infections. Most reported data on susceptibility and resistance to anti-HIV therapies are from subtype B HIV infections, which are prevalent in developed countries but account for only ~12% of all global HIV infections, whereas non-B subtype HIV infections that account for ~88% of all HIV infections are prevalent primarily in low and middle-income countries. Although the treatments for subtype B infections are generally effective against non-B subtype infections, there are differences in response to therapies. Here, we review how polymorphisms, transmission efficiency of drug-resistant strains, and differences in genetic barrier for drug resistance can differentially alter the response to reverse transcriptase-targeting therapies in various subtypes.
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Affiliation(s)
- Kamalendra Singh
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Jacqueline A Flores
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Karen A Kirby
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Atsuko Hachiya
- Clinical Research Center, Department of Infectious Diseases and Immunology, National Hospital Organization, Nagoya Medical Center, Nagoya 460-0001, Japan.
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Carole McArthur
- Department of Oral and Craniofacial Science , School of Dentistry, University of Missouri, Kansas City, MO 64108, USA.
| | - Michael Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Stefan G Sarafianos
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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Liegler T, Abdel-Mohsen M, Bentley LG, Atchison R, Schmidt T, Javier J, Mehrotra M, Eden C, Glidden DV, McMahan V, Anderson PL, Li P, Wong JK, Buchbinder S, Guanira JV, Grant RM. HIV-1 drug resistance in the iPrEx preexposure prophylaxis trial. J Infect Dis 2014; 210:1217-27. [PMID: 24740633 PMCID: PMC4176446 DOI: 10.1093/infdis/jiu233] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The iPrEx study demonstrated that combination oral emtricitabine and tenofovir disoproxil fumarate (FTC/TDF) as preexposure prophylaxis (PrEP) protects against HIV acquisition in men who have sex with men and transgender women. Selection for drug resistance could offset PrEP benefits. METHODS Phenotypic and genotypic clinical resistance assays characterized major drug resistant mutations. Minor variants with FTC/TDF mutations K65R, K70E, M184V/I were measured using 454 deep sequencing and a novel allele-specific polymerase chain reaction (AS-PCR) diagnostic tolerant to sequence heterogeneity. RESULTS Control of primer-binding site heterogeneity resulted in improved accuracy of minor variant measurements by AS-PCR. Of the 48 on-study infections randomized to FTC/TDF, none showed FTC/TDF mutations by clinical assays despite detectable drug levels in 8 participants. Two randomized to FTC/TDF had minor variant M184I detected at 0.53% by AS-PCR or 0.75% by deep sequencing, only 1 of which had low but detectable drug levels. Among those with acute infection at randomization to FTC/TDF, M184V or I mutations that were predominant at seroconversion waned to background levels within 24 weeks after discontinuing drug. CONCLUSIONS Drug resistance was rare in iPrEx on-study FTC/TDF-randomized seroconverters, and only as low-frequency minor variants. FTC resistance among those initiating PrEP with acute infection waned rapidly after drug discontinuation. Clinical Trials Registration.NCT00458393.
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Affiliation(s)
- Teri Liegler
- Department of Medicine, University of California AIDS Research Institute, University of California
| | | | | | | | | | | | | | | | - David V Glidden
- Department of Epidemiology, University of California, San Francisco
| | | | - Peter L Anderson
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora
| | - Peilin Li
- Veterans Affairs Medical Center, San Francisco
| | | | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, California
| | | | - Robert M Grant
- Department of Medicine, University of California J. David Gladstone Institutes
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Heredia A, Davis CE, Reitz MS, Le NM, Wainberg MA, Foulke JS, Wang LX, Redfield RR. Targeting of the purine biosynthesis host cell pathway enhances the activity of tenofovir against sensitive and drug-resistant HIV-1. J Infect Dis 2013; 208:2085-94. [PMID: 23922365 PMCID: PMC3836462 DOI: 10.1093/infdis/jit395] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 06/11/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Targeting host-cell pathways to increase the potency of nucleoside/nucleotide analog reverse transcriptase inhibitors (NRTIs) is an important strategy for clinical investigation. Resveratrol is a natural product that inhibits cellular ribonucleotide reductase, prolonging the S phase of the cell cycle and preferentially lowering dATP levels. METHODS We performed in vitro evaluation of resveratrol on the antiviral activity of adenosine analog tenofovir (TFV) against sensitive and drug-resistant human immunodeficiency virus type 1 (HIV-1), from subtypes B and C, in primary cells. RESULTS Resveratrol enhanced the antiviral activity of TFV by up to 10-fold and restored susceptibility of TFV-resistant viruses. Resveratrol prevented wild-type HIV-1 from developing phenotypic resistance to TFV. Notably, resveratrol enhanced TFV activity against sensitive and resistant HIV-1 from both subtypes B and C. CONCLUSIONS Prolonged wide-scale use of thymidine analogs in the setting of viral failure has limited the efficacy of second-line NRTI-based regimens in Africa. Moreover, the extensive use of ddI and d4T has led to high frequencies of the K65R mutation, further compromising TFV efficacy. In light of increasing resistance to commonly used NRTIs in global HIV treatment programs, targeting nucleoside biosynthesis with resveratrol, or derivatives with improved bioavailabilities, is a potential strategy to maintain, enhance, and restore susceptibility of commonly used NRTIs.
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Affiliation(s)
- Alonso Heredia
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Charles E. Davis
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Marvin S. Reitz
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Nhut M. Le
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Mark A. Wainberg
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - James S. Foulke
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Lai-Xi Wang
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Robert R. Redfield
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
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McCallum M, Oliveira M, Ibanescu RI, Kramer VG, Moisi D, Asahchop EL, Brenner BG, Harrigan PR, Xu H, Wainberg MA. Basis for early and preferential selection of the E138K mutation in HIV-1 reverse transcriptase. Antimicrob Agents Chemother 2013; 57:4681-8. [PMID: 23856772 PMCID: PMC3811420 DOI: 10.1128/aac.01029-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/05/2013] [Indexed: 12/13/2022] Open
Abstract
E138K, a G→A mutation in HIV-1 reverse transcriptase (RT), is preferentially selected by etravirine (ETR) and rilpivirine over other substitutions at position E138 that offer greater drug resistance. We hypothesized that there was a mutational bias for the E138K substitution and designed an allele-specific PCR to monitor the emergence of E138A/G/K/Q/R/V during ETR selection experiments. We also performed competition experiments using mutated viruses and quantified the prevalence of E138 minority species in drug-naive patients. E138K, as well as E138G, consistently emerged first during ETR selection experiments, followed by E138A and E138Q; E138R was never selected. Surprisingly, E138K was identified as a tiny minority in 23% of drug-naive subtype B patients, a result confirmed by ultradeep sequencing (UDS). This result could reflect a low fitness cost of E138K; however, E138K was one of the least fit substitutions at codon E138, even after taking into account the deoxynucleoside triphosphate pools of the cells used in competition experiments. Further UDS analysis revealed other minority species in a pattern consistent with the mutational bias of HIV RT. There was no evidence of APOBEC3-hypermutation in these selection experiments or in patients. Our results confirm the mutational bias of HIV-1 in patients and highlight the importance of G→A mutations in HIV-1 drug resistance evolution.
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Affiliation(s)
- Matthew McCallum
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Victor G. Kramer
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniela Moisi
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Eugene L. Asahchop
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Bluma G. Brenner
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - P. Richard Harrigan
- BC Center for Excellence in HIV/AIDS, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hongtao Xu
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A. Wainberg
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
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Tang MW, Rhee SY, Bertagnolio S, Ford N, Holmes S, Sigaloff KC, Hamers RL, de Wit TFR, Fleury HJ, Kanki PJ, Ruxrungtham K, Hawkins CA, Wallis CL, Stevens W, van Zyl GU, Manosuthi W, Hosseinipour MC, Ngo-Giang-Huong N, Belec L, Peeters M, Aghokeng A, Bunupuradah T, Burda S, Cane P, Cappelli G, Charpentier C, Dagnra AY, Deshpande AK, El-Katib Z, Eshleman SH, Fokam J, Gody JC, Katzenstein D, Koyalta DD, Kumwenda JJ, Lallemant M, Lynen L, Marconi VC, Margot NA, Moussa S, Ndung'u T, Nyambi PN, Orrell C, Schapiro JM, Schuurman R, Sirivichayakul S, Smith D, Zolfo M, Jordan MR, Shafer RW. Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine. J Infect Dis 2013; 207 Suppl 2:S70-7. [PMID: 23687292 DOI: 10.1093/infdis/jit114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The World Health Organization Antiretroviral Treatment Guidelines recommend phasing-out stavudine because of its risk of long-term toxicity. There are two mutational pathways of stavudine resistance with different implications for zidovudine and tenofovir cross-resistance, the primary candidates for replacing stavudine. However, because resistance testing is rarely available in resource-limited settings, it is critical to identify the cross-resistance patterns associated with first-line stavudine failure. METHODS We analyzed HIV-1 resistance mutations following first-line stavudine failure from 35 publications comprising 1,825 individuals. We also assessed the influence of concomitant nevirapine vs. efavirenz, therapy duration, and HIV-1 subtype on the proportions of mutations associated with zidovudine vs. tenofovir cross-resistance. RESULTS Mutations with preferential zidovudine activity, K65R or K70E, occurred in 5.3% of individuals. Mutations with preferential tenofovir activity, ≥ two thymidine analog mutations (TAMs) or Q151M, occurred in 22% of individuals. Nevirapine increased the risk of TAMs, K65R, and Q151M. Longer therapy increased the risk of TAMs and Q151M but not K65R. Subtype C and CRF01_AE increased the risk of K65R, but only CRF01_AE increased the risk of K65R without Q151M. CONCLUSIONS Regardless of concomitant nevirapine vs. efavirenz, therapy duration, or subtype, tenofovir was more likely than zidovudine to retain antiviral activity following first-line d4T therapy.
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Affiliation(s)
- Michele W Tang
- Division Infectious Diseases, Department of Medicine, Stanford University, California 94305, USA.
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Santoro MM, Perno CF. HIV-1 Genetic Variability and Clinical Implications. ISRN MICROBIOLOGY 2013; 2013:481314. [PMID: 23844315 PMCID: PMC3703378 DOI: 10.1155/2013/481314] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
Despite advances in antiretroviral therapy that have revolutionized HIV disease management, effective control of the HIV infection pandemic remains elusive. Beyond the classic non-B endemic areas, HIV-1 non-B subtype infections are sharply increasing in previous subtype B homogeneous areas such as Europe and North America. As already known, several studies have shown that, among non-B subtypes, subtypes C and D were found to be more aggressive in terms of disease progression. Luckily, the response to antiretrovirals against HIV-1 seems to be similar among different subtypes, but these results are mainly based on small or poorly designed studies. On the other hand, differences in rates of acquisition of resistance among non-B subtypes are already being observed. This different propensity, beyond the type of treatment regimens used, as well as access to viral load testing in non-B endemic areas seems to be due to HIV-1 clade specific peculiarities. Indeed, some non-B subtypes are proved to be more prone to develop resistance compared to B subtype. This phenomenon can be related to the presence of subtype-specific polymorphisms, different codon usage, and/or subtype-specific RNA templates. This review aims to provide a complete picture of HIV-1 genetic diversity and its implications for HIV-1 disease spread, effectiveness of therapies, and drug resistance development.
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Affiliation(s)
- Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- INMI L Spallanzani Hospital, Antiretroviral Therapy Monitoring Unit, Via Portuense 292, 00149 Rome, Italy
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Invernizzi CF, Coutsinos D, Oliveira M, Schildknecht RS, Xu H, Gaseitsiwe S, Moisi D, Brenner BG, Wainberg MA. The preferential selection of K65R in HIV-1 subtype C is attenuated by nucleotide polymorphisms at thymidine analogue mutation sites. J Antimicrob Chemother 2013; 68:2192-6. [PMID: 23749954 DOI: 10.1093/jac/dkt204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We recently reported the preferential selection of the K65R resistance mutation in subtype C HIV-1 compared with subtype B and showed the underlying mechanism to be dependent on subtype C-specific silent nucleotide polymorphisms, i.e. genomic mutations that change the genotype but not the phenotype. The number of clinical reports demonstrating elevated numbers of K65R nevertheless suggests the existence of factors limiting the increased incidence of K65R mutations. Thus, we investigated the contributions of subtype C-specific silent nucleotide polymorphisms at thymidine analogue mutation (TAM) sites 70, 210 and/or 219 that might reduce the previously described preferential selection of K65R in subtype C HIV-1 associated with subtype C-specific nucleotide polymorphisms at sites 64/65. METHODS Cell culture drug selections were performed with various drugs in MT2 cells. RESULTS The use of nucleoside/nucleotide reverse transcriptase inhibitors [N(t)RTIs] as single drugs or in combination confirmed the more frequent selection of K65R by multiple N(t)RTIs in a subtype B virus that contained the 64/65 nucleotide polymorphisms of subtype C than in a wild-type subtype B virus. This effect was attenuated in the presence of several silent TAM nucleotide polymorphisms, except when stavudine was employed in the selection protocol. CONCLUSIONS These results further demonstrate that stavudine can preferentially select for K65R in subtype C virus and also provide a basis for understanding the importance of silent nucleotide polymorphisms in regard to altered HIV drug resistance profiles.
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Affiliation(s)
- Cédric F Invernizzi
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
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Das K, Arnold E. HIV-1 reverse transcriptase and antiviral drug resistance. Part 2. Curr Opin Virol 2013; 3:119-28. [PMID: 23602470 DOI: 10.1016/j.coviro.2013.03.014] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/12/2013] [Accepted: 03/20/2013] [Indexed: 11/29/2022]
Abstract
Structures of RT and its complexes combined with biochemical and clinical data help in illuminating the molecular mechanisms of different drug-resistance mutations. The NRTI drugs that are used in combinations have different primary mutation sites. RT mutations that confer resistance to one drug can be hypersensitive to another RT drug. Structure of an RT-DNA-nevirapine complex revealed how NNRTI binding forbids RT from forming a polymerase competent complex. Collective knowledge about various mechanisms of drug resistance by RT has broader implications for understanding and targeting drug resistance in general. In Part 1, we discussed the role of RT in developing HIV-1 drug resistance, structural and functional states of RT, and the nucleoside/nucleotide analog (NRTI) and non-nucleoside (NNRTI) drugs used in treating HIV-1 infections. In this part, we discuss structural understanding of various mechanisms by which RT confers antiviral drug resistance.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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Menéndez-Arias L. Molecular basis of human immunodeficiency virus type 1 drug resistance: overview and recent developments. Antiviral Res 2013; 98:93-120. [PMID: 23403210 DOI: 10.1016/j.antiviral.2013.01.007] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/26/2013] [Accepted: 01/29/2013] [Indexed: 12/15/2022]
Abstract
The introduction of potent combination therapies in the mid-90s had a tremendous effect on AIDS mortality. However, drug resistance has been a major factor contributing to antiretroviral therapy failure. Currently, there are 26 drugs approved for treating human immunodeficiency virus (HIV) infections, although some of them are no longer prescribed. Most of the available antiretroviral drugs target HIV genome replication (i.e. reverse transcriptase inhibitors) and viral maturation (i.e. viral protease inhibitors). Other drugs in clinical use include a viral coreceptor antagonist (maraviroc), a fusion inhibitor (enfuvirtide) and two viral integrase inhibitors (raltegravir and elvitegravir). Elvitegravir and the nonnucleoside reverse transcriptase inhibitor rilpivirine have been the most recent additions to the antiretroviral drug armamentarium. An overview of the molecular mechanisms involved in antiretroviral drug resistance and the role of drug resistance-associated mutations was previously presented (Menéndez-Arias, L., 2010. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res. 85, 210-231). This article provides now an updated review that covers currently approved drugs, new experimental agents (e.g. neutralizing antibodies) and selected drugs in preclinical or early clinical development (e.g. experimental integrase inhibitors). Special attention is dedicated to recent research on resistance to reverse transcriptase and integrase inhibitors. In addition, recently discovered interactions between HIV and host proteins and novel strategies to block HIV assembly or viral entry emerge as promising alternatives for the development of effective antiretroviral treatments.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa"-Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain.
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Bansode V, McCormack GP, Crampin AC, Ngwira B, Shrestha RK, French N, Glynn JR, Travers SA. Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing. BMC Infect Dis 2013; 13:52. [PMID: 23363532 PMCID: PMC3740783 DOI: 10.1186/1471-2334-13-52] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 01/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The role of HIV-1 RNA in the emergence of resistance to antiretroviral therapies (ARTs) is well documented while less is known about the role of historical viruses stored in the proviral DNA. The primary focus of this work was to characterize the genetic diversity and evolution of HIV drug resistant variants in an individual's provirus during antiretroviral therapy using next generation sequencing. METHODS Blood samples were collected prior to antiretroviral therapy exposure and during the course of treatment from five patients in whom drug resistance mutations had previously been identified using consensus sequencing. The spectrum of viral variants present in the provirus at each sampling time-point were characterized using 454 pyrosequencing from multiple combined PCR products. The prevalence of viral variants containing drug resistant mutations (DRMs) was characterized at each time-point. RESULTS Low abundance drug resistant viruses were identified in 14 of 15 sampling time-points from the five patients. In all individuals DRMs against current therapy were identified at one or more of the sampling time-points. In two of the five individuals studied these DRMs were present prior to treatment exposure and were present at high prevalence within the amplified and sequenced viral population. DRMs to drugs other than those being currently used were identified in four of the five individuals. CONCLUSION The presence of DRMs in the provirus, regardless of their observed prevalence did not appear to have an effect on clinical outcomes in the short term suggesting that the drug resistant viral variants present in the proviral DNA do not appear to play a role in the short term in facilitating the emergence of drug resistance.
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Affiliation(s)
- Vijay Bansode
- Molecular Evolution and Systematics laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Grace P McCormack
- Molecular Evolution and Systematics laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Amelia C Crampin
- Karonga Prevention Study, Chilumba, Malawi, South Africa
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Bagrey Ngwira
- Karonga Prevention Study, Chilumba, Malawi, South Africa
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Ram K Shrestha
- South African National Bioinformatics Institute, University of the Western, Cape, Bellville, South Africa
| | - Neil French
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Simon A Travers
- South African National Bioinformatics Institute, University of the Western, Cape, Bellville, South Africa
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Emerging HIV-1 drug resistance after roll-out of antiretroviral therapy in sub-Saharan Africa. Curr Opin HIV AIDS 2013; 8:19-26. [DOI: 10.1097/coh.0b013e32835b7f94] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gonzalez S, Tully DC, Gondwe C, Wood C. Low-abundance resistant mutations in HIV-1 subtype C antiretroviral therapy-naive individuals as revealed by pyrosequencing. Curr HIV Res 2013; 11:43-49. [PMID: 23305169 PMCID: PMC4005869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 06/01/2023]
Abstract
Given the recent scale-up of antiretroviral therapy (ART) in sub-Saharan Africa, we sought to determine how often and at what levels do drug-resistant mutant variants exist in ART-naive HIV subtype C infected individuals. Samples from 10 ART-naive Zambian individuals were subjected to ultra-deep pyrosequencing (UDPS) to characterize the frequency of low-abundance drug resistance mutations in the pol gene. Low-abundance clinically relevant variants were detected for nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) in eight of the ten subjects. Intermediate to high-level resistance was predicted for the majority of NRTIs. Mutations conferring resistance to most first-line and some second-line therapy drugs were also observed. UDPS detected a number of additional major resistant mutations suggesting that these individuals may have an increased risk of virological failure after initiating ART. Moreover, the effectiveness of first-line and even some secondline ART may be compromised in this setting.
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Affiliation(s)
- Sandra Gonzalez
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, 4240 Fair St, Lincoln, NE 68583-0900, USA
| | - Damien C. Tully
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, 4240 Fair St, Lincoln, NE 68583-0900, USA
| | - Clement Gondwe
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, 4240 Fair St, Lincoln, NE 68583-0900, USA
- Virology Department, University Teaching Hospital, P.O. Box 50223, Lusaka, 10101, Zambia
| | - Charles Wood
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, 4240 Fair St, Lincoln, NE 68583-0900, USA
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Abstract
The efficacy of an antiretroviral (ARV) treatment regimen depends on the activity of the regimen's individual ARV drugs and the number of HIV-1 mutations required for the development of resistance to each ARV - the genetic barrier to resistance. ARV resistance impairs the response to therapy in patients with transmitted resistance, unsuccessful initial ARV therapy and multiple virological failures. Genotypic resistance testing is used to identify transmitted drug resistance, provide insight into the reasons for virological failure in treated patients, and help guide second-line and salvage therapies. In patients with transmitted drug resistance, the virological response to a regimen selected on the basis of standard genotypic testing approaches the responses observed in patients with wild-type viruses. However, because such patients are at a higher risk of harbouring minority drug-resistant variants, initial ARV therapy in this population should contain a boosted protease inhibitor (PI) - the drug class with the highest genetic barrier to resistance. In patients receiving an initial ARV regimen with a high genetic barrier to resistance, the most common reasons for virological failure are nonadherence and, potentially, pharmacokinetic factors or minority transmitted drug-resistant variants. Among patients in whom first-line ARVs have failed, the patterns of drug-resistance mutations and cross-resistance are often predictable. However, the extent of drug resistance correlates with the duration of uncontrolled virological replication. Second-line therapy should include the continued use of a dual nucleoside/nucleotide reverse transcriptase inhibitor (NRTI)-containing backbone, together with a change in the non-NRTI component, most often to an ARV belonging to a new drug class. The number of available fully active ARVs is often diminished with each successive treatment failure. Therefore, a salvage regimen is likely to be more complicated in that it may require multiple ARVs with partial residual activity and compromised genetic barriers of resistance to attain complete virological suppression. A thorough examination of the patient's ARV history and prior resistance tests should be performed because genotypic and/or phenotypic susceptibility testing is often not sufficient to identify drug-resistant variants that emerged during past therapies and may still pose a threat to a new regimen. Phenotypic testing is also often helpful in this subset of patients. ARVs used for salvage therapy can be placed into the following hierarchy: (i) ARVs belonging to a previously unused drug class; (ii) ARVs belonging to a previously used drug class that maintain significant residual antiviral activity; (iii) NRTI combinations, as these often appear to retain in vivo virological activity, even in the presence of reduced in vitro NRTI susceptibility; and rarely (iv) ARVs associated with previous virological failure and drug resistance that appear to have possibly regained their activity as a result of viral reversion to wild type. Understanding the basic principles of HIV drug resistance is helpful in guiding individual clinical decisions and the development of ARV treatment guidelines.
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Affiliation(s)
- Michele W Tang
- Stanford University, Division of Infectious Diseases, Stanford, CA 94305-5107, USA.
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Götte M. The distinct contributions of fitness and genetic barrier to the development of antiviral drug resistance. Curr Opin Virol 2012; 2:644-50. [DOI: 10.1016/j.coviro.2012.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 08/15/2012] [Indexed: 01/14/2023]
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Santoro MM, Alteri C, Ronga L, Flandre P, Fabeni L, Mercurio F, D'Arrigo R, Gori C, Palamara G, Bertoli A, Forbici F, Salpini R, Boumis E, Tozzi V, Visco-Comandini U, Zaccarelli M, Van Houtte M, Pattery T, Narciso P, Antinori A, Ceccherini-Silberstein F, Perno CF. Comparative analysis of drug resistance among B and the most prevalent non-B HIV type 1 subtypes (C, F, and CRF02_AG) in Italy. AIDS Res Hum Retroviruses 2012; 28:1285-93. [PMID: 22417570 DOI: 10.1089/aid.2011.0142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, increasing numbers of patients infected with HIV-1 non-B subtypes have been treated with modern antiretroviral regimens. Therefore, a better knowledge of HIV drug resistance in non-B strains is crucial. Thus, we compared the mutational pathways involved in drug resistance among the most common non-B subtypes in Italy (F, C, and CRF02_AG) and the B subtype. In total, 2234 pol sequences from 1231 virologically failing patients from Central Italy were analyzed. The prevalence of resistance mutations in protease and reverse transcriptase between non-B and B subtypes has been evaluated. Among patients treated with nucleoside/nucleotide reverse transcriptase inhibitors (NRTI) and with thymidine analogues (TA) experience, TAMs1 M41L and L210W were less prevalent in CRF02_AG, while TAMs2 T215F and K219E were more prevalent in the F subtype. In NRTI-treated patients having experience with abacavir, didanosine, tenofovir, or stavudine the K65R mutation was mostly prevalent in the C subtype. In non-NRTI (NNRTI)-treated patients infected by the C subtype the prevalence of K103N was lower than in patients infected with other subtypes, while the prevalence of Y181C and Y188L was higher compared to subtype B. The prevalence of Y181C was higher also in subtype F as compared to subtype B. In patients treated with protease inhibitors, L89V was predominantly found in CRF02_AG, while the TPV resistance mutation T74P was predominantly found in the C subtype. Some differences in the genotypic drug resistance have been found among patients infected with B, C, F, and CRF02_AG subtypes in relationship to treatment. These results may be useful for the therapeutic management of individuals infected with HIV-1 non-B strains.
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Affiliation(s)
- Maria Mercedes Santoro
- University of Rome Tor Vergata, Experimental Medicine and Biochemical Sciences, Rome, Italy
| | - Claudia Alteri
- University of Rome Tor Vergata, Experimental Medicine and Biochemical Sciences, Rome, Italy
| | - Luigi Ronga
- University of Rome Tor Vergata, Experimental Medicine and Biochemical Sciences, Rome, Italy
- Department of Pathology and Laboratory Medicine, Section of Microbiology, University of Parma, Parma, Italy
| | | | | | - Fabio Mercurio
- University of Rome Tor Vergata, Experimental Medicine and Biochemical Sciences, Rome, Italy
| | | | | | | | - Ada Bertoli
- University Hospital Tor Vergata, Molecular Virology, Rome, Italy
| | | | - Romina Salpini
- University of Rome Tor Vergata, Experimental Medicine and Biochemical Sciences, Rome, Italy
| | | | | | | | | | | | | | | | | | | | - Carlo Federico Perno
- University of Rome Tor Vergata, Experimental Medicine and Biochemical Sciences, Rome, Italy
- INMI L Spallanzani, Rome, Italy
- University Hospital Tor Vergata, Molecular Virology, Rome, Italy
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Intersubtype differences in the effect of a rare p24 gag mutation on HIV-1 replicative fitness. J Virol 2012; 86:13423-33. [PMID: 23015721 DOI: 10.1128/jvi.02171-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Certain immune-driven mutations in HIV-1, such as those arising in p24(Gag), decrease viral replicative capacity. However, the intersubtype differences in the replicative consequences of such mutations have not been explored. In HIV-1 subtype B, the p24(Gag) M250I mutation is a rare variant (0.6%) that is enriched among elite controllers (7.2%) (P = 0.0005) and appears to be a rare escape variant selected by HLA-B58 supertype alleles (P < 0.01). In contrast, in subtype C, it is a relatively common minor polymorphic variant (10 to 15%) whose appearance is not associated with a particular HLA allele. Using site-directed mutant viruses, we demonstrate that M250I reduces in vitro viral replicative capacity in both subtype B and subtype C sequences. However, whereas in subtype C downstream compensatory mutations at p24(Gag) codons 252 and 260 reduce the adverse effects of M250I, fitness costs in subtype B appear difficult to restore. Indeed, patient-derived subtype B sequences harboring M250I exhibited in vitro replicative defects, while those from subtype C did not. The structural implications of M250I were predicted by protein modeling to be greater in subtype B versus C, providing a potential explanation for its lower frequency and enhanced replicative defects in subtype B. In addition to accounting for genetic differences between HIV-1 subtypes, the design of cytotoxic-T-lymphocyte-based vaccines may need to account for differential effects of host-driven viral evolution on viral fitness.
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Margeridon-Thermet S, Shafer RW. Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C. Viruses 2012; 2:2696-739. [PMID: 21243082 PMCID: PMC3020796 DOI: 10.3390/v2122696] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) are the most prevalent deadly chronic viral diseases. HIV is treated by small molecule inhibitors. HBV is treated by immunomodulation and small molecule inhibitors. HCV is currently treated primarily by immunomodulation but many small molecules are in clinical development. Although HIV is a retrovirus, HBV is a double-stranded DNA virus, and HCV is a single-stranded RNA virus, antiviral drug resistance complicates the development of drugs and the successful treatment of each of these viruses. Although their replication cycles, therapeutic targets, and evolutionary mechanisms are different, the fundamental approaches to identifying and characterizing HIV, HBV, and HCV drug resistance are similar. This review describes the evolution of HIV, HBV, and HCV within individuals and populations and the genetic mechanisms associated with drug resistance to each of the antiviral drug classes used for their treatment.
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High rate of K65R for antiretroviral therapy-naive patients with subtype C HIV infection failing a tenofovir-containing first-line regimen. AIDS 2012; 26:1679-84. [PMID: 22739389 DOI: 10.1097/qad.0b013e328356886d] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We sought to determine the rate of the K65R mutation in patients receiving tenofovir (TDF)-based antiretroviral therapy (ART) with subtype C HIV infection. DESIGN Retrospective cohort study. METHODS All patients initiated on stavudine (d4T) with lamivudine (3TC) or TDF with 3TC and a nonnucleoside reverse transcriptase inhibitor at McCord Hospital in Durban, South Africa had their charts reviewed. All patients with virologic failure, defined as a viral load more than 1000 copies/ml after 5 months of a first ART regimen, had genotypic resistance testing performed prospectively using a validated in-house assay. Important resistance mutations were selected based upon published mutations in subtype B virus in the Stanford HIV Drug Resistance database. RESULTS A total of 585 patients were initiated on TDF-containing first-line ART from 3 August 2010 to 17 March 2011. Thirty-five (6.0%) of these patients had virologic failure and 23 of 33 (69.7%) of the virologic failure patients had the K65R mutation. The median (interquartile range) for the baseline CD4 cell count was 105 cells/μl (49-209) and viral load at virologic failure was 47 571 copies/ml (20 708-202 000). During the same period, 53 patients were initiated on d4T-containing regimens. Two (3.8%) of these patients had virologic failure and one of the virologic failure patients had the K65R mutation. CONCLUSION Preliminary data show very high rates (>65%) of K65R for patients failing TDF-based first-line regimens at McCord Hospital with few additional nucleoside reverse transcriptase inhibitor mutations compared with subtype B. These rates may reflect faster in-vivo selection, longer time on a failing regimen or transmitted drug resistance.
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The Impact of HIV Genetic Polymorphisms and Subtype Differences on the Occurrence of Resistance to Antiretroviral Drugs. Mol Biol Int 2012; 2012:256982. [PMID: 22792462 PMCID: PMC3390109 DOI: 10.1155/2012/256982] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 04/12/2012] [Indexed: 12/20/2022] Open
Abstract
The vast majority of reports on drug resistance deal with subtype B infections in developed countries, and this is largely due to historical delays in access to antiretroviral therapy (ART) on a worldwide basis. This notwithstanding the concept that naturally occurring polymorphisms among different non-B subtypes can affect HIV-1 susceptibility to antiretroviral drugs (ARVs) is supported by both enzymatic and virological data. These findings suggest that such polymorphisms can affect both the magnitude of resistance conferred by some major mutations as well as the propensity to acquire certain resistance mutations, even though such differences are sometimes difficult to demonstrate in phenotypic assays. It is mandatory that tools are optimized to assure accurate measurements of drug susceptibility in non-B subtypes and to recognize that each subtype may have a distinct resistance profile and that differences in resistance pathways may also impact on cross-resistance and the choice of regimens to be used in second-line therapy. Although responsiveness to first-line therapy should not theoretically be affected by considerations of viral subtype and drug resistance, well-designed long-term longitudinal studies involving patients infected by viruses of different subtypes should be carried out.
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Recordon-Pinson P, Papuchon J, Reigadas S, Deshpande A, Fleury H. K65R in subtype C HIV-1 isolates from patients failing on a first-line regimen including d4T or AZT: comparison of Sanger and UDP sequencing data. PLoS One 2012; 7:e36549. [PMID: 22615779 PMCID: PMC3353948 DOI: 10.1371/journal.pone.0036549] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/09/2012] [Indexed: 12/03/2022] Open
Abstract
Background We and others have shown that subtype C HIV-1 isolates from patients failing on a regimen containing stavudine (d4T) or zidovudine (AZT) exhibit thymidine-associated mutations (TAMs) and K65R which can impair the efficacy of Tenofovir (TDF) at second line. Depending on the various studies, the prevalence of K65R substitution as determined by the Sanger method ranges from 4 to 30%. Our aim was to determine whether ultra-deep pyrosequencing (UDPS) could provide more information than the Sanger method about selection of K65R in this population of patients. Methods 27 subtype C HIV-1 isolates from treated patients failing on a regimen with d4T or AZT plus lamivudine (3TC) plus nevirapine (NVP) or efavirenz (EFV) and who had been sequenced by Sanger were investigated by UDPS at codon 65 of the reverse transcriptase (RT). 18 isolates from naïve patients and dilutions of a control K65R plasmid were analysed by Sanger plus UDPS. Results Analysis of Sanger sequences of subtype C HIV-1 isolates from naïve patients exhibited expected polymorphic substitutions compared to subtype B but no drug resistance mutations (DRMs). Quantitation of K65R variants by UDPS ranged from <0.4% to 3.08%. Sanger sequences of viral isolates from patients at failure of d4T or AZT plus 3TC plus NVP or EFV showed numerous DRMs to nucleoside reverse transcriptase inhibitors (NRTIs) including M184V, thymidine-associated mutations (TAMs) plus DRMs to non- nucleoside reverse transcriptase inhibitors (NNRTIs). Two K65R were observed by Sanger in this series of 27 samples with UDPS percentages of 27 and 87%. Other samples without K65R by Sanger exhibited quantities of K65R variants ranging from <0.4% to 0.80%, which were below the values observed in isolates from naïve patients. Conclusions While Sanger sequencing of subtype C isolates from treated patients at failure of d4T or AZT plus 3TC plus NVP or EFV exhibited numerous mutations including TAMs and 8% K65R, UDPS quantitation of K65R variants in the same series did not provide any more information than Sanger.
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Affiliation(s)
- Patricia Recordon-Pinson
- CNRS, UMR 5234, Bordeaux, France
- Laboratoire de Virologie (WHO accredited), CHU de Bordeaux, Bordeaux, France
| | - Jennifer Papuchon
- CNRS, UMR 5234, Bordeaux, France
- Laboratoire de Virologie (WHO accredited), CHU de Bordeaux, Bordeaux, France
| | - Sandrine Reigadas
- CNRS, UMR 5234, Bordeaux, France
- Laboratoire de Virologie (WHO accredited), CHU de Bordeaux, Bordeaux, France
| | | | - Hervé Fleury
- CNRS, UMR 5234, Bordeaux, France
- Laboratoire de Virologie (WHO accredited), CHU de Bordeaux, Bordeaux, France
- * E-mail:
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Hamers RL, Sigaloff KCE, Wensing AM, Wallis CL, Kityo C, Siwale M, Mandaliya K, Ive P, Botes ME, Wellington M, Osibogun A, Stevens WS, Rinke de Wit TF, Schuurman R. Patterns of HIV-1 drug resistance after first-line antiretroviral therapy (ART) failure in 6 sub-Saharan African countries: implications for second-line ART strategies. Clin Infect Dis 2012; 54:1660-9. [PMID: 22474222 DOI: 10.1093/cid/cis254] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) drug resistance may limit the benefits of antiretroviral therapy (ART). This cohort study examined patterns of drug-resistance mutations (DRMs) in individuals with virological failure on first-line ART at 13 clinical sites in 6 African countries and predicted their impact on second-line drug susceptibility. METHODS A total of 2588 antiretroviral-naive individuals initiated ART consisting of different nucleoside reverse transcriptase inhibitor (NRTI) backbones (zidovudine, stavudine, tenofovir, or abacavir, plus lamivudine or emtricitabine) with either efavirenz or nevirapine. Population sequencing after 12 months of ART was retrospectively performed if HIV RNA was >1000 copies/mL. The 2010 International Antiviral Society-USA list was used to score major DRMs. The Stanford algorithm was used to predict drug susceptibility. RESULTS HIV-1 sequences were generated for 142 participants who virologically failed ART, of whom 70% carried ≥1 DRM and 49% had dual-class resistance, with an average of 2.4 DRMs per sequence (range, 1-8). The most common DRMs were M184V (53.5%), K103N (28.9%), Y181C (15.5%), and G190A (14.1%). Thymidine analogue mutations were present in 8.5%. K65R was frequently selected by stavudine (15.0%) or tenofovir (27.7%). Among participants with ≥1 DRM, HIV-1 susceptibility was reduced in 93% for efavirenz/nevirapine, in 81% for lamivudine/emtricitabine, in 59% for etravirine/rilpivirine, in 27% for tenofovir, in 18% for stavudine, and in 10% for zidovudine. CONCLUSIONS Early failure detection limited the accumulation of resistance. After stavudine failure in African populations, zidovudine rather than tenofovir may be preferred in second-line ART. Strategies to prevent HIV-1 resistance are a global priority.
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Affiliation(s)
- Raph L Hamers
- PharmAccess Foundation, Academic Medical Center of the University of Amsterdam, The Netherlands.
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van Zyl GU, van der Merwe L, Claassen M, Zeier M, Preiser W. Antiretroviral resistance patterns and factors associated with resistance in adult patients failing NNRTI-based regimens in the Western Cape, South Africa. J Med Virol 2012; 83:1764-9. [PMID: 21837793 DOI: 10.1002/jmv.22189] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Antiretroviral drug resistance in patients failing non-nucleoside reverse transcriptase inhibitor (NNRTI)-based first-line combination antiretroviral treatment (ART) is influenced by: regimen choice, HIV-1 subtype, detection of and response to therapy failure. In order to describe resistance patterns by genotypic testing, at the time of first-line ART failure and to describe associations with having M184I/V, K65R, three or more thymidine analog mutations (TAMs) and etravirine (ETV) resistance, the prevalence of antiretroviral drug resistance associated mutations in a cross-sectional study, at two South African public health clinic settings, at the time of virologic failure (HIV-1 RNA load >400 copies/ml) are described. Also reported are associations of therapy choice, prolonged virologic failure, and concurrent HIV viral load and CD4 count with the presence of M184I/V, TAMs, K65R, and resistance to ETV. Of 167 adult patients with virologic failure on first-line ART, 28 (17%) had no resistance, 137 (82%) had NNRTI resistance, 101 (60%) M184I/V, 20 (12%) TAMs, of which 4 had 3 or more TAMs, and 7 (4%) had K65R, of which 6 were on D4T and one on AZT. A prolonged estimated period of failure was associated with having ≥3 TAMs. Patients treated with nevirapine (NVP) were more likely to have ETV resistance than those treated with efavirenz (EFV). Major protease inhibitor mutations were not detected. A delayed response to ART failure may risk accumulation of TAMs in patients on an NNRTI-based regimen. The use of NVP rather than EFV was associated with ETV resistance.
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Affiliation(s)
- Gert U van Zyl
- Division of Medical Virology, Stellenbosch University, Tygerberg, Cape Town, South Africa.
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Kozal MJ, Chiarella J, St John EP, Moreno EA, Simen BB, Arnold TE, Lataillade M. Prevalence of low-level HIV-1 variants with reverse transcriptase mutation K65R and the effect of antiretroviral drug exposure on variant levels. Antivir Ther 2012; 16:925-9. [PMID: 21900725 DOI: 10.3851/imp1851] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND It has been reported that treatment-naive individuals infected with HIV-1 subtype C may be more likely to harbour viral variants possessing a K65R reverse transcriptase gene mutation. The objectives of this study were to determine the prevalence of low-level K65R variants within different HIV-1 subtypes and to assess the effects of antiretroviral exposure on K65R variant levels. METHODS Treatment-naive individuals infected with different HIV-1 subtypes were genotyped by ultra-deep sequencing. Samples were evaluated for low-level variants to 0.4% or 1% levels depending upon viral load. Estimated mutational load was calculated by multiplying the percentage of the variant by the plasma viral load. RESULTS A total of 411 treatment-naive individuals were evaluated by ultra-deep sequencing to 1% levels; 4 subjects (0.97%) had K65R variants at ≥1% or had a very high mutation load. All four subjects had variants with linked drug resistance mutations suggesting transmitted resistant variants. 147 ARV-naive subjects were sequenced to 0.4% levels; 8.8% (13/147) had K65R low-level variants identified: 2.2% (2/92) in subtype B, 35.7% (10/28) in subtype C (P<0.001 for B versus C) and 3.7% (1/27) in non-B/C subtypes. The 13 ARV-naive subjects with K65R variants at <1% received tenofovir plus emtricitabine plus a ritonavir-boosted protease inhibitor (TDF+FTC+PI/r) and 5 subsequently experienced virological failure. There was no enhancement in K65R levels by percentage or mutational load compared to pre-therapy levels. CONCLUSIONS Low-level K65R variants were more frequently identified in subtype C. K65R variants at >1% levels likely represent transmitted resistant variants. The clinical implication of low-level K65R variants below 1% in treatment-naive subjects who receive TDF+FTC+PI/r remains to be determined as the majority are very low-level and did not increase after antiretroviral exposure.
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Affiliation(s)
- Michael J Kozal
- Yale University School of Medicine and Veterans Affairs Connecticut Healthcare System, New Haven, CT, USA.
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Wallis CL, Papathanasopolous MA, Fox M, Conradie F, Ive P, Orrell C, Zeinecker J, Sanne I, Wood R, McIntyre J, Stevens W. Low rates of nucleoside reverse transcriptase inhibitor resistance in a well-monitored cohort in South Africa on antiretroviral therapy. Antivir Ther 2011; 17:313-20. [PMID: 22293461 DOI: 10.3851/imp1985] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2011] [Indexed: 10/15/2022]
Abstract
BACKGROUND The emergence of complex HIV-1 drug resistance mutations has been linked to the duration of time patients are on a failing antiretroviral drug regimen. This study reports on resistance profiles in a closely monitored subtype C infected cohort. METHODS A total of 812 participants were enrolled into the CIPRA-SA 'safeguard the household' study, viral loads were determined at 12-weekly intervals for 96 weeks. Virological failure was defined as either a <1.5 log decrease in viral load at week 12 or two consecutive viral load measurements of >1,000 RNA copies/ml after week 24. Regimens prescribed were in line with the South African roll-out programme (stavudine, lamivudine, efavirenz or nevirapine). Viral RNA was extracted from patients with virological failure, and pol reverse-transcriptase PCR and sequence analysis were performed to determine drug-resistant mutations. RESULTS Virological failure was observed in 83 participants on the first-line regimen during the study period, of which 61 (73%) had HIV-1 drug-resistant mutations. The M184V mutation was the most frequent (n=46; 65%), followed by K103N (46%) and Y181C (21%). Thymidine analogue mutations were infrequent (1%) and Q151M was not observed. CONCLUSIONS Drug resistance profiles were less complex than has been previously reported in South Africa using the same antiretroviral drug regimens. These data suggest that frequent viral load monitoring limits the level and complexity of resistance observed in HIV-1 subtype C, preserving susceptibility to second-line options.
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Affiliation(s)
- Carole L Wallis
- University of the Witwatersrand, Johannesburg, South Africa.
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Affiliation(s)
- Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
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Lawyer G, Altmann A, Thielen A, Zazzi M, Sönnerborg A, Lengauer T. HIV-1 mutational pathways under multidrug therapy. AIDS Res Ther 2011; 8:26. [PMID: 21794106 PMCID: PMC3162516 DOI: 10.1186/1742-6405-8-26] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/27/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genotype-derived drug resistance profiles are a valuable asset in HIV-1 therapy decisions. Therapy decisions could be further improved, both in terms of predicting length of current therapy success and in preserving followup therapy options, through better knowledge of mutational pathways- here defined as specific locations on the viral genome which, when mutant, alter the risk that additional specific mutations arise. We limit the search to locations in the reverse transcriptase region of the HIV-1 genome which host resistance mutations to nucleoside (NRTI) and non-nucleoside (NNRTI) reverse transcriptase inhibitors (as listed in the 2008 International AIDS Society report), or which were mutant at therapy start in 5% or more of the therapies studied. METHODS A Cox proportional hazards model was fit to each location with the hazard of a mutation at that location during therapy proportional to the presence/absence of mutations at the remaining locations at therapy start. A pathway from preexisting to occurring mutation was indicated if the covariate was both selected as important via smoothly clipped absolute deviation (a form of regularized regression) and had a small p-value. The Cox model also allowed controlling for non-genetic parameters and potential nuisance factors such as viral resistance and number of previous therapies. Results were based on 1981 therapies given to 1495 distinct patients drawn from the EuResist database. RESULTS The strongest influence on the hazard of developing NRTI resistance was having more than four previous therapies, not any one existing resistance mutation. Known NRTI resistance pathways were shown, and previously speculated inhibition between the thymidine analog pathways was evidenced. Evidence was found for a number of specific pathways between NRTI and NNRTI resistance sites. A number of common mutations were shown to increase the hazard of developing both NRTI and NNRTI resistance. Viral resistance to the therapy compounds did not materially effect the hazard of mutation in our model. CONCLUSIONS The accuracy of therapy outcome prediction tools may be increased by including the number of previous treatments, and by considering locations in the HIV genome which increase the hazard of developing resistance mutations.
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Mascolini M, Mellors JW, Richman DD, Boucher CAB, Larder BA. HIV and hepatitis virus resistance to antivirals: review of data from the XIX International HIV and Hepatitis Virus Drug Resistance Workshop and curative strategies. Antivir Ther 2011; 16:263-86. [PMID: 21447877 DOI: 10.3851/imp1761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The XIX International HIV and Hepatitis Virus Drug Resistance Workshop offered scientists, clinical investigators, physicians and others an opportunity to present study results selected in a rigorous peer-review process and to discuss those data in an open forum. In 2010, Workshop organizers expanded the programme to include hepatitis B and C viruses, reasoning that workers in all three fields could benefit from shared experience, positive and negative. Slide sessions at the 2010 Workshop focused on hepatitis virus resistance to current and experimental antivirals; epidemiology of HIV resistance; HIV pathogenesis, fitness and resistance; resistance to new antiretrovirals; markers of response to HIV entry inhibitors; HIV persistence, reservoirs and elimination strategies; application of new viral sequencing techniques; and mechanisms of HIV drug resistance. This article summarizes all slide presentations at the Workshop.
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Ibe S, Sugiura W. Clinical significance of HIV reverse-transcriptase inhibitor-resistance mutations. Future Microbiol 2011; 6:295-315. [PMID: 21449841 DOI: 10.2217/fmb.11.7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this article, we summarize recent knowledge on drug-resistance mutations within HIV reverse transcriptase (RT). Several large-scale HIV-1 genotypic analyses have revealed that the most prevalent nucleos(t)ide analog RT inhibitor (NRTI)-resistance mutation is M184V/I followed by a series of thymidine analog-associated mutations: M41L, D67N, K70R, L210W, T215Y/F and K219Q/E. Among non-nucleoside RT inhibitor (NNRTI)-resistance mutations, K103N was frequently observed, followed by Y181C and G190A. Interestingly, V106M was identified in HIV-1 subtype C as a subtype-specific multi-NNRTI-resistance mutation. Regarding mutations in the HIV-1 RT C-terminal region, including the connection subdomain and RNase H domain, their clinical impacts are still controversial, although their effects on NRTI and NNRTI resistance have been confirmed in vitro. In HIV-2 infections, the high prevalence of the Q151M mutation associated with multi-NRTI resistance has been frequently observed.
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Affiliation(s)
- Shiro Ibe
- Department of Infection & Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
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50
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Coutsinos D, Invernizzi CF, Moisi D, Oliveira M, Martinez-Cajas JL, Brenner BG, Wainberg MA. A template-dependent dislocation mechanism potentiates K65R reverse transcriptase mutation development in subtype C variants of HIV-1. PLoS One 2011; 6:e20208. [PMID: 21655292 PMCID: PMC3105016 DOI: 10.1371/journal.pone.0020208] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 04/15/2011] [Indexed: 01/11/2023] Open
Abstract
Numerous studies have suggested that the K65R reverse transcriptase (RT) mutation develops more readily in subtype C than subtype B HIV-1. We recently showed that this discrepancy lies partly in the subtype C template coding sequence that predisposes RT to pause at the site of K65R mutagenesis. However, the mechanism underlying this observation and the elevated rates of K65R development remained unknown. Here, we report that DNA synthesis performed with subtype C templates consistently produced more K65R-containing transcripts than subtype B templates, regardless of the subtype-origin of the RT enzymes employed. These findings confirm that the mechanism involved is template-specific and RT-independent. In addition, a pattern of DNA synthesis characteristic of site-specific primer/template slippage and dislocation was only observed with the subtype C sequence. Analysis of RNA secondary structure suggested that the latter was unlikely to impact on K65R development between subtypes and that Streisinger strand slippage during DNA synthesis at the homopolymeric nucleotide stretch of the subtype C K65 region might occur, resulting in misalignment of the primer and template. Consequently, slippage would lead to a deletion of the middle adenine of codon K65 and the production of a -1 frameshift mutation, which upon dislocation and realignment of the primer and template, would lead to development of the K65R mutation. These findings provide additional mechanistic evidence for the facilitated development of the K65R mutation in subtype C HIV-1.
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Affiliation(s)
- Dimitrios Coutsinos
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
- Departments of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Cédric F. Invernizzi
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
- Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Daniela Moisi
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
| | - Maureen Oliveira
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
| | - Jorge L. Martinez-Cajas
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
- Department of Medicine, Infectious Diseases, Queen's University, Kingston, Ontario, Canada
| | - Bluma G. Brenner
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
- Departments of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Mark A. Wainberg
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
- Departments of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Department of Medicine, McGill University, Montréal, Québec, Canada
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