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Pimentel V, Pingarilho M, Sebastião CS, Miranda M, Gonçalves F, Cabanas J, Costa I, Diogo I, Fernandes S, Costa O, Corte-Real R, Martins MRO, Seabra SG, Abecasis AB, Gomes P. Applying Next-Generation Sequencing to Track HIV-1 Drug Resistance Mutations Circulating in Portugal. Viruses 2024; 16:622. [PMID: 38675962 PMCID: PMC11054263 DOI: 10.3390/v16040622] [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: 02/27/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The global scale-up of antiretroviral treatment (ART) offers significant health benefits by suppressing HIV-1 replication and increasing CD4 cell counts. However, incomplete viral suppression poses a potential threat for the emergence of drug resistance mutations (DRMs), limiting ART options, and increasing HIV transmission. OBJECTIVE We investigated the patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) among HIV-1 patients in Portugal. METHODS Data were obtained from 1050 HIV-1 patient samples submitted for HIV drug resistance (HIVDR) testing from January 2022 to June 2023. Evaluation of DRM affecting viral susceptibility to nucleoside/tide reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and integrase strand transfer inhibitors (INSTIs) was performed using an NGS technology, the Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay. RESULTS About 71% of patients were ART naïve and 29% were experienced. Overall, 20% presented with any DRM. The prevalence of TDR and ADR was 12.6% and 41.1%, respectively. M184V, T215S, and M41L mutations for NRTI, K103N for NNRTI, and M46I/L for PIs were frequent in naïve and treated patients. E138K and R263K mutations against INSTIs were more frequent in naïve than treated patients. TDR and ADR to INSTIs were 0.3% and 7%, respectively. Patients aged 50 or over (OR: 1.81, p = 0.015), originating from Portuguese-speaking African countries (PALOPs) (OR: 1.55, p = 0.050), HIV-1 subtype G (OR: 1.78, p = 0.010), and with CD4 < 200 cells/mm3 (OR: 1.70, p = 0.043) were more likely to present with DRMs, while the males (OR: 0.63, p = 0.003) with a viral load between 4.1 to 5.0 Log10 (OR: 0.55, p = 0.003) or greater than 5.0 Log10 (OR: 0.52, p < 0.001), had lower chances of presenting with DRMs. CONCLUSIONS We present the first evidence on TDR and ADR to INSTI regimens in followed up patients presenting for healthcare in Portugal. We observed low levels of TDR to INSTIs among ART-naïve and moderate levels in ART-exposed patients. Regimens containing PIs could be an alternative second line in patients with intermediate or high-level drug resistance, especially against second-generation INSTIs (dolutegravir, bictegravir, and cabotegravir).
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Affiliation(s)
- Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Cruz S. Sebastião
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
- Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Fátima Gonçalves
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Joaquim Cabanas
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Inês Costa
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Olga Costa
- Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar de Lisboa Central, 1150-199 Lisbon, Portugal; (O.C.); (R.C.-R.)
| | - Rita Corte-Real
- Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar de Lisboa Central, 1150-199 Lisbon, Portugal; (O.C.); (R.C.-R.)
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Sofia G. Seabra
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Ana B. Abecasis
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Caparica, 2829-511 Almada, Portugal
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Rossetti B, Incardona F, Di Teodoro G, Mommo C, Saladini F, Kaiser R, Sönnerborg A, Lengauer T, Zazzi M. Cohort Profile: A European Multidisciplinary Network for the Fight against HIV Drug Resistance (EuResist Network). Trop Med Infect Dis 2023; 8:tropicalmed8050243. [PMID: 37235291 DOI: 10.3390/tropicalmed8050243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
The EuResist cohort was established in 2006 with the purpose of developing a clinical decision-support tool predicting the most effective antiretroviral therapy (ART) for persons living with HIV (PLWH), based on their clinical and virological data. Further to continuous extensive data collection from several European countries, the EuResist cohort later widened its activity to the more general area of antiretroviral treatment resistance with a focus on virus evolution. The EuResist cohort has retrospectively enrolled PLWH, both treatment-naïve and treatment-experienced, under clinical follow-up from 1998, in nine national cohorts across Europe and beyond, and this article is an overview of its achievement. A clinically oriented treatment-response prediction system was released and made available online in 2008. Clinical and virological data have been collected from more than one hundred thousand PLWH, allowing for a number of studies on the response to treatment, selection and spread of resistance-associated mutations and the circulation of viral subtypes. Drawing from its interdisciplinary vocation, EuResist will continue to investigate clinical response to antiretroviral treatment against HIV and monitor the development and circulation of HIV drug resistance in clinical settings, along with the development of novel drugs and the introduction of new treatment strategies. The support of artificial intelligence in these activities is essential.
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Affiliation(s)
- Barbara Rossetti
- Infectious Diseases Department, Infectious Diseases Unit, USL SUDEST Toscana, Misericordia Hospital, 58100 Grosseto, Italy
| | | | - Giulia Di Teodoro
- EuResist Network, 00152 Rome, Italy
- Department of Computer Control and Management Engineering Antonio Ruberti, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Rolf Kaiser
- Institute of Virology, University and University Hospital Cologne, University of Cologne, 50923 Cologne, Germany
| | - Anders Sönnerborg
- Department of Medicine Huddinge, Karolinska Institutet, Division of Infectious Diseases, 17177 Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Division of Clinical Microbiology, 17177 Stockholm, Sweden
| | - Thomas Lengauer
- Institute of Virology, University and University Hospital Cologne, University of Cologne, 50923 Cologne, Germany
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
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Smith J, Bansi-Matharu L, Cambiano V, Dimitrov D, Bershteyn A, van de Vijver D, Kripke K, Revill P, Boily MC, Meyer-Rath G, Taramusi I, Lundgren JD, van Oosterhout JJ, Kuritzkes D, Schaefer R, Siedner MJ, Schapiro J, Delany-Moretlwe S, Landovitz RJ, Flexner C, Jordan M, Venter F, Radebe M, Ripin D, Jenkins S, Resar D, Amole C, Shahmanesh M, Gupta RK, Raizes E, Johnson C, Inzaule S, Shafer R, Warren M, Stansfield S, Paredes R, Phillips AN. Predicted effects of the introduction of long-acting injectable cabotegravir pre-exposure prophylaxis in sub-Saharan Africa: a modelling study. Lancet HIV 2023; 10:e254-e265. [PMID: 36642087 PMCID: PMC10065903 DOI: 10.1016/s2352-3018(22)00365-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Long-acting injectable cabotegravir pre-exposure prophylaxis (PrEP) is recommended by WHO as an additional option for HIV prevention in sub-Saharan Africa, but there is concern that its introduction could lead to an increase in integrase-inhibitor resistance undermining treatment programmes that rely on dolutegravir. We aimed to project the health benefits and risks of cabotegravir-PrEP introduction in settings in sub-Saharan Africa. METHODS With HIV Synthesis, an individual-based HIV model, we simulated 1000 setting-scenarios reflecting both variability and uncertainty about HIV epidemics in sub-Saharan Africa and compared outcomes for each with and without cabotegravir-PrEP introduction. PrEP use is assumed to be risk-informed and to be used only in 3-month periods (the time step for the model) when having condomless sex. We consider three groups at risk of integrase-inhibitor resistance emergence: people who start cabotegravir-PrEP after (unknowingly) being infected with HIV, those who seroconvert while on PrEP, and those with HIV who have residual cabotegravir drugs concentrations during the early tail period after recently stopping PrEP. We projected the outcomes of policies of cabotegravir-PrEP introduction and of no introduction in 2022 across 50 years. In 50% of setting-scenarios we considered that more sensitive nucleic-acid-based HIV diagnostic testing (NAT), rather than regular antibody-based HIV rapid testing, might be used to reduce resistance risk. For cost-effectiveness analysis we assumed in our base case a cost of cabotegravir-PrEP drug to be similar to oral PrEP, resulting in a total annual cost of USD$144 per year ($114 per year and $264 per year considered in sensitivity analyses), a cost-effectiveness threshold of $500 per disability-adjusted life years averted, and a discount rate of 3% per year. FINDINGS Reflecting our assumptions on the appeal of cabotegravir-PrEP, its introduction is predicted to lead to a substantial increase in PrEP use with approximately 2·6% of the adult population (and 46% of those with a current indication for PrEP) receiving PrEP compared with 1·5% (28%) without cabotegravir-PrEP introduction across 20 years. As a result, HIV incidence is expected to be lower by 29% (90% range across setting-scenarios 6-52%) across the same period compared with no introduction of cabotegravir-PrEP. In people initiating antiretroviral therapy, the proportion with integrase-inhibitor resistance after 20 years is projected to be 1·7% (0-6·4%) without cabotegravir-PrEP introduction but 13·1% (4·1-30·9%) with. Cabotegravir-PrEP introduction is predicted to lower the proportion of all people on antiretroviral therapy with viral loads less than 1000 copies per mL by 0·9% (-2·5% to 0·3%) at 20 years. For an adult population of 10 million an overall decrease in number of AIDS deaths of about 4540 per year (-13 000 to -300) across 50 years is predicted, with little discernible benefit with NAT when compared with standard antibody-based rapid testing. AIDS deaths are predicted to be averted with cabotegravir-PrEP introduction in 99% of setting-scenarios. Across the 50-year time horizon, overall HIV programme costs are predicted to be similar regardless of whether cabotegravir-PrEP is introduced (total mean discounted annual HIV programme costs per year across 50 years is $151·3 million vs $150·7 million), assuming the use of standard antibody testing. With antibody-based rapid HIV testing, the introduction of cabotegravir-PrEP is predicted to be cost-effective under an assumed threshold of $500 per disability-adjusted life year averted in 82% of setting-scenarios at the cost of $144 per year, in 52% at $264, and in 87% at $114. INTERPRETATION Despite leading to increases in integrase-inhibitor drug resistance, cabotegravir-PrEP introduction is likely to reduce AIDS deaths in addition to HIV incidence. Long-acting cabotegravir-PrEP is predicted to be cost-effective if delivered at similar cost to oral PrEP with antibody-based rapid HIV testing. FUNDING Bill & Melinda Gates Foundation, National Institute of Allergy and Infectious Diseases of the National Institutes of Health.
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Affiliation(s)
- Jennifer Smith
- Institute for Global Health, University College London, London, UK
| | | | | | - Dobromir Dimitrov
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anna Bershteyn
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | | | | | - Paul Revill
- Centre for Health Economics, University of York, York, UK
| | - Marie-Claude Boily
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Gesine Meyer-Rath
- Health Economics and Epidemiology Research Office (HE2RO), Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Jens D Lundgren
- Department of Clinical Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Joep J van Oosterhout
- Partners in Hope, Lilongwe, Malawi; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Daniel Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Robin Schaefer
- Global HIV, Hepatitis, and STIs Programmes, WHO, Geneva, Switzerland
| | - Mark J Siedner
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Clinical Research Department, Africa Health Research Institute, Mtubatuba, South Africa
| | | | - Sinead Delany-Moretlwe
- Wits RHI, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Raphael J Landovitz
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Center for Clinical AIDS Research and Education, University of California, Los Angeles, CA, USA
| | - Charles Flexner
- Johns Hopkins University School of Medicine and Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Michael Jordan
- Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Francois Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mopo Radebe
- Regional Office for Africa, WHO, Gauteng, South Africa
| | - David Ripin
- Infectious Diseases Program, Clinton Health Access Initiative, New York, NY, USA
| | - Sarah Jenkins
- Infectious Diseases Program, Clinton Health Access Initiative, New York, NY, USA
| | - Danielle Resar
- Infectious Diseases Program, Clinton Health Access Initiative, New York, NY, USA
| | - Carolyn Amole
- Infectious Diseases Program, Clinton Health Access Initiative, New York, NY, USA
| | - Maryam Shahmanesh
- Institute for Global Health, University College London, London, UK; Clinical Research Department, Africa Health Research Institute, Mtubatuba, South Africa
| | - Ravindra K Gupta
- Clinical Research Department, Africa Health Research Institute, Mtubatuba, South Africa; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Elliot Raizes
- US Department of Health and Human Services, Centers for Disease Control, Atlanta, GA, USA
| | - Cheryl Johnson
- Global HIV, Hepatitis, and STIs Programmes, WHO, Geneva, Switzerland
| | - Seth Inzaule
- Global HIV, Hepatitis, and STIs Programmes, WHO, Geneva, Switzerland
| | - Robert Shafer
- Department of Medicine, Stanford University, Palo Alto, CA, USA
| | | | - Sarah Stansfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Roger Paredes
- Department of Infectious Diseases, Irsi Caixa Institut de Recerca de la SIDA, Barcelona, Spain
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A clinical review of HIV integrase strand transfer inhibitors (INSTIs) for the prevention and treatment of HIV-1 infection. Retrovirology 2022; 19:22. [PMID: 36273165 PMCID: PMC9588231 DOI: 10.1186/s12977-022-00608-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) have improved the treatment of human immunodeficiency virus (HIV). There are currently four approved for use in treatment-naïve individuals living with HIV; these include first generation raltegravir, elvitegravir, and second generation dolutegravir and bictegravir. The most recent INSTI, cabotegravir, is approved for (1) treatment of HIV infection in adults to replace current antiretroviral therapy in individuals who maintain virologic suppression on a stable antiretroviral regimen without history of treatment failure and no known resistance to its components and (2) pre-exposure prophylaxis in individuals at risk of acquiring HIV-1 infection. Cabotegravir can be administered intramuscularly as a monthly or bi-monthly injection depending on the indication. This long-acting combination has been associated with treatment satisfaction in clinical studies and may be helpful for individuals who have difficulty taking daily oral medications. Worldwide, second generation INSTIs are preferred for treatment-naïve individuals. Advantages of these INSTIs include their high genetic barrier to resistance, limited drug-drug interactions, excellent rates of virologic suppression, and favorable tolerability. Few INSTI resistance-associated mutations have been reported in clinical trials involving dolutegravir, bictegravir and cabotegravir. Other advantages of specific INSTIs include their use in various populations such as infants and children, acute HIV infection, and individuals of childbearing potential. The most common adverse events observed in clinical studies involving INSTIs included diarrhea, nausea, insomnia, fatigue, and headache, with very low rates of treatment discontinuation versus comparator groups. The long-term clinical implications of weight gain associated with second generation INSTIs dolutegravir and bictegravir warrants further study. This review summarizes key clinical considerations of INSTIs in terms of clinical pharmacology, drug-drug interactions, resistance, and provides perspective on clinical decision-making. Additionally, we summarize major clinical trials evaluating the efficacy and safety of INSTIs in treatment-naïve patients living with HIV as well as individuals at risk of acquiring HIV infection.
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