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Bailey AJ, Rhee SY, Shafer RW. Integrase Strand Transfer Inhibitor Resistance in Integrase Strand Transfer Inhibitor-Naive Persons. AIDS Res Hum Retroviruses 2021; 37:736-743. [PMID: 33683148 DOI: 10.1089/aid.2020.0261] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There has been no systematic review of the prevalence of transmitted integrase strand transfer inhibitor (INSTI) resistance. We systematically searched the English-language PubMed database and GenBank to identify studies published since 2010 reporting 50 or more INSTI-naive HIV-1-infected adults undergoing integrase genotyping. We extracted data related to country, sample year, specimen type, sequencing method, and subtype. For studies with sequences in GenBank, we determined the prevalence of three categories of INSTI-associated resistance mutations: (1) nonpolymorphic INSTI-selected drug resistance mutations (DRMs) that we refer to as surveillance DRMs; (2) rarely selected nonpolymorphic INSTI-associated DRMs; and (3) common polymorphic accessory INSTI-selected DRMs. A total of 103 studies met inclusion criteria including 75 studies in GenBank containing integrase sequences from 16,481 INSTI-naive persons. The median sample year was 2013 (interquartile range: 2008-2014). The prevalence of INSTI surveillance DRMs, rarely selected DRMs, and common polymorphic accessory INSTI-selected DRMs were 0.5%, 0.8%, and 6.2%, respectively. There was no association between the presence of nonpolymorphic surveillance DRM and region, sample year, or subtype. Two surveillance DRMs, E138K and R263K occurred in 0.15% and 0.10% of naive sequences, respectively. Several lines of evidence suggested that the 0.5% prevalence of surveillance DRMs partly reflects the cumulative natural occurrence of these mutations in the absence of selective drug pressure. There was an unexplained temporal increase in the proportion of sequences with polymorphic accessory mutations. The prevalence of INSTI-associated surveillance DRMs is low even in regions where INSTIs have been a major component of antiretroviral therapy for several years. The presence of INSTI-associated surveillance DRMs in INSTI-naive persons likely results from actual cases of transmitted INSTI resistance and from a low background level reflecting the cumulative rare natural occurrence of several nonpolymorphic mutations.
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Affiliation(s)
| | - Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, California, USA
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, California, USA
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Andreatta K, Willkom M, Martin R, Chang S, Wei L, Liu H, Liu YP, Graham H, Quirk E, Martin H, White KL. Switching to bictegravir/emtricitabine/tenofovir alafenamide maintained HIV-1 RNA suppression in participants with archived antiretroviral resistance including M184V/I. J Antimicrob Chemother 2020; 74:3555-3564. [PMID: 31430369 PMCID: PMC6857193 DOI: 10.1093/jac/dkz347] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/01/2019] [Accepted: 07/16/2019] [Indexed: 12/12/2022] Open
Abstract
Objectives Studies 1878 and 1844 demonstrated non-inferior efficacy of switching suppressed HIV-1-infected adults to bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) versus continuing boosted PI-based triple regimens or dolutegravir/abacavir/lamivudine (DTG/ABC/3TC). Here, detailed analyses of pre-existing resistance in the two BIC/FTC/TAF switch studies and efficacy at week 48 are described. Methods Pre-existing resistance was assessed from historical genotypes (documented resistance to study drugs was excluded) and by retrospective baseline proviral archive DNA genotyping from whole blood. Outcomes were based on HIV-1 RNA at week 48 with missing values imputed using the last on-treatment observation carried forward method. Results Cumulative pre-existing resistance data from historical and proviral genotypes were obtained for 95% (543/570) of participants who switched to BIC/FTC/TAF. Altogether, 40% (217/543) had one or more pre-existing primary resistance substitutions in protease, reverse transcriptase and/or integrase. Pre-switch NRTI resistance was detected in 16% (89/543) of BIC/FTC/TAF-treated participants, with M184V or M184I detected by proviral genotyping in 10% (54/543). At week 48, 98% (561/570) of all BIC/FTC/TAF-treated participants versus 98% (213/217) with pre-existing resistance and 96% (52/54) with archived M184V/I had HIV-1 RNA <50 copies/mL. No BIC/FTC/TAF-treated participants developed treatment-emergent resistance to study drugs. Conclusions Pre-existing resistance substitutions, notably M184V/I, were unexpectedly common among suppressed participants who switched to BIC/FTC/TAF. High rates of virological suppression were maintained in the overall study population and in those with pre-existing resistance, including M184V/I, for up to 48 weeks of BIC/FTC/TAF treatment with no resistance development. These results indicate that BIC/FTC/TAF is an effective treatment option for suppressed patients, including those with evidence of archived NRTI resistance.
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Affiliation(s)
- Kristen Andreatta
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Madeleine Willkom
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Ross Martin
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Silvia Chang
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Lilian Wei
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Hui Liu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Ya-Pei Liu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Hiba Graham
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Erin Quirk
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Hal Martin
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Kirsten L White
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
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Orta-Resendiz A, Rodriguez-Diaz RA, Angulo-Medina LA, Hernandez-Flores M, Soto-Ramirez LE. HIV-1 acquired drug resistance to integrase inhibitors in a cohort of antiretroviral therapy multi-experienced Mexican patients failing to raltegravir: a cross-sectional study. AIDS Res Ther 2020; 17:6. [PMID: 32041622 PMCID: PMC7011548 DOI: 10.1186/s12981-020-0262-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 01/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In resource-limited settings, multi-experienced HIV infected patients are often prescribed raltegravir for salvage therapy. Patients failing raltegravir-containing regimens require other drugs including other integrase inhibitors. In this context, real-life data about the resistance and cross-resistance pathways between integrase inhibitors is limited. The aim of this study was to investigate integrase resistance pathways in a cohort of Mexican multi-experienced patients failing of a raltegravir-containing salvage regimen. METHODS Twenty-five plasma samples from subjects failing antiretroviral regimens which included raltegravir were obtained from various healthcare centres from 2009 to 2017 in Mexico. Antiretroviral history and demographics were collected. Samples were processed for integrase resistance genotyping testing by sequencing. The viral sequences were analysed with the Stanford HIV drug resistance database algorithm. Data was analysed with SPSS Statistics software. RESULTS We found a mean viral load of 4.17 log10 c/mL (SD 1.11) at the time of virologic failure. Forty-eight percent of the samples were raltegravir resistant. The Y143R/H/C substitutions were the most prevalent, followed by the N155H, and both Q148H/K and G140S/A in the same proportion. The Q148 + G140 combination was found in (12%) of the samples. Cross-resistance to elvitegravir was found in 83.3% and in 18.2% for both dolutegravir and bictegravir. Thirteen samples (52%) were susceptible to the four integrase strand-transfer inhibitors. CONCLUSIONS Our findings suggest a high occurrence of resistance and cross-resistance to other integrase inhibitors among multi-experienced subjects failing raltegravir. We found a modestly lower proportion of cross-resistance to dolutegravir than data from clinical trials. Likely this drug could be used for salvage therapy. Explanations for the absence of mutations in half of the samples, other than reduced adherence, should be further investigated. Close surveillance is needed.
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Policicchio BB, Sette P, Xu C, Haret-Richter G, Dunsmore T, Pandrea I, Ribeiro RM, Apetrei C. Emergence of resistance mutations in simian immunodeficiency virus (SIV)-infected rhesus macaques receiving non-suppressive antiretroviral therapy (ART). PLoS One 2018; 13:e0190908. [PMID: 29466356 PMCID: PMC5821307 DOI: 10.1371/journal.pone.0190908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/21/2017] [Indexed: 01/31/2023] Open
Abstract
Two SIVmac251-infected rhesus macaques received tenofovir/emtricitabine with raltegravir intensification. Viral rebound occurred during treatment and sequencing of reverse transcriptase and integrase genes identified multiple resistance mutations. Similar to HIV infection, antiretroviral-resistance mutations may occur in SIV-infected nonhuman primates receiving nonsuppressive ART. As ART administration to nonhuman primates is currently dramatically expanding, fueled by both cure research and the study of HIV-related comorbidities, viral resistance should be factored in the study design and data interpretation.
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Affiliation(s)
- Benjamin Bruno Policicchio
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pennsylvania, United States of America
| | - Paola Sette
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Cuiling Xu
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - George Haret-Richter
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tammy Dunsmore
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ivona Pandrea
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pennsylvania, United States of America
- Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Laboratorio de Biomatemática, Faculdade de Medicina, Universidade de Lisbo, Lisboa, Portugal
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pennsylvania, United States of America
- Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Pham HT, Mesplède T, Wainberg MA. Effect on HIV-1 viral replication capacity of DTG-resistance mutations in NRTI/NNRTI resistant viruses. Retrovirology 2016; 13:31. [PMID: 27130466 PMCID: PMC4851780 DOI: 10.1186/s12977-016-0265-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/19/2016] [Indexed: 12/15/2022] Open
Abstract
Background Recommended regimens for HIV-positive individuals include the co-administration of dolutegravir (DTG) with two reverse transcriptase inhibitors (RTIs). Although rare, emerging resistance against DTG is often associated with the R263K substitution in integrase. In-vitro-selected R263K was associated with impaired viral replication capacity, DNA integration, and integrase strand-transfer activity, especially when accompanied by the secondary mutation H51Y. Given the reduced fitness of RTI-resistant viruses, we investigated potential impacts on viral replication of combining R263K and H51Y/R263K with major RTI-resistance substitutions including K65R, L74V, K103N, E138K, and M184I/V. Results We combined the R263K or H51Y/R263K with RTI-resistance mutations into the proviral plasmid pNL4.3 and measured the resulting viral infectiousness, replication capacity, and ability to integrate viral DNA into host cells. Infectiousness was determined by luciferase assay in TZM-bl cells. Replicative capacity was monitored over 7 days and viral DNA integration was studied by real-time Alu-qPCR in PM1 cells. We found that viral infectiousness, replication capacities and integration levels were greatly reduced in triple mutants, i.e. H51Y/R263K plus a RT mutation, and moderately reduced in double mutants, i.e. R263K plus a RT mutation, compared to wild-type and single RT-mutant viruses. Conclusions Our findings help to explain the absence of RTI mutations in individuals who experienced DTG-treatment failure.
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Affiliation(s)
- Hanh T Pham
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Côte-Ste-Catherine, Montreal, QC, H3T 1E2, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Thibault Mesplède
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Côte-Ste-Catherine, Montreal, QC, H3T 1E2, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Côte-Ste-Catherine, Montreal, QC, H3T 1E2, Canada. .,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada. .,Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, QC, Canada.
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