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Murphy RA, Bedesi PH, Perumal N, Gosnell BI, Hatlen TJ, Brijkumar J. Dolutegravir Resistance in African Programmatic Settings Among Patients With Failure of Dolutegravir-based ART. Open Forum Infect Dis 2024; 11:ofae321. [PMID: 38947737 PMCID: PMC11214099 DOI: 10.1093/ofid/ofae321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024] Open
Abstract
Dolutegravir resistance is emerging in routine clinical contexts in southern Africa, primarily in patients with prior treatment experience failing dolutegravir-based antiretroviral therapy (ART). This potential issue was raised by The Nucleosides and Darunavir/Dolutegravir in Africa trial that compared dolutegravir and boosted protease inhibitor-based therapy as second-line ART, in which new dolutegravir resistance was observed at failure. However, recent data suggest that also at risk are patients who were transitioned to dolutegravir from non-nucleoside reverse transcriptase inhibitor-based ART while viremic. Identifying patients experiencing failure of dolutegravir with resistance will be difficult given current gaps in viral load monitoring and limited capacity for genotypic resistance testing. As a result, in the short term, most patients affected will go unrecognized, with particularly important implications for patients affected who have advanced HIV or who are pregnant/breastfeeding. Prospective research is needed to understand the scope of the problem, identify additional risk factors, and determine best management. In the short term, for most patients with dolutegravir resistance and prior non-nucleoside reverse transcriptase inhibitor exposure, the best option will be a timely switch to a regimen anchored by a boosted protease inhibitor, with a high genetic barrier to resistance.
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Affiliation(s)
- Richard A Murphy
- Division of Infectious Diseases, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- Division of Infectious Diseases, White River Junction Veterans Affairs Medical Center, White River Junction, Vermont, USA
| | | | | | - Bernadett I Gosnell
- Department of Infectious Diseases, University of KwaZulu-Natal, Durban, South Africa
| | - Timothy J Hatlen
- Division of HIV, Lundquist Institute for Biomedical Innovation at Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
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Wang Y, Kingwara L, Wagner AD, Yongo N, Hassan SA, Liu S, Oyaro P, Patel RC. Optimising HIV drug resistance testing laboratory networks in Kenya: insights from systems engineering modelling. BMJ Open 2024; 14:e079988. [PMID: 38569688 PMCID: PMC11146353 DOI: 10.1136/bmjopen-2023-079988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND HIV drug resistance (DR) is a growing threat to the durability of current and future HIV treatment success. DR testing (DRT) technologies are very expensive and specialised, relying on centralised laboratories in most low and middle-income countries. Modelling for laboratory network with point-of-care (POC) DRT assays to minimise turnaround time (TAT), is urgently needed to meet the growing demand. METHODS We developed a model with user-friendly interface using integer programming and queueing theory to improve the DRT system in Kisumu County, Kenya. We estimated DRT demand based on both current and idealised scenarios and evaluated a centralised laboratory-only network and an optimised POC DRT network. A one-way sensitivity analysis of key user inputs was conducted. RESULTS In a centralised laboratory-only network, the mean TAT ranged from 8.52 to 8.55 working days, and the system could not handle a demand proportion exceeding 1.6%. In contrast, the mean TAT for POC DRT network ranged from 1.13 to 2.11 working days, with demand proportion up to 4.8%. Sensitivity analyses showed that expanding DRT hubs reduces mean TAT substantially while increasing the processing rate at national labs had minimal effect. For instance, doubling the current service rate at national labs reduced the mean TAT by only 0.0%-1.9% in various tested scenarios, whereas doubling the current service rate at DRT hubs reduced the mean TAT by 37.5%-49.8%. In addition, faster batching modes and transportation were important factors influencing the mean TAT. CONCLUSIONS Our model offers decision-makers an informed framework for improving the DRT system using POC in Kenya. POC DRT networks substantially reduce mean TAT and can handle a higher demand proportion than a centralised laboratory-only network, especially for children and pregnant women living with HIV, where there is an immediate push to use DRT results for patient case management.
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Affiliation(s)
- Yinsheng Wang
- Department of Industrial & Systems Engineering, University of Washington, Seattle, Washington, USA
| | - Leonard Kingwara
- National HIV Reference Laboratory, Kenya Ministry of Health, Nairobi, Kenya
| | - Anjuli Dawn Wagner
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Nashon Yongo
- University of Washington Kenya Research and Training Center, Seattle, Washington, USA
| | | | - Shan Liu
- Department of Industrial and Systems Engineering, University of Washington, Seattle, Washington, USA
| | | | - Rena C Patel
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Abimbola Salubi C, Abbo HS, Jahed N, Titinchi S. Medicinal chemistry perspectives on the development of piperazine-containing HIV-1 inhibitors. Bioorg Med Chem 2024; 99:117605. [PMID: 38246116 DOI: 10.1016/j.bmc.2024.117605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
The Human immunodeficiency virus (HIV) is the causative agent of acquired immunodeficiency syndrome (AIDS), one of the most perilous diseases known to humankind. A 2023 estimate put the number of people living with HIV around 40 million worldwide, with the majority benefiting from various antiretroviral therapies. Consequently, the urgent need for the development of effective drugs to combat this virus cannot be overstated. In the realm of medicinal and organic chemistry, the synthesis and identification of novel compounds capable of inhibiting HIV enzymes at different stages of their life cycle are of paramount importance. Notably, the spotlight is on the progress made in enhancing the potency of HIV inhibitors through the use of piperazine-based compounds. Multiple studies have revealed that the incorporation of a piperazine moiety results in a noteworthy enhancement of anti-HIV activity. The piperazine ring assumes a pivotal role in shaping the pharmacophore responsible for inhibiting HIV-1 at critical stage, including attachment, reverse transcription, integration, and protease activity. This review also sheds light on the various opportunities that can be exploited to develop effective antiretroviral targets and eliminate latent HIV reservoirs. The advancement of highly potent analogues in HIV inhibitor research has been greatly facilitated by contemporary medicinal strategies, including molecular/fragment hybridization, structure-based drug design, and bioisosterism. These techniques have opened up new avenues for the development of compounds with enhanced efficacy in combating the virus.
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Affiliation(s)
- Christiana Abimbola Salubi
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Hanna S Abbo
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Nazeeen Jahed
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Salam Titinchi
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa.
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Branda F, Giovanetti M, Sernicola L, Farcomeni S, Ciccozzi M, Borsetti A. Comprehensive Analysis of HIV-1 Integrase Resistance-Related Mutations in African Countries. Pathogens 2024; 13:102. [PMID: 38392840 PMCID: PMC10892843 DOI: 10.3390/pathogens13020102] [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: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The growing emergence of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance in sub-Saharan Africa (SSA) led to the World Health Organization (WHO) recommending, in 2018, a transition to dolutegravir (DTG) as a first-line antiretroviral therapy (ART) in SSA. The broad HIV-1 genetic diversity in SSA could shape DTG effectiveness and the pattern of drug resistance mutations (DRMs) in this region. This study evaluated HIV-1 integrase (IN) DRMs and conserved regions among published groups M, N, O, and P HIV-1 sequences spanning forty years of the HIV epidemic during the transition of DTG-based ART. Overall, we found low levels of integrase strand transfer inhibitor (INSTI)-DRMs (<1%) across HIV groups between the years 1983 and 2023; however, it was unexpected to detect DRMs at statistically significantly higher frequencies in pre-INSTI (1983-2007) than in the INSTI (2008-2023) era. The variability of accessory INSTI-DRMs depended on the HIV subtypes, with implications for susceptibility to DTG. Our findings provide new perspectives on the molecular epidemiology and drug resistance profiles of INSTIs in SSA, emphasizing the need for ongoing surveillance and customized treatment approaches to address the continent's varied HIV subtypes and changing resistance patterns.
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Affiliation(s)
- Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, Brazil
| | - Leonardo Sernicola
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| | - Stefania Farcomeni
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
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Loaiza JD, Chvatal-Medina M, Hernandez JC, Rugeles MT. Integrase inhibitors: current protagonists in antiretroviral therapy. Immunotherapy 2023; 15:1477-1495. [PMID: 37822251 DOI: 10.2217/imt-2023-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Since HIV was identified as the etiological agent of AIDS, there have been significant advances in antiretroviral therapy (ART) that has reduced morbidity/mortality. Still, the viral genome's high mutation rate, suboptimal ART regimens, incomplete adherence to therapy and poor control of the viral load generate variants resistant to multiple drugs. Licensing over 30 anti-HIV drugs worldwide, including integrase inhibitors, has marked a milestone since they are potent and well-tolerated drugs. In addition, they favor a faster recovery of CD4+ T cells. They also increase the diversity profile of the gut microbiota and reduce inflammatory markers. All of these highlight the importance of including them in different ART regimens.
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Affiliation(s)
- John D Loaiza
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan C Hernandez
- Infettare, Facultad de medicina, Universidad Cooperativa de Colombia, Medellín, 050012, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
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Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, d'Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos RD. HIV-1 drug resistance in people on dolutegravir-based antiretroviral therapy: a collaborative cohort analysis. Lancet HIV 2023; 10:e733-e741. [PMID: 37832567 PMCID: PMC10913014 DOI: 10.1016/s2352-3018(23)00228-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND The widespread use of the integrase strand transfer inhibitor (INSTI) dolutegravir in first-line and second-line antiretroviral therapy (ART) might facilitate emerging resistance. The DTG RESIST study combined data from HIV cohorts to examine patterns of drug resistance mutations (DRMs) and identify risk factors for dolutegravir resistance. METHODS We included cohorts with INSTI resistance data from two collaborations (ART Cohort Collaboration, International epidemiology Databases to Evaluate AIDS in Southern Africa), and the UK Collaborative HIV Cohort. Eight cohorts from Canada, France, Germany, Italy, the Netherlands, Switzerland, South Africa, and the UK contributed data on individuals who were viraemic on dolutegravir-based ART and underwent genotypic resistance testing. Individuals with unknown dolutegravir initiation date were excluded. Resistance levels were categorised using the Stanford algorithm. We identified risk factors for resistance using mixed-effects ordinal logistic regression models. FINDINGS We included 599 people with genotypic resistance testing on dolutegravir-based ART between May 22, 2013, and Dec 20, 2021. Most had HIV-1 subtype B (n=351, 59%), a third had been exposed to first-generation INSTIs (n=193, 32%), 70 (12%) were on dolutegravir dual therapy, and 18 (3%) were on dolutegravir monotherapy. INSTI DRMs were detected in 86 (14%) individuals; 20 (3%) had more than one mutation. Most (n=563, 94%) were susceptible to dolutegravir, seven (1%) had potential low, six (1%) low, 17 (3%) intermediate, and six (1%) high-level dolutegravir resistance. The risk of dolutegravir resistance was higher on dolutegravir monotherapy (adjusted odds ratio [aOR] 34·1, 95% CI 9·93-117) and dolutegravir plus lamivudine dual therapy (aOR 9·21, 2·20-38·6) compared with combination ART, and in the presence of potential low or low (aOR 5·23, 1·32-20·7) or intermediate or high-level (aOR 13·4, 4·55-39·7) nucleoside reverse transcriptase inhibitor (NRTI) resistance. INTERPRETATION Among people with viraemia on dolutegravir-based ART, INSTI DRMs and dolutegravir resistance were rare. NRTI resistance substantially increased the risk of dolutegravir resistance, which is of concern, notably in resource-limited settings. Monitoring is important to prevent resistance at the individual and population level and ensure the long-term sustainability of ART. FUNDING US National Institutes of Health, Swiss National Science Foundation.
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Affiliation(s)
- Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefanie Hossmann
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Suzanne M Ingle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hajra Okhai
- Institute for Global Health, University College London, London, UK
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Johannes Mouton
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Melanie Stecher
- German Center for Infection Research (DZIF), Partner-Site Cologne-Bonn, Cologne, Germany; Department I of Internal Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | - M John Gill
- Southern Alberta Clinic, Calgary, AB, Canada; Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jonathan A C Sterne
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Herd CL, Mellet J, Mashingaidze T, Durandt C, Pepper MS. Consequences of HIV infection in the bone marrow niche. Front Immunol 2023; 14:1163012. [PMID: 37497228 PMCID: PMC10366613 DOI: 10.3389/fimmu.2023.1163012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Dysregulation of the bone marrow niche resulting from the direct and indirect effects of HIV infection contributes to haematological abnormalities observed in HIV patients. The bone marrow niche is a complex, multicellular environment which functions primarily in the maintenance of haematopoietic stem/progenitor cells (HSPCs). These adult stem cells are responsible for replacing blood and immune cells over the course of a lifetime. Cells of the bone marrow niche support HSPCs and help to orchestrate the quiescence, self-renewal and differentiation of HSPCs through chemical and molecular signals and cell-cell interactions. This narrative review discusses the HIV-associated dysregulation of the bone marrow niche, as well as the susceptibility of HSPCs to infection by HIV.
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Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, d’Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos R. sHIV-1 drug resistance in people on dolutegravir-based ART: Collaborative analysis of cohort studies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.05.23288183. [PMID: 37066200 PMCID: PMC10104228 DOI: 10.1101/2023.04.05.23288183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Background The widespread use of the integrase strand transfer inhibitor (INSTI) dolutegravir (DTG) in first- and second-line antiretroviral therapy (ART) may facilitate emerging resistance. We combined data from HIV cohorts to examine patterns of drug resistance mutations (DRMs) and identify risk factors for DTG resistance. Methods Eight cohorts from Canada, Europe, and South Africa contributed data on individuals with genotypic resistance testing on DTG-based ART. Resistance levels were categorised using the Stanford algorithm. We identified risk factors for resistance using mixed-effects ordinal logistic regression models. Results We included 750 people with genotypic resistance testing on DTG-based ART between 2013 and 2022. Most had HIV subtype B (N=444, 59·2%) and were treatment-experienced; 134 (17.9%) were on DTG dual and 19 (2.5%) on DTG monotherapy. INSTI DRMs were detected in 100 (13·3%) individuals; 21 (2·8%) had more than one mutation. Most (N=713, 95·1%) were susceptible to DTG, 8 (1·1%) had potential-low, 5 (0·7%) low, 18 (2·4%) intermediate and 6 (0·8%) high-level DTG resistance. The risk of DTG resistance was higher on DTG monotherapy (adjusted odds ratio (aOR) 37·25, 95% CI 11·17 to 124·2) and DTG lamivudine dual therapy (aOR 6·59, 95% CI 1·70 to 25·55) compared to combination ART, and higher in the presence of potential-low/low (aOR 4.62, 95% CI 1.24 to 17.2) or intermediate/high-level (aOR 7·01, 95% CI 2·52 to 19·48) nucleoside reverse transcriptase inhibitors (NRTI) resistance. Viral load on DTG showed a trend towards increased DTG resistance (aOR 1·42, 95% CI 0·92 to 2·19 per standard deviation of log10 area under the viral load curve). Interpretation Among people experiencing virological failure on DTG-based ART, INSTI DRMs were uncommon, and DTG resistance was rare. DTG monotherapy and NRTI resistance substantially increased the risk for DTG resistance, which is of concern, notably in resource-limited settings.
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Affiliation(s)
- Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefanie Hossmann
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Switzerland
| | - Suzanne M. Ingle
- Population Health Sciences, Bristol Medical School, University of Bristol, UK
| | - Hajra Okhai
- Institute for Global Health, University College London, UK
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Johannes Mouton
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Melanie Stecher
- German Center for Infection Research (DZIF), Partner-Site Cologne-Bonn, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf
| | - Antonella d’Arminio Monforte
- Italian Cohort Naive Antiretrovirals, (ICONA) L’Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Milano, Italy
| | - M. John Gill
- Southern Alberta Clinic, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Gary Maartens
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Richard Lessells
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Switzerland
- Population Health Sciences, Bristol Medical School, University of Bristol, UK
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Roger Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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HIV and Drug-Resistant Subtypes. Microorganisms 2023; 11:microorganisms11010221. [PMID: 36677513 PMCID: PMC9861097 DOI: 10.3390/microorganisms11010221] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/03/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Acquired Immunodeficiency Syndrome (AIDS) is a human viral infectious disease caused by the positive-sense single-stranded (ss) RNA Human Immunodeficiency Virus (HIV) (Retroviridae family, Ortervirales order). HIV-1 can be distinguished into various worldwide spread groups and subtypes. HIV-2 also causes human immunodeficiency, which develops slowly and tends to be less aggressive. HIV-2 only partially homologates to HIV-1 despite the similar derivation. Antiretroviral therapy (ART) is the treatment approved to control HIV infection, based on multiple antiretroviral drugs that belong to different classes: (i) NNRTIs, (ii) NRTIs, (iii) PIs, (iv) INSTIs, and (v) entry inhibitors. These drugs, acting on different stages of the HIV life cycle, decrease the patient's total burden of HIV, maintain the function of the immune system, and prevent opportunistic infections. The appearance of several strains resistant to these drugs, however, represents a problem today that needs to be addressed as best as we can. New outbreaks of strains show a widespread geographic distribution and a highly variable mortality rate, even affecting treated patients significantly. Therefore, novel treatment approaches should be explored. The present review discusses updated information on HIV-1- and HIV-2-resistant strains, including details on different mutations responsible for drug resistance.
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Ghasabi F, Hashempour A, Khodadad N, Bemani S, Keshani P, Shekiba MJ, Hasanshahi Z. First report of computational protein-ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients. Biochem Biophys Rep 2022; 30:101254. [PMID: 35368742 PMCID: PMC8968007 DOI: 10.1016/j.bbrep.2022.101254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/04/2022] Open
Abstract
Background Iran has recently included integrase (INT) inhibitors (INTIs) in the first-line treatment regimen in human immunodeficiency virus (HIV)-infected patients. However, there is no bioinformatics data to elaborate the impact of resistance-associated mutations (RAMs) and naturally occurring polymorphisms (NOPs) on INTIs treatment outcome in Iranian patients. Method In this cross-sectional survey, 850 HIV-1-infected patients enrolled; of them, 78 samples had successful sequencing results for INT gene. Several analyses were performed including docking screening, genotypic resistance, secondary/tertiary structures, post-translational modification (PTM), immune epitopes, etc. Result The average docking energy (E value) of different samples with elvitegravir (EVG) and raltegravir (RAL) was more than other INTIs. Phylogenetic tree analysis and Stanford HIV Subtyping program revealed HIV-1 CRF35-AD was the predominant subtype (94.9%) in our cases; in any event, online subtyping tools confirmed A1 as the most frequent subtype. For the first time, CRF-01B and BF were identified as new subtypes in Iran. Decreased CD4 count was associated with several factors: poor or unstable adherence, naïve treatment, and drug user status. Conclusion As the first bioinformatic report on HIV-integrase from Iran, this study indicates that EVG and RAL are the optimal INTIs in first-line antiretroviral therapy (ART) in Iranian patients. Some conserved motifs and specific amino acids in INT-protein binding sites have characterized that mutation(s) in them may disrupt INT-drugs interaction and cause a significant loss in susceptibility to INTIs. Good adherence, treatment of naïve patients, and monitoring injection drug users are fundamental factors to control HIV infection in Iran effectively.
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Key Words
- Antiretroviral therapy, ART
- Behavioral Diseases Consultation Center, BDCC
- Bictegravir, BIC
- C-terminal domain, CTD
- CRF35-AD
- Cabotegravir, CBT
- Catalytic core domain, CCD
- Dolutegravir, DTG
- Drug resistance
- Elvitegravir, EVG
- Grand average hydropathy, GRAVY
- HIV
- Human immunodeficiency virus, HIV
- INT, Integrase
- INTIs, Integrase inhibitors (INTIs)
- Injecting drug users, IDUs
- Integrase
- Integrase inhibitors
- Molecular docking
- N-terminal domain, NTD
- Naturally occurring polymorphisms, NOPs
- Post-translational modification, PTM
- Raltegravir, RAL
- Resistance-associated mutations, RAMs
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Affiliation(s)
- Farzane Ghasabi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soudabeh Bemani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parisa Keshani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Javad Shekiba
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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11
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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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Giovanetti M, Farcomeni S, Sernicola L, Virtuoso S, Sulekova LF, Maggiorella MT, Buttò S, Taliani G, Ciccozzi M, Borsetti A. Analysis of HIV‐1 integrase genotypes and polymorphisms among integrase inhibitors‐based antiretroviral treatment naïve patients in South Sudan. J Med Virol 2022; 94:3320-3327. [DOI: 10.1002/jmv.27713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Marta Giovanetti
- Reference Laboratory of Flavivirus, Oswaldo Cruz Institute, Fundação Oswaldo CruzRio de JaneiroBrazil
- Laboratório de Genética Celular e Molecular, ICBUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrazil
- Medical Statistics and Molecular EpidemiologyUniversity Campus Bio‐Medico of RomeRomeItaly
| | - Stefania Farcomeni
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | - Leonardo Sernicola
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | - Sara Virtuoso
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | | | - Maria T. Maggiorella
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | - Stefano Buttò
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | - Gloria Taliani
- Chronic Infectious Diseases Unit, Policlinico Umberto I“Sapienza” University of RomeRomeItaly
| | - Massimo Ciccozzi
- Medical Statistics and Molecular EpidemiologyUniversity Campus Bio‐Medico of RomeRomeItaly
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
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13
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Ngoufack Jagni Semengue E, Santoro MM, Ndze VN, Ka'e AC, Yagai B, Nka AD, Dambaya B, Takou D, Teto G, Fabeni L, Colizzi V, Perno CF, Ceccherini-Silberstein F, Fokam J. HIV-1 integrase resistance associated mutations and the use of dolutegravir in Sub-Saharan Africa: A systematic review and meta-analysis. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000826. [PMID: 36962573 PMCID: PMC10021461 DOI: 10.1371/journal.pgph.0000826] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/12/2022] [Indexed: 11/12/2022]
Abstract
As sub-Saharan Africa (SSA) countries are transitioning to dolutegravir (DTG)-based ART, baseline data are required for optimal monitoring of therapeutic response. In this frame, we sought to generate up-to-date evidence on the use of integrase-strand transfer inhibitors (INSTI) and associated drug resistance mutations (DRMs) within SSA. In this systematic review and meta-analysis, we included randomized and non-randomized trials, cohort-studies, cross-sectional studies, and case-reports published on INSTI or integrase DRMs in SSA. We included studies of patients exposed to DTG, raltegravir (RAL) or elvitegravir (EVG). Primary outcomes were "the rate of virological control (VC:<50copies/ml)" and "the presence of DRMs" on INSTI-based regimens among patients in SSA. We synthesised extracted data using subgroup analysis, and random effect models were used where appropriate. Additional analyses were conducted to assess study heterogeneity. We identified 1,916 articles/citations through database searches, of which 26 were included in the analysis pertaining to 5,444 patients (mean age: 37±13 years), with 67.62% (3681/5444) female. Specifically, 46.15% (12/26) studies focused on DTG, 26.92% (7/26) on RAL, 23.08% (6/26) on both DTG and RAL, and 3.85% (1/26) on EVG. We found an increasing use of DTG overtime (0% before 2018 to 100% in 2021). Median treatment duration under INSTI-based regimens was 12 [9-36] months. Overall, the rate of VC was 88.51% [95%CI: 73.83-97.80] with DTG vs. 82.49% [95%CI: 55.76-99.45] and 96.55% [95%CI: 85.7-100.00] with RAL and EVG, respectively. In univariate analysis, VC with DTG-containing vs. other INSTI-regimens was significantly higher (OR = 1.44 [95%CI: 1.15-1.79], p = 0.0014). Among reported DRMs at failure, the only DTG resistance-mutations were G118R and R263K. In SSA, DTG presents a superiority effect in VC compared to other INSTIs. Nonetheless, the early detection of INSTI-DRMs calls for sentinel surveillance for a successful transition and a sustained efficacy of DTG in SSA. PROSPERO Registration Number: CRD42019122424.
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Affiliation(s)
- Ezechiel Ngoufack Jagni Semengue
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Evangelical University of Cameroon, Bandjoun, Cameroon
- University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Aude Christelle Ka'e
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Evangelical University of Cameroon, Bandjoun, Cameroon
- Doctoral School of Microbiology, Immunology, Infectious Diseases and Transplants, MIMIT, University of Rome "Tor Vergata", Rome, Italy
| | - Bouba Yagai
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Alex Durand Nka
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Evangelical University of Cameroon, Bandjoun, Cameroon
- University of Rome "Tor Vergata", Rome, Italy
| | - Beatrice Dambaya
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Desiré Takou
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Georges Teto
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" -IRCCS, Rome, Italy
| | - Vittorio Colizzi
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Evangelical University of Cameroon, Bandjoun, Cameroon
- University of Rome "Tor Vergata", Rome, Italy
- Chair of Biotechnology-UNESCO, University of Rome "Tor Vergata", Rome, Italy
| | - Carlo-Federico Perno
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Bambino Gesu Children's Hospital, Rome, Italy
| | - Francesca Ceccherini-Silberstein
- University of Rome "Tor Vergata", Rome, Italy
- Doctoral School of Microbiology, Immunology, Infectious Diseases and Transplants, MIMIT, University of Rome "Tor Vergata", Rome, Italy
| | - Joseph Fokam
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
- National HIV Drug Resistance Working Group, Ministry of Public Health, Yaounde, Cameroon
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14
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Got FEB, Recordon-Pinson P, Loubano-Voumbi G, Ebourombi D, Blondot ML, Metifiot M, Ondzotto G, Andreola ML. Absence of Resistance Mutations in the Integrase Coding Region among ART-Experienced Patients in the Republic of the Congo. Microorganisms 2021; 9:2355. [PMID: 34835480 PMCID: PMC8620905 DOI: 10.3390/microorganisms9112355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND HIV infects around one hundred thousand patients in the Republic of the Congo. Approximately 25% of them receive an antiretroviral treatment; current first-line regimens include two NRTIs and one NNRTI, reverse transcriptase inhibitors. Recently, protease inhibitors (PIs) were also introduced as second-line therapy upon clinical signs of treatment failure. Due to the limited number of molecular characterizations and amount of drug resistance data available in the Republic of the Congo, this study aims to evaluate the prevalence of circulating resistance mutations within the pol region. METHODS HIV-positive, ART-experienced patients have been enrolled in four semi-urban localities in the Republic of the Congo. Plasma samples were collected, and viral RNA was extracted. The viral load for each patient was evaluated by RT-qPCR, following the general diagnostic procedures of the University Hospital of Bordeaux. Finally, drug resistance genotyping and phylogenetic analysis were conducted following Sanger sequencing of the pol region. RESULTS A high diversity of HIV-1 strains was observed with many recombinant forms. Drug resistance mutations in RT and PR genes were determined and correlated to HAART. Because integrase inhibitors are rarely included in treatments in the Republic of the Congo, the prevalence of integrase drug resistance mutations before treatment was also determined. Interestingly, very few mutations were observed. CONCLUSIONS We confirmed a high diversity of HIV-1 in the Republic of the Congo. Most patients presented an accumulation of mutations conferring resistance against NRTIs, NNRTIs and PIs. Nonetheless, the absence of integrase mutations associated with drug resistance suggests that the introduction of integrase inhibitors into therapy will be highly beneficial to patients in the Republic of the Congo.
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Affiliation(s)
- Ferdinand Emaniel Brel Got
- Faculté des Sciences de la Santé, Université Marien Ngouabi, Brazzaville BP69, Democratic Republic of the Congo; (F.E.B.G.); (G.L.-V.); (D.E.); (G.O.)
- UMR 5234 Microbiologie Fondamentale et Pathogénicité, CNRS, Univ. Bordeaux, F-33000 Bordeaux, France; (M.-L.B.); (M.M.); (M.-L.A.)
| | - Patricia Recordon-Pinson
- UMR 5234 Microbiologie Fondamentale et Pathogénicité, CNRS, Univ. Bordeaux, F-33000 Bordeaux, France; (M.-L.B.); (M.M.); (M.-L.A.)
- Virology Laboratory, WHO HIV Center, CHU Bordeaux, F-33000 Bordeaux, France
| | - Ghislain Loubano-Voumbi
- Faculté des Sciences de la Santé, Université Marien Ngouabi, Brazzaville BP69, Democratic Republic of the Congo; (F.E.B.G.); (G.L.-V.); (D.E.); (G.O.)
| | - Dagene Ebourombi
- Faculté des Sciences de la Santé, Université Marien Ngouabi, Brazzaville BP69, Democratic Republic of the Congo; (F.E.B.G.); (G.L.-V.); (D.E.); (G.O.)
| | - Marie-Lise Blondot
- UMR 5234 Microbiologie Fondamentale et Pathogénicité, CNRS, Univ. Bordeaux, F-33000 Bordeaux, France; (M.-L.B.); (M.M.); (M.-L.A.)
| | - Mathieu Metifiot
- UMR 5234 Microbiologie Fondamentale et Pathogénicité, CNRS, Univ. Bordeaux, F-33000 Bordeaux, France; (M.-L.B.); (M.M.); (M.-L.A.)
| | - Gontran Ondzotto
- Faculté des Sciences de la Santé, Université Marien Ngouabi, Brazzaville BP69, Democratic Republic of the Congo; (F.E.B.G.); (G.L.-V.); (D.E.); (G.O.)
| | - Marie-Line Andreola
- UMR 5234 Microbiologie Fondamentale et Pathogénicité, CNRS, Univ. Bordeaux, F-33000 Bordeaux, France; (M.-L.B.); (M.M.); (M.-L.A.)
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15
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Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Comput Biol 2021; 17:e1008363. [PMID: 34491984 PMCID: PMC8448360 DOI: 10.1371/journal.pcbi.1008363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 09/17/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Although combination antiretroviral therapies seem to be effective at controlling HIV-1 infections regardless of the viral subtype, there is increasing evidence for subtype-specific drug resistance mutations. The order and rates at which resistance mutations accumulate in different subtypes also remain poorly understood. Most of this knowledge is derived from studies of subtype B genotypes, despite not being the most abundant subtype worldwide. Here, we present a methodology for the comparison of mutational networks in different HIV-1 subtypes, based on Hidden Conjunctive Bayesian Networks (H-CBN), a probabilistic model for inferring mutational networks from cross-sectional genotype data. We introduce a Monte Carlo sampling scheme for learning H-CBN models for a larger number of resistance mutations and develop a statistical test to assess differences in the inferred mutational networks between two groups. We apply this method to infer the temporal progression of mutations conferring resistance to the protease inhibitor lopinavir in a large cross-sectional cohort of HIV-1 subtype C genotypes from South Africa, as well as to a data set of subtype B genotypes obtained from the Stanford HIV Drug Resistance Database and the Swiss HIV Cohort Study. We find strong support for different initial mutational events in the protease, namely at residue 46 in subtype B and at residue 82 in subtype C. The inferred mutational networks for subtype B versus C are significantly different sharing only five constraints on the order of accumulating mutations with mutation at residue 54 as the parental event. The results also suggest that mutations can accumulate along various alternative paths within subtypes, as opposed to a unique total temporal ordering. Beyond HIV drug resistance, the statistical methodology is applicable more generally for the comparison of inferred mutational networks between any two groups. There is a disparity in the distribution of infections by HIV-1 subtype in the world. Subtype B is predominant in America, Australia and western and central Europe, and most therapeutic strategies are based on research and clinical studies on this subtype. However, non-B subtypes represent the majority of global HIV-1 infections; e.g., subtype C alone accounts for nearly half of all HIV-1 infections. We present a statistical framework enabling the comparison of patterns of accumulating mutations in different HIV-1 subtypes. Specifically, we compare the temporal ordering of lopinavir resistance mutations in HIV-1 subtypes B versus C. To this end, we combine the Hidden Conjunctive Bayesian Network (H-CBN) model with an approximate inference scheme enabling comparisons of larger networks. We show that the development of resistance to lopinavir differs significantly between subtypes B and C, such that findings based on subtype B sequences can not always be applied to sybtype C. The described methodology is suitable for comparing different subgroups in the context of other evolutionary processes.
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16
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Characterizing HIV-1 Genetic Subtypes and Drug Resistance Mutations among Children, Adolescents and Pregnant Women in Sierra Leone. Genes (Basel) 2021; 12:genes12091314. [PMID: 34573296 PMCID: PMC8469552 DOI: 10.3390/genes12091314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/15/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) drug resistance (HIVDR) is widespread in sub-Saharan Africa. Children and pregnant women are particularly vulnerable, and laboratory testing capacity remains limited. We, therefore, used a cross-sectional design and convenience sampling to characterize HIV subtypes and resistance-associated mutations (RAMs) in these groups in Sierra Leone. In total, 96 children (age 2–9 years, 100% ART-experienced), 47 adolescents (age 10–18 years, 100% ART-experienced), and 54 pregnant women (>18 years, 72% ART-experienced) were enrolled. Median treatment durations were 36, 84, and 3 months, respectively, while the sequencing success rates were 45%, 70%, and 59%, respectively, among children, adolescents, and pregnant women. Overall, the predominant HIV-1 subtype was CRF02_AG (87.9%, 95/108), with minority variants constituting 12%. Among children and adolescents, the most common RAMs were M184V (76.6%, n = 49/64), K103N (45.3%, n = 29/64), Y181C/V/I (28.1%, n = 18/64), T215F/Y (25.0%, n = 16/64), and V108I (18.8%, n = 12/64). Among pregnant women, the most frequent RAMs were K103N (20.6%, n = 7/34), M184V (11.8%, n = 4/34), Y181C/V/I (5.9%, n = 2/34), P225H (8.8%, n = 3/34), and K219N/E/Q/R (5.9%, n = 2/34). Protease and integrase inhibitor-RAMs were relatively few or absent. Based on the genotype susceptibility score distributions, 73%, 88%, and 14% of children, adolescents, and pregnant women, respectively, were not susceptible to all three drug components of the WHO preferred first-line regimens per 2018 guidelines. These findings suggest that routine HIVDR surveillance and access to better ART choices may improve treatment outcomes in Sierra Leone.
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17
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Semengue ENJ, Armenia D, Inzaule S, Santoro MM, Dambaya B, Takou D, Teto G, Nka AD, Yagai B, Fabeni L, Chenwi C, Angong Beloumou G, Djupsa Ndjeyep SC, Colizzi V, Perno CF, Ceccherini-Silberstein F, Fokam J. Baseline integrase drug resistance mutations and conserved regions across HIV-1 clades in Cameroon: implications for transition to dolutegravir in resource-limited settings. J Antimicrob Chemother 2021; 76:1277-1285. [PMID: 33501504 DOI: 10.1093/jac/dkab004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Transition to dolutegravir-based regimens in resource-limited settings (RLS) requires prior understanding of HIV-1 integrase variants and conserved regions. Therefore, we evaluated integrase drug resistance mutations (DRMs) and conserved regions amongst integrase strand transfer inhibitor (INSTI)-naive patients harbouring diverse HIV-1 clades in Cameroon. METHODS A cross-sectional study was conducted amongst 918 INSTI-naive patients from Cameroon (89 ART-naive and 829 ART-experienced patients). HIV-1 sequences were interpreted regarding INSTI-DRMs using the Stanford HIVdb v8.9-1 and the 2019 IAS-USA list. Amino acid positions with <1% variability were considered as highly conserved. Subtyping was performed by phylogeny. RESULTS Overall prevalence (95% CI) of INSTI-DRMs was 0.8% (0.4-1.7), with 0.0% (0.0-4.0) amongst ART-naive versus 0.9% (0.5-1.9) amongst ART-experienced patients; P = 0.44. Accessory mutations (95% CI) were found in 33.8% (30.9-37.0), with 38.2% (28.1-49.1) amongst ART-naive versus 33.4% (30.4-36.7) amongst ART-experienced patients; P = 0.21. Of 288 HIV-1 integrase amino acid positions, 58.3% were highly conserved across subtypes in the following major regions: V75-G82, E85-P90, H114-G118, K127-W132, E138-G149, Q168-L172, T174-V180, W235-A239 and L241-D253. Wide genetic diversity was found (37 clades), including groups M (92.3%), N (1.4%), O (6.2%) and P (0.1%). Amongst group M, CRF02_AG was predominant (47.4%), with a significantly higher frequency (95% CI) of accessory mutations compared with non-AG [41.4% (36.8-46.0) versus 27.1% (23.3-31.2) respectively; P < 0.001]. CONCLUSIONS The low baseline of INSTI-DRMs (<1%) in Cameroon suggests effectiveness of dolutegravir-based regimens. In spite of high conservation across clades, the variability of accessory mutations between major circulating strains underscores the need for monitoring the selection of INSTI-DRMs while scaling up dolutegravir-based regimens in RLS.
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Affiliation(s)
- Ezechiel Ngoufack Jagni Semengue
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Daniele Armenia
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
| | - Seth Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | | | - Béatrice Dambaya
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Désiré Takou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Georges Teto
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Alex Durand Nka
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Bouba Yagai
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Collins Chenwi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Grâce Angong Beloumou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Sandrine Claire Djupsa Ndjeyep
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Vittorio Colizzi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Carlo-Federico Perno
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Bambino Gesu Children's Hospital, IRCCS, Rome, Italy
| | | | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon.,National HIV Drug Resistance Working Group, Ministry of Public Health, Cameroon.,Faculty of Health Sciences, University of Buea, Buea, Cameroon
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18
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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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Mikasi SG, Isaacs D, Chitongo R, Ikomey GM, Jacobs GB, Cloete R. Interaction analysis of statistically enriched mutations identified in Cameroon recombinant subtype CRF02_AG that can influence the development of Dolutegravir drug resistance mutations. BMC Infect Dis 2021; 21:379. [PMID: 33892628 PMCID: PMC8063366 DOI: 10.1186/s12879-021-06059-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/08/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The Integrase (IN) strand transfer inhibitor (INSTI), Dolutegravir (DTG), has been given the green light to form part of first-line combination antiretroviral therapy (cART) by the World Health Organization (WHO). DTG containing regimens have shown a high genetic barrier against HIV-1 isolates carrying specific resistance mutations when compared with other class of regimens. METHODS We evaluated the HIV-1 CRF02_AG IN gene sequences from Cameroon for the presence of resistance-associated mutations (RAMs) against INSTIs and naturally occurring polymorphisms (NOPs), using study sequences (n = 20) and (n = 287) sequences data derived from HIV Los Alamos National Laboratory database. The possible impact of NOPs on protein structure caused by HIV-1 CRF02_AG variations was addressed within the context of a 3D model of the HIV-1 IN complex and interaction analysis was performed using PyMol to validate DTG binding to the Wild type and seven mutant structures. RESULTS We observed 12.8% (37/287) sequences to contain RAMs, with only 1.0% (3/287) of the sequences having major INSTI RAMs: T66A, Q148H, R263K and N155H. Of these,11.8% (34/287) of the sequences contained five different IN accessory mutations; namely Q95K, T97A, G149A, E157Q and D232N. NOPs occurred at a frequency of 66% on the central core domain (CCD) position, 44% on the C-terminal domain (CTD) position and 35% of the N-terminal domain (NTD) position. The interaction analysis revealed that DTG bound to DNA, 2MG ions and DDE motif residues for T66A, T97A, Q148H, N155H and R263K comparable to the WT structure. Except for accessory mutant structure E157Q, only one MG contact was made with DTG, while DTG had no MG ion contacts and no DDE motif residue contacts for structure D232N. CONCLUSIONS Our analysis indicated that all RAM's that resulted in a change in the number of interactions with encompassing residues does not affect DTG binding, while accessory mutations E157Q and D232N could affect DTG binding leading to possible DTG resistance. However, further experimental validation is required to validate the in silico findings of our study.
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Affiliation(s)
- Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Darren Isaacs
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa
| | - Rumbidzai Chitongo
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa
| | - George Mondide Ikomey
- Centre for the Study and Control of Communicable Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa.
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20
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Lan Y, Li L, Chen W, Deng X, Li J, Fan Q, Cai X, Cai W, Hu F. Absence of Integrase Inhibitor-Associated Resistance Among Antiretroviral Therapy-Naïve HIV-1-Infected Adults in Guangdong Province, China, in 2018. Infect Drug Resist 2020; 13:4389-4394. [PMID: 33324078 PMCID: PMC7733411 DOI: 10.2147/idr.s284917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/25/2020] [Indexed: 11/24/2022] Open
Abstract
Background Antiretroviral therapy (ART) containing an integrase strand transfer inhibitor (INSTI) plus two nucleoside reverse-transcriptase inhibitors has been recommended as a first-line regimen for ART-naïve HIV-1-infected patients in the latest Chinese Guidelines for Diagnosis and Treatment of HIV/AIDS. Objective To determine the prevalence of INSTI-related mutations among ART-naïve HIV-1-infected adults in Guangdong, China, in 2018. Methods The entire integrase gene was amplified from blood plasma. Demographic and epidemiological information was collected. INSTI mutations and antiretroviral susceptibility were interpreted using the Stanford University HIV Drug Resistance Database HIVdb program. Results Of 927 samples, 827 integrase sequences were successfully obtained. Among them, no major resistance mutations to INSTIs were identified, and four accessory mutations, including T97A (0.12%, 1/827), A128T (0.24%, 2/827), E157Q (0.85%, 7/827), and G163R (0.24%, 2/827), were found in twelve individuals. Two patient samples contained the G163R mutation conferring low-level resistance to elvitegravir and raltegravir. Conclusion The overall prevalence of INSTI mutations remains low. Drug resistance mutation testing for the detection of INSTI drug resistance mutations in HIV treatment-naïve patients should be considered due to the circulation of polymorphisms contributing to INSTI resistance and the expected increasing use of this class of drugs.
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Affiliation(s)
- Yun Lan
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Linghua Li
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Weilie Chen
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Xizi Deng
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Junbin Li
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Qinghong Fan
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Xiaoli Cai
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Weiping Cai
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Fengyu Hu
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
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21
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Structural Comparison of Diverse HIV-1 Subtypes using Molecular Modelling and Docking Analyses of Integrase Inhibitors. Viruses 2020; 12:v12090936. [PMID: 32858802 PMCID: PMC7552036 DOI: 10.3390/v12090936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 12/27/2022] Open
Abstract
The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA). Due to high HIV-1 diversity, it is not well understood how specific naturally occurring polymorphisms (NOPs) in IN may affect the structure/function and binding affinity of integrase strand transfer inhibitors (INSTIs). We applied computational methods of molecular modelling and docking to analyze the effect of NOPs on the full-length IN structure and INSTI binding. We identified 13 NOPs within the Cameroonian-derived CRF02_AG IN sequences and further identified 17 NOPs within HIV-1C South African sequences. The NOPs in the IN structures did not show any differences in INSTI binding affinity. However, linear regression analysis revealed a positive correlation between the Ki and EC50 values for DTG and BIC as strong inhibitors of HIV-1 IN subtypes. All INSTIs are clinically effective against diverse HIV-1 strains from INSTI treatment-naïve populations. This study supports the use of second-generation INSTIs such as DTG and BIC as part of first-line combination antiretroviral therapy (cART) regimens, due to a stronger genetic barrier to the emergence of drug resistance.
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22
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El Bouzidi K, Kemp SA, Datir RP, Murtala-Ibrahim F, Aliyu A, Kwaghe V, Frampton D, Roy S, Breuer J, Sabin CA, Ogbanufe O, Charurat ME, Bonsall D, Golubchik T, Fraser C, Dakum P, Ndembi N, Gupta RK. High prevalence of integrase mutation L74I in West African HIV-1 subtypes prior to integrase inhibitor treatment. J Antimicrob Chemother 2020; 75:1575-1579. [PMID: 32105319 PMCID: PMC7225870 DOI: 10.1093/jac/dkaa033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES HIV-1 integrase inhibitors are recommended as first-line therapy by WHO, though efficacy and resistance data for non-B subtypes are limited. Two recent trials have identified the integrase L74I mutation to be associated with integrase inhibitor treatment failure in HIV-1 non-B subtypes. We sought to define the prevalence of integrase resistance mutations, including L74I, in West Africa. METHODS We studied a Nigerian cohort of recipients prior to and during receipt of second-line PI-based therapy, who were integrase inhibitor-naive. Illumina next-generation sequencing with target enrichment was used on stored plasma samples. Drug resistance was interpreted using the Stanford Resistance Database and the IAS-USA 2019 mutation lists. RESULTS Of 115 individuals, 59.1% harboured CRF02_AG HIV-1 and 40.9% harboured subtype G HIV-1. Four participants had major IAS-USA integrase resistance-associated mutations detected at low levels (2%-5% frequency). Two had Q148K minority variants and two had R263K (one of whom also had L74I). L74I was detected in plasma samples at over 2% frequency in 40% (46/115). Twelve (26.1%) had low-level minority variants of between 2% and 20% of the viral population sampled. The remaining 34 (73.9%) had L74I present at >20% frequency. L74I was more common among those with subtype G infection (55.3%, 26/47) than those with CRF02_AG infection (29.4%, 20/68) (P = 0.005). CONCLUSIONS HIV-1 subtypes circulating in West Africa appear to have very low prevalence of major integrase mutations, but significant prevalence of L74I. A combination of in vitro and clinical studies is warranted to understand the potential implications.
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Affiliation(s)
- Kate El Bouzidi
- Division of Infection & Immunity, University College London, London, UK
- Institute for Global Health, University College London, London, UK
| | - Steven A Kemp
- Division of Infection & Immunity, University College London, London, UK
| | | | | | - Ahmad Aliyu
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Vivian Kwaghe
- University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Dan Frampton
- Division of Infection & Immunity, University College London, London, UK
| | - Sunando Roy
- Division of Infection & Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection & Immunity, University College London, London, UK
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Obinna Ogbanufe
- U.S. Centers for Disease Control and Prevention, Diplomatic Drive, Abuja, Nigeria
| | - Man E Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Bonsall
- Big Data Institute, University of Oxford, Oxford, UK
| | | | | | | | | | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, KZN, South Africa
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23
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Semengue ENJ, Santoro MM, Ndze VN, Dambaya B, Takou D, Teto G, Nka AD, Fabeni L, Wiyeh A, Ceccherini-Silberstein F, Colizzi V, Perno CF, Fokam J. HIV-1 integrase resistance associated mutations and the use of dolutegravir in Sub-Saharan Africa: a systematic review and meta-analysis protocol. Syst Rev 2020; 9:93. [PMID: 32334643 PMCID: PMC7183126 DOI: 10.1186/s13643-020-01356-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 04/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sub-Saharan Africa carries the greatest burden of HIV-infection with increasing drug resistance burden, which requires improved patient management and monitoring. Current WHO recommendations suggest transitioning to dolutegravir-based (adults) or raltegravir-based-regimens (neonates) for initial antiretroviral therapy (ART) and as a suitable alternative in cases of multi-resistance in resource-limited settings. This review aims at synthesizing the current knowledge on dolutegravir use and integrase resistance-associated mutations found before the wide use of dolutegravir-based regimens. METHODS This systematic review will include randomized and non-randomized trials, cohort, and cross-sectional studies published on dolutegravir use or integrase resistance-associated mutations in Sub-Saharan Africa. Searches will be conducted (from 2007 onwards) in PubMed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Latin American and Caribbean Health Sciences Literature (LILAC), Web of Science, African Journals Online, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) databases. Hand searching of the reference lists of relevant reviews and trials will be conducted and we will also look for conference abstracts. We will include studies of adults and/or children exposed to integrase inhibitors-based therapies; especially dolutegravir or raltegravir (which is our intervention of interest as compared to other antiretroviral regimens). We will exclude studies of patients with specific co-morbidities such as tuberculosis or opportunistic infections. Primary outcomes will be "the rate of viral suppression" and "the level of drug resistance" on integrase inhibitor-based regimens among patients in Sub-Saharan Africa. Secondary outcomes will be "the effect of baseline viremia on viral suppression," "the effect of treatment duration on viral suppression," "the proportion of patients with immune recovery," "the rate of non-adherence," "rate of adverse events;" "drug resistance according to different integrase inhibitor-based regimens," and "drug resistance according to viral subtypes/recombinants." Two reviewers will independently screen titles and abstracts, assess the full texts for eligibility, and extract data. If data permits, random effects models will be used where appropriate. Subgroup and additional analyses will be conducted to explore the potential sources of heterogeneity (e.g., age, sex, baseline viremia, CD4 following treatment, treatment duration, and adherence level). DISCUSSION This review will help to strengthen evidence on the effectiveness of integrase strand transfer inhibitors by contributing to current knowledge on the use of dolutegravir and/or raltegravir (especially for neonates) in Sub-Saharan Africa. Results will therefore help in setting-up baseline data for an optimal management of people living with HIV as Sub-Saharan African countries are transitioning to dolutegravir-based regimens. Evidence will also support HIV/AIDS programs in identifying gaps and actions to be undertaken for improved long-term care and treatment of people living with HIV in Sub-Saharan Africa. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42019122424.
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Affiliation(s)
- Ezechiel Ngoufack Jagni Semengue
- Chantal Biya International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
- Evangelical University of Cameroon, Bandjoun, Cameroon
- University of Rome “Tor Vergata”, Rome, Italy
| | | | - Valantine Ngum Ndze
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Beatrice Dambaya
- Chantal Biya International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Desiré Takou
- Chantal Biya International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Georges Teto
- Chantal Biya International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - Alex Durand Nka
- Chantal Biya International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
- Evangelical University of Cameroon, Bandjoun, Cameroon
- University of Rome “Tor Vergata”, Rome, Italy
| | | | - Alison Wiyeh
- South African Medical Research Council (MRC), Cochrane South Africa, Pretoria, South Africa
| | | | - Vittorio Colizzi
- Evangelical University of Cameroon, Bandjoun, Cameroon
- Chair of Biotechnology-UNESCO, University of Rome “Tor Vergata”, Rome, Italy
| | | | - Joseph Fokam
- Chantal Biya International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
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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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Acharya A, Tagny CT, Mbanya D, Fonsah JY, Nchindap E, Kenmogne L, Jihyun M, Njamnshi AK, Kanmogne GD. Variability in HIV-1 Integrase Gene and 3'-Polypurine Tract Sequences in Cameroon Clinical Isolates, and Implications for Integrase Inhibitors Efficacy. Int J Mol Sci 2020; 21:ijms21051553. [PMID: 32106437 PMCID: PMC7084836 DOI: 10.3390/ijms21051553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 01/06/2023] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs) are now included in preferred first-line antiretroviral therapy (ART) for HIV-infected adults. Studies of Western clade-B HIV-1 show increased resistance to INSTIs following mutations in integrase and nef 3′polypurine tract (3′-PPT). With anticipated shifts in Africa (where 25.6-million HIV-infected people resides) to INSTIs-based ART, it is critical to monitor patients in African countries for resistance-associated mutations (RAMs) affecting INSTIs efficacy. We analyzed HIV-1 integrase and 3′-PPT sequences in 345 clinical samples from INSTIs-naïve HIV-infected Cameroonians for polymorphisms and RAMs that affect INSTIs. Phylogeny showed high genetic diversity, with the predominance of HIV-1 CRF02_AG. Major INSTIs RAMs T66A and N155K were found in two (0.6%) samples. Integrase polymorphic and accessory RAMs found included T97A, E157Q, A128T, M50I, S119R, L74M, L74I, S230N, and E138D (0.3′23.5% of samples). Ten (3.2%) samples had both I72V+L74M, L74M+T97A, or I72V+T97A mutations; thirty-one (9.8%) had 3′-PPT mutations. The low frequency of major INSTIs RAMs shows that INSTIs-based ART can be successfully used in Cameroon. Several samples had ≥1 INSTIs accessory RAMs known to reduce INSTIs efficacy; thus, INSTIs-based ART would require genetic surveillance. The 3′-PPT mutations could also affect INSTIs. For patients failing INSTIs-based ART with no INSTIs RAMs, monitoring 3′-PPT sequences could reveal treatment failure etiology.
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Affiliation(s)
- Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Claude T. Tagny
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Julius Y. Fonsah
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Department of Neurology, Yaoundé Central Hospital/Brain Research Africa Initiative (BRAIN), P.O. Box 25625 Yaoundé, Cameroon
| | - Emilienne Nchindap
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Léopoldine Kenmogne
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Ma Jihyun
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Alfred K. Njamnshi
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Department of Neurology, Yaoundé Central Hospital/Brain Research Africa Initiative (BRAIN), P.O. Box 25625 Yaoundé, Cameroon
| | - Georgette D. Kanmogne
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Correspondence: ; Tel.: +402-559-4084
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An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors. Antimicrob Agents Chemother 2019; 63:AAC.00539-19. [PMID: 31109980 DOI: 10.1128/aac.00539-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/15/2019] [Indexed: 12/19/2022] Open
Abstract
Viral pathogens causing global disease burdens are often characterized by high rates of evolutionary changes. The extensive viral diversity at baseline can shorten the time to escape from therapeutic or immune selective pressure and alter mutational pathways. The impact of genotypic background on the barrier to resistance can be difficult to capture, particularly for agents in experimental stages or that are recently approved or expanded into new patient populations. We developed an evolutionary model-based counting method to quickly quantify the population genetic potential to resistance and assess population differences. We demonstrate its applicability to HIV-1 integrase inhibitors, as their increasing use globally contrasts with limited availability of non-B subtype resistant sequence data and corresponding knowledge gap. A large sequence data set encompassing most prevailing HIV-1 subtypes and resistance-associated mutations of currently approved integrase inhibitors was investigated. A complex interplay between codon predominance, polymorphisms, and associated evolutionary costs resulted in a subtype-dependent varied genetic potential for 15 resistance mutations against integrase inhibitors. While we confirm the lower genetic barrier of subtype B for G140S, we convincingly discard a similar effect previously suggested for G140C. A supplementary analysis for HIV-1 reverse transcriptase inhibitors identified a lower genetic barrier for K65R in subtype C through differential codon usage not reported before. To aid evolutionary interpretations of genomic differences for antiviral strategies, we advanced existing counting methods with increased sensitivity to identify subtype dependencies of resistance emergence. Future applications include novel HIV-1 drug classes or vaccines, as well as other viral pathogens.
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Abbas UL, Glaubius RL, Ding Y, Hood G. Drug resistance from preferred antiretroviral regimens for HIV infection in South Africa: A modeling study. PLoS One 2019; 14:e0218649. [PMID: 31269034 PMCID: PMC6609148 DOI: 10.1371/journal.pone.0218649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 06/06/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Tenofovir-containing regimens comprise the preferred first-line antiretroviral therapy (ART) in many countries including South Africa, where utilization of second-line regimens is limited. Considerable HIV drug resistance has occurred among persons failing tenofovir-containing first-line ART. We evaluated drug resistance at the population level using mathematical modeling. SETTING Heterosexual HIV epidemic in KwaZulu-Natal, South Africa. METHODS We constructed a stochastic individual-based model and simulated scenarios of ART implementation, either CD4-based (threshold < 500 cells/mL) or Fast-track (81% coverage by 2020), with consideration of major drug-associated mutations (M184V, K65R and non-nucleoside reverse transcriptase inhibitor (NNRTI)). Using base case and uncertainty analyses, we assessed (majority) drug resistance levels. RESULTS By 2030, the median total resistance (proportion of HIV-infected persons with drug resistance) is predicted to reach 31.4% (interquartile range (IQR): 16.5%-50.2%) with CD4-based ART, decreasing to 14.5% (IQR: 7.7%-25.8%) with Fast-track implementation. In both scenarios, we find comparably high prevalence (~80%) of acquired NNRTI-associated, M184V and K65R mutations. Over 48% of individuals with acquired resistance harbor dual, 44% triple and 7% just single drug mutations. Drug-resistant HIV is predicted to comprise 40% (IQR: 27%-50%) of incident infections, while 70% of prevalent transmitted resistance is NNRTI-associated. At 2018, the projected total resistance is 15% (IQR: 7.5%-25%), with 18% (IQR: 13%-24%) of incident infections from transmitted drug-resistant HIV. CONCLUSIONS WHO-recommended preferred first-line ART could lead to substantial drug resistance. Effective surveillance of HIV drug resistance and utilization of second-line as well as alternative first-line regimens is crucial.
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Affiliation(s)
- Ume L. Abbas
- Department of Medicine, Section of Infectious Diseases and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Quantitative Health Sciences and Infectious Disease, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Robert L. Glaubius
- Departments of Quantitative Health Sciences and Infectious Disease, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Yajun Ding
- Department of Medicine, Section of Infectious Diseases and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Gregory Hood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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Inzaule SC, Hamers RL, Noguera-Julian M, Casadellà M, Parera M, Rinke de Wit TF, Paredes R. Primary resistance to integrase strand transfer inhibitors in patients infected with diverse HIV-1 subtypes in sub-Saharan Africa. J Antimicrob Chemother 2019; 73:1167-1172. [PMID: 29462322 DOI: 10.1093/jac/dky005] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023] Open
Abstract
Objectives To investigate the prevalence and patterns of major and accessory resistance mutations associated with integrase strand transfer inhibitors (INSTIs), across diverse HIV-1 subtypes in sub-Saharan Africa. Methods pol gene sequences were obtained using Illumina next-generation sequencing from 425 INSTI-naive HIV-infected adults from Kenya (21.2%), Nigeria (7.3%), South Africa (22.8%), Uganda (25.2%) and Zambia (23.5%). Drug resistance interpretation was based on the IAS 2017 mutation list and accessory mutations from Stanford HIVdb with resistance penalty scores of ≥10 to at least 1 INSTI. Resistance was further classified based on sensitivity thresholds of ≥20% (Sanger sequencing) and 1%-20% for low-frequency variants (next-generation sequencing). Results Of 425 genotypes, 48.7% were subtype C, 28.5% A, 10.1% D, 2.8% G and 9.9% were recombinants. Major INSTI resistance mutations were detected only at <20% threshold, at a prevalence of 2.4% (2.5% in subtype A, 2.4% C, 0% D, 8.3% G and 2.4% in recombinants) and included T66A/I (0.7%), E92G (0.5%), Y143C/S (0.7%), S147G (0.2%) and Q148R (0.5%). Accessory mutations occurred at a prevalence of 15.1% at the ≥20% threshold (23.1% in subtype A, 8.7% C, 11.6% D, 25% G and 23.8% in recombinants), and included L74I/M (10.4%), Q95K (0.5%), T97A (4%), E157Q (0.7%) and G163R/K (0.7%). Conclusions Major INSTI resistance mutations were rare and only occurred at low-level resistance detection thresholds. INSTI-based regimens are expected to be effective across the different major HIV-1 subtypes in the region.
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Affiliation(s)
- Seth C Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands.,Joep Lange Institute, Department of Global Health, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands
| | - Raph L Hamers
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands.,Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia, and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marc Noguera-Julian
- Infectious Diseases Unit & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500 Vic, Catalonia, Spain
| | - Maria Casadellà
- Infectious Diseases Unit & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - Mariona Parera
- Infectious Diseases Unit & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - Tobias F Rinke de Wit
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands.,Joep Lange Institute, Department of Global Health, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands
| | - Roger Paredes
- Infectious Diseases Unit & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500 Vic, Catalonia, Spain
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Hamers RL, Rinke de Wit TF, Holmes CB. HIV drug resistance in low-income and middle-income countries. Lancet HIV 2018; 5:e588-e596. [PMID: 30193863 DOI: 10.1016/s2352-3018(18)30173-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/02/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
Abstract
After 15 years of global scale-up of antiretroviral therapy (ART), rising prevalence of HIV drug resistance in many low-income and middle-income countries (LMICs) poses a growing threat to the HIV response, with the potential to drive an increase in mortality, HIV incidence, and costs. To achieve UNAIDS global targets, enhanced strategies are needed to improve quality of ART services and durability of available ART regimens, and to curb resistance. These strategies include roll out of drugs with greater efficacy and higher genetic barriers to resistance than those that are currently widely used, universal access to and improved effectiveness of viral load monitoring, patient-centred care delivery models, and reliable drug supply chains, in conjunction with frameworks for resistance monitoring and prevention. In this Review, we assess contemporary data on HIV drug resistance in LMICs and their implications for the HIV response, highlighting the potential impact and resistance risks of novel ART strategies and knowledge gaps.
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Affiliation(s)
- Raph L Hamers
- Eijkman-Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Global Health, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands.
| | - Tobias F Rinke de Wit
- Department of Global Health, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands; Joep Lange Institute, Amsterdam, Netherlands
| | - Charles B Holmes
- Centre for Infectious Diseases Research Zambia, Lusaka, Zambia; Center for Global Health and Quality, Georgetown University Medical Center, Washington, DC, USA; Johns Hopkins University School of Medicine and Bloomberg School of Public Health, Baltimore, MD, USA
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Durable suppression of HIV-1 with resistance mutations to integrase inhibitors by dolutegravir following drug washout. AIDS 2018; 32:1773-1780. [PMID: 29894388 DOI: 10.1097/qad.0000000000001903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Dolutegravir (DTG) has achieved better long-term suppression of HIV-1 replication than other integrase strand transfer inhibitors (INSTIs), such as raltegravir (RAL) and elvitegravir (EVG). In in-vitro drug washout experiments, we previously showed that removal of DTG from pretreated MT-2 cells infected with wild-type HIV-1 showed slower rebound in viral replication as compared to removal of RAL. Now, we performed DTG, EVG and RAL washout experiments to compare the recovery of viral integration and production of 2-long terminal repeat (LTR) circles using wild-type HIV-1 clones, R263K viruses with low-level resistance to DTG and viruses with G140S/Q148H mutations showing cross-resistance against all currently approved INSTIs. DESIGN AND METHODS MT-2 cells infected with wild-type, R263K or G140S/Q148H HIV-1 clones were treated with DTG, RAL or EVG for 3 days. Viral rebound following drug washout was assessed, monitoring viral integration and 2-LTR circle production by qPCR. RESULTS Viral integration did not resume for up to 8 days after DTG washout from the wild-type or R263K infections but increased soon after washout of either RAL or EVG. With the G140S/Q148H virus, levels of integration were not significantly affected by the presence of either RAL or EVG. With DTG, integration was much lower at 3 days after infection than for the no-drug control. At 8 days after DTG washout, viral integration resumed but remained relatively low. CONCLUSION DTG antiretroviral activity in tissue culture is more durable than that of either RAL or EVG after drug washout and this is true for both wild-type and drug-resistant viruses.
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Alessandri-Gradt E, Collin G, Tourneroche A, Bertine M, Leoz M, Charpentier C, Unal G, Descamps D, Plantier JC. HIV-1 non-group M phenotypic susceptibility to integrase strand transfer inhibitors. J Antimicrob Chemother 2018; 72:2431-2437. [PMID: 28859447 DOI: 10.1093/jac/dkx190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/23/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives To determine natural phenotypic susceptibility of non-group M HIV-1 to integrase strand transfer inhibitors (INSTIs) in a large panel of 39 clinical strains from groups O, N and P and to identify genotypic polymorphisms according to susceptibility levels. Methods Susceptibility to raltegravir, elvitegravir and dolutegravir was evaluated in 36 HIV-1/O, 2 HIV-1/N and 1 HIV-1/P strains plus an HIV-1/M reference strain. IC50 values were determined after 3 days, and fold changes (FCs) were calculated relative to the HIV-1/M strain. Genotypic polymorphism was determined by amplification of codons 19-263 of the integrase; the natural occurrence of resistance-associated mutations was analysed using the main resistance algorithms and the IAS-USA list. VESPA analysis of the strain sequences was used to determine a signature pattern associated with higher FC. Results Similar IC50 results were observed for the three drugs. Based on the value for the HIV-1/M reference strain, the data showed FC values <2.5 for raltegravir and dolutegravir, whereas the distribution for elvitegravir was heterogeneous, with FC > 10 for six strains (15%). Analysis of the non-M integrase sequences showed a high level of polymorphism without a major genotypic impact; it also revealed mutations that may be associated with the highest FC values obtained for elvitegravir. Conclusions Our phenotypic data showed that non-M strains are globally susceptible to the three currently used INSTIs, but the impact of the high FC values observed for some strains with elvitegravir needs to be explored. Clinical data are now needed to confirm these phenotypic results.
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Affiliation(s)
- E Alessandri-Gradt
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
| | - G Collin
- IAME, UMR 1137, Univ. Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France.,IAME, UMR 1137, INSERM, F-75018 Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - A Tourneroche
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
| | - M Bertine
- IAME, UMR 1137, Univ. Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France.,IAME, UMR 1137, INSERM, F-75018 Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - M Leoz
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
| | - C Charpentier
- IAME, UMR 1137, Univ. Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France.,IAME, UMR 1137, INSERM, F-75018 Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - G Unal
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
| | - D Descamps
- IAME, UMR 1137, Univ. Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France.,IAME, UMR 1137, INSERM, F-75018 Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - J C Plantier
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
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Affiliation(s)
| | - Anton Pozniak
- Chelsea and Westminster Hospital, London, United Kingdom
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Ex-vivo antiretroviral potency of newer integrase strand transfer inhibitors cabotegravir and bictegravir in HIV type 1 non-B subtypes. AIDS 2018; 32:469-476. [PMID: 29239896 DOI: 10.1097/qad.0000000000001726] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To determine the antiretroviral activity of the integrase strand transfer inhibitors (INSTIs), raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), cabotegravir (CAB) and bictegravir (BIC), against different subtypes as well as primary and acquired drug resistance mutations (DRMs) in a patient-cohort infected with diverse subtypes. DESIGN Biochemical and virological drug sensitivity analyses using patient-derived HIV type 1 (HIV-1) genes and cross-sectional/longitudinal clinical study. METHODS Assays for 50% inhibition of 3'-end processing (IC50-3EP), strand transfer (IC50-ST) and drug sensitivity for five INSTIs were done using patient-derived integrase or gag-pol genes from subtypes A1, B, C, 01_AE and 02_AG. Integrase from INSTI-naive (n = 270) and experienced (n = 96) patients were sequenced. RESULTS RAL had higher IC50-ST than the other INSTIs for all subtypes. EVG had higher IC50-ST for HIV 1 subtype C (P < 0.05) and 02_AG (P < 0.05) than HIV 1 subtype B (HIV-1B). DTG showed lower IC50-ST in HIV 1 subtype C than HIV-1B (P = 0.003). In CAB , the non-B subtypes showed lower IC50-ST (P < 0.05) than HIV-1B. In BIC, lower IC50-ST in 01_AE (P = 0.017) and 02_AG (P = 0.045) than HIV-1B. In drug sensitivity assay, inhibiting virus replication by 50% for DTG [median (IQR) 2.14 (1.3-2.56)], CAB [1.68 (1.34-2.55)] and BIC [1.07 (0.22-2.53)] were lower than RAL and EVG. One patient had a primary DRMs (0.3%, 1/270), but 17 (6.3%) had one major accessory DRM, of which 12 were E157Q. CONCLUSION The equal or higher potency in non-B subtypes of DTG, CAB and BIC compared with RAL and EVG confirms their suitability for use in countries dominated by non-B subtypes. Any impact of the high prevalence of major accessory mutations, especially E157Q, requires long-term follow-up studies.
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Initial treatment response among HIV subtype F infected patients who started antiretroviral therapy based on integrase inhibitors. AIDS 2018; 32:121-125. [PMID: 29112068 DOI: 10.1097/qad.0000000000001679] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
: HIV-1 subtype B (54.4%) and subtype F (27.2%) are the most prevalent variants in patients who started antiretroviral therapy including an integrase inhibitor in the last 2 years in Northwest Spain. Virological response rates to antiretroviral therapy based on integrase inhibitor were significantly lower among F subtypes compared with B subtypes at weeks 12 (25.0% vs. 75.0%) and 24 (59.1% vs. 95.0%). Subtype F was independently associated with virological response at 24 weeks [odds ratio 11.8 (95% confidence interval 1.1-119.9); P = 0.037].
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HIV drug resistance against strand transfer integrase inhibitors. Retrovirology 2017; 14:36. [PMID: 28583191 PMCID: PMC5460515 DOI: 10.1186/s12977-017-0360-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/30/2017] [Indexed: 12/03/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are the newest class of antiretroviral drugs to be approved for treatment and act by inhibiting the essential HIV protein integrase from inserting the viral DNA genome into the host cell’s chromatin. Three drugs of this class are currently approved for use in HIV-positive individuals: raltegravir (RAL), elvitegravir (EVG), and dolutegravir (DTG), while cabotegravir (CAB) and bictegravir (BIC) are currently in clinical trials. RAL and EVG have been successful in clinical settings but have relatively low genetic barriers to resistance. Furthermore, they share a high degree of cross-resistance, which necessitated the development of so-called second-generation drugs of this class (DTG, CAB, and BIC) that could retain activity against these resistant variants. In vitro selection experiments have been instrumental to the clinical development of INSTIs, however they cannot completely recapitulate the situation in an HIV-positive individual. This review summarizes and compares all the currently available information as it pertains to both in vitro and in vivo selections with all five INSTIs, and the measured fold-changes in resistance of resistant variants in in vitro assays. While the selection of resistance substitutions in response to RAL and EVG bears high similarity in patients as compared to laboratory studies, there is less concurrence regarding the “second-generation” drugs of this class. This highlights the unpredictability of HIV resistance to these inhibitors, which is of concern as CAB and BIC proceed in their clinical development.
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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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