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De Castro N, Chazallon C, Brites C, Messou E, Khosa C, Laureillard D, Chau GD, Pilotto JH, Eholié S, Delaugerre C, Molina JM, Wittkop L, Grinsztejn B, Marcy O. Virologic response to antiretroviral therapy in people with HIV and tuberculosis in high tuberculosis burden countries. AIDS 2023; 37:1837-1842. [PMID: 36928120 DOI: 10.1097/qad.0000000000003521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
OBJECTIVE We sought to compare virologic outcomes on antiretroviral therapy (ART) between people with HIV (PWH) also treated for tuberculosis in the different countries who participated to two randomized trials. DESIGN Pooled analysis of two randomized clinical trials. METHODS In the phase II Reflate TB and phase III Reflate TB2 trials conducted in Brazil, Côte d'Ivoire, Mozambique and Vietnam, ART-naïve PWH treated for tuberculosis were randomized to receive raltegravir or efavirenz. We assessed country differences in baseline characteristic using Wilcoxon tests and chi-square, or Fisher's exact test. We used logistic regression to analyze determinants of virologic success, defined as week-48 plasma HIV-1 RNA <50 copies/ml. RESULTS Of 550 participants (140 from Brazil, 170 from Côte d'Ivoire, 129 from Mozambique and 111 from Vietnam) with median baseline HIV-1 RNA of 5.4 log 10 copies/ml, 362 (65.8%) achieved virologic success at week 48. Virologic success rates were: 105/140 (75.0%) in Brazil, 99/170 (58.2%) in Côte d'Ivoire, 84/129 (65.1%) in Mozambique and 74/111 (66.7%) in Vietnam ( P = 0.0233). Baseline HIV-1 RNA, but not the country, was independently associated with virologic success: baseline HIV-1 RNA ≥500 000 copies/ml (reference), HIV RNA <100 000 copies/ml odds ratio 3.12 [95% confidence interval (CI) 1.94; 5.01] and HIV-1 RNA 100 000-499 999 copies/ml odds ratio: 1.80 (95% CI 1.19; 2.73). Overall, 177/277 (63.9%) patients treated with raltegravir and 185/273 (67.9%) patients treated with efavirenz had a plasma HIV-1 RNA <50 copies/ml at week 48. CONCLUSIONS Virologic response to antiretroviral therapy in PWH with TB varied across countries but was mainly driven by levels of pretreatment HIV-1 RNA.
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Affiliation(s)
- Nathalie De Castro
- University of Bordeaux, National Institute for Health and Medical Research (INSERM) UMR 1219, Research Institute for Sustainable Development (IRD) EMR 271, Bordeaux Population Health Centre, Bordeaux, France
- Infectious Diseases Department, AP-HP-Hôpital Saint-Louis Lariboisière, Paris, France
| | - Corine Chazallon
- University of Bordeaux, National Institute for Health and Medical Research (INSERM) UMR 1219, Research Institute for Sustainable Development (IRD) EMR 271, Bordeaux Population Health Centre, Bordeaux, France
| | - Carlos Brites
- Laboratório de Pesquisa em Doenças Infecciosas, Hospital Universitário Prof Edgar Santos, Bahia, Brazil
| | - Eugène Messou
- Programme PACCI/ANRS Research Center
- Centre de Prise en Charge de Recherche et de Formation, CePReF-Aconda-VS, Abidjan, Cote D'Ivoire
- Département de Dermatologie et d'Infectiologie, UFR des Sciences Médicales, Université Félix Houphouët Boigny, Abidjan, Cote d'Ivoire
| | - Celso Khosa
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Didier Laureillard
- Department of Infectious and Tropical Diseases, Nimes University Hospital, Nimes
- Research Unit 1058, Pathogenesis and Control Chronical Infections, INSERM, French Blood Center, University of Montpellier, Montpellier, France
| | - Giang D Chau
- Pham Ngoc Thach Hospital, Ho Chi Minh City, Vietnam
| | - José H Pilotto
- Laboratorio de AIDS e Imunologia Molecular-IOC/Fiocruz, Rio de Janeiro, Brazil
| | - Serge Eholié
- Programme PACCI/ANRS Research Center
- Département de Dermatologie et d'Infectiologie, UFR des Sciences Médicales, Université Félix Houphouët Boigny, Abidjan, Cote d'Ivoire
| | - Constance Delaugerre
- Virology department, APHP-Hôpital Saint-Louis
- INSERM U944
- Université Paris Cité, Paris
| | - Jean-Michel Molina
- Infectious Diseases Department, AP-HP-Hôpital Saint-Louis Lariboisière, Paris, France
- INSERM U944
- Université Paris Cité, Paris
| | - Linda Wittkop
- University Bordeaux, INSERM, Institut Bergonié, Bordeaux
- INRIA SISTM team, Talence
- CHU de Bordeaux, Service d'information médicale, INSERM, Institut Bergonié, Bordeaux, France
| | - Beatriz Grinsztejn
- National Institute of Infectious Diseases Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Olivier Marcy
- University of Bordeaux, National Institute for Health and Medical Research (INSERM) UMR 1219, Research Institute for Sustainable Development (IRD) EMR 271, Bordeaux Population Health Centre, Bordeaux, France
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Ndashimye E, Reyes PS, Arts EJ. New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates? FEMS Microbiol Rev 2023; 47:fuac040. [PMID: 36130204 PMCID: PMC9841967 DOI: 10.1093/femsre/fuac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 01/21/2023] Open
Abstract
Combined HIV antiretroviral therapy (cART) has been effective except if drug resistance emerges. As cART has been rolled out in low-income countries, drug resistance has emerged at higher rates than observed in high income countries due to factors including initial use of these less tolerated cART regimens, intermittent disruptions in drug supply, and insufficient treatment monitoring. These socioeconomic factors impacting drug resistance are compounded by viral mechanistic differences by divergent HIV-1 non-B subtypes compared to HIV-1 subtype B that largely infects the high-income countries (just 10% of 37 million infected). This review compares the inhibition and resistance of diverse HIV-1 subtypes and strains to the various approved drugs as well as novel inhibitors in clinical trials. Initial sequence variations and differences in replicative fitness between HIV-1 subtypes pushes strains through different fitness landscapes to escape from drug selective pressure. The discussions here provide insight to patient care givers and policy makers on how best to use currently approved ART options and reduce the emergence of drug resistance in ∼33 million individuals infected with HIV-1 subtype A, C, D, G, and recombinants forms. Unfortunately, over 98% of the literature on cART resistance relates to HIV-1 subtype B.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
- Joint Clinical Research Centre, -Center for AIDS Research Laboratories, 256, Kampala, Uganda
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
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Gil H, Delgado E, Benito S, Moreno-Lorenzo M, Thomson MM. Factors associated with HIV-1 resistance to integrase strand transfer inhibitors in Spain: Implications for dolutegravir-containing regimens. Front Microbiol 2022; 13:1051096. [PMID: 36578581 PMCID: PMC9792149 DOI: 10.3389/fmicb.2022.1051096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Integrase strand transfer inhibitor (INSTI)-containing regimens in HIV-1-infected patients have experienced a global increase. Recently, WHO has emphasized the need to fast-track the transition to dolutegravir (DTG)-based antiretroviral (ARV) treatments. However, continued surveillance of INSTI resistance is recommended. In this study, clinical, epidemiological, and virological features associated with INSTI resistance diagnosed in Spain were analyzed. Samples collected between 2008 and 2021 from HIV-1-infected patients were analyzed in integrase, protease, and reverse transcriptase using Sanger population sequencing. ARV drug resistance was evaluated with the Stanford University HIVdb program. Among 2,696 patients, 174 (6.5%) had INSTI resistance, all of them to first-generation INSTIs, and 71 (2.6%) had also resistance to second-generation INSTIs. Of these, only 5 individuals were exposed to DTG as the only INSTI, in whom resistance development was associated with poor treatment adherence and/or resistance to other ARV classes. Of newly HIV-1-diagnosed individuals, 0.92% harbored INSTI-resistant viruses, with low prevalences maintained along time, and only one had low-level resistance to DTG. Persons who inject drugs, age over 39 years, resistance to other ARV classes, and longer time from diagnosis were associated with INSTI resistance (p < 0.001). Non-subtype B INSTI-resistant viruses lacked the Q148H + G140S resistance pathway and showed lower INSTI resistance levels than subtype B viruses. In conclusion, INSTI resistance is uncommon and associated with long-term infections, older age and additional resistance to other ARV drug classes, and is rare in newly diagnosed HIV-1 infections. Our results also support the preferential use of DTG-containing regimens in first-line treatments, although surveillance of INSTI resistance is encouraged.
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Pre-Treatment Integrase Inhibitor Resistance and Natural Polymorphisms among HIV-1 Subtype C Infected Patients in Ethiopia. Viruses 2022; 14:v14040729. [PMID: 35458459 PMCID: PMC9029575 DOI: 10.3390/v14040729] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Dolutegravir-based antiretroviral therapy (ART) has been scaled up in many developing countries, including Ethiopia. However, subtype-dependent polymorphic differences might influence the occurrence of HIV-drug-resistance mutations (HIVDRMs). We analyzed the prevalence of pre-treatment integrase strand transfer inhibitor (INSTI) HIVDRMs and naturally occurring polymorphisms (NOPs) of the integrase gene, using plasma samples collected as part of the national HIVDR survey in Ethiopia in 2017. We included a total of 460 HIV-1 integrase gene sequences from INSTI-naïve (n = 373 ART-naïve and n = 87 ART-experienced) patients. No dolutegravir-associated HIVDRMs were detected, regardless of previous exposure to ART. However, we found E92G in one ART-naïve patient specimen and accessory mutations in 20/460 (4.3%) of the specimens. Moreover, among the 288 integrase amino acid positions of the subtype C, 187/288 (64.9%) were conserved (<1.0% variability). Analysis of the genetic barrier showed that the Q148H/K/R dolutegravir resistance pathway was less selected in subtype C. Docking analysis of the dolutegravir showed that protease- and reverse-transcriptase-associated HIVDRMs did not affect the native structure of the HIV-1 integrase. Our results support the implementation of a wide scale-up of dolutegravir-based regimes. However, the detection of polymorphisms contributing to INSTI warrants the continuous surveillance of INSTI resistance.
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Sánchez D, Arazi Caillaud S, Zapiola I, Fernandez Giuliano S, Bologna R, Mangano A, Aulicino PC. Impact of genotypic diversity on selection of subtype-specific drug resistance profiles during raltegravir-based therapy in individuals infected with B and BF recombinant HIV-1 strains. J Antimicrob Chemother 2021; 75:1567-1574. [PMID: 32125378 DOI: 10.1093/jac/dkaa042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Current knowledge on HIV-1 resistance to integrase inhibitors (INIs) is based mostly on subtype B strains. This contrasts with the increasing use of INIs in low- and middle-income countries, where non-B subtypes predominate. MATERIALS AND METHODS HIV-1 drug resistance genotyping was performed in 30 HIV-1-infected individuals undergoing virological failure to raltegravir. Drug resistance mutations (DRMs) and HIV-1 subtype were characterized using Stanford HIVdb and phylogenetic analyses. RESULTS Of the 30 integrase (IN) sequences, 14 were characterized as subtype F (47%), 8 as subtype B (27%), 7 as BF recombinants (23%) and 1 as a putative CRF05_DF (3%). In 25 cases (83%), protease and reverse transcriptase (PR-RT) sequences from the same individuals confirmed the presence of different BF recombinants. Stanford HIVdb genotyping was concordant with phylogenetic inference in 70% of IN and 60% of PR-RT sequences. INI DRMs differed between B and F IN subtypes, with Q148K/R/H, G140S and E138K/A being more prevalent in subtype B (63% versus 0%, P = 0.0021; 50% versus 0%, P = 0.0096; and 50% versus 0%, P = 0.0096, respectively). These differences were independent of the time on raltegravir therapy or viral load at the time of genotyping. INI DRMs in subtype F IN genomes predicted a lower level of resistance to raltegravir and no cross-resistance to second-generation INIs. CONCLUSIONS Alternative resistance pathways to raltegravir develop in subtypes B and F IN genomes, with implications for clinical practice. Evaluating the role of HIV-1 subtype in development and persistence of mutations that confer resistance to INIs will be important to improve algorithms for resistance testing and optimize the use of INIs.
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Affiliation(s)
- Daniela Sánchez
- Laboratorio de Biología Celular y Retrovirus-CONICET, Unidad de Virología y Epidemiología Molecular, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina.,Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Solange Arazi Caillaud
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Ines Zapiola
- Unidad de Virología, Hospital de Infecciosas "Francisco J. Muñiz", Buenos Aires, Argentina
| | | | - Rosa Bologna
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus-CONICET, Unidad de Virología y Epidemiología Molecular, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus-CONICET, Unidad de Virología y Epidemiología Molecular, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
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Ojwach DBA, Madlala P, Gordon M, Ndung'u T, Mann JK. Vulnerable targets in HIV-1 Pol for attenuation-based vaccine design. Virology 2021; 554:1-8. [PMID: 33316731 PMCID: PMC7931244 DOI: 10.1016/j.virol.2020.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 11/24/2022]
Abstract
Identification of viral immune escape mutations that compromise HIV's ability to replicate may aid rational attenuation-based vaccine design. Previously we reported amino acids associated with altered viral replication capacity (RC) from a sequence-function analysis of 487 patient-derived RT-integrase sequences. In this study, site-directed mutagenesis experiments were performed to validate the effect of these mutations on RC. Viral reverse transcripts were measured by quantitative PCR and structural modelling was performed to gain further insight into the effect of reverse transcriptase (RT) mutations on reverse transcription. RT-integrase variants in or flanking cytotoxic T cell epitopes in the RT palm (158S), RT thumb (241I and 257V) and integrase catalytic core domain (124N) were confirmed to significantly reduce RC. RT mutants showed a delayed initiation of viral DNA synthesis. Structural models provide insight into how these attenuating RT mutations may affect amino acid interactions in the helix clamp, primer grip and catalytic site regions.
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Affiliation(s)
- Doty B A Ojwach
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Paradise Madlala
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle Gordon
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Africa Health Research Institute, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany; Division of Infection and Immunity, University College London, London, UK
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
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Santos-Pereira A, Magalhães C, Araújo PMM, Osório NS. Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: "The Tortoise and the Hare". Microorganisms 2021; 9:147. [PMID: 33440808 PMCID: PMC7827287 DOI: 10.3390/microorganisms9010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral "mutant cloud" is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.
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Affiliation(s)
- Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Pedro M. M. Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
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Lai A, Franzetti M, Bergna A, Saladini F, Bruzzone B, Di Giambenedetto S, Di Biagio A, Lo Caputo S, Santoro MM, Maggiolo F, Parisi SG, Rusconi S, Gianotti N, Balotta C. Marked decrease in acquired resistance to antiretrovirals in latest years in Italy. Clin Microbiol Infect 2020; 27:1038.e1-1038.e6. [PMID: 32979570 DOI: 10.1016/j.cmi.2020.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate acquired drug resistance in Italy in the 2009-2018 period. METHODS We analysed 3094 patients from the Italian ARCA database who had failed antiretroviral treatment and who had received a genotypic test after 6 months of treatment. Drug resistance mutations were identified using International AIDS Society (IAS)-USA tables and the Stanford HIVdb algorithm. The global burden of acquired resistance was calculated among all subjects with antiretroviral failure. Time trends and correlates of resistance were analysed using standard statistical tests. RESULTS Patients of non-European origin and non-B subtypes increased significantly from 11.5% (103/896) to 19.2% (33/172) and from 13.1% (141/1079) to 23.8% (53/223), respectively, over time. Overall, 14.5% (448/3094), 12.1% (374/3094) and 37.8% (1169/3094) of patients failed first, second and later lines, respectively. According to both IAS and HIVdb, in the study period resistance to any class, nucleoside reverse inhibitor, non-nucleoside reverse inhibitor, and protease inhibitors (PIs) declined significantly. Integrase strand transfer inhibitor (INSTI) resistance declined significantly from 31% (36/116) to 20.8% (41/197) according to HIVdb but not to IAS. Divergent data were highlighted regarding the proportion of non-European patients carrying any, PI and INSTI resistance using IAS tables compared with the Stanford HIVdb algorithm, as the former failed to detect a decrease in resistance while the latter indicates a reduction of 1.6-, 5- and 1.8-fold resistance for such drug classes. In the multivariate analysis, the risk of resistance increased in patients with a larger number of treatment lines and higher viraemia and decreased in those starting therapy in the last biennium of the study. DISCUSSION A marked reduction in drug resistance was observed over 10 years, compatible with higher genetic barrier and potency of new antiretrovirals. Nonetheless, concerns remain for subjects with non-B subtypes when using mutation lists instead of interpretation systems because of the extensive polymorphism of the protease region.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
| | - Marco Franzetti
- Infectious Diseases Unit, 'A. Manzoni' Hospital, Lecco, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Bianca Bruzzone
- Hygiene Unit, Policlinico San Martino Hospital, Genoa, Italy
| | - Simona Di Giambenedetto
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart of Rome, Rome, Italy
| | - Antonio Di Biagio
- Infectious Diseases Clinic, Department of Health Sciences, University of Genoa, San Martino Hospital-IRCCS, Genoa, Italy
| | - Sergio Lo Caputo
- Clinic of Infectious Diseases, University Hospital Policlinico, University of Bari, Bari, Italy
| | | | - Franco Maggiolo
- Clinic of Infectious Diseases, Ospedali Riuniti, Bergamo, Italy
| | - Saverio G Parisi
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Stefano Rusconi
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | | | - Claudia Balotta
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
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Kirichenko A, Lapovok I, Baryshev P, van de Vijver DAMC, van Kampen JJA, Boucher CAB, Paraskevis D, Kireev D. Genetic Features of HIV-1 Integrase Sub-Subtype A6 Predominant in Russia and Predicted Susceptibility to INSTIs. Viruses 2020; 12:v12080838. [PMID: 32752001 PMCID: PMC7472261 DOI: 10.3390/v12080838] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023] Open
Abstract
The increasing use of the integrase strand transfer inhibitor (INSTI) class for the treatment of HIV-infection has pointed to the importance of analyzing the features of HIV-1 subtypes for an improved understanding of viral genetic variability in the occurrence of drug resistance (DR). In this study, we have described the prevalence of INSTI DR in a Russian cohort and the genetic features of HIV-1 integrase sub-subtype A6. We included 408 HIV infected patients who were not exposed to INSTI. Drug resistance mutations (DRMs) were detected among 1.3% of ART-naïve patients and among 2.7% of INSTI-naïve patients. The prevalence of 12 polymorphic mutations was significantly different between sub-subtypes A6 and A1. Analysis of the genetic barriers determined two positions in which subtype A (A1 and A6) showed a higher genetic barrier (G140C and V151I) compared with subtype B, and one position in which subtypes A1 and B displayed a higher genetic barrier (L74M and L74I) than sub-subtype A6. Additionally, we confirmed that the L74I mutation was selected at the early stage of the epidemic and subsequently spread as a founder effect in Russia. Our data have added to the overall understanding of the genetic features of sub-subtype A6 in the context of drug resistance.
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Affiliation(s)
- Alina Kirichenko
- Central Research Institute of Epidemiology, 111123 Moscow, Russia; (I.L.); (P.B.); (D.K.)
- Correspondence:
| | - Ilya Lapovok
- Central Research Institute of Epidemiology, 111123 Moscow, Russia; (I.L.); (P.B.); (D.K.)
| | - Pavel Baryshev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia; (I.L.); (P.B.); (D.K.)
| | - David A. M. C. van de Vijver
- Viroscience Department, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands; (D.A.M.C.v.d.V.); (J.J.A.v.K.); (C.A.B.B.)
| | - Jeroen J. A. van Kampen
- Viroscience Department, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands; (D.A.M.C.v.d.V.); (J.J.A.v.K.); (C.A.B.B.)
| | - Charles A. B. Boucher
- Viroscience Department, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands; (D.A.M.C.v.d.V.); (J.J.A.v.K.); (C.A.B.B.)
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Goudi, Athens, Greece;
| | - Dmitry Kireev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia; (I.L.); (P.B.); (D.K.)
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Masoud S, Kamori D, Barabona G, Mahiti M, Sunguya B, Lyamuya E, Ueno T. Circulating HIV-1 Integrase Genotypes in Tanzania: Implication on the Introduction of Integrase Inhibitors-Based Antiretroviral Therapy Regimen. AIDS Res Hum Retroviruses 2020; 36:539-543. [PMID: 32126792 DOI: 10.1089/aid.2020.0021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Tanzania has recently adapted World Health Organization antiretroviral guidelines that include integrase strand transfer inhibitors (INSTIs) in the first-line regimen. However, there is lack of evidence on integrase (IN) gene polymorphisms in viral strains circulating in Tanzania. In this study, we characterize IN gene polymorphisms in viral strains circulating in Dar es Salaam, Tanzania, before introduction of INSTIs. Plasma viral RNAs were prepared from 158 HIV-1-infected subjects, including 111 treated, but viremic (INSTI-naïve), subjects. A part of the pol gene encompassing the IN-coding region was amplified and directly sequenced by the Sanger sequencing method. Subtype analysis revealed that subtypes A1, C, and D and intersubtype recombinants were 42%, 38%, 11%, and 9%, respectively. Although multiple subtypes cocirculate, the IN gene exhibited a relatively conserved amino acid sequence pattern with an average Shannon entropy score of 0.16. No major INSTI resistance mutations were found; however, accessory resistance mutations at positions T97A, E157Q, G163E/K, and 128A/T were detected in 5% of subjects.
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Affiliation(s)
- Salim Masoud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Doreen Kamori
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Godfrey Barabona
- Division of Infection and Immunity, Joint Sciences Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Macdonald Mahiti
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Bruno Sunguya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Eligius Lyamuya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Takamasa Ueno
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Division of Infection and Immunity, Joint Sciences Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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11
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Younger J, Raboud J, Szadkowski L, Harrigan R, Walmsley S, Bayoumi AM, Klein MB, Cooper C, Burchell AN, Loutfy M, Hull M, Wong A, Thomas R, Hogg R, Montaner J, Tsoukas C, Antoniou T. Tenofovir and emtricitabine resistance among antiretroviral-naive patients in the Canadian Observational Cohort Collaboration: implications for PrEP. Antivir Ther 2020; 24:211-220. [PMID: 30873953 DOI: 10.3851/imp3302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND The real-world effectiveness of pre-exposure prophylaxis (PrEP) may be influenced by circulating HIV strains resistant to either tenofovir or emtricitabine. Yet, few studies have examined rates of resistance to these drugs in clinical settings. METHODS We conducted a retrospective cohort study of antiretroviral-naive participants in the Canadian Observational Cohort collaboration who initiated antiretroviral therapy between 2006 and 2014. In separate analyses, we determined the prevalence of pretherapy resistance and cumulative incidence of follow-up resistance to tenofovir and emtricitabine. We used multivariable proportional hazards models to examine associations between baseline variables and the development of resistance. RESULTS We studied 6,622 antiretroviral-naive participants initiating therapy, of whom 5,428 (82.0%) had a baseline resistance test. Baseline resistance to tenofovir and emtricitabine was observed in 83 (1.5%) and 21 (0.4%) patients, respectively. Among patients without baseline resistance, the cumulative incidence of resistance to tenofovir and emtricitabine 5 years following treatment initiation was 0.0070 (95% CI 0.0046, 0.0095) and 0.033 (95% CI 0.028, 0.038), respectively. Following multivariable analysis, a baseline viral load ≥100,000 copies/ml was associated with emergence of tenofovir (hazard ratio [HR] 2.88; 95% CI 1.35, 6.15) and emtricitabine (HR 2.27; 95% CI 1.64, 3.15) resistance. Initiating an integrase inhibitor-based regimen and CD4+ T-cell count below 200 cells/mm3 were also associated with resistance to each drug. CONCLUSIONS We observed a low prevalence of baseline resistance and a low incidence of emergence of resistance to tenofovir and emtricitabine among antiretroviral-naive patients in routine clinical care.
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Affiliation(s)
- Jaime Younger
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Janet Raboud
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Leah Szadkowski
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sharon Walmsley
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,CIHR Canadian HIV Trials Network, Vancouver, BC, Canada
| | - Ahmed M Bayoumi
- Department of Medicine, University of Toronto, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Marina B Klein
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Department of Medicine, McGill University Health Centre Research Institute, Montréal, QC, Canada
| | - Curtis Cooper
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Ann N Burchell
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada.,Department of Family and Community Medicine, St Michael's Hospital and University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Mona Loutfy
- Department of Medicine, University of Toronto, Toronto, ON, Canada.,CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Women's College Research Institute, Women's College Hospital, Toronto, ON, Canada.,Maple Leaf Medical Clinic, Toronto, ON, Canada
| | - Mark Hull
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Alex Wong
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Division of Infectious Diseases, Department of Medicine, University of Saskatchewan, Regina, SK, Canada
| | | | - Robert Hogg
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Faculty of Health Sciences, Simon Fraser University, Vancouver, BC, Canada
| | - Julio Montaner
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Chris Tsoukas
- Faculty of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Tony Antoniou
- Department of Family and Community Medicine, St Michael's Hospital and University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
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12
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Celotti A, Gargiulo F, Quiros-Roldan E, Properzi M, De Francesco MAD, Coletto D, Caccuri F, Izzo I, Caruso A, Castelli F, Focà E. Presence of V72I, G123S and R127K Integrase Inhibitor polymorphisms could reduce ART effectiveness: a retrospective longitudinal study. HIV Res Clin Pract 2020; 21:24-33. [PMID: 32141388 DOI: 10.1080/25787489.2020.1734753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Objectives: Structural aspects of HIV-1 integrase complex and role of integrase minor mutations and polymorphisms in ART effectiveness is still unknown. The objective of this study was to assess the 24 and 48 weeks (W) effectiveness of ART regimens in patients with Integrase Inhibitors (InSTI) minor mutations and polymorphisms receiving InSTI-based regimens.Methods: We enrolled all ART-naïve or InSTI-naïve HIV-infected patients, with a baseline InSTI genotypic resistances test between 2011 and 2016. We analyzed integrase resistance mutations using the Stanford University HIV Drug Resistance Database (HIVdb Program, version 6.3.0). The outcome was virological response at 24 and 48 W of follow up (FU) according to snapshot analysis. We defined virological failure as two consecutive HIV-RNA > 50 copies/ml, or one >1000 copies/ml. Patients were divided in those presenting InSTI minor mutations (Group 1), and those with only polymorphisms or wild type (Group 2).Results: We enrolled 83 patients. 81 patients reached 24 W of FU: 2/20 (10%) and 4/61 (6.5%) showed virological failure in Group 1 and 2 respectively. 66 patients reached 48 W of FU: 0/17 (0%) and 2/49 (4%) showed virological failure in Group 1 and 2 respectively. Interestingly, patients with polymorphisms G123S and R127K had higher risk of failure at 24 W (respectively, relative risk - RR - 36, IQR 2.1-613, p = 0.01; RR 36, IQR 2.1-613, p = 0.01) and patients with V72I had an higher risk of failure both at 24 W (RR 6.52, IQR 1.29-32.9, p = 0.02) and 48 W (RR 21.1, IQR 1.07-414, p = 0.04).Conclusions: Our study showed that the presence of V72I, G123S and R127K polymorphisms could play a role in reducing InSTI effectiveness.
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Affiliation(s)
- Anna Celotti
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Franco Gargiulo
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Martina Properzi
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Maria Antonia De De Francesco
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Davide Coletto
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Francesca Caccuri
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Ilaria Izzo
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Arnaldo Caruso
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Emanuele Focà
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
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Machado LDA, Gomes MFDC, Guimarães ACR. Raltegravir-Induced Adaptations of the HIV-1 Integrase: Analysis of Structure, Variability, and Mutation Co-occurrence. Front Microbiol 2019; 10:1981. [PMID: 31551948 PMCID: PMC6733956 DOI: 10.3389/fmicb.2019.01981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/12/2019] [Indexed: 11/13/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) has several proteins of therapeutic importance, many of which are currently used as drug targets in antiretroviral therapy. Among these proteins is the integrase, which is responsible for the integration of the viral DNA into the host genome - a crucial step for HIV-1 replication. Given the importance of this protein in the replication process, three integrase inhibitors are currently used as an option for antiretroviral therapy: Raltegravir, Elvitegravir, and Dolutegravir. However, the crescent emergence of mutations that cause resistance to these drugs has become a worldwide health problem. In this study, we compared the variability of each position of the HIV-1 integrase sequence in clinical isolates of Raltegravir-treated and drug-naïve patients by calculating their Shannon entropies. A co-occurrence network was created to explore how mutations co-occur in patients treated with Raltegravir. Then, by building tridimensional models of the HIV-1 integrase intasomes, we investigated the relationship between variability, architecture, and co-occurrence. We observed that positions bearing some of the major resistance pathways are highly conserved among non-treated patients and variable among the treated ones. The residues involved in the three main resistance-related mutations could be identified in the same group when the positions were clustered according to their entropies. Analysis of the integrase architecture showed that the high-entropy residues S119, T124, and T125, are in contact with the host DNA, and their variations may have impacts in the protein-DNA recognition. The co-occurrence network revealed that the major resistance pathways N155H and Q148HR share more mutations with each other than with the Y143R pathway, this observation corroborates the fact that the N155H pathway is most commonly converted into Q148HRK than into Y143RCH pathway in patients' isolates. The network and the structure analysis also support the hypothesis that the resistance-related E138K mutation may be a mechanism to compensate for mutations in neighbor lysine residues to maintain DNA binding. The present study reveals patterns by which the HIV-1 integrase adapts during Raltegravir therapy. This information can be useful to comprehend the impacts of the drug in the enzyme, as well as help planning new therapeutic approaches.
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Affiliation(s)
- Lucas de Almeida Machado
- Laboratory for Functional Genomics and Bioinformatics, Instituto Oswaldo Cruz, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | | | - Ana Carolina Ramos Guimarães
- Laboratory for Functional Genomics and Bioinformatics, Instituto Oswaldo Cruz, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
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14
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E157Q integrase strand-transfer inhibitor substitution in patients with acute/recent HIV infection. AIDS 2019; 33:1613-1617. [PMID: 31090546 DOI: 10.1097/qad.0000000000002243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Integrase strand-transfer inhibitor (InSTI)-based regimens are the preferred combinations for naïve HIV-infected individuals. Polymorphic substitutions that reduce InSTIs activity have been described, with E157Q being one of the most frequently found. This study aimed to evaluate the prevalence of E157Q substitution in newly diagnosed acute/recent HIV cases and the presence of transmission clusters. DESIGN Prospective cohort study in patients with acute/recent HIV infection. METHODS Genotypic drug resistance tests were performed in all consecutive patients prospectively enrolled with a documented infection of less than 6 months from May 2015 to May 2017. Sequences were obtained by ultra-deep sequencing. Phylogenetic inferences were performed using maximum likelihood trees constructed with Mega 6.06. Bootstrap values of 75% or greater were defined for cluster assignment. Follow-up was, at least, 1 year. RESULTS In six out of 67 consecutive patients (8.95%, 95% confidence interval 4.17-18.19) with acute/recent HIV infection, strains carrying the E157Q InSTI substitution were detected. All cases were MSM patients infected with subtype B strains. No other resistance substitutions were detected in these cases. Median viral load was 5.33 (interquartile range: 4.54-5.71) log10 copies/ml and, in all cases, the mutational viral load was high (>95%). Three cases were included in transmission clusters. Three cases responded to dolutegravir-based regimens; nonnucleoside reverse transcriptase inhibitor-based regimens were used for the other case(s). CONCLUSION E157Q substitution, reducing raltegravir and elvitegravir activity, was frequently found in acute/recent HIV cases. All cases were infected with subtype B, and some were included in clusters. Cases treated with dolutegravir-based regimens had good virological response.
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15
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Chung YS, Choi JY, Yoo MS, Seong JH, Choi BS, Kang C. Phylogenetic transmission clusters among newly diagnosed antiretroviral drug-naïve patients with human immunodeficiency virus-1 in Korea: A study from 1999 to 2012. PLoS One 2019; 14:e0217817. [PMID: 31166970 PMCID: PMC6550428 DOI: 10.1371/journal.pone.0217817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 05/21/2019] [Indexed: 11/29/2022] Open
Abstract
Population-level phylogenetic patterns reflect both transmission dynamics and genetic changes, which accumulate because of selection or drift. In this study, we determined whether a longitudinally sampled dataset derived from human immunodeficiency virus (HIV)-1-infected individuals over a 14-year period (1999–2012) could shed light on the transmission processes involved in the initiation of the HIV-1 epidemic in Korea. In total, 927 sequences were acquired from 1999 to 2012; each sequence was acquired from an individual patient who had not received treatment. Sequences were used for drug resistance and phylogenetic analyses. Phylogenetic and other analyses were conducted using MEGA version 6.06 based on the GTR G+I parameter model and SAS. Of the 927 samples, 863 (93.1%) were classified as subtype B and 64 were classified as other subtypes. Phylogenetic analysis demonstrated that 104 of 927 patient samples (11.2%) were grouped into 37 clusters. Being part of a transmission cluster was significantly associated with subtype-B viruses, infection via sexual contact, and the infection of young males. Of all clusters, three (~8.1%) that comprised 10 individual samples (22.2% of 45 individuals) included at least one member with total transmitted drug resistance (TDR). In summary, HIV transmission cluster analyses can integrate laboratory data with behavioral data to enable the identification of key transmission patterns to develop tailored interventions aimed at interrupting transmission chains.
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Affiliation(s)
- Yoon-Seok Chung
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Ju-Yeon Choi
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Myoung-Su Yoo
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Jae Hyun Seong
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Byeong-Sun Choi
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Chun Kang
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
- * E-mail:
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16
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Integrase Resistance-Associated Mutations on Raltegravir Failure in Western India: A Preliminary Analysis. J Acquir Immune Defic Syndr 2019; 77:e42-e45. [PMID: 29315113 DOI: 10.1097/qai.0000000000001625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Parveen N, Moodie EEM, Cox J, Lambert G, Otis J, Roger M, Brenner B. New Challenges in HIV Research: Combining Phylogenetic Cluster Size and Epidemiological Data. ACTA ACUST UNITED AC 2018. [DOI: 10.1515/em-2017-0017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
An exciting new direction in HIV research is centered on using molecular phylogenetics to understand the social and behavioral drivers of HIV transmission. SPOT was an intervention designed to offer HIV point of care testing to men who have sex with men at a community-based site in Montreal, Canada; at the time of testing, a research questionnaire was also deployed to collect data on socio-demographic and behavioral characteristics of participating men. The men taking part in SPOT could be viewed, from the research perspective, as having been recruited via a convenience sample. Among men who were found to be HIV positive, phylogenetic cluster size was measured using a large cohort of HIV-positive individuals in the province of Quebec. The cluster size is likely subject to under-estimation. In this paper, we use SPOT data to evaluate the association between HIV transmission cluster size and the number of sex partners for MSM, after adjusting for the SPOT sampling scheme and correcting for measurement error in cluster size by leveraging external data sources. The sampling weights for SPOT participants were calculated from another study of men who have sex with men in Montreal by fitting a weight-adjusted model, whereas measurement error was corrected using the simulation-extrapolation conditional on covariates approach.
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Affiliation(s)
- Nabila Parveen
- Epidemiology & Biostatistics , McGill University , Montreal , Quebec , Canada
| | - Erica E. M. Moodie
- Epidemiology & Biostatistics , McGill University , 1020 Pine Ave W , Montreal , Quebec , Canada
| | - Joseph Cox
- Epidemiology & Biostatistics , McGill University , Montreal , Quebec , Canada
| | - Gilles Lambert
- Institut national de sante publique du Quebec , Montreal , Quebec , Canada
| | - Joanne Otis
- Universite du Quebec a Montreal , Montreal , Quebec , Canada
| | - Michel Roger
- Department of Microbiology and Immunology , Université de Montréal , Montreal , Quebec , Canada
| | - Bluma Brenner
- McGill AIDS Centre , Lady Davis Institute for Medical Research , Montreal , Quebec , Canada
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18
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Oliveira M, Ibanescu RI, Anstett K, Mésplède T, Routy JP, Robbins MA, Brenner BG. Selective resistance profiles emerging in patient-derived clinical isolates with cabotegravir, bictegravir, dolutegravir, and elvitegravir. Retrovirology 2018; 15:56. [PMID: 30119633 PMCID: PMC6098636 DOI: 10.1186/s12977-018-0440-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/11/2018] [Indexed: 11/26/2022] Open
Abstract
Background Integrase strand transfer inhibitors (INSTIs) are recommended for first-line HIV therapy based on their relatively high genetic barrier to resistance. Although raltegravir (RAL) and elvitegravir (EVG) resistance profiles are well-characterized, resistance patterns for dolutegravir (DTG), bictegravir (BIC), and cabotegravir (CAB) remain largely unknown. Here, in vitro drug selections compared the development of resistance to DTG, BIC, CAB, EVG and RAL using clinical isolates from treatment-naïve primary HIV infection (PHI) cohort participants (n = 12), and pNL4.3 recombinant strains encoding patient-derived Integrase with (n = 5) and without (n = 5) the E157Q substitution. Results Patient-derived viral isolates were serially passaged in PHA-stimulated cord blood mononuclear cells in the presence of escalating concentrations of INSTIs over the course of 36–46 weeks. Drug resistance arose more rapidly in primary clinical isolates with EVG (12/12), followed by CAB (8/12), DTG (8/12) and BIC (6/12). For pNL4.3 recombinant strains encoding patient-derived integrase, the comparative genetic barrier to resistance was RAL > EVG > CAB > DTG and BIC. The E157Q substitution in integrase delayed the advent of resistance to INSTIs. With EVG, T66I/A, E92G/V/Q, T97A or R263K (n = 16, 3, 2 and 1, respectively) arose by weeks 8–16, followed by 1–4 accessory mutations, conferring high-level resistance (> 100-fold) by week 36. With DTG and BIC, solitary R263K (n = 27), S153F/Y (n = 7) H51Y (n = 2), Q146 R (n = 3) or S147G (n = 1) mutations conferred low-level (< 3-fold) resistance at weeks 36–46. Similarly, most CAB selections (n = 18) resulted in R263K, S153Y, S147G, H51Y, or Q146L solitary mutations. However, three CAB selections resulted in Q148R/K followed by secondary mutations conferring high-level cross-resistance to all INSTIs. EVG-resistant viruses (T66I/R263K, T66I/E157Q/R263K, and S153A/R263K) retained residual susceptibility when switched to DTG, BIC or CAB, losing T66I by week 27. Two EVG-resistant variants developed resistance to DTG, BIC and CAB through the additional acquisition of E138A/Q148R and S230N, respectively. One EVG-resistant variant (T66I) acquired L74M/G140S/S147G, L74M/E138K/S147G and H51Y with DTG CAB and BIC, respectively. Conclusions Second generation INSTIs show a higher genetic barrier to resistance than EVG and RAL. The potency of CAB was lower than BIC and DTG. The development of Q148R/K with CAB can result in high-level cross-resistance to all INSTIs.
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Affiliation(s)
- Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Kaitlin Anstett
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Thibault Mésplède
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Jean-Pierre Routy
- Faculty of Medicine (Surgery, Experimental Medicine, Infectious Disease), McGill University, Montreal, QC, Canada
| | | | - Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada. .,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada. .,Faculty of Medicine (Surgery, Experimental Medicine, Infectious Disease), McGill University, Montreal, QC, Canada.
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Yebra G, Frampton D, Gallo Cassarino T, Raffle J, Hubb J, Ferns RB, Waters L, Tong CYW, Kozlakidis Z, Hayward A, Kellam P, Pillay D, Clark D, Nastouli E, Leigh Brown AJ. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project. PLoS One 2018; 13:e0192081. [PMID: 29389981 PMCID: PMC5794160 DOI: 10.1371/journal.pone.0192081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND & METHODS The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. RESULTS The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. CONCLUSIONS The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.
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Affiliation(s)
- Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Dan Frampton
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
| | | | - Jade Raffle
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
| | - Jonathan Hubb
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
| | - R. Bridget Ferns
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
- NIHR UCLH/UCL Biomedical Research Centre, London, United Kingdom
| | - Laura Waters
- Department of HIV Medicine, Mortimer Market Centre, Central & North West London NHS Trust, London, United Kingdom
| | - C. Y. William Tong
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- Queen Mary University, London, United Kingdom
| | - Zisis Kozlakidis
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
- UCL Institute of Disease Informatics, Farr Institute of Health Informatics Research, London, United Kingdom
| | - Andrew Hayward
- UCL Institute of Epidemiology and Health Care, London, United Kingdom
| | - Paul Kellam
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Deenan Pillay
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
| | - Duncan Clark
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- School of Life Sciences, University of Glasgow. Glasgow, United Kingdom
| | - Eleni Nastouli
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
- Department of Population, Policy and Practice, UCL GOS Institute of Child Health, London, United Kingdom
| | - Andrew J. Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
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Brenner BG, Ibanescu RI, Oliveira M, Roger M, Hardy I, Routy JP, Kyeyune F, Quiñones-Mateu ME, Wainberg MA. HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters. J Antimicrob Chemother 2018; 72:2171-2183. [PMID: 28472323 PMCID: PMC7263826 DOI: 10.1093/jac/dkx118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/22/2017] [Indexed: 12/20/2022] Open
Abstract
Objectives: Viral phylogenetics revealed two patterns of HIV-1 spread among
MSM in Quebec. While most HIV-1 strains (n = 2011) were
associated with singleton/small clusters (cluster size 1–4), 30 viral lineages formed
large networks (cluster size 20–140), contributing to 42% of diagnoses between 2011 and
2015. Herein, tissue culture selections ascertained if large cluster lineages possessed
higher replicative fitness than singleton/small cluster isolates, allowing for viral
escape from integrase inhibitors. Methods: Primary HIV-1 isolates from large 20+ cluster
(n = 11) or singleton/small cluster
(n = 6) networks were passagedin
vitro in escalating concentrations of dolutegravir, elvitegravir and lamivudine
for 24–36 weeks. Sanger and deep sequencing assessed genotypic changes under selective
drug pressure. Results: Large cluster HIV-1 isolates selected for resistance to
dolutegravir, elvitegravir and lamivudine faster than HIV-1 strains forming small
clusters. With dolutegravir, large cluster HIV-1 variants acquired solitary R263K
(n = 7), S153Y
(n = 1) or H51Y
(n = 1) mutations as the dominant quasi-species within
8–12 weeks as compared with small cluster lineages where R263K
(n = 1/6), S153Y (1/6) or WT species (4/6) were
observed after 24 weeks. Interestingly, dolutegravir-associated mutations compromised
viral replicative fitness, precluding escalations in concentrations beyond 5–10 nM. With
elvitegravir, large cluster variants more rapidly acquired first mutations (T66I, A92G,
N155H or S147G) by week 8 followed by sequential accumulation of multiple mutations
leading to viral escape (>10 μM) by week 24. Conclusions: Further studies are needed to understand virological features of
large cluster viruses that may favour their transmissibility, replicative competence and
potential to escape selective antiretroviral drug pressure.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Isabelle Hardy
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | | | - Fred Kyeyune
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,University Hospitals Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Brenner BG, Ibanescu RI, Hardy I, Roger M. Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in "Real-World" Settings. Viruses 2017; 10:v10010010. [PMID: 29283390 PMCID: PMC5795423 DOI: 10.3390/v10010010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 12/22/2017] [Accepted: 12/24/2017] [Indexed: 12/15/2022] Open
Abstract
HIV continues to spread among vulnerable heterosexual (HET), Men-having-Sex with Men (MSM) and intravenous drug user (IDU) populations, influenced by a complex array of biological, behavioral and societal factors. Phylogenetics analyses of large sequence datasets from national drug resistance testing programs reveal the evolutionary interrelationships of viral strains implicated in the dynamic spread of HIV in different regional settings. Viral phylogenetics can be combined with demographic and behavioral information to gain insights on epidemiological processes shaping transmission networks at the population-level. Drug resistance testing programs also reveal emergent mutational pathways leading to resistance to the 23 antiretroviral drugs used in HIV-1 management in low-, middle- and high-income settings. This article describes how genotypic and phylogenetic information from Quebec and elsewhere provide critical information on HIV transmission and resistance, Cumulative findings can be used to optimize public health strategies to tackle the challenges of HIV in “real-world” settings.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
| | - Isabelle Hardy
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC H2X 0A9, Canada.
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC H2X 0A9, Canada.
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Antiviral Activity of Bictegravir and Cabotegravir against Integrase Inhibitor-Resistant SIVmac239 and HIV-1. Antimicrob Agents Chemother 2017; 61:AAC.01695-17. [PMID: 28923862 DOI: 10.1128/aac.01695-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/08/2017] [Indexed: 01/26/2023] Open
Abstract
Animal models are essential to study novel antiretroviral drugs, resistance-associated mutations (RAMs), and treatment strategies. Bictegravir (BIC) is a novel potent integrase strand transfer inhibitor (INSTI) that has shown promising results against HIV-1 infection in vitro and in vivo and against clinical isolates with resistance against INSTIs. BIC has a higher genetic barrier to the development of resistance than two clinically approved INSTIs, termed raltegravir and elvitegravir. Another clinically approved INSTI, dolutegravir (DTG) also possesses a high genetic barrier to resistance, while a fourth compound, termed cabotegravir (CAB), is currently in late phases of clinical development. Here we report the susceptibilities of simian immunodeficiency virus (SIV) and HIV-1 integrase (IN) mutants containing various RAMs to BIC, CAB, and DTG. BIC potently inhibited SIV and HIV-1 in single cycle infection with 50% effective concentrations (EC50s) in the low nM range. In single cycle SIV infections, none of the E92Q, T97A, Y143R, or N155H substitutions had a significant effect on susceptibility to BIC (≤4-fold increase in EC50), whereas G118R and R263K conferred ∼14-fold and ∼6-fold increases in EC50, respectively. In both single and multiple rounds of HIV-1 infections, BIC remained active against the Y143R, N155H, R263K, R263K/M50I, and R263K/E138K mutants (≤4-fold increase in EC50). In multiple rounds of infection, the G140S/Q148H combination of substitutions decreased HIV-1 susceptibility to BIC 4.8-fold compared to 16.8- and 7.4-fold for CAB and DTG, respectively. BIC possesses an excellent resistance profile in regard to HIV and SIV and could be useful in nonhuman primate models of HIV infection.
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Meixenberger K, Yousef KP, Smith MR, Somogyi S, Fiedler S, Bartmeyer B, Hamouda O, Bannert N, von Kleist M, Kücherer C. Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors. Virol J 2017; 14:223. [PMID: 29137637 PMCID: PMC5686839 DOI: 10.1186/s12985-017-0887-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Detailed knowledge of the evolutionary potential of polymorphic sites in a viral protein is important for understanding the development of drug resistance in the presence of an inhibitor. We therefore set out to analyse the molecular evolution of the HIV-1 subtype B integrase at the inter-patient level in Germany during a 20-year period prior to the first introduction of integrase strand inhibitors (INSTIs). METHODS We determined 337 HIV-1 integrase subtype B sequences (amino acids 1-278) from stored plasma samples of antiretroviral treatment-naïve individuals newly diagnosed with HIV-1 between 1986 and 2006. Shannon entropy was calculated to determine the variability at each amino acid position. Time trends in the frequency of amino acid variants were identified by linear regression. Direct coupling analysis was applied to detect covarying sites. RESULTS Twenty-two time trends in the frequency of amino acid variants demonstrated either single amino acid exchanges or variation in the degree of polymorphy. Covariation was observed for 17 amino acid variants with a temporal trend. Some minor INSTI resistance mutations (T124A, V151I, K156 N, T206S, S230 N) and some INSTI-selected mutations (M50I, L101I, T122I, T124 N, T125A, M154I, G193E, V201I) were identified at overall frequencies >5%. Among these, the frequencies of L101I, T122I, and V201I increased over time, whereas the frequency of M154I decreased. Moreover, L101I, T122I, T124A, T125A, M154I, and V201I covaried with non-resistance-associated variants. CONCLUSIONS Time-trending, covarying polymorphisms indicate that long-term evolutionary changes of the HIV-1 integrase involve defined clusters of possibly structurally or functionally associated sites independent of selective pressure through INSTIs at the inter-patient level. Linkage between polymorphic resistance- and non-resistance-associated sites can impact the selection of INSTI resistance mutations in complex ways. Identification of these sites can help in improving genotypic resistance assays, resistance prediction algorithms, and the development of new integrase inhibitors.
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Affiliation(s)
| | - Kaveh Pouran Yousef
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Maureen Rebecca Smith
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Sybille Somogyi
- HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Stefan Fiedler
- HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Barbara Bartmeyer
- HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | - Osamah Hamouda
- HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | - Norbert Bannert
- HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Claudia Kücherer
- HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
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A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012. PLoS One 2017; 12:e0170601. [PMID: 28489920 PMCID: PMC5425008 DOI: 10.1371/journal.pone.0170601] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/06/2017] [Indexed: 12/12/2022] Open
Abstract
Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005–2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.
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Lack of impact of pre-existing T97A HIV-1 integrase mutation on integrase strand transfer inhibitor resistance and treatment outcome. PLoS One 2017; 12:e0172206. [PMID: 28212411 PMCID: PMC5315389 DOI: 10.1371/journal.pone.0172206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 01/05/2023] Open
Abstract
T97A is an HIV-1 integrase polymorphism associated with integrase strand transfer inhibitor (INSTI) resistance. Using pooled data from 16 clinical studies, we investigated the prevalence of T97A (pre-existing and emergent) and its impact on INSTI susceptibility and treatment response in INSTI-naive patients who enrolled on elvitegravir (EVG)- or raltegravir (RAL)-based regimens. Prior to INSTI-based therapy, primary INSTI resistance-associated mutations (RAMs) were absent and T97A pre-existed infrequently (1.4%; 47 of 3367 integrase sequences); most often among non-B (5.3%) than B (0.9%) HIV-1 subtypes. During INSTI-based therapy, few patients experienced virologic failure with emergent INSTI RAMs (3%; 122 of 3881 patients), among whom T97A emerged infrequently in the presence (n = 6) or absence (n = 8) of primary INSTI RAMs. A comparison between pre-existing and emergent T97A patient populations (i.e., in the absence of primary INSTI RAMs) showed no significant differences in EVG or RAL susceptibility in vitro. Furthermore, among all T97A-containing viruses tested, only 38-44% exhibited reduced susceptibility to EVG and/or RAL (all of low magnitude; <11-fold), while all maintained susceptibility to dolutegravir. Of the patients with pre-existing T97A, 17 had available clinical follow-up: 16 achieved virologic suppression and 1 maintained T97A and INSTI sensitivity without further resistance development. Overall, T97A is an infrequent integrase polymorphism that is enriched among non-B HIV-1 subtypes and can confer low-level reduced susceptibility to EVG and/or RAL. However, detection of T97A does not affect response to INSTI-based therapy with EVG or RAL. These results suggest a very low risk of initiating INSTI-based therapy in patients with pre-existing T97A.
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Brenner BG, Wainberg MA. Clinical benefit of dolutegravir in HIV-1 management related to the high genetic barrier to drug resistance. Virus Res 2016; 239:1-9. [PMID: 27422477 DOI: 10.1016/j.virusres.2016.07.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 01/08/2023]
Abstract
This manuscript reviews the reasons why Integrase inhibitors should now routinely constitute a part of first line antiretroviral therapy for the treatment of HIV disease. The use of these drugs that are generally well tolerated has resulted in far less drug resistance than was the case with most other categories of antiviral compounds. In addition, the integrase inhibitor family of drugs has been less prone to the problem of transmitted drug resistance which is due to a wide variety of substitutions in the HIV genome that can be sexually transmitted from one person to another. However, the use of integrase inhibitors in first line therapy may unfortunately not soon happen in developing country settings where non-nucleoside reverse transcriptase inhibitors continue to be a mainstay of initial therapy, primarily for reasons of cost. As long as this situation continues, problems of drug resistance and transmitted drug resistance will be common in such settings. Current evidence also suggests that the use of dolutegravir as a first line integrase inhibitor may limit development of drug resistance to an extent that exceeds the use of other members of this family of drugs. This may be due to particular patterns of resistance involving dolutegravir, whereby the mutations that are associated with resistance against this compound may actually diminish both HIV replication capacity as well as integrase enzymatic activity in a far-reaching and unique manner. This gives potential hope that the use of dolutegravir in first line therapy could actually form part of the long-sought goal of attainment of a functional cure for HIV disease.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
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Differences among HIV-1 subtypes in drug resistance against integrase inhibitors. INFECTION GENETICS AND EVOLUTION 2016; 46:286-291. [PMID: 27353185 DOI: 10.1016/j.meegid.2016.06.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 11/22/2022]
Abstract
Three integrase strand transfer inhibitors (INSTIs), raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG), have been approved by the FDA. Resistance against these three INSTIs have been reported and cross-resistance among them has been documented. Due to extensive and dynamic genetic diversity in different HIV-1 variants, significant differences in susceptibility to the INSTIs have been observed among HIV subtypes. This review summarizes what is known about this topic and discusses possible clinical implications.
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Brenner BG, Thomas R, Blanco JL, Ibanescu RI, Oliveira M, Mesplède T, Golubkov O, Roger M, Garcia F, Martinez E, Wainberg MA. Development of a G118R mutation in HIV-1 integrase following a switch to dolutegravir monotherapy leading to cross-resistance to integrase inhibitors. J Antimicrob Chemother 2016; 71:1948-53. [PMID: 27029845 DOI: 10.1093/jac/dkw071] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/17/2016] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Dolutegravir shows a high barrier to resistance with no previously reported cases of acquired integrase mutations during first-line therapy. In this study, rapid development of the G118R mutation arose following a switch from first-line elvitegravir/cobicistat/tenofovir disoproxil fumarate/emtricitabine to dolutegravir monotherapy. The G118R mutation also arose in a treatment-experienced patient switched to dolutegravir monotherapy. The genetic basis for G118R selection and potential phenotypic outcome was ascertained. PATIENT AND METHODS Genotypic analysis was performed on patients with virological failure (<1000 copies/mL) on dolutegravir-containing regimens. The Los Alamos database was queried for glycine codon 118 polymorphisms. Cell culture selections and phenotypic drug susceptibility assays assessed resistance via the G118R pathway. RESULTS We report on two patients who developed viral failure while on dolutegravir monotherapy. Both patients had been on a current or previous regimen containing integrase inhibitors. Virological failure (<1000 copies/mL) emerged early within 2 months following the dolutegravir switch. The appearance of G118R in these two cases and subtype C and CRF02_AG in vitro selections were related to a rare GGA natural polymorphism at codon 118 (1.5% prevalence), facilitating a GGA to AGA transition. Cell culture selections were used to assess the in vitro progression of the G118R pathway leading to cross-resistance to all integrase inhibitors. CONCLUSIONS Although resistance to dolutegravir is typically rare, genetic polymorphisms and monotherapy can facilitate the acquisition of G118R.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Réjean Thomas
- Clinique Médicale l'Actuel, Montreal, Quebec, Canada
| | - José Luis Blanco
- Infectious Disease and AIDS Unit, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Thibault Mesplède
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Olga Golubkov
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Federico Garcia
- Microbiology Department, Complejo Hospitalario Universitario Granada, Granada, Spain Hospital Universitario San Cecilio, Instituto de Investigación Ibs, Granada, Spain
| | - Esteban Martinez
- Infectious Disease and AIDS Unit, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Mortality of treated HIV-1 positive individuals according to viral subtype in Europe and Canada: collaborative cohort analysis. AIDS 2016; 30:503-13. [PMID: 26562844 PMCID: PMC4711384 DOI: 10.1097/qad.0000000000000941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVES To estimate prognosis by viral subtype in HIV-1-infected individuals from start of antiretroviral therapy (ART) and after viral failure. DESIGN Collaborative analysis of data from eight European and three Canadian cohorts. METHODS Adults (N>20 000) who started triple ART between 1996 and 2012 and had data on viral subtype were followed for mortality. We estimated crude and adjusted (for age, sex, regimen, CD4 cell count, and AIDS at baseline, period of starting ART, stratified by cohort, region of origin and risk group) mortality hazard ratios (MHR) by subtype. We estimated MHR subsequent to viral failure defined as two HIV-RNA measurements greater than 500 copies/ml after achieving viral suppression. RESULTS The most prevalent subtypes were B (15 419; 74%), C (2091; 10%), CRF02AG (1057; 5%), A (873; 4%), CRF01AE (506; 2.4%), G (359; 1.7%), and D (232; 1.1%). Subtypes were strongly patterned by region of origin and risk group. During 104 649 person-years of observation, 1172/20 784 patients died. Compared with subtype B, mortality was higher for subtype A, but similar for all other subtypes. MHR for A versus B were 1.13 (95% confidence interval 0.85,1.50) when stratified by cohort, increased to 1.78 (1.27,2.51) on stratification by region and risk, and attenuated to 1.59 (1.14,2.23) on adjustment for covariates. MHR for A versus B was 2.65 (1.64,4.28) and 0.95 (0.57,1.57) for patients who started ART with CD4 cell count below, or more than, 100 cells/μl, respectively. There was no difference in mortality between subtypes A, B and C after viral failure. CONCLUSION Patients with subtype A had worse prognosis, an observation which may be confounded by socio-demographic factors.
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Mulu A, Maier M, Liebert UG. Lack of integrase inhibitors associated resistance mutations among HIV-1C isolates. J Transl Med 2015; 13:377. [PMID: 26626277 PMCID: PMC4665939 DOI: 10.1186/s12967-015-0734-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Although biochemical analysis of HIV-1 integrase enzyme suggested the use of integrase inhibitors (INIs) against HIV-1C, different viral subtypes may favor different mutational pathways potentially leading to varying levels of drug resistance. Thus, the aim of this study was to search for the occurrence and natural evolution of integrase polymorphisms and/or resistance mutations in HIV-1C Ethiopian clinical isolates prior to the introduction of INIs. Methods Plasma samples from chronically infected drug naïve patients (N = 45), of whom the PR and RT sequence was determined previously, were used to generate population based sequences of HIV-1 integrase. HIV-1 subtype was determined using the REGA HIV-1 subtyping tool. Resistance mutations were interpreted according to the Stanford HIV drug resistance database (http://hivdb.stanford.edu) and the updated International Antiviral Society (IAS)-USA mutation lists. Moreover, rates of polymorphisms in the current isolates were compared with South African and global HIV-1C isolates. Results All subjects were infected with HIV-1C concordant to the protease (PR) and reverse transcriptase (RT) regions. Neither major resistance-associated IN mutations (T66I/A/K, E92Q/G, T97A, Y143HCR, S147G, Q148H/R/K, and N155H) nor silent mutations known to change the genetic barrier were observed. Moreover, the DDE-catalytic motif (D64G/D116G/E152 K) and signature HHCC zinc-binding motifs at codon 12, 16, 40 and 43 were found to be highly conserved. However, compared to other South African subtype C isolates, the rate of polymorphism was variable at various positions. Conclusion Although the sample size is small, the findings suggest that this drug class could be effective in Ethiopia and other southern African countries where HIV-1C is predominantly circulating. The data will contribute to define the importance of integrase polymorphism and to improve resistance interpretation algorithms in HIV-1C isolates.
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Affiliation(s)
- Andargachew Mulu
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany. .,Department of Microbiology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
| | - Melanie Maier
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.
| | - Uwe Gerd Liebert
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.
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Abstract
BACKGROUND HIV-1 group O (HIV-O) is a rare variant that is characterized by a high number of natural polymorphisms in the integrase coding region that may impact on susceptibility to integrase strand transfer inhibitors (INSTIs) and on the emergence of resistance substitutions. We previously reported that HIV-O is more susceptible to RAL than HIV-1 group M (HIV-M). METHODS The aim of this study was to assess pathways of resistance to INSTIs in group 0 variants. Accordingly, we selected for resistance to each of raltegravir (RAL), elvitegravir (EVG), and dolutegravir (DTG) in cord blood mononuclear cells using HIV group O subtypes A and B, an HIV-O divergent isolate, and HIV-1 group M (subtype B, which served as a reference). Site-directed mutagenesis was performed on the pCOM2.5 HIV group 0 infectious clone to ascertain the impact of INSTI resistance substitutions at positions Q148R, N155H, and R263K within integrase on susceptibility to INSTIs and infectiousness. RESULTS Cell culture selections of group O variants yielded similar patterns of resistance to RAL, EVG, and DTG as observed for subtype B. In the DTG selections, subtype B yielded S153Y, whereas a natural S153A polymorphism sometimes led to A153V in group O. The pCMO2.5/Q148R and pCMO2.5/N155H variants displayed far higher levels of resistance to DTG (>1000 FC) than was seen for group M viruses. CONCLUSIONS HIV-O harboring Q148R and N155H shows higher resistance to DTG compared with HIV-M subtype B.
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Doyle T, Dunn DT, Ceccherini-Silberstein F, De Mendoza C, Garcia F, Smit E, Fearnhill E, Marcelin AG, Martinez-Picado J, Kaiser R, Geretti AM. Integrase inhibitor (INI) genotypic resistance in treatment-naive and raltegravir-experienced patients infected with diverse HIV-1 clades. J Antimicrob Chemother 2015; 70:3080-6. [PMID: 26311843 PMCID: PMC4613743 DOI: 10.1093/jac/dkv243] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/14/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The aim of this study was to characterize the prevalence and patterns of genotypic integrase inhibitor (INI) resistance in relation to HIV-1 clade. METHODS The cohort comprised 533 INI-naive subjects and 255 raltegravir recipients with viraemia who underwent integrase sequencing in routine care across Europe, including 134/533 (25.1%) and 46/255 (18.0%), respectively, with non-B clades (A, C, D, F, G, CRF01, CRF02, other CRFs, complex). RESULTS No major INI resistance-associated mutations (RAMs) occurred in INI-naive subjects. Among raltegravir recipients with viraemia (median 3523 HIV-1 RNA copies/mL), 113/255 (44.3%) had one or more major INI RAMs, most commonly N155H (45/255, 17.6%), Q148H/R/K + G140S/A (35/255, 13.7%) and Y143R/C/H (12/255, 4.7%). In addition, four (1.6%) raltegravir recipients showed novel mutations at recognized resistance sites (E92A, S147I, N155D, N155Q) and novel mutations at other integrase positions that were statistically associated with raltegravir exposure (K159Q/R, I161L/M/T/V, E170A/G). Comparing subtype B with non-B clades, Q148H/R/K occurred in 42/209 (20.1%) versus 2/46 (4.3%) subjects (P = 0.009) and G140S/A occurred in 36/209 (17.2%) versus 1/46 (2.2%) subjects (P = 0.005). Intermediate- to high-level cross-resistance to twice-daily dolutegravir was predicted in 40/255 (15.7%) subjects, more commonly in subtype B versus non-B clades (39/209, 18.7% versus 1/46, 2.2%; P = 0.003). A glycine (G) to serine (S) substitution at integrase position 140 required one nucleotide change in subtype B and two nucleotide changes in all non-B clades. CONCLUSIONS No major INI resistance mutations occurred in INI-naive subjects. Reduced occurrence of Q148H/R/K + G140S/A was seen in non-B clades versus subtype B, and was explained by the higher genetic barrier to the G140S mutation observed in all non-B clades analysed.
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Affiliation(s)
- Tomas Doyle
- Department of Infectious Diseases, King's College London, London, UK
| | | | | | | | | | - Erasmus Smit
- Heart of England NHS Foundation Trust, Birmingham, UK
| | | | - Anne-Genevieve Marcelin
- AP-HP, Hôpital Pitié-Salpêtrière, INSERM-Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Paris, France
| | | | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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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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Hardy I, Brenner B, Quashie P, Thomas R, Petropoulos C, Huang W, Moisi D, Wainberg MA, Roger M. Evolution of a novel pathway leading to dolutegravir resistance in a patient harbouring N155H and multiclass drug resistance. J Antimicrob Chemother 2014; 70:405-11. [PMID: 25281399 DOI: 10.1093/jac/dku387] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Dolutegravir has been recently approved for treatment-naive and -experienced HIV-infected subjects, including integrase inhibitor (INI)-experienced patients. Dolutegravir is a second-generation INI that can overcome many prior raltegravir and elvitegravir failures. Here, we report the evolution of resistance to dolutegravir in a highly treatment-experienced patient harbouring the major N155H mutation consequent to raltegravir treatment failure. METHODS Genotypic and phenotypic analyses were done on longitudinal samples to determine viral resistance to INIs. Integrase amino acid sequence interactions with raltegravir and dolutegravir were assessed by molecular modelling and docking simulations. RESULTS Five mutations (A49P, L68FL, T97A, E138K and L234V) were implicated in emergent dolutegravir resistance, with a concomitant severe compromise in viral replicative capacity. Molecular modelling and docking simulations revealed that dolutegravir binding to integrase was affected by these acquired dolutegravir mutations. CONCLUSIONS Our findings identify a novel mutational pathway involving integrase mutations A49P and L234V, leading to dolutegravir resistance in a patient with the N155H raltegravir mutation.
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Affiliation(s)
- Isabelle Hardy
- Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Bluma Brenner
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Peter Quashie
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Réjean Thomas
- Clinique Médicale L'Actuel, Montréal, Québec, Canada
| | | | - Wei Huang
- Monogram Biosciences, South San Francisco, CA, USA
| | - Daniela Moisi
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Mark A Wainberg
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Michel Roger
- Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
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Bellecave P, Malato L, Calmels C, Reigadas S, Parissi V, Andreola ML, Fleury H. In vitro analysis of the susceptibility of HIV-1 subtype A and CRF01_AE integrases to raltegravir. Int J Antimicrob Agents 2014; 44:168-72. [DOI: 10.1016/j.ijantimicag.2014.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/26/2014] [Accepted: 04/04/2014] [Indexed: 11/29/2022]
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Resistance mutations against dolutegravir in HIV integrase impair the emergence of resistance against reverse transcriptase inhibitors. AIDS 2014; 28:813-9. [PMID: 24463394 DOI: 10.1097/qad.0000000000000199] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Among 1222 antiretroviral-naive patients who received dolutegravir (DTG) as part of first-line therapy, none has developed resistance against this compound after 48-96 weeks of follow-up. Moreover, only four occurrences of virological failure with resistance mutations have been documented in previously drug-experienced patients who received DTG as a first time integrase inhibitor as a component of a second-line regimen. The R263K integrase resistance mutation was observed in two of these individuals who received suboptimal background regimens. We have previously selected mutations at position R263K, G118R, H51Y, and E138K as being associated with low-level resistance to DTG. Now, we sought to investigate the facility with which resistance on the part of R263K-containing viruses might develop. DESIGN AND METHODS We tested the ability of DTG-resistant viruses containing either the R263K or G118R and/or H51Y mutations to develop further resistance against several reverse transcriptase inhibitors during in-vitro selection experiments. RESULTS Our results show that DTG-resistant viruses are impaired in their ability to acquire further resistance to each of nevirapine and lamivudine as a consequence of their relative inability to develop resistance mutations associated with these two compounds. CONCLUSION Our findings provide an explanation for the fact that no individual has yet progressed to virological failure with resistance mutations associated with dolutegravir in clinical trials in which patients received dolutegravir together with an optimized background regimen.
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Shadrina O, Krotova O, Agapkina J, Knyazhanskaya E, Korolev S, Starodubova E, Viklund A, Lukashov V, Magnani M, Medstrand P, Karpov V, Gottikh M, Isaguliants M. Consensus HIV-1 subtype A integrase and its raltegravir-resistant variants: design and characterization of the enzymatic properties. Biochimie 2014; 102:92-101. [PMID: 24594066 DOI: 10.1016/j.biochi.2014.02.013] [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] [Received: 11/01/2013] [Accepted: 02/21/2014] [Indexed: 11/28/2022]
Abstract
Model studies of the subtype B and non-subtype B integrases are still required to compare their susceptibility to antiretroviral drugs, evaluate the significance of resistance mutations and identify the impact of natural polymorphisms on the level of enzymatic reactivity. We have therefore designed the consensus integrase of the HIV-1 subtype A strain circulating in the former Soviet Union territory (FSU-A) and two of its variants with mutations of resistance to the strand transfer inhibitor raltegravir. Their genes were synthesized, and expressed in E coli; corresponding His-tagged proteins were purified using the affinity chromatography. The enzymatic properties of the consensus integrases and their sensitivity to raltegravir were examined in a series of standard in vitro reactions and compared to the properties of the integrase of HIV-1 subtype B strain HXB2. The consensus enzyme demonstrated similar DNA-binding properties, but was significantly more active than HXB-2 integrase in the reactions of DNA cleavage and integration. All integrases were equally susceptible to inhibition by raltegravir and elvitegravir, indicating that the sporadic polymorphisms inherent to the HXB-2 enzyme have little effect on its susceptibility to drugs. Insensitivity of the mutated enzymes to the inhibitors of strand transfer occurred at a cost of a 30-90% loss of the efficacies of both 3'-processing and strand transfer. This is the first study to describe the enzymatic properties of the consensus integrase of HIV-1 clade A and the effects of the resistance mutations when the complex actions of sporadic sequence polymorphisms are excluded.
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Affiliation(s)
- Olga Shadrina
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Olga Krotova
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia; Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Julia Agapkina
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Ekaterina Knyazhanskaya
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Sergey Korolev
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Elizaveta Starodubova
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Alecia Viklund
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Vladimir Lukashov
- Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mauro Magnani
- Department of Biomolecular Science, University of Urbino "Carla Bo", Via Saffi, 2, 61029 Urbino, Italy
| | - Patrik Medstrand
- Department of Laboratory Medicine, Lund University, Sölvegatan 19, SE-205 02 Malmö, Sweden
| | - Vadim Karpov
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia
| | - Marina Gottikh
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia.
| | - Maria Isaguliants
- Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden.
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Increasing HIV subtype diversity and its clinical implications in a sentinel North American population. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2014; 24:69-73. [PMID: 24421804 DOI: 10.1155/2013/230380] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND HIV-1 is a highly diverse virus; subtypes may exhibit differences in rates of transmission, disease progression, neurotoxicity, antiretroviral treatment failure profiles and accuracy of viral load measurements. To date, the HIV epidemic in Canada and the rest of the developed world has been largely due to subtype B; however, shifts in subtype epidemiology could have significant implications. OBJECTIVE To determine whether there has been an increase in HIV subtype diversity in southern Alberta, Canada. METHODS All 2358 patients receiving any HIV care between December 31, 2001 and December 31, 2010 were included in a retrospective analysis of subtype prevalence and incidence. In an indexed analysis, subtype trends from 1994 to 2010 were also evaluated. RESULTS Between 2001 and 2010, the prevalence of non-B HIV subtypes in patients with a known subtype increased from 7% to 24%. In 2010, the most prevalent non-B subtypes were C (65%), A (11%), CRF02_AG (9.7%), CRF01_AE (4.9%), D (3.9%), G (2.9%) and CRF06_cpx (1.5%). In the indexed analysis, there was an overall proportional increase in non-B subtypes of 2.3% per year. The year-over-year increase in the prevalence of patients infected with a nonsubtype B virus increased from 13% from 1995 to 2002 to 27% from 2003 to 2010 (P=0.01). Incident non-B subtype cases increased from 9.6% to 32.4% over these time periods. CONCLUSIONS This recent and dramatic shift in HIV strain diversity in Canada is unprecedented and may have important public health, research and clinical consequences.
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Performance comparison of an in-house integrase genotyping assay versus the ViroSeq™ Integra48, and study of HIV-1 integrase polymorphisms in Hong Kong. J Clin Virol 2013; 58:299-302. [DOI: 10.1016/j.jcv.2013.06.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/17/2013] [Accepted: 06/17/2013] [Indexed: 11/17/2022]
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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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Abstract
PURPOSE OF REVIEW Integrase strand transfer inhibitors (INSTIs) have become a key component of antiretroviral therapy since the approval of twice-daily raltegravir in 2007 and the more recent approval of elvitegravir in 2012. At the same time, a third compound, dolutegravir, is in late-phase clinical trials, being tested as part of a multidrug once-daily formulation comprising this INSTI and two other antiretroviral (ARV) drugs. This review focuses on the factors leading to the development of drug resistance mutations (DRMs) against INSTIs, evidence of cross-resistance among them, and the results of regimen simplification in regard to this topic. RECENT FINDINGS Sequencing data show that DRMs are highly dynamic in patients failing INSTI therapy. Considerations of viral fitness and drug resistance can together determine the evolution of drug resistance mutations, and in this regard the Y143 and Q148 pathways are superior to the N155 pathway in the promotion of resistance. Preventing the emergence of DRMs requires that effective reverse transcriptase or other inhibitors be used together with INSTIs and that high-level adherence to treatment be maintained. SUMMARY Because of the susceptibility to drug resistance, INSTIs should always be used together with other effective ARV drugs.
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Dimonte S, Babakir-Mina M, Aquaro S, Perno CF. Natural polymorphisms of HIV-1 subtype-C integrase coding region in a large group of ARV-naïve infected individuals. Infection 2013; 41:1097-102. [PMID: 23620062 DOI: 10.1007/s15010-013-0464-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/15/2013] [Indexed: 11/30/2022]
Abstract
PURPOSE Integrase (IN) is an enzyme produced by human immunodeficiency virus (HIV)-1 that enables its genetic material to be integrated into the DNA of the infected cell. Still now, few data are available with detailed analysis of the natural IN polymorphisms of HIV-1 subtype-C in datasets retrieved from antiretroviral-naïve patients; this study focuses on these polymorphisms. METHODS The analysis included 335 HIV-1 subtype-C IN sequences (one per patient). Multi-alignment of IN sequences was performed, and for the definition of a polymorphism, only amino acid changes with prevalence ≥3 % among treatment-naïve patients were considered. RESULTS Seventy IN amino acid positions were fully conserved. Differently, forty-six IN amino acid polymorphic positions were observed, 12 within the N-terminal domain and 13 within the C-terminal domain. In the DDE-catalytic motif, only one mutation per site (D64G/D116G/E152K) was found, while a low variability (<1 %) was observed for IN positions interacting with LEDGF/p75. A major drug resistance mutation for raltegravir (RAL) and elvitegravir (EVG), Q148H, was retrieved from one patient and another RAL primary resistance mutation, Y143H, was also retrieved from another patient. CONCLUSIONS The results from the IN sequences analyzed underlined that some unexpected baseline substitutions affecting the susceptibility to RAL/EVG could be detected in drug-naïve individuals, and, therefore, it should be genotyped before the consideration of HIV-1 IN inhibitors (INIs). The impact of these mutations on the baseline drug susceptibility of HIV-1 subtype-C to INIs may need to be addressed prior to the introduction of these drugs in some Asiatic and African countries.
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Affiliation(s)
- S Dimonte
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00133, Rome, Italy,
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Abstract
PURPOSE OF REVIEW This review highlights recent data on the pathways of resistance that impact the clinical activity of first-generation and second-generation integrase inhibitors. RECENT FINDINGS Raltegravir (RAL) and elvitegravir (EVG) are highly efficacious in first-line antiretroviral therapy, with small numbers of virological failures observed in clinical trials. Durable activity in treatment-experienced patients requires a fully supportive background regimen. RAL and EVG show a low-to-moderate genetic barrier to resistance and extensive cross-resistance, which preclude their sequential use. Resistance to dolutegravir (DTG) is not selected as readily in vitro and has not emerged in studies of treatment-naïve patients to date. Both in vitro and in vivo, DTG retains activity against several RAL and EVG resistant strains, but susceptibility is variably impaired by multiple mutations within the G148 pathway, which are common after RAL or EVG failure. Cross-resistance can be partially overcome by doubling DTG dosing to twice daily, but durability of responses remains dependent on a supportive background regimen. There is variability in the integrase gene of circulating HIV strains, which does not appear to reduce drug activity, although it may influence the emergence and evolution of integrase resistance. Transmission of integrase resistance remains rare but surveillance is required. SUMMARY Integrase inhibitors provide a potent option for the treatment of HIV infection. Drug resistance remains a challenge, which may be partially overcome by the introduction of second-generation compounds. Prompt management of RAL and EVG failure is required to prevent the accumulation of multiple resistance mutations that reduce DTG susceptibility.
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44
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Quashie PK, Mesplède T, Wainberg MA. HIV Drug Resistance and the Advent of Integrase Inhibitors. Curr Infect Dis Rep 2013. [PMID: 23180144 DOI: 10.1007/s11908-012-0305-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review focuses on the topic of HIV integrase inhibitors that are potent antiretroviral drugs that efficiently decrease viral load in patients. However, emergence of resistance mutations against this new class of drugs represents a threat to their long-term efficacy. Here, we provide new information about the most recent mutations identified and other mutations that confer resistance to several integrase inhibitors, such as new resistance mutations-for example, G118R, R263K, and S153Y-that have been identified through in vitro selection studies with second-generation integrase strand transfer inhibitors (INSTIs). These add to the three main resistance pathways involving mutations at positions Y143, N155, and Q148. Deep sequencing, structural modeling, and biochemical analyses are methods that currently help in the understanding of the mechanisms of resistance conferred by these mutations. Although the new resistance mutations appear to confer only low levels of cross-resistance to second-generation drugs, the Q148 pathway with numerous secondary mutations has the potential to significantly decrease susceptibility to all drugs of the INSTI family of compounds.
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Affiliation(s)
- Peter K Quashie
- McGill University AIDS Centre, Lady Davis for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Wainberg MA. The Need for Development of New HIV-1 Reverse Transcriptase and Integrase Inhibitors in the Aftermath of Antiviral Drug Resistance. SCIENTIFICA 2012; 2012:238278. [PMID: 24278679 PMCID: PMC3820659 DOI: 10.6064/2012/238278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 11/01/2012] [Indexed: 05/20/2023]
Abstract
The use of highly active antiretroviral therapy (HAART) involves combinations of drugs to achieve maximal virological response and reduce the potential for the emergence of antiviral resistance. There are two broad classes of reverse transcriptase inhibitors, the nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs). Since the first classes of such compounds were developed, viral resistance against them has necessitated the continuous development of novel compounds within each class. This paper considers the NRTIs and NNRTIs currently in both preclinical and clinical development or approved for second line therapy and describes the patterns of resistance associated with their use, as well as the underlying mechanisms that have been described. Due to reasons of both affordability and availability, some reverse transcriptase inhibitors with low genetic barrier are more commonly used in resource-limited settings. Their use results to the emergence of specific patterns of antiviral resistance and so may require specific actions to preserve therapeutic options for patients in such settings. More recently, the advent of integrase strand transfer inhibitors represents another major step forward toward control of HIV infection, but these compounds are also susceptible to problems of HIV drug resistance.
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Affiliation(s)
- Mark A. Wainberg
- Lady Davis Institute, McGill University AIDS Centre, Jewish General Hospital, Montreal, QC, Canada H3T 1E2
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Turriziani O, Montagna C, Falasca F, Bucci M, Russo G, Lichtner M, Sobze MS, Vullo V, Pistello M, Antonelli G. Short communication: analysis of the integrase gene from HIV type 1-positive patients living in a rural area of West Cameroon. AIDS Res Hum Retroviruses 2012; 28:1729-33. [PMID: 22214532 DOI: 10.1089/aid.2011.0266] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Major mutations associated with HIV-I integrase inhibitors (INI) resistance are rare in INI-naive patients. However, polymorphisms at positions that may influence the genetic barrier and/or drive the selection of specific INI resistance pathways are common in HIV non-B subtypes. The aim was to evaluate the presence of natural polymorphisms and/or INI resistance mutations in HIV-1 non-B subtype samples obtained from INI-naive patients living in rural west Cameroon. Thirty-three HIV-1 non-B samples were obtained from INI-naive African women and, as controls, 15 samples of HIV-1 subtype B were obtained from antiretroviral-naive Italian patients. The integrase gene was amplified and sequenced using Trugene Core Reagents. Several amino acid positions in B and non-B subtypes were found to be polymorphic. Interestingly, two patients infected with the CRF02_AG subtype had the resistance mutations N155H and E157Q/E and 12% of African samples had an amino acid substitution at position 143. Silent mutations leading to a higher increment of genetic barriers were detected at 140 and 151 positions in non B-subtypes. Although most polymorphisms may have little effect on INI susceptibility, the IN gene variations found in the present study should be taken into consideration as they may facilitate or delay the emergence of variants fully resistant to INIs.
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Affiliation(s)
| | - Claudia Montagna
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesca Falasca
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Mauro Bucci
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Gianluca Russo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Miriam Lichtner
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Vincenzo Vullo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Mauro Pistello
- Department of Experimental Pathology, Retrovirus Center and Virology Section, University of Pisa, Pisa, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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47
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Raltegravir-based regimens are effective in HIV-1 group O-infected patients. J Acquir Immune Defic Syndr 2012; 61:e1-3. [PMID: 22918125 DOI: 10.1097/qai.0b013e31826327c4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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48
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Lessells RJ, Katzenstein DK, de Oliveira T. Are subtype differences important in HIV drug resistance? Curr Opin Virol 2012; 2:636-43. [PMID: 23006584 DOI: 10.1016/j.coviro.2012.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/26/2022]
Abstract
The diversity of human immunodeficiency virus type 1 (HIV-1) has given rise to multiple subtypes and recombinant strains. The majority of research into antiretroviral agents and drug resistance has been performed on subtype B viruses, yet non-subtype B strains are responsible for 90% of global infections. Although it seems that combination antiretroviral regimens are effective against all HIV-1 subtypes, there is emerging evidence of subtype differences in drug resistance, relevant to antiretroviral strategies in different parts of the world. For this purpose, extensive sampling of HIV genetic diversity, curation and analyses are required to inform antiretroviral strategies in different parts of the world.
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Affiliation(s)
- R J Lessells
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Somkhele, South Africa
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Tramuto F, Mazzucco W, Maida CM, Affronti A, Affronti M, Montalto G, Vitale F. Serological pattern of Hepatitis B, C, and HIV infections among immigrants in Sicily: epidemiological aspects and implication on public health. J Community Health 2012; 37:547-53. [PMID: 21922163 DOI: 10.1007/s10900-011-9477-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The objective of this study was to describe the prevalence of Hepatitis B virus (HBV), Hepatitis C virus (HCV), and human immunodeficiency virus (HIV) infections in a cohort of immigrants living in Palermo, Sicily. The study was carried out in the period May 2006-June 2010 and recruited a total of 393 patients (59.8% males-median age of 32.6 years). All patients were tested for serological markers of HBV, HCV, and HIV infection. One-hundred thirty-eight (35.1%) individuals did not show any HBV/HCV/HIV serological marker, while 186 (47.3%) were indicative of past or current HBV infection. A total of 42 (10.7%) subjects were HBsAg positive, 59 (15.0%) showed the serological profile "anti-HBc alone", and only 40 (10.1%) were anti-HBs alone. Overall, 22/393 (5.6%) immigrants were anti-HCV positive and 13/327 (4.0%) were infected with HIV. Findings from this study suggest that a suitable screening protocol for the viral blood/sexually transmissible diseases is recommended on entering Italy, and the adoption of health control strategies should also be considered to safeguard the health of the local population.
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Affiliation(s)
- Fabio Tramuto
- Department of Sciences for the Health Promotion "G. D'Alessandro"-Hygiene Section, University of Palermo, 133, via del Vespro, 90127, Palermo, Italy.
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Winters MA, Lloyd RM, Shafer RW, Kozal MJ, Miller MD, Holodniy M. Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations. PLoS One 2012; 7:e40514. [PMID: 22815755 PMCID: PMC3399858 DOI: 10.1371/journal.pone.0040514] [Citation(s) in RCA: 29] [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: 01/30/2012] [Accepted: 06/12/2012] [Indexed: 12/04/2022] Open
Abstract
Failure of antiretroviral regimens containing elvitegravir (EVG) and raltegravir (RAL) can result in the appearance of integrase inhibitor (INI) drug-resistance mutations (DRMs). While several INI DRMs have been identified, the evolution of EVG DRMs and the linkage of these DRMs with protease inhibitor (PI) and reverse transcriptase inhibitor (RTI) DRMs have not been studied at the clonal level. We examined the development of INI DRMs in 10 patients failing EVG-containing regimens over time, and the linkage of INI DRMs with PI and RTI DRMs in these patients plus 6 RAL-treated patients. A one-step RT-nested PCR protocol was used to generate a 2.7 kB amplicon that included the PR, RT, and IN coding region, and standard cloning and sequencing techniques were used to determine DRMs in 1,277 clones (mean 21 clones per time point). Results showed all patients had multiple PI, NRTI, and/or NNRTI DRMs at baseline, but no primary INI DRM. EVG-treated patients developed from 2 to 6 strains with different primary INI DRMs as early as 2 weeks after initiation of treatment, predominantly as single mutations. The prevalence of these strains fluctuated and new strains, and/or strains with new combinations of INI DRMs, developed over time. Final failure samples (weeks 14 to 48) typically showed a dominant strain with multiple mutations or N155H alone. Single N155H or multiple mutations were also observed in RAL-treated patients at virologic failure. All patient strains showed evidence of INI DRM co-located with single or multiple PI and/or RTI DRMs on the same viral strand. Our study shows that EVG treatment can select for a number of distinct INI-resistant strains whose prevalence fluctuates over time. Continued appearance of new INI DRMs after initial INI failure suggests a potent, highly dynamic selection of INI resistant strains that is unaffected by co-location with PI and RTI DRMs.
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Affiliation(s)
- Mark A Winters
- AIDS Research Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America.
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