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Kemp SA, Kamelian K, Cuadros DF, Cheng MTK, Okango E, Hanekom W, Ndung'u T, Pillay D, Bonsall D, Wong EB, Tanser F, Siedner MJ, Gupta RK. HIV transmission dynamics and population-wide drug resistance in rural South Africa. Nat Commun 2024; 15:3644. [PMID: 38684655 PMCID: PMC11059351 DOI: 10.1038/s41467-024-47254-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
Despite expanded antiretroviral therapy (ART) in South Africa, HIV-1 transmission persists. Integrase strand transfer inhibitors (INSTI) and long-acting injectables offer potential for superior viral suppression, but pre-existing drug resistance could threaten their effectiveness. In a community-based study in rural KwaZulu-Natal, prior to widespread INSTI usage, we enroled 18,025 individuals to characterise HIV-1 drug resistance and transmission networks to inform public health strategies. HIV testing and reflex viral load quantification were performed, with deep sequencing (20% variant threshold) used to detect resistance mutations. Phylogenetic and geospatial analyses characterised transmission clusters. One-third of participants were HIV-positive, with 21.7% having detectable viral loads; 62.1% of those with detectable viral loads were ART-naïve. Resistance to older reverse transcriptase (RT)-targeting drugs was found, but INSTI resistance remained low (<1%). Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance, particularly to rilpivirine (RPV) even in ART-naïve individuals, was concerning. Twenty percent of sequenced individuals belonged to transmission clusters, with geographic analysis highlighting higher clustering in peripheral and rural areas. Our findings suggest promise for INSTI-based strategies in this setting but underscore the need for RPV resistance screening before implementing long-acting cabotegravir (CAB) + RPV. The significant clustering emphasises the importance of geographically targeted interventions to effectively curb HIV-1 transmission.
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Affiliation(s)
- Steven A Kemp
- Department of Medicine, University of Cambridge, Cambridge, UK
- Pandemic Science Institute, Big Data Institute, University of Oxford, Oxford, UK
| | - Kimia Kamelian
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Diego F Cuadros
- Digital Epidemiology Laboratory, Digital Futures, University of Cincinnati, Cincinnati, OH, USA
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Elphas Okango
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- University College London, London, UK
| | - Thumbi Ndung'u
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- University College London, London, UK
| | | | - David Bonsall
- Pandemic Science Institute, Big Data Institute, University of Oxford, Oxford, UK
| | - Emily B Wong
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | - Frank Tanser
- University of Stellenbosch, Cape Town, South Africa
| | - Mark J Siedner
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- University of KwaZulu-Natal, Durban, South Africa
- Harvard University, Cambridge, MA, England
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa.
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2
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Gbadamosi SO, Boyce G, Trepka MJ, Edwards RJ. The Burden of Pretreatment HIV Drug Resistance in Trinidad and Tobago. AIDS Res Hum Retroviruses 2024; 40:189-197. [PMID: 37409403 PMCID: PMC11040187 DOI: 10.1089/aid.2022.0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
Strategies to improve the scale-up of antiretroviral therapy (ART) for patients with HIV in Trinidad and Tobago, including the adoption of the "Test and Treat All" policy, have accompanied an increase in the number of patients with pretreatment HIV drug resistance (PDR) in the country. However, the scale of this public health problem is not well established. The objective of this study was to estimate the prevalence of PDR and evaluate its impact on viral suppression among patients with HIV receiving care at a large HIV treatment center in Trinidad and Tobago. We retrospectively analyzed data from the Medical Research Foundation of Trinidad and Tobago of patients newly diagnosed with HIV who had HIV genotyping performed. PDR was defined as having at least one drug-resistant mutation. We assessed the impact of PDR on achieving viral suppression within 12 months of ART initiation, using a Cox extended model. Among 99 patients, 31.3% had PDR to any drug, 29.3% to a non-nucleoside reverse transcriptase inhibitor (NNRTI), 3.0% to a nucleoside reverse transcriptase inhibitor, and 3.0% to a protease inhibitor. Overall, 67.1% of the patients who initiated ART (n = 82) and 66.7% (16/24) of patients with PDR achieved viral suppression within 12 months. We found no significant association between PDR status and achieving viral suppression within 12 months [adjusted hazard ratio: 1.08 (95% confidence interval: 0.57-2.04)]. There is a high prevalence of PDR in Trinidad and Tobago, specifically driven by NNRTI resistance. Although we found no difference in virologic suppression by PDR status, there is an urgent need for an effective HIV response to address the many drivers of virologic failure. Accelerating access to affordable, quality-assured generic dolutegravir and adopting it as the preferred first-line ART therapy are critical.
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Affiliation(s)
- Semiu O. Gbadamosi
- Department of Epidemiology, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, Florida, USA
| | - Gregory Boyce
- Medical Research Foundation of Trinidad and Tobago, Port of Spain, Trinidad
| | - Mary Jo Trepka
- Department of Epidemiology, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, Florida, USA
- Research Center in Minority Institutions (RCMI), Florida International University, Miami, Florida, USA
| | - Robert Jeffrey Edwards
- Medical Research Foundation of Trinidad and Tobago, Port of Spain, Trinidad
- Department of Paraclinical Sciences, University of the West Indies, St. Augustine, Trinidad
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3
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Chu C, Tao K, Kouamou V, Avalos A, Scott J, Grant PM, Rhee SY, McCluskey SM, Jordan MR, Morgan RL, Shafer RW. Prevalence of Emergent Dolutegravir Resistance Mutations in People Living with HIV: A Rapid Scoping Review. Viruses 2024; 16:399. [PMID: 38543764 PMCID: PMC10975848 DOI: 10.3390/v16030399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Dolutegravir (DTG) is a cornerstone of global antiretroviral (ARV) therapy (ART) due to its high efficacy and favorable tolerability. However, limited data exist regarding the risk of emergent integrase strand transfer inhibitor (INSTI) drug-resistance mutations (DRMs) in individuals receiving DTG-containing ART. METHODS We performed a PubMed search using the term "Dolutegravir", last updated 18 December 2023, to estimate the prevalence of VF with emergent INSTI DRMs in people living with HIV (PLWH) without previous VF on an INSTI who received DTG-containing ART. RESULTS Of 2131 retrieved records, 43 clinical trials, 39 cohorts, and 6 cross-sectional studies provided data across 6 clinical scenarios based on ART history, virological status, and co-administered ARVs: (1) ART-naïve PLWH receiving DTG plus two NRTIs; (2) ART-naïve PLWH receiving DTG plus lamivudine; (3) ART-experienced PLWH with VF on a previous regimen receiving DTG plus two NRTIs; (4) ART-experienced PLWH with virological suppression receiving DTG plus two NRTIs; (5) ART-experienced PLWH with virological suppression receiving DTG and a second ARV; and (6) ART-experienced PLWH with virological suppression receiving DTG monotherapy. The median proportion of PLWH in clinical trials with emergent INSTI DRMs was 1.5% for scenario 3 and 3.4% for scenario 6. In the remaining four trial scenarios, VF prevalence with emergent INSTI DRMs was ≤0.1%. Data from cohort studies minimally influenced prevalence estimates from clinical trials, whereas cross-sectional studies yielded prevalence data lacking denominator details. CONCLUSIONS In clinical trials, the prevalence of VF with emergent INSTI DRMs in PLWH receiving DTG-containing regimens has been low. Novel approaches are required to assess VF prevalence with emergent INSTI DRMs in PLWH receiving DTG in real-world settings.
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Affiliation(s)
- Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, CA 94110, USA;
| | - Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
| | - Vinie Kouamou
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare 00263, Zimbabwe;
| | - Ava Avalos
- Careena Center for Health, Gaborone, Botswana
| | - Jake Scott
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
| | - Philip M. Grant
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
| | | | - Michael R. Jordan
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Collaboratory for Emerging Infectious Diseases and Response (CEIDR), Tufts University, Medford, MA 02155, USA
| | - Rebecca L. Morgan
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
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Gupta R, Kemp S, Kamelian K, Cuadros D, Gupta R, Cheng M, Okango E, Hanekom W, Ndung'u T, Pillay D, Bonsall D, Wong E, Tanser F, Siedner M. HIV transmission dynamics and population-wide drug resistance in rural South Africa. RESEARCH SQUARE 2023:rs.3.rs-3640717. [PMID: 38076835 PMCID: PMC10705695 DOI: 10.21203/rs.3.rs-3640717/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Despite the scale-up of antiretroviral therapy (ART) in South Africa, HIV-1 incidence remains high. The anticipated use of potent integrase strand transfer inhibitors and long-acting injectables aims to enhance viral suppression at the population level and diminish transmission. Nevertheless, pre-existing drug resistance could impede the efficacy of long-acting injectable ART combinations, such as rilpivirine (an NNRTI) and cabotegravir (an INSTI). Consequently, a thorough understanding of transmission networks and geospatial distributions is vital for tailored interventions, including pre-exposure prophylaxis with long-acting injectables. However, empirical data on background resistance and transmission networks remain limited. In a community-based study in rural KwaZulu-Natal (2018-2019), prior to the widespread use of integrase inhibitor-based first-line ART, we performed HIV testing with reflex HIV-1 RNA viral load quantification on 18,025 participants. From this cohort, 6,096 (33.9%) tested positive for HIV via ELISA, with 1,323 (21.7%) exhibiting detectable viral loads (> 40 copies/mL). Of those with detectable viral loads, 62.1% were ART-naïve, and the majority of the treated were on an efavirenz + cytosine analogue + tenofovir regimen. Deep sequencing analysis, with a variant abundance threshold of 20%, revealed NRTI resistance mutations such as M184V in 2% of ART-naïve and 32% of treated individuals. Tenofovir resistance mutations K65R and K70E were found in 12% and 5% of ART-experienced individuals, respectively, and in less than 1% of ART-naïve individuals. Integrase inhibitor resistance mutations were notably infrequent (< 1%). Prevalence of pre-treatment drug resistance to NNRTIs was 10%, predominantly consisting of the K103N mutation. Among those with viraemic ART, NNRTI resistance was 50%, with rilpivirine-associated mutations observed in 9% of treated and 6% of untreated individuals. Cluster analysis revealed that 20% (205/1,050) of those sequenced were part of a cluster. We identified 171 groups with at least two linked participants; three quarters of clusters had only two individuals, and a quarter had 3-6 individuals. Integrating phylogenetic with geospatial analyses, we revealed a complex transmission network with significant clustering in specific regions, notably peripheral and rural areas. These findings derived from population scale genomic analyses are encouraging in terms of the limited resistance to DTG, but indicate that transitioning to long-acting cabotegravir + rilpivirine for transmission reduction should be accompanied by prior screening for rilpivirine resistance. Whole HIV-1 genome sequencing allowed identification of significant proportions of clusters with multiple individuals, and geospatial analyses suggesting decentralised networks can inform targeting public health interventions to effectively curb HIV-1 transmission.
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Mandt REK, Luth MR, Tye MA, Mazitschek R, Ottilie S, Winzeler EA, Lafuente-Monasterio MJ, Gamo FJ, Wirth DF, Lukens AK. Diverse evolutionary pathways challenge the use of collateral sensitivity as a strategy to suppress resistance. eLife 2023; 12:e85023. [PMID: 37737220 PMCID: PMC10695565 DOI: 10.7554/elife.85023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/21/2023] [Indexed: 09/23/2023] Open
Abstract
Drug resistance remains a major obstacle to malaria control and eradication efforts, necessitating the development of novel therapeutic strategies to treat this disease. Drug combinations based on collateral sensitivity, wherein resistance to one drug causes increased sensitivity to the partner drug, have been proposed as an evolutionary strategy to suppress the emergence of resistance in pathogen populations. In this study, we explore collateral sensitivity between compounds targeting the Plasmodium dihydroorotate dehydrogenase (DHODH). We profiled the cross-resistance and collateral sensitivity phenotypes of several DHODH mutant lines to a diverse panel of DHODH inhibitors. We focus on one compound, TCMDC-125334, which was active against all mutant lines tested, including the DHODH C276Y line, which arose in selections with the clinical candidate DSM265. In six selections with TCMDC-125334, the most common mechanism of resistance to this compound was copy number variation of the dhodh locus, although we did identify one mutation, DHODH I263S, which conferred resistance to TCMDC-125334 but not DSM265. We found that selection of the DHODH C276Y mutant with TCMDC-125334 yielded additional genetic changes in the dhodh locus. These double mutant parasites exhibited decreased sensitivity to TCMDC-125334 and were highly resistant to DSM265. Finally, we tested whether collateral sensitivity could be exploited to suppress the emergence of resistance in the context of combination treatment by exposing wildtype parasites to both DSM265 and TCMDC-125334 simultaneously. This selected for parasites with a DHODH V532A mutation which were cross-resistant to both compounds and were as fit as the wildtype parent in vitro. The emergence of these cross-resistant, evolutionarily fit parasites highlights the mutational flexibility of the DHODH enzyme.
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Affiliation(s)
- Rebecca EK Mandt
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Madeline R Luth
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Mark A Tye
- Center for Systems Biology, Massachusetts General HospitalBostonUnited States
- Harvard Graduate School of Arts and SciencesCambridgeUnited States
| | - Ralph Mazitschek
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Center for Systems Biology, Massachusetts General HospitalBostonUnited States
| | - Sabine Ottilie
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Elizabeth A Winzeler
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
- Skaggs School of Pharmaceutical Sciences, University of California, San DiegoLa JollaUnited States
| | | | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKlineMadridSpain
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Infectious Disease and Microbiome Program, The Broad InstituteCambridgeUnited States
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Infectious Disease and Microbiome Program, The Broad InstituteCambridgeUnited States
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Abdullahi A, Kida IM, Maina UA, Ibrahim AH, Mshelia J, Wisso H, Adamu A, Onyemata JE, Edun M, Yusuph H, Aliyu SH, Charurat M, Abimiku A, Abeler-Dorner L, Fraser C, Bonsall D, Kemp SA, Gupta RK. Limited emergence of resistance to integrase strand transfer inhibitors (INSTIs) in ART-experienced participants failing dolutegravir-based antiretroviral therapy: a cross-sectional analysis of a Northeast Nigerian cohort. J Antimicrob Chemother 2023; 78:2000-2007. [PMID: 37367727 PMCID: PMC10393879 DOI: 10.1093/jac/dkad195] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Due to the high prevalence of resistance to NNRTI-based ART since 2018, consolidated recommendations from the WHO have indicated dolutegravir as the preferred drug of choice for HIV treatment globally. There is a paucity of resistance outcome data from HIV-1 non-B subtypes circulating across West Africa. AIMS We characterized the mutational profiles of persons living with HIV from a cross-sectional cohort in North-East Nigeria failing a dolutegravir-based ART regimen. METHODS WGS of plasma samples collected from 61 HIV-1-infected participants following virological failure of dolutegravir-based ART were sequenced using the Illumina platform. Sequencing was successfully completed for samples from 55 participants. Following quality control, 33 full genomes were analysed from participants with a median age of 40 years and median time on ART of 9 years. HIV-1 subtyping was performed using SNAPPy. RESULTS Most participants had mutational profiles reflective of exposure to previous first- and second-line ART regimens comprised NRTIs and NNRTIs. More than half of participants had one or more drug resistance-associated mutations (DRMs) affecting susceptibility to NRTIs (17/33; 52%) and NNRTIs (24/33; 73%). Almost a quarter of participants (8/33; 24.4%) had one or more DRMs affecting tenofovir susceptibility. Only one participant, infected with HIV-1 subtype G, had evidence of DRMs affecting dolutegravir susceptibility-this was characterized by the T66A, G118R, E138K and R263K mutations. CONCLUSIONS This study found a low prevalence of resistance to dolutegravir; the data are therefore supportive of the continual rollout of dolutegravir as the primary first-line regimen for ART-naive participants and the preferred switch to second-line ART across the region. However, population-level, longer-term data collection on dolutegravir outcomes are required to further guide implementation and policy action across the region.
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Affiliation(s)
- Adam Abdullahi
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Ibrahim Musa Kida
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Umar Abdullahi Maina
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Maiduguri, Borno, Nigeria
| | | | - James Mshelia
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Haruna Wisso
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Abdullahi Adamu
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Maiduguri, Borno, Nigeria
| | | | - Martin Edun
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Haruna Yusuph
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Sani H Aliyu
- Department of Microbiology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | | | - Lucie Abeler-Dorner
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - David Bonsall
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Steven A Kemp
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Ravindra K Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
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7
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Rugemalila J, Kamori D, Kunambi P, Mizinduko M, Sabasaba A, Masoud S, Msafiri F, Mugusi S, Mutagonda R, Mlunde L, Amani D, Mboya E, Mahiti M, Ruhago G, Mushi J, Sambu V, Mgomella G, Jullu B, Maokola W, Njau P, Mutayoba B, Barabona G, Ueno T, Pembe A, Nagu T, Sunguya B, Aboud S. HIV virologic response, patterns of drug resistance mutations and correlates among adolescents and young adults: A cross-sectional study in Tanzania. PLoS One 2023; 18:e0281528. [PMID: 36821538 PMCID: PMC9949668 DOI: 10.1371/journal.pone.0281528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/25/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND The emergence of HIV drug resistance mutations (DRMs) is of significant threat to achieving viral suppression (VS) in the quest to achieve global elimination targets. We hereby report virologic outcomes and patterns of acquired DRMs and its associated factors among adolescents and young adults (AYA) from a broader HIV drug resistance surveillance conducted in Tanzania. METHODS Data of AYA was extracted from a cross-sectional study conducted in 36 selected facilities using a two-stage cluster sampling design. Dried blood spot (DBS) samples were collected and samples with a viral load (VL) ≥1000 copies/mL underwent genotyping for the HIV-1 pol gene. Stanford HIV database algorithm predicted acquired DRMs, Fisher's exact test and multivariable logistic regression assessed factors associated with DRMs and VS, respectively. FINDINGS We analyzed data of 578 AYA on antiretroviral therapy (ART) for 9-15 and ≥ 36 months; among them, 91.5% and 88.2% had VS (VL<1000copies/mL) at early and late time points, respectively. Genotyping of 64 participants (11.2%) who had VL ≥1000 copies/ml detected 71.9% of any DRM. Clinically relevant DRMs were K103N, M184V, M41L, T215Y/F, L210W/L, K70R, D67N, L89V/T, G118R, E138K, T66A, T97A and unexpectedly absent K65R. Participants on a protease inhibitor (PI) based regimen were twice as likely to not achieve VS compared to those on integrase strand transfer inhibitors (INSTI). The initial VL done 6 months after ART initiation of ≥1000copies/mL was the primary factor associated with detecting DRMs (p = .019). CONCLUSIONS VS amongst AYA is lower than the third UNAIDs target. Additionally, a high prevalence of ADR and high levels of circulating clinically relevant DRMs may compromise the long-term VS in AYA. Furthermore, the first VL result of ≥1000copies/ml after ART initiation is a significant risk factor for developing DRMs. Thus, strict VL monitoring for early identification of treatment failure and genotypic testing during any ART switch is recommended to improve treatment outcomes for AYA.
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Affiliation(s)
- Joan Rugemalila
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Internal Medicine, Muhimbili National Hospital, Dar es Salaam, Tanzania
- * E-mail:
| | - Doreen Kamori
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Peter Kunambi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Mucho Mizinduko
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Amon Sabasaba
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Salim Masoud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Frank Msafiri
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sabina Mugusi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Rita Mutagonda
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Linda Mlunde
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Davis Amani
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Erick Mboya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Macdonald Mahiti
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - George Ruhago
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Veryeh Sambu
- National AIDS Control Programme, Dodoma, Tanzania
| | - George Mgomella
- Centers for Disease Control and Prevention, Dar es Salaam, Tanzania
| | - Boniface Jullu
- Management and Development for Health, Dar es Salaam, Tanzania
| | | | - Prosper Njau
- National AIDS Control Programme, Dodoma, Tanzania
| | | | - Godfrey Barabona
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takamasa Ueno
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Andrea Pembe
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Tumaini Nagu
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Bruno Sunguya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Said Aboud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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8
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Parbie PK, Abana CZY, Kushitor D, Asigbee TW, Ntim NAA, Addo-Tetebo G, Ansong MRD, Ofori SB, Mizutani T, Runtuwene LR, Nishizawa M, Ishikawa K, Kiyono H, Ampofo WK, Matano T, Bonney EY, Kikuchi T. High-level resistance to non-nucleos(t)ide reverse transcriptase inhibitor based first-line antiretroviral therapy in Ghana; A 2017 study. Front Microbiol 2022; 13:973771. [PMID: 36090108 PMCID: PMC9459847 DOI: 10.3389/fmicb.2022.973771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
Expanding access to effective antiretroviral therapy (ART) is a major tool for management of Human Immunodeficiency Virus (HIV) infection. However, rising levels of HIV drug-resistance have significantly hampered the anticipated success of ART in persons living with HIV (PLWH), particularly those from Africa. Though great strides have been made in Ghana toward achieving the UNAIDS “95-95-95” target, a substantial number of PLWH receiving ART have not attained viral suppression. This study investigated patterns of drug resistance mutations in ART naïve as well as ART-experienced PLWH receiving first-line regimen drugs from Ghana. In a cross-sectional study, blood samples were collected from HIV-1 infected adults (≥18 years) attending HIV/AIDS clinic at the Eastern Regional Hospital, Koforidua, Ghana from September to October 2017. Viral RNA isolated from plasma were subjected to genotypic drug resistance testing for Protease Inhibitors (PI), Reverse Transcriptase Inhibitors (RTI), and Integrase Strand Transfer Inhibitors (INSTI). A total of 95 (84 ART experienced, 11 ART naïve) HIV-1 infected participants were sampled in this study. Sixty percent (50/84) of the ART-experienced participants were controlling viremia (viral load < 1,000 copies/ml). Of the 95 patient samples, 32, 34, and 33 were successfully sequenced for protease, reverse-transcriptase, and integrase regions, respectively. The dominant HIV-1 subtypes detected were CRF02_AG (70%), and A3 (10%). Major drug resistance associated mutations were only detected for reverse transcriptase inhibitors. The predominant drug resistance mutations were against nucleos(t)ide reverse transcriptase inhibitors (NRTI)—M184V/I and non-nucleos(t)ide reverse transcriptase inhibitors (NNRTI)—K103N. In the ART-experienced group, M184V/I and K103N were detected in 54% (15/28) and 46% (13/28) of individuals, respectively. Both mutations were each detected in 33% (2/6) of ART naïve individuals. Multiclass resistance to NRTI and NNRTI was detected in 57% of ART-experienced individuals and two ART naïve individuals. This study reports high-level resistance to NNRTI-based antiretroviral therapy in PLWH in Ghana. However, the absence of major PI and INSTI associated-mutations is a good signal that the current WHO recommendation of Dolutegravir in combination with an NRTI backbone will yield maximum benefits as first-line regimen for PLWH in Ghana.
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Affiliation(s)
- Prince Kofi Parbie
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Christopher Zaab-Yen Abana
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Center for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Dennis Kushitor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Theodore Worlanyo Asigbee
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Nana Afia Asante Ntim
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Gifty Addo-Tetebo
- Eastern Regional Hospital Koforidua, Ghana Health Service, Koforidua, Ghana
| | | | - Sampson Badu Ofori
- Eastern Regional Hospital Koforidua, Ghana Health Service, Koforidua, Ghana
| | | | | | - Masako Nishizawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Kiyono
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Future Medicine Education and Research Organization, Institute for Global Prominent Research, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Medicine, Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV) University of California San Diego, San Diego, CA, United States
| | | | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Evelyn Yayra Bonney
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- *Correspondence: Evelyn Yayra Bonney,
| | - Tadashi Kikuchi
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Tadashi Kikuchi,
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9
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Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK. HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy. mBio 2022; 13:e0026922. [PMID: 35446121 PMCID: PMC9239331 DOI: 10.1128/mbio.00269-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 12/19/2022] Open
Abstract
Prolonged virologic failure on 2nd-line protease inhibitor (PI)-based antiretroviral therapy (ART) without emergence of major protease mutations is well recognized and provides an opportunity to study within-host evolution in long-term viremic individuals. Using next-generation sequencing and in silico haplotype reconstruction, we analyzed whole-genome sequences from longitudinal plasma samples of eight chronically infected HIV-1-positive individuals failing 2nd-line regimens from the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) trial. On nonsuppressive ART, there were large fluctuations in synonymous and nonsynonymous variant frequencies despite stable viremia. Reconstructed haplotypes provided evidence for selective sweeps during periods of partial adherence, and viral haplotype competition, during periods of low drug exposure. Drug resistance mutations in reverse transcriptase (RT) were used as markers of viral haplotypes in the reservoir, and their distribution over time indicated recombination. We independently observed linkage disequilibrium decay, indicative of recombination. These data highlight dramatic changes in virus population structure that occur during stable viremia under nonsuppressive ART. IMPORTANCE HIV-1 infections are most commonly initiated with a single founder virus and are characterized by extensive inter- and intraparticipant genetic diversity. However, existing literature on HIV-1 intrahost population dynamics is largely limited to untreated infections, predominantly in subtype B-infected individuals. The manuscript characterizes viral population dynamics in long-term viremic treatment-experienced individuals, which has not been previously characterized. These data are particularly relevant for understanding HIV dynamics but can also be applied to other RNA viruses. With this unique data set we propose that the virus is highly unstable, and we have found compelling evidence of HIV-1 within-host viral diversification, recombination, and haplotype competition during nonsuppressive ART.
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Affiliation(s)
- Steven A. Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
| | - Oscar J. Charles
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, Durban, South Africa
| | - Werner Smidt
- Africa Health Research Institute, Durban, South Africa
| | - Darren P. Martin
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Collins Iwuji
- Africa Health Research Institute, Durban, South Africa
- Research Department of Infection and Population Health, University College London, United Kingdom
| | - John Adamson
- Africa Health Research Institute, Durban, South Africa
| | | | - Tulio de Oliveira
- Africa Health Research Institute, Durban, South Africa
- KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa
| | - Francois Dabis
- INSERM U1219-Centre Inserm Bordeaux Population Health, Université de Bordeaux, France
- Université de Bordeaux, ISPED, Centre INSERM U1219-Bordeaux Population Health, France
| | - Deenan Pillay
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Richard A. Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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10
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Spooner E, Reddy T, Mchunu N, Reddy S, Daniels B, Ngomane N, Luthuli N, Kiepiela P, Coutsoudis A. Point-of-care CD4 testing: Differentiated care for the most vulnerable. J Glob Health 2022; 12:04004. [PMID: 35136596 PMCID: PMC8818294 DOI: 10.7189/jogh.12.04004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background South Africa, with the highest burden of HIV infection globally, has made huge strides in its HIV/ART programme, but AIDS deaths have not decreased proportionally to ART uptake. Advanced HIV disease (CD4 < 200 cells/mm3) persists, and CD4 count testing is being overlooked since universal test-and-treat was implemented. Point-of-care CD4 testing could address this gap and assure differentiated care to these vulnerable patients with low CD4 counts. Methods A time randomised implementation trial was conducted, enrolling 603 HIV positive non-ART, not pregnant patients at a primary health care clinic in Durban, South Africa. Weeks were randomised to either point-of-care CD4 testing (n = 305 patients) or standard-of-care central laboratory CD4 testing (n = 298 patients) to assess the proportion initiating ART at 3 months. Cox regression, with robust standard errors adjusting for clustering by week, were used to assess the relationship between treatment initiation and arm. Results Among the 578 (299 point-of-care and 279 standard-of-care) patients eligible for analysis, there was no significant difference in the number of eligible patients initiating ART within 3 months in the point-of-care (73%) and the standard-of-care (68%) groups (P = 0.112). The time-to-treat analysis was not significantly different in patients with CD4 counts of 201-500 cells/mm3 which could have been due to appointment scheduling to cope with the large burden of cases. However, in patients with advanced HIV disease (CD4 < 200cells/mm3) 65% more patients started ART earlier in the point-of-care group (HR 1.65 (95% confidence interval (CI) = 0.99-2.75; P = 0.052) compared to the standard-of-care group. Conclusions Point-of-care testing decreased time-to-treatment in those with advanced HIV disease. With universal test and treat for HIV, rollout of simple point-of-care CD4 testing would ensure early diagnosis of advanced HIV disease and facilitate differentiated care for these vulnerable patients as per the World Health Organisation 2020 target product profile for point-of-care CD4 testing. Trial registration ISRCTN14220457.
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Affiliation(s)
- Elizabeth Spooner
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council, HIV Prevention Research Unit, Durban, South Africa
| | - Tarylee Reddy
- South African Medical Research Council, Biostatistics Unit, Durban, South Africa
| | - Nobuhle Mchunu
- South African Medical Research Council, Biostatistics Unit, Durban, South Africa
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Brodie Daniels
- South African Medical Research Council, HIV Prevention Research Unit, Durban, South Africa
| | | | | | | | - Anna Coutsoudis
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
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11
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Henerico S, Mikasi SG, Kalluvya SE, Brauner JM, Abdul S, Lyimo E, Desderius B, Korn K, van Zyl G, Jacobs GB, Preiser W, Kasang C. Prevalence and patterns of HIV drug resistance in patients with suspected virological failure in North-Western Tanzania. J Antimicrob Chemother 2022; 77:483-491. [PMID: 35107140 PMCID: PMC8809186 DOI: 10.1093/jac/dkab406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND More than 15 million people in sub-Saharan Africa receive ART. Treatment failure is common, but the role of HIV drug resistance in treatment failure is largely unknown because drug resistance testing is not routinely done. This study determined the prevalence and patterns of HIV drug resistance in patients with suspected virological failure. MATERIALS AND METHODS A single high viral load of >1000 viral RNA copies/mL of plasma at any point during ART was considered as suspected virological failure. HIV-1 RNA was extracted from plasma samples of these patients using the QIAamp Viral RNA kit. The protease and part of the RT regions of the HIV pol gene were characterized. RESULTS Viral load was determined in 317 patients; 64 (20.2%) had suspected virological failure. We successfully genotyped 56 samples; 48 (85.7%) had at least one major resistance-associated mutation (RAM). Common mutations in RT were M184V (75%), T215Y (41.1%), K103N (39.3%), M41L (32.1%), D67DN (30.3%), G190A (28.6%) and A98G (26.8%). No RAMs were detected in ART regimens based on a ritonavir-boosted PI. CONCLUSIONS The Tanzanian national guidelines define 'virological failure' as two consecutive viral load measurement results, at 3 month intervals, above the WHO threshold (1000 copies/mL). Here, we show that a single viral load above the WHO threshold is associated with high rates of RAMs. This suggests that a single high viral load measurement could be used to predict virological failure and avoid delays in switching patients from first-line to higher genetic barrier second-line regimens.
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Affiliation(s)
- Shimba Henerico
- Bugando Medical Centre, Mwanza, United Republic of Tanzania.,Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Sello Given Mikasi
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Samuel Elias Kalluvya
- Catholic University of Health and Allied Sciences, Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - Jan M Brauner
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Seif Abdul
- Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - Eric Lyimo
- National Institute of Medical Research, Mwanza, United Republic of Tanzania
| | - Bernard Desderius
- Bugando Medical Centre, Mwanza, United Republic of Tanzania.,Catholic University of Health and Allied Sciences, Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - Klaus Korn
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Christa Kasang
- German Leprosy and Tuberculosis Relief Association, Wuerzburg, Germany.,Medical Mission Institute, Wuerzburg, Germany
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12
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Boyer PL, Rehm CA, Sneller MC, Mican J, Caplan MR, Dewar R, Ferris AL, Clark P, Johnson A, Maldarelli F, Hughes SH. A Combination of Amino Acid Mutations Leads to Resistance to Multiple Nucleoside Analogs in Reverse Transcriptases from HIV-1 Subtypes B and C. Antimicrob Agents Chemother 2022; 66:e0150021. [PMID: 34723625 PMCID: PMC8765311 DOI: 10.1128/aac.01500-21] [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: 08/02/2021] [Accepted: 10/28/2021] [Indexed: 11/20/2022] Open
Abstract
Resistance to anti-HIV drugs has been a problem from the beginning of antiviral drug treatments. The recent expansion of combination antiretroviral therapy worldwide has led to an increase in resistance to antiretrovirals; understanding the mechanisms of resistance is increasingly important. In this study, we analyzed reverse transcriptase (RT) variants based on sequences derived from an individual who had low-level rebound viremia while undergoing therapy with abacavir, azidothymidine (AZT) (zidovudine), and (-)-l-2',3'-dideoxy-3'-thiacytidine (3TC) (lamivudine). The RT had mutations at positions 64, 67, 70, 184, and 219 and a threonine insertion after amino acid 69 in RT. The virus remained partially susceptible to the nucleoside RT inhibitor (NRTI) regimen. We show how these mutations affect the ability of NRTIs to inhibit DNA synthesis by RT. The presence of the inserted threonine reduced the susceptibility of the RT mutant to inhibition by tenofovir.
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Affiliation(s)
- Paul L. Boyer
- Retroviral Replication Laboratory, National Cancer Institute, Frederick, Maryland, USA
| | - Catherine A. Rehm
- Clinical Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Michael C. Sneller
- Clinical and Molecular Retrovirology Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - JoAnn Mican
- Clinical Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Margaret R. Caplan
- Division of Infectious Disease, Department of Medicine, Harbor-UCLA Medical Center, Los Angeles, California, USA
| | - Robin Dewar
- Division of Infectious Disease, Department of Medicine, Harbor-UCLA Medical Center, Los Angeles, California, USA
| | - Andrea L. Ferris
- Retroviral Replication Laboratory, National Cancer Institute, Frederick, Maryland, USA
| | - Patrick Clark
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Adam Johnson
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Frank Maldarelli
- Clinical Retrovirology Section, National Cancer Institute, Frederick, Maryland, USA
| | - Stephen H. Hughes
- Retroviral Replication Laboratory, National Cancer Institute, Frederick, Maryland, USA
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13
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McCluskey SM, Pepperrell T, Hill A, Venter WDF, Gupta RK, Siedner MJ. Adherence, resistance, and viral suppression on dolutegravir in sub-Saharan Africa: implications for the TLD era. AIDS 2021; 35:S127-S135. [PMID: 34848579 PMCID: PMC8647784 DOI: 10.1097/qad.0000000000003082] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dolutegravir (DTG) is now a component of preferred first-line antiretroviral therapy (ART) worldwide. ADVANCE and NAMSAL were two landmark clinical trials conducted exclusively in sub-Saharan Africa, which studied the effectiveness of DTG-based first-line regimens for ART-naive individuals. In this review, we examine the data from these studies to consider the contributions of adherence and HIV drug resistance to treatment failure on DTG-based ART, as compared with efavirenz (EFV)-based ART, which has a lower genetic barrier to resistance. We also discuss the implications of virologic failure on DTG and consolidate currently available data to conclude with recommendations for virologic monitoring on DTG-based ART.
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Affiliation(s)
- Suzanne M McCluskey
- Medical Practice Evaluation Center
- Division of Infectious Diseases, Massachusetts General Hospital
- Harvard Medical School, Boston, MA, USA
| | | | - Andrew Hill
- Department of Translational Medicine, Liverpool University, Liverpool, United Kingdom
| | - Willem D F Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Ravindra K Gupta
- Africa Health Research Institute, Durban, South Africa
- Cambridge University, Cambridge, United Kingdom
| | - Mark J Siedner
- Medical Practice Evaluation Center
- Division of Infectious Diseases, Massachusetts General Hospital
- Harvard Medical School, Boston, MA, USA
- Africa Health Research Institute, Durban, South Africa
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14
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Jin X, Wang Z, Zhang Z, Wu H, Ruan Y, Zhang C, Kang R, Xing H, Lou J. The transmission of drug-resistant strains of HIV in heterosexual populations based on genetic sequences. PLoS One 2021; 16:e0259023. [PMID: 34851959 PMCID: PMC8635345 DOI: 10.1371/journal.pone.0259023] [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: 02/17/2021] [Accepted: 10/11/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND China's National Free Antiretroviral Treatment Program (NFATP) has substantially reduced morbidity and HIV/AIDS incidence since 2003. However, HIV resistance to antiretroviral drugs (ARVs) has been a major challenge for the current treatment of HIV/AIDS in China. METHODS In the current study, we established a nested dynamic model to predict the multi-drug resistance dynamics of HIV among the heterosexual population and evaluated the impact of intervention measures on the transmission of drug resistance. We obtained an effective reproductive number [Formula: see text] from each sub-model held at different stages of the dynamic model. Meanwhile, we applied Bayesian phylogenetic methods to infer the weighted average effective reproductive number [Formula: see text] from four HIV subtypes that sampled from 912 HIV-positive patients in China. It is an original and innovative method by fitting [Formula: see text] to [Formula: see text] by Markov Chain Monte Carlo (MCMC) to generate unknown parameters in [Formula: see text]. RESULTS By analyzing the HIV gene sequences, we inferred that the most recent common ancestor of CRF01AE, CRF07BC, CRF08BC, and CRFBC dated from 1994, 1990, 1993 and 1990, respectively. The weighted average effective reproductive number [Formula: see text] dropped from 1.95 in 1994 to 1.73 in 2018. Considering different interventions, we used a macro dynamic model to predict the trend of HIV resistance. The results show that the number of new infections and total drug resistance under the baseline parameter (S1) are 253,422 and 213,250 in 2025, respectively. Comparing with the numbers under the target treatment rate (S2), they were 219,717 and 236,890, respectively. However, under the ideal treatment target (S3, the treatment rate reaches 90% and the treatment success rate reaches 90%), the number of new infections shows a declining trend and will decrease to 46,559 by 2025. Compared with S1 and S2, the total number of resistance also decreased to 160,899 in 2025. CONCLUSION With the promotion of NFATP in China, HIV resistance to ARVs is inevitable. The strategy of increasing the treatment rate would not only ineffectively curb the epidemic, but also deteriorate drug resistance issue. Whereas, a combination of intervention strategies (the treatment rate reaches 90% and the treatment success rate reaches 90%) can greatly reduce both infection and drug resistance rate than applying one strategy alone.
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Affiliation(s)
- Xin Jin
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Zhen Wang
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Zhiyuan Zhang
- Department of Statistics, Columbia University, New York, NY, United States of America
| | - Hui Wu
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Yuhua Ruan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chen Zhang
- School of Nursing, University of Rochester, Rochester, NY, United States of America
| | - Ruihua Kang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Disease Prevention and Control, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Lou
- Department of Mathematics, Shanghai University, Shanghai, China
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15
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El Bouzidi K, Datir RP, Kwaghe V, Roy S, Frampton D, Breuer J, Ogbanufe O, Murtala-Ibrahim F, Charurat M, Dakum P, Sabin CA, Ndembi N, Gupta RK. Deep sequencing of HIV-1 reveals extensive subtype variation and drug resistance after failure of first-line antiretroviral regimens in Nigeria. J Antimicrob Chemother 2021; 77:474-482. [PMID: 34741609 PMCID: PMC8809188 DOI: 10.1093/jac/dkab385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/28/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Deep sequencing could improve understanding of HIV treatment failure and viral population dynamics. However, this tool is often inaccessible in low- and middle-income countries. OBJECTIVES To determine the genetic patterns of resistance emerging in West African HIV-1 subtypes during first-line virological failure, and the implications for future antiretroviral options. PATIENTS AND METHODS Participants were selected from a Nigerian cohort of people living with HIV who had failed first-line ART and subsequently switched to second-line therapy. Whole HIV-1 genome sequences were generated from first-line virological failure samples with Illumina MiSeq. Mutations detected at ≥2% frequency were analysed and compared by subtype. RESULTS HIV-1 sequences were obtained from 101 participants (65% female, median age 30 years, median 32.9 months of nevirapine- or efavirenz-based ART). Thymidine analogue mutations (TAMs) were detected in 61%, other core NRTI mutations in 92% and NNRTI mutations in 99%. Minority variants (<20% frequency) comprised 18% of all mutations. K65R was more prevalent in CRF02_AG than G subtypes (33% versus 7%; P = 0.002), and ≥3 TAMs were more common in G than CRF02_AG (52% versus 24%; P = 0.004). Subtype G viruses also contained more RT cleavage site mutations. Cross-resistance to at least one of the newer NNRTIs, doravirine, etravirine or rilpivirine, was predicted in 81% of participants. CONCLUSIONS Extensive drug resistance had accumulated in people with West African HIV-1 subtypes, prior to second-line ART. Deep sequencing significantly increased the detection of resistance-associated mutations. Caution should be used if considering newer-generation NNRTI agents in this setting.
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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
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Vivian Kwaghe
- University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Sunando Roy
- Division of Infection & Immunity, University College London, London, UK
| | - Dan Frampton
- Division of Infection & Immunity, University College London, London, UK.,Farr Institute of Health Informatics Research, University College London, London, UK
| | - Judith Breuer
- Division of Infection & Immunity, University College London, London, UK
| | - Obinna Ogbanufe
- U.S. Centers for Disease Control and Prevention, U.S. Embassy, Abuja, Nigeria
| | | | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | | | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Nicaise Ndembi
- Institute of Human Virology Nigeria, Abuja, Nigeria.,Africa Centres for Disease Control and Prevention, African Union Commission, Addis Ababa, Ethiopia
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.,Africa Health Research Institute, Durban, South Africa
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16
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Kouamou V, Mavetera J, Manasa J, Ndhlovu CE, Katzenstein D, McGregor AM. Pretreatment HIV Drug Resistance Among Adults Initiating or Re-Initiating First-Line Antiretroviral Therapy in Zimbabwe: Fast-Tracking the Transition to Dolutegravir-Based First-Line Regimens? AIDS Res Hum Retroviruses 2021; 37:776-783. [PMID: 33430681 DOI: 10.1089/aid.2020.0242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pretreatment drug resistance (PDR) can compromise antiretroviral therapy (ART) efficacy and undermine the WHO targets to end the AIDS epidemic as a public health threat by 2030. Thus, we examined the level of PDR in Harare, Zimbabwe. Eligible study participants were adults who were ART naive or individuals with previous ART exposure reinitiating treatment, recruited between October 2018 and February 2020 in a HIV ART treatment clinic, in Harare. HIV drug resistance tests were performed for all specimens with viral load ≥400 copies/mL and interpreted using the Stanford HIVDB Algorithm. Chi-square test or Fisher's exact test was used for comparison of proportions of PDR across ART-naive or prior ART-exposed participants. All statistical analyses were performed using Stata version 14. Overall, 120 samples were genotyped of whom 104 were ART naive and 16 reported previous ART exposure. The overall PDR frequency among all participants was 31% [95% confidence interval (CI): 22.5-39.6]. PDR to any non-nucleotide reverse transcriptase inhibitor (NNRTI) was reported in 29% (95% CI: 21.0-37.9). PDR to nucleotide reverse transcriptase inhibitors (NRTIs) and protease inhibitors were low, found in 3% (95% CI: 0.9-8.2) and 1% (95% CI: 0.02-4.52), respectively. PDR to NNRTIs [efavirenz/nevirapine (EFV/NVP)] was found in 17% (95% CI: 10.5-24.6) and was more than six times higher among people with previous ART exposure than ART-naive people: 63% versus 10%, p < .001. Our study shows that PDR to NNRTIs in Zimbabwe has remarkably increased from the 10.9% prevalence reported in the 2016 WHO survey. Addressing PDR at a national level is a critical need and will be facilitated by fast-tracking the transition to dolutegravir in first-line ART regimens.
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Affiliation(s)
- Vinie Kouamou
- Department of Medicine, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Justice Mavetera
- Department of Medicine, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Justen Manasa
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | | | - David Katzenstein
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Alan Michael McGregor
- Department of Medicine, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
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Kikaire B, Ssemanda M, Asiimwe A, Nakanwagi M, Rwegyema T, Seruwagi G, Lawoko S, Asiimwe E, Wamundu C, Musinguzi A, Lugada E, Turesson E, Laverentz M, Bwayo D. HIV viral load suppression following intensive adherence counseling among people living with HIV on treatment at military-managed health facilities in Uganda. Int J Infect Dis 2021; 112:45-51. [PMID: 34481969 DOI: 10.1016/j.ijid.2021.08.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND Uniformed service personnel have an increased risk of poor viral load suppression (VLS). This study was performed to evaluate the outcomes of interventions to improve VLS in the 28 military health facilities in Uganda. METHODS This operational research was conducted between October 2018 and September 2019, among people living with HIV (PLHIV) in the 28 health facilities managed by the military in Uganda. Patients with a viral load (VL) >1000 copies/ml received three sessions of intensive adherence counselling (IAC), 1 month apart, after which a repeat VL was done. The main outcome was the proportion with a suppressed VL following IAC. RESULTS Of the 965 participants included in this analysis, 592 (61.4%) were male and 367 (38.3%) were female. Average age was 35.5 ± 13.7 years, and 87.8% had at least one IAC session. At least 48.2% had a suppressed repeat VL. IAC increased the odds of VLS by 82% (P = 0.004), with adjusted OR of 1.56 (P = 0.054). An initial VL >10 000 copies/ml, being on antiretroviral therapy for at least 2 years, being male, and being <18 years of age were associated with repeat VL non-suppression. CONCLUSIONS IAC marginally improved VL suppression. There is a need to improve IAC in military health facilities.
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Affiliation(s)
- Bernard Kikaire
- Makerere University College of Health Sciences, Kampala, Uganda.
| | - Michael Ssemanda
- University Research Co., LLC, Department of Defense HIV/AIDS Prevention Program (DHAPP), Kampala, Uganda
| | - Alex Asiimwe
- University Research Co., LLC, Department of Defense HIV/AIDS Prevention Program (DHAPP), Kampala, Uganda; Directorate of HIV, Uganda Peoples Defense Force (UPDF), Kampala, Uganda
| | - Miriam Nakanwagi
- University Research Co., LLC, Department of Defense HIV/AIDS Prevention Program (DHAPP), Kampala, Uganda
| | - Twaha Rwegyema
- University Research Co., LLC, Department of Defense HIV/AIDS Prevention Program (DHAPP), Kampala, Uganda
| | - Gloria Seruwagi
- Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Evarlyne Asiimwe
- Directorate of HIV, Uganda Peoples Defense Force (UPDF), Kampala, Uganda
| | - Cassette Wamundu
- Directorate of HIV, Uganda Peoples Defense Force (UPDF), Kampala, Uganda
| | - Ambrose Musinguzi
- Directorate of HIV, Uganda Peoples Defense Force (UPDF), Kampala, Uganda
| | - Eric Lugada
- University Research Co., LLC, Department of Defense HIV/AIDS Prevention Program (DHAPP), Kampala, Uganda
| | - Elizabeth Turesson
- University Research Co., LLC, Department of Defense HIV/AIDS Prevention Program (DHAPP), Kampala, Uganda
| | - Marni Laverentz
- University Research Co., LLC, Department of Defense HIV/AIDS Prevention Program (DHAPP), Kampala, Uganda
| | - Denis Bwayo
- University Research Co., LLC, Department of Defense HIV/AIDS Prevention Program (DHAPP), Kampala, Uganda
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Ndashimye E, Arts EJ. Dolutegravir response in antiretroviral therapy naïve and experienced patients with M184V/I: Impact in low-and middle-income settings. Int J Infect Dis 2021; 105:298-303. [PMID: 33722682 DOI: 10.1016/j.ijid.2021.03.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Dolutegravir (DTG) is now recommended to all HIV infected adults, adolescents, and children of right age by WHO. The low cost of $75 per year for generic DTG-based combination, has allowed 3.9 million people living with HIV (PLWH) in low and middle-income countries (LMICs) access to DTG. Lamivudine and emtricitabine associated M184V/I mutation is highly prevalent in PLWH and the majority of HIV infected individuals receiving DTG regimens may already be carrying M184V/I mutation. DISCUSSION Despite high prevalence of M184V/I in antiretroviral therapy (ART) experienced patients, DTG treatment outcomes will likely not be adversely affected by this mutation. The use of DTG in ART naïve has been largely characterised by rare emergence of resistance and virological failure. DTG-based regimens have to great extent been effective at maintaining viral suppression in treatment experienced PLWH carrying M184V/I. CONCLUSIONS Initiating patients on DTG may help preserve more treatment options for HIV infected individuals living in LMICs. High genetic barrier to the development of resistance associated with DTG and progressive viral suppression in patients switched to DTG-based therapy with M184V/I, may encourage better DTG outcomes and help in curbing increasing levels of HIV drug resistance in LMICs.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada; Joint Clinical Research Centre, Center for AIDS Research Uganda Laboratories, Kampala, Uganda.
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Canada.
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Addressing Antiretroviral Drug Resistance with Host-Targeting Drugs-First Steps towards Developing a Host-Targeting HIV-1 Assembly Inhibitor. Viruses 2021; 13:v13030451. [PMID: 33802145 PMCID: PMC8001593 DOI: 10.3390/v13030451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
The concerning increase in HIV-1 resistance argues for prioritizing the development of host-targeting antiviral drugs because such drugs can offer high genetic barriers to the selection of drug-resistant viral variants. Targeting host proteins could also yield drugs that act on viral life cycle events that have proven elusive to inhibition, such as intracellular events of HIV-1 immature capsid assembly. Here, we review small molecule inhibitors identified primarily through HIV-1 self-assembly screens and describe how all act either narrowly post-entry or broadly on early and late events of the HIV-1 life cycle. We propose that a different screening approach could identify compounds that specifically inhibit HIV-1 Gag assembly, as was observed when a potent rabies virus inhibitor was identified using a host-catalyzed rabies assembly screen. As an example of this possibility, we discuss an antiretroviral small molecule recently identified using a screen that recapitulates the host-catalyzed HIV-1 capsid assembly pathway. This chemotype potently blocks HIV-1 replication in T cells by specifically inhibiting immature HIV-1 capsid assembly but fails to select for resistant viral variants over 37 passages, suggesting a host protein target. Development of such small molecules could yield novel host-targeting antiretroviral drugs and provide insight into chronic diseases resulting from dysregulation of host machinery targeted by these drugs.
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Identification of an Antiretroviral Small Molecule That Appears To Be a Host-Targeting Inhibitor of HIV-1 Assembly. J Virol 2021; 95:JVI.00883-20. [PMID: 33148797 PMCID: PMC7925099 DOI: 10.1128/jvi.00883-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/25/2020] [Indexed: 12/16/2022] Open
Abstract
Given the projected increase in multidrug-resistant HIV-1, there is an urgent need for development of antiretrovirals that act on virus life cycle stages not targeted by drugs currently in use. Host-targeting compounds are of particular interest because they can offer a high barrier to resistance. Here, we report identification of two related small molecules that inhibit HIV-1 late events, a part of the HIV-1 life cycle for which potent and specific inhibitors are lacking. This chemotype was discovered using cell-free protein synthesis and assembly systems that recapitulate intracellular host-catalyzed viral capsid assembly pathways. These compounds inhibit replication of HIV-1 in human T cell lines and peripheral blood mononuclear cells, and are effective against a primary isolate. They reduce virus production, likely by inhibiting a posttranslational step in HIV-1 Gag assembly. Notably, the compound colocalizes with HIV-1 Gag in situ; however, unexpectedly, selection experiments failed to identify compound-specific resistance mutations in gag or pol, even though known resistance mutations developed upon parallel nelfinavir selection. Thus, we hypothesized that instead of binding to Gag directly, these compounds localize to assembly intermediates, the intracellular multiprotein complexes containing Gag and host factors that form during immature HIV-1 capsid assembly. Indeed, imaging of infected cells shows compound colocalized with two host enzymes found in assembly intermediates, ABCE1 and DDX6, but not two host proteins found in other complexes. While the exact target and mechanism of action of this chemotype remain to be determined, our findings suggest that these compounds represent first-in-class, host-targeting inhibitors of intracellular events in HIV-1 assembly.IMPORTANCE The success of antiretroviral treatment for HIV-1 is at risk of being undermined by the growing problem of drug resistance. Thus, there is a need to identify antiretrovirals that act on viral life cycle stages not targeted by drugs in use, such as the events of HIV-1 Gag assembly. To address this gap, we developed a compound screen that recapitulates the intracellular events of HIV-1 assembly, including virus-host interactions that promote assembly. This effort led to the identification of a new chemotype that inhibits HIV-1 replication at nanomolar concentrations, likely by acting on assembly. This compound colocalized with Gag and two host enzymes that facilitate capsid assembly. However, resistance selection did not result in compound-specific mutations in gag, suggesting that the chemotype does not directly target Gag. We hypothesize that this chemotype represents a first-in-class inhibitor of virus production that acts by targeting a virus-host complex important for HIV-1 Gag assembly.
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Datir R, Kemp S, El Bouzidi K, Mlchocova P, Goldstein R, Breuer J, Towers GJ, Jolly C, Quiñones-Mateu ME, Dakum PS, Ndembi N, Gupta RK. In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix. mBio 2020; 11:e02036-20. [PMID: 33144375 PMCID: PMC7642677 DOI: 10.1128/mbio.02036-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
Protease inhibitors (PIs) are the second- and last-line therapy for the majority of HIV-infected patients worldwide. Only around 20% of individuals who fail PI regimens develop major resistance mutations in protease. We sought to explore the role of mutations in gag-pro genotypic and phenotypic changes in viruses from six Nigerian patients who failed PI-based regimens without known drug resistance-associated protease mutations in order to identify novel determinants of PI resistance. Target enrichment and next-generation sequencing (NGS) with the Illumina MiSeq system were followed by haplotype reconstruction. Full-length Gag-protease gene regions were amplified from baseline (pre-PI) and virologic failure (VF) samples, sequenced, and used to construct gag-pro-pseudotyped viruses. Phylogenetic analysis was performed using maximum-likelihood methods. Susceptibility to lopinavir (LPV) and darunavir (DRV) was measured using a single-cycle replication assay. Western blotting was used to analyze Gag cleavage. In one of six participants (subtype CRF02_AG), we found 4-fold-lower LPV susceptibility in viral clones during failure of second-line treatment. A combination of four mutations (S126del, H127del, T122A, and G123E) in the p17 matrix of baseline virus generated a similar 4-fold decrease in susceptibility to LPV but not darunavir. These four amino acid changes were also able to confer LPV resistance to a subtype B Gag-protease backbone. Western blotting demonstrated significant Gag cleavage differences between sensitive and resistant isolates in the presence of drug. Resistant viruses had around 2-fold-lower infectivity than sensitive clones in the absence of drug. NGS combined with haplotype reconstruction revealed that resistant, less fit clones emerged from a minority population at baseline and thereafter persisted alongside sensitive fitter viruses. We used a multipronged genotypic and phenotypic approach to document emergence and temporal dynamics of a novel protease inhibitor resistance signature in HIV-1 matrix, revealing the interplay between Gag-associated resistance and fitness.
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Affiliation(s)
| | - Steven Kemp
- University College London, London, United Kingdom
| | | | - Petra Mlchocova
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Judy Breuer
- University College London, London, United Kingdom
| | | | - Clare Jolly
- University College London, London, United Kingdom
| | | | - Patrick S Dakum
- Institute for Human Virology, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nicaise Ndembi
- Institute for Human Virology, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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Ndembi N, Murtala-Ibrahim F, Tola M, Jumare J, Aliyu A, Alabi P, Mensah C, Abimiku A, Quiñones-Mateu ME, Crowell TA, Rhee SY, Shafer RW, Gupta R, Blattner W, Charurat ME, Dakum P. Predictors of first-line antiretroviral therapy failure among adults and adolescents living with HIV/AIDS in a large prevention and treatment program in Nigeria. AIDS Res Ther 2020; 17:64. [PMID: 33143751 PMCID: PMC7640637 DOI: 10.1186/s12981-020-00317-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/10/2020] [Indexed: 01/09/2023] Open
Abstract
Background A substantial number of persons living with HIV (PLWH) in Nigeria do not experience durable viral suppression on first-line antiretroviral therapy (ART). Understanding risk factors for first-line treatment failure informs patient monitoring practices and distribution of limited resources for second-line regimens. We determined predictors of immunologic and virologic failures in a large ART delivery program in Abuja, Nigeria. Methods A retrospective cohort study was conducted at the University of Abuja Teaching Hospital, a tertiary health care facility, using data from February 2005 to December 2014 in Abuja, Nigeria. All PLWH aged ≥ 15 years who initiated ART with at least 6-month follow-up and one CD4 measurement were included. Immunologic failure was defined as a CD4 decrease to or below pre-ART level or persistent CD4 < 100 cells per mm3 after 6 months on ART. Virologic failure (VF) was defined as two consecutive HIV-1 RNA levels > 1000 copies/mL after at least 6 months of ART and enhanced adherence counselling. HIV drug resistance (Sanger sequences) was analyzed using the Stanford HIV database algorithm and scored for resistance to common nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). Univariate and multivariate log binomial regression models were used to estimate relative risks (RRs) and 95% confidence intervals (CIs). Results Of 12,452 patients followed, a total of 5928 initiated ART with at least 6 months of follow-up and one CD4 measurement. The entry point for 3924 (66.2%) was through the program’s own voluntary counseling and testing (VCT) center, while 1310 (22.1%) were referred from an outside clinic/program, 332 (5.6%) in-patients, and 373 (6.3%) through other entry points including prevention of mother to child transmission (PMTCT) and transferred from other programs. The mean CD4 at enrollment in care was 268 ± 23.7 cells per mm3, and the mean HIV-1 RNA was 3.3 ± 1.3.log10 copies/mL. A total of 3468 (80.5%) received nevirapine (NVP) and 2260 (19.5%) received efavirenz (EFV)—based regimens. A total of 2140 (36.1%) received tenofovir (TDF); 2662 (44.9%) zidovudine (AZT); and 1126 (19.0%) stavudine (d4T). Among those receiving TDF, 45.0% also received emtricitabine (FTC). In a multivariate model, immunologic failure was more common among PLWH with female gender as compared to male [RR (95% CI) 1.22 (1.07–1.40)] and less common among those who entered care at the program’s VCT center as compared to other entry points [0.79 (0.64–0.91)], WHO stage 3/4 as compared to 1/2 [0.19 (0.16–0.22)], or CD4 200 + cells per mm3 as compared to lower [0.19 (0.16–0.22)]. Virologic failure was more common among PLWH who entered care at the program’s VCT center as compared to other entry points [RR (95% CI) 1.45 (1.11–1.91) and those with CD4 < 200 cells per mm3 at entry into care as compared to higher [1.71 (1.36–2.16)]. Of 198 patient-derived samples sequenced during virologic failure, 42 (21%) were wild-type; 145 (73%) carried NNRTI drug resistance mutations; 151 (76.3%) M184I/V; 29 (14.6%) had ≥ 3 TAMs, and 37 (18.7%) had K65R, of whom all were on TDF-containing first-line regimens. Conclusions In this cohort of Nigerian PLWH followed for a period of 9 years, immunologic criteria poorly predicted virologic failure. Furthermore, a subset of samples showed that patients failing ART for extended periods of time had HIV-1 strains harboring drug resistance mutations.
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Tenofovir resistance in early and long-term treated patients on first-line antiretroviral therapy in eight low-income and middle-income countries. AIDS 2020; 34:1965-1969. [PMID: 32694410 DOI: 10.1097/qad.0000000000002623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We aimed to assess the frequency of tenofovir (TDF) resistance in people failing tenofovir/lamivudine or emtricitabine (XTC)/nonnucleotide reverse-transcriptase inhibitor-based first-line antiretroviral treatment (ART) using data from 15 nationally representative surveys of HIV drug resistance conducted between 2014 and 2018 in Cameroon, Guatemala, Honduras, Nicaragua, Senegal, Uganda, Vietnam and Zambia. METHODS Prevalence of nucleoside reverse-transcriptase inhibitor resistance among participants with virological nonsuppression (viral load ≥1000 copies/ml) who had received TDF-based ART for 12-24 months (early ART group) and at least 40 months (long-term ART group) was assessed using Sanger sequencing and resistance was interpreted using the Stanford HIVdb algorithm. For each group, we estimated a pooled prevalence using random effect meta-analysis. RESULTS Of 4677 participants enrolled in the surveys, 640 (13.7%) had virological nonsuppression, 431 (67.3%) were successfully genotyped and were included in the analysis; of those, 60.3% (260) were participants in the early ART group. Overall, 39.1, 57.9, 38.5 and 3.6% patients in the early ART group and 42.9, 69.3, 42.9 and 10.0% patients on long-term ART had resistance to TDF, XTC, TDF + XTC and TDF + XTC + zidovudine, respectively. Overall, tenofovir resistance was mainly due to K65R or K70E/G/N/A/S/T/Y115F mutations (79%) but also due to thymidine analogue mutations (21%) which arise from exposure to thymidine analogues but causing cross-resistance to TDF. CONCLUSION Dual resistance to TDF + XTC occurred in more than 40% of the people with viral nonsuppression receiving tenofovir-based first-line ART, supporting WHO recommendation to optimize the nucleoside backbone in second-line treatment and cautioning against single drug substitutions in people with unsuppressed viral load.
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Gupta-Wright A, Fielding K, van Oosterhout JJ, Alufandika M, Grint DJ, Chimbayo E, Heaney J, Byott M, Nastouli E, Mwandumba HC, Corbett EL, Gupta RK. Virological failure, HIV-1 drug resistance, and early mortality in adults admitted to hospital in Malawi: an observational cohort study. Lancet HIV 2020; 7:e620-e628. [PMID: 32890497 PMCID: PMC7487765 DOI: 10.1016/s2352-3018(20)30172-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Antiretroviral therapy (ART) scale-up in sub-Saharan Africa combined with weak routine virological monitoring has driven increasing HIV drug resistance. We investigated ART failure, drug resistance, and early mortality among patients with HIV admitted to hospital in Malawi. METHODS This observational cohort study was nested within the rapid urine-based screening for tuberculosis to reduce AIDS-related mortality in hospitalised patients in Africa (STAMP) trial, which recruited unselected (ie, irrespective of clinical presentation) adult (aged ≥18 years) patients with HIV-1 at admission to medical wards. Patients were included in our observational cohort study if they were enrolled at the Malawi site (Zomba Central Hospital) and were taking ART for at least 6 months at admission. Patients who met inclusion criteria had frozen plasma samples tested for HIV-1 viral load. Those with HIV-1 RNA of at least 1000 copies per mL had drug resistance testing by ultra-deep sequencing, with drug resistance defined as intermediate or high-level resistance using the Stanford HIVDR program. Mortality risk was calculated 56 days from enrolment. Patients were censored at death, at 56 days, or at last contact if lost to follow-up. The modelling strategy addressed the causal association between HIV multidrug resistance and mortality, excluding factors on the causal pathway (most notably, CD4 cell count, clinical signs of advanced HIV, and poor functional and nutritional status). FINDINGS Of 1316 patients with HIV enrolled in the STAMP trial at the Malawi site between Oct 26, 2015, and Sept 19, 2017, 786 had taken ART for at least 6 months. 252 (32%) of 786 patients had virological failure (viral load ≥1000 copies per mL). Mean age was 41·5 years (SD 11·4) and 528 (67%) of 786 were women. Of 237 patients with HIV drug resistance results available, 195 (82%) had resistance to lamivudine, 128 (54%) to tenofovir, and 219 (92%) to efavirenz. Resistance to at least two drugs was common (196, 83%), and this was associated with increased mortality (adjusted hazard ratio 1·7, 95% CI 1·2-2·4; p=0·0042). INTERPRETATION Interventions are urgently needed and should target ART clinic, hospital, and post-hospital care, including differentiated care focusing on patients with advanced HIV, rapid viral load testing, and routine access to drug resistance testing. Prompt diagnosis and switching to alternative ART could reduce early mortality among inpatients with HIV. FUNDING Joint Global Health Trials Scheme of the Medical Research Council, UK Department for International Development, and Wellcome Trust.
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Affiliation(s)
- Ankur Gupta-Wright
- Department of Infection and Immunity, University College London, London UK; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.
| | - Katherine Fielding
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Joep J van Oosterhout
- Department of Medicine, University of Malawi College of Medicine, Blantyre, Malawi; Dignitas International, Zomba, Malawi
| | - Melanie Alufandika
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Dignitas International, Zomba, Malawi
| | - Daniel J Grint
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Elizabeth Chimbayo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Judith Heaney
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Matthew Byott
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Eleni Nastouli
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Henry C Mwandumba
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Elizabeth L Corbett
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK; Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
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Segujja F, Omooja J, Lunkuse S, Nanyonjo M, Nabirye SE, Nassolo F, Bugembe DL, Bbosa N, Kateete DP, Ssenyonga W, Mayanja Y, Nsubuga RN, Seeley J, Kaleebu P, Ssemwanga D. High Levels of Acquired HIV Drug Resistance Following Virological Nonsuppression in HIV-Infected Women from a High-Risk Cohort in Uganda. AIDS Res Hum Retroviruses 2020; 36:782-791. [PMID: 32475121 DOI: 10.1089/aid.2019.0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV drug resistance (HIVDR) is of increasing health concern, especially among key populations. We investigated the prevalence of virological suppression (VS), prevalence and correlates of HIVDR in HIV-infected women, enrolled in a high-risk cohort. We enrolled 267 women initiated on first-line antiretroviral therapy (ART) between 2015 and 2018. Participants' plasma samples were analyzed for HIV RNA viral load (VL) and genotypic resistance testing was performed on those with VL nonsuppression (defined as VL ≥1,000 copies/mL). We used the Stanford HIVDR database-algorithm to assess HIVDR mutations and logistic regression to assess risk factors for VL nonsuppression and HIVDR. We observed an overall VS prevalence of 76.0% (203/267) and detected respective acquired drug resistance prevalence to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs) of 81.3% [confidence interval (CI) 67.4-91.1] and 45.8% (CI 31.4-60.8) among the 48 successfully genotyped VL nonsuppressors. NNRTI mutations were observed in 81.3% (39/48) of the genotyped participants and 45.8% (22/48) had both NRTI and NNRTI mutations. The mutation K103N was detected in 62.5% (30/48) of participants, 41.7% (20/48) had M184V/I, 14.6% had K65R, and 12.5% (6/48) had thymidine analog mutations (TAMs). None of the analyzed potential risk factors, including age and duration on ART, was significantly correlated with VL nonsuppression or HIVDR. Although high levels of NNRTI mutations support the transition to dolutegravir, the presence of NRTI mutations, especially TAMs, may compromise dolutegravir-based regimens or other second-line ART options. The moderate VS prevalence and high HIVDR prevalence therefore call for timely ART switching and intensive adherence counseling.
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Affiliation(s)
- Farouk Segujja
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Jonah Omooja
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sandra Lunkuse
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Maria Nanyonjo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Stella E. Nabirye
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Faridah Nassolo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Daniel L. Bugembe
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - David P. Kateete
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - William Ssenyonga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Yunia Mayanja
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N. Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Janet Seeley
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
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Gregson J, Rhee SY, Datir R, Pillay D, Perno CF, Derache A, Shafer RS, Gupta RK. Human Immunodeficiency Virus-1 Viral Load Is Elevated in Individuals With Reverse-Transcriptase Mutation M184V/I During Virological Failure of First-Line Antiretroviral Therapy and Is Associated With Compensatory Mutation L74I. J Infect Dis 2020; 222:1108-1116. [PMID: 31774913 PMCID: PMC7459140 DOI: 10.1093/infdis/jiz631] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/26/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND M184V/I cause high-level lamivudine (3TC) and emtricitabine (FTC) resistance and increased tenofovir disoproxil fumarate (TDF) susceptibility. Nonetheless, 3TC and FTC (collectively referred to as XTC) appear to retain modest activity against human immunodeficiency virus-1 with these mutations possibly as a result of reduced replication capacity. In this study, we determined how M184V/I impacts virus load (VL) in patients failing therapy on a TDF/XTC plus nonnucleoside reverse-transcriptase inhibitor (NNRTI)-containing regimen. METHODS We compared VL in the absence and presence of M184V/I across studies using random effects meta-analysis. The effect of mutations on virus reverse-transcriptase activity and infectiousness was analyzed in vitro. RESULTS M184I/V was present in 817 (56.5%) of 1445 individuals with virologic failure (VF). Virus load was similar in individuals with or without M184I/V (difference in log10 VL, 0.18; 95% confidence interval, .05-.31). CD4 count was lower both at initiation of antiretroviral therapy and at VF in participants who went on to develop M184V/I. L74I was present in 10.2% of persons with M184V/I but absent in persons without M184V/I (P < .0001). In vitro, L74I compensated for defective replication of M184V-mutated virus. CONCLUSIONS Virus loads were similar in persons with and without M184V/I during VF on a TDF/XTC/NNRTI-containing regimen. Therefore, we did not find evidence for a benefit of XTC in the context of first-line failure on this combination.
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Affiliation(s)
- J Gregson
- Department of Biostatistics, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - S Y Rhee
- Department of Medicine, Stanford University, Stanford, California, USA
| | - R Datir
- Division of Infection and Immunity, UCL, London, United Kingdom
| | - D Pillay
- Division of Infection and Immunity, UCL, London, United Kingdom
- Africa Health Research Institute, Durban, South Africa
| | - C F Perno
- Department of Oncology and Haematoncology, University of Milan, Milan, Italy
| | - A Derache
- Africa Health Research Institute, Durban, South Africa
| | - R S Shafer
- Department of Medicine, Stanford University, Stanford, California, USA
| | - R K Gupta
- Africa Health Research Institute, Durban, South Africa
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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27
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Barabona G, Mahiti M, Masoud S, Mbelele P, Mgunya AS, Minja L, Sunguya B, Shigemi U, Matsuda M, Hachiya A, Iwatani Y, Lyamuya E, Ueno T. Pre-treatment and acquired HIV drug resistance in Dar es Salaam, Tanzania in the era of tenofovir and routine viral load monitoring. J Antimicrob Chemother 2020; 74:3016-3020. [PMID: 31273377 DOI: 10.1093/jac/dkz272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES We investigated the prevalence and patterns of pre-treatment and acquired HIV drug resistance mutations (DRMs) in Tanzania as a 'treat all' strategy, virological monitoring and the progressive increase in usage of tenofovir are being implemented in HIV treatment programmes. METHODS Viral RNA was isolated from plasma of 60 ART-naive and 166 treated-but-viraemic (>400 copies/mL) HIV-1-infected adults attending a care and treatment clinic at Muhimbili National Hospital, Dar es Salaam, Tanzania, between June and October 2017. Viral genes encoding protease and reverse transcriptase were amplified by PCR and directly sequenced. RESULTS Viral genotyping of successfully amplified samples revealed pre-treatment DRMs in 14/47 (29.8%) ART-naive subjects. Of these, 7/47 (14.9%) harboured mutations that confer high-level resistance to at least one drug of the default first-line regimen. In treated-but-viraemic subjects, DRMs were found in 100/111 (90%), where DRMs against NNRTI, NRTI and PI were observed in 95/100 (95%), 92/100 (92%) and 13/100 (13%), respectively. Tenofovir-resistance mutations K65R and K70G/E or ≥3 thymidine analogue resistance mutations including M41L and L210W were found in 18/36 (50%) subjects on a tenofovir-containing regimen at failure. Four patients harboured multiple DRMs, which can confer resistance to all available ART regimens in Tanzania. CONCLUSIONS Taken together, pre-treatment and acquired DRMs were highly prevalent, which represents a major risk for the efficacy of ART programmes in Tanzania. Availability of a newer generation of antiretroviral drugs with a higher genetic barrier to resistance and robust treatment monitoring is warranted for effective and sustainable HIV treatment.
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Affiliation(s)
- Godfrey Barabona
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Macdonald Mahiti
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,St Francis University College of Health and Allied Sciences, Ifakara, Tanzania.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Salim Masoud
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Peter Mbelele
- Kibong'oto Infectious Diseases Hospital, Moshi, Tanzania
| | | | - Lilian Minja
- Muhimbili National Hospital, Dar es Salaam, Tanzania
| | - Bruno Sunguya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan.,Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eligius Lyamuya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Takamasa Ueno
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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28
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Datir R, El Bouzidi K, Dakum P, Ndembi N, Gupta RK. Baseline PI susceptibility by HIV-1 Gag-protease phenotyping and subsequent virological suppression with PI-based second-line ART in Nigeria. J Antimicrob Chemother 2020; 74:1402-1407. [PMID: 30726945 PMCID: PMC6477990 DOI: 10.1093/jac/dkz005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/14/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022] Open
Abstract
Objectives Previous work showed that gag-protease-derived phenotypic susceptibility to PIs differed between HIV-1 subtype CRF02_AG/subtype G-infected patients who went on to successfully suppress viral replication versus those who experienced virological failure of lopinavir/ritonavir monotherapy as first-line treatment in a clinical trial. We analysed the relationship between PI susceptibility and outcome of second-line ART in Nigeria, where subtypes CRF02_AG/G dominate the epidemic. Methods Individuals who experienced second-line failure with ritonavir-boosted PI-based ART were matched (by subtype, sex, age, viral load, duration of treatment and baseline CD4 count) to those who achieved virological response (‘successes’). Successes were defined by viral load <400 copies of HIV-1 RNA/mL by week 48. Full-length Gag-protease was amplified from patient samples for in vitro phenotypic susceptibility testing, with PI susceptibility expressed as IC50 fold change (FC) relative to a subtype B reference strain. Results The median (IQR) lopinavir IC50 FC was 4.04 (2.49–7.89) for virological failures and 4.13 (3.14–8.17) for virological successes (P = 0.94). One patient had an FC >10 for lopinavir at baseline and experienced subsequent virological failure with ritonavir-boosted lopinavir as the PI. There was no statistically significant difference in single-round replication efficiency between the two groups (P = 0.93). There was a moderate correlation between single-round replication efficiency and FC for lopinavir (correlation coefficient 0.32). Conclusions We found no impact of baseline HIV-1 Gag-protease-derived phenotypic susceptibility on outcomes of PI-based second-line ART in Nigeria.
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Affiliation(s)
- R Datir
- Division of Infection and Immunity, University College London, London, UK
| | - K El Bouzidi
- Division of Infection and Immunity, University College London, London, UK
| | - P Dakum
- Institute of Human Virology, Abuja, Nigeria
| | - N Ndembi
- Institute of Human Virology, Abuja, Nigeria
| | - R K Gupta
- Division of Infection and Immunity, University College London, London, UK.,Africa Health Research Institute, Durban, South Africa
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29
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Hudson FP, Mulenga L, Westfall AO, Warrier R, Mweemba A, Saag MS, Stringer JS, Eron JJ, Chi BH. Evolution of HIV-1 drug resistance after virological failure of first-line antiretroviral therapy in Lusaka, Zambia. Antivir Ther 2020; 24:291-300. [PMID: 30977467 DOI: 10.3851/imp3299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND HIV viral load (VL) and resistance testing are limited in sub-Saharan Africa, so individuals may have prolonged time on failing first-line antiretroviral therapy (ART). Our objective was to describe the evolution of drug resistance mutations among adults failing first-line ART in Zambia. METHODS We analysed data from a trial of VL monitoring in Lusaka, Zambia. From 2006 to 2011, 12 randomized sites provided either routine VL monitoring (intervention) or discretionary (control) after ART initiation. Samples were collected prospectively following the same schedule in each arm but analysed retrospectively in the control group. For those with virological failure (VF; >400 copies/ml), HIV genotyping was performed retrospectively on baseline (BL) and on all subsequent specimens until censored due to study completion, withdrawal or death. RESULTS Of 1,973 enrollees, 165 (8.4%) developed VF. 464 genotype results were available including 132 (80%) at BL, 116 (70%) at VF and 125 (76%) had at least one result between VF and censoring. Major nucleoside reverse transcriptase inhibitor (NRTI) or non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations increased from 26% (BL) to 82% (VF) to 89% at last genotype (LG). M184 mutations increased from 2% to 59% to 71%; K65R from 2% to 11% to 13%; 2 or more thymidine analogue mutations from 1% to 3% to 12%. Among those on a failing tenofovir disoproxil fumarate (TDF)-based regimen, TDF resistance increased from 42% to 58%. CONCLUSIONS We found substantial resistance to NRTIs and NNRTIs at VF with incremental increases after VF while still on a failing first-line ART; this resistance may compromise attainment of the UNAIDS 90-90-90 goals.
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Affiliation(s)
- F Parker Hudson
- Department of Internal Medicine, University of Texas at Austin, Austin, TX, USA
| | - Lloyd Mulenga
- School of Medicine, University of Zambia, Lusaka, Zambia
| | - Andrew O Westfall
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ranjit Warrier
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Aggrey Mweemba
- School of Medicine, University of Zambia, Lusaka, Zambia
| | - Michael S Saag
- Department of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey Sa Stringer
- UNC Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph J Eron
- Department of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin H Chi
- UNC Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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30
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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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31
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Liu P, Xing H, Liao L, Feng Y, Leng X, Wang J, Kan W, Yan J, Li Y, Zuo Z, You Y, Ruan Y, Shao Y. HIV drug resistance in patients in China's national HIV treatment programme who have been on first-line ART for at least 9 months. AIDS Res Ther 2020; 17:9. [PMID: 32138739 PMCID: PMC7059326 DOI: 10.1186/s12981-020-00264-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 02/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to assess trends in drug resistance and associated clinical and programmatic factors at a national level during the rapid scale up of ART. METHODS Logistic regression was used to identify the factors associated with HIVDR. Variables associated with drug resistance in multivariable logistic regression were included in the Cochran-Armitage test for trend. RESULTS A total of 11,976 patients were enrolled in the study. The prevalence of HIVDR among patients who received ART for 9-24 months during 2003-2008, 2009-2012, and 2013-2015 significantly decreased (15.5%, 6.3%, and 2.3%, respectively, P < 0.01). With respect to the class of antiretroviral, there were substantial increases in resistance to both non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs) (2003-2008, 2009-2012, and 2013-2015: 49.7%, 58.9%, and 73.0%, respectively, P < 0.01). The prevalence of DR to protease inhibitors (PIs) was low, which supported their continued use as second-line therapy in China. CONCLUSIONS Our results provide evidence for the effectiveness of China's "Treat All" approach to guide policy makers to improve training for healthcare providers and education on ART adherence among patients.
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32
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Collier DA, Monit C, Gupta RK. The Impact of HIV-1 Drug Escape on the Global Treatment Landscape. Cell Host Microbe 2019; 26:48-60. [PMID: 31295424 DOI: 10.1016/j.chom.2019.06.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The rising prevalence of HIV drug resistance (HIVDR) could threaten gains made in combating the HIV epidemic and compromise the 90-90-90 target proposed by United Nations Programme on HIV/AIDS (UNAIDS) to have achieved virological suppression in 90% of all persons receiving antiretroviral therapy (ART) by the year 2020. HIVDR has implications for the persistence of HIV, the selection of current and future ART drug regimens, and strategies of vaccine and cure development. Focusing on drug classes that are in clinical use, this Review critically summarizes what is known about the mechanisms the virus utilizes to escape drug control. Armed with this knowledge, strategies to limit the expansion of HIVDR are proposed.
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Affiliation(s)
- D A Collier
- Division of Infection and Immunity, University College London, London, UK
| | - C Monit
- Division of Infection and Immunity, University College London, London, UK
| | - R K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
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33
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Birungi J, Cui Z, Okoboi S, Kapaata A, Munderi P, Mukajjanga C, Nanfuka M, Nyonyintono MS, Kim J, Zhu J, Kaleebu P, Moore DM. Lack of effectiveness of adherence counselling in reversing virological failure among patients on long-term antiretroviral therapy in rural Uganda. HIV Med 2019; 21:21-29. [PMID: 31432614 PMCID: PMC6916407 DOI: 10.1111/hiv.12790] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 11/27/2022]
Abstract
Objectives The current World Health Organization and Uganda Ministry of Health HIV treatment guidelines recommend that asymptomatic patients who have a viral load (VL) ≥ 1000 HIV‐1 RNA copies/mL should receive adherence counselling and repeat VL testing before switching to second‐line therapy. We evaluated the effectiveness of this strategy in a large HIV treatment programme of The AIDS Support Organisation Jinja in Jinja, Uganda. Methods We measured the HIV VL at enrolment, and for participants with VL ≥ 1000 copies/mL we informed them of their result, offered enhanced adherence counselling and repeated the VL measurement after 3 months. All blood samples with VL ≥ 1000 copies/mL were sequenced in the polymerase (pol) region, a 1257‐bp fragment spanning the protease and reverse transcriptase genes. Results One thousand and ninety‐one participants were enrolled in the study; 74.7% were female and the median age was 44 years [interquartile range (IQR) 39–50 years]. The median time on antiretroviral therapy (ART) at enrolment was 6.75 years (IQR 5.3–7.6 years) and the median CD4 cell count was 494 cells/μL (IQR 351–691 cells/μL). A total of 113 participants (10.4%) had VLs ≥ 1000 copies/mL and were informed of the VL result and its implications and given adherence counselling. Of these 113 participants, 102 completed 3 months of follow‐up and 93 (91%) still had VLs ≥ 1000 copies/mL. We successfully genotyped HIV for 105 patients (93%) and found that 103 (98%) had at least one mutation: eight (7.6%) had only one mutation, 94 (89.5%) had two mutations and one sample (1%) had three mutations. Conclusions In this study, enhanced adherence counselling was not effective in reversing virologically defined treatment failure for patients on long‐term ART who had not previously had a VL test.
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Affiliation(s)
- J Birungi
- The AIDS Support Organisation (TASO), Kampala, Uganda.,Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Z Cui
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - S Okoboi
- Infectious Diseases Institute, Makerere, Uganda
| | - A Kapaata
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - P Munderi
- International Association of Providers of AIDS Care, Washington, DC, USA
| | - C Mukajjanga
- The AIDS Support Organisation (TASO), Kampala, Uganda
| | - M Nanfuka
- The AIDS Support Organisation (TASO), Kampala, Uganda
| | | | - J Kim
- University of British Columbia, Vancouver, BC, Canada
| | - J Zhu
- University of British Columbia, Vancouver, BC, Canada
| | - P Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - D M Moore
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,University of British Columbia, Vancouver, BC, Canada
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Shroufi A, Van Cutsem G, Cambiano V, Bansi-Matharu L, Duncan K, Murphy RA, Maman D, Phillips A. Simplifying switch to second-line antiretroviral therapy in sub Saharan Africa: predicted effect of using a single viral load to define efavirenz-based first-line failure. AIDS 2019; 33:1635-1644. [PMID: 31305331 PMCID: PMC6641111 DOI: 10.1097/qad.0000000000002234] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background: Many individuals failing first-line antiretroviral therapy (ART) in sub-Saharan Africa never initiate second-line ART or do so after significant delay. For people on ART with a viral load more than 1000 copies/ml, the WHO recommends a second viral load measurement 3 months after the first viral load and enhanced adherence support. Switch to a second-line regimen is contingent upon a persistently elevated viral load more than 1000 copies/ml. Delayed second-line switch places patients at increased risk for opportunistic infections and mortality. Methods: To assess the potential benefits of a simplified second-line ART switch strategy, we use an individual-based model of HIV transmission, progression and the effect of ART which incorporates consideration of adherence and drug resistance, to compare predicted outcomes of two policies, defining first-line regimen failure for patients on efavirenz-based ART as either two consecutive viral load values more than 1000 copies/ml, with the second after an enhanced adherence intervention (implemented as per current WHO guidelines) or a single viral load value more than 1000 copies/ml. We simulated a range of setting-scenarios reflecting the breadth of the sub-Saharan African HIV epidemic, taking into account potential delays in defining failure and switch to second-line ART. Findings: The use of a single viral load more than 1000 copies/ml to define ART failure would lead to a higher proportion of persons with nonnucleoside reverse-transcriptase inhibitor resistance switched to second-line ART [65 vs. 48%; difference 17% (90% range 14–20%)], resulting in a median 18% reduction in the rate of AIDS-related death over setting scenarios (90% range 6–30%; from a median of 3.1 to 2.5 per 100 person-years) over 3 years. The simplified strategy also is predicted to reduce the rate of AIDS conditions by a median of 31% (90% range 8–49%) among people on first-line ART with a viral load more than 1000 copies/ml in the past 6 months. For a country of 10 million adults (and a median of 880 000 people with HIV), we estimate that this approach would lead to a median of 1322 (90% range 67–3513) AIDS deaths averted per year over 3 years. For South Africa this would represent around 10 215 deaths averted annually. Interpretation: As a step towards reducing unnecessary mortality associated with delayed second-line ART switch, defining failure of first-line efavirenz-based regimens as a single viral load more than 1000 copies/ml should be considered.
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Inzaule SC, Hamers RL, Bertagnolio S, Siedner MJ, Rinke de Wit TF, Gupta RK. Pretreatment HIV drug resistance in low- and middle-income countries. Future Virol 2019. [DOI: 10.2217/fvl-2018-0208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pretreatment HIV drug resistance (PDR) has been increasing with scale-up of antiretroviral therapy (ART) in low- and middle-income countries. Delay in responding to rising levels of PDR is projected to fuel a worldwide increase in mortality, HIV incidence and ART costs. Strategies to curb the rise in PDR include using antiretrovirals (ARVs) with high-genetic barrier to resistance in first-line therapy and for prophylaxis in HIV exposed infants, enhancing HIV drug resistance surveillance in populations initiating, receiving ART, and in those on pre-exposure prophylaxis, universal access and effective use of viral-load tests, improving adherence and retention and minimizing ART programmatic quality gaps. In this review, we assess the drivers of PDR, and potential strategies to mitigate its rise in prevalence and impact in low- and middle-income countries.
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Affiliation(s)
- Seth C Inzaule
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
| | - Raph L Hamers
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
- Eijkman-Oxford Clinical Research Unit, and Faculty of Medicine Universitas Indonesia, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Nuffield Department of Medicine, Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Silvia Bertagnolio
- HIV/AIDS Department & Global Hepatitis Programme, World Health Organization, 20 avenue Appia, 1211 Geneva, 27, Switzerland
| | - Mark J Siedner
- Massachusetts General Hospital, Harvard University, 02114 Boston, MA, USA
- Department of Medicine, University of Cambridge, Cambridge, CB2 OXY, UK
| | - Tobias F Rinke de Wit
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
- Joep Lange Institute, 1105 BM, North Holland, The Netherlands
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, CB2 OXY, UK
- Africa Health Research Institute, 719 Umbilo Road, Durban, KZN, South Africa
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Ntlantsana V, Hift RJ, Mphatswe WP. HIV viraemia during pregnancy in women receiving preconception antiretroviral therapy in KwaDukuza, KwaZulu-Natal. South Afr J HIV Med 2019; 20:847. [PMID: 31061722 PMCID: PMC6494933 DOI: 10.4102/sajhivmed.v20i1.847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 02/05/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Preconception antiretroviral therapy (PCART) followed by sustained viral suppression is effective in preventing mother-to-child transmission of HIV. The rates of persistent and transient viraemia in such patients have not been prospectively assessed in South Africa. OBJECTIVES We determined the prevalence of transient and persistent viraemia in HIV-positive women entering antenatal care on PCART and studied variables associated with viraemia. METHODS We performed a prospective cross-sectional observational study of HIV-positive pregnant women presenting to a primary healthcare facility in KwaZulu-Natal. All had received at least 6 months of first-line PCART. Viral load (VL) was measured, patients were interviewed, adherence estimated using a visual analogue scale and adherence counselling provided. Viral load was repeated after 4 weeks where baseline VL exceeded 50 copies/mL. RESULTS We enrolled 82 participants. Of them, 59 (72%) pregnancies were unplanned. Fifteen participants (18.3%) were viraemic at presentation with VL > 50 copies/mL. Of these, seven (8.5%) had viral suppression (VL < 50 copies/mL), and eight remained viraemic at the second visit. Adherence correlated significantly with viraemia at baseline. Level of knowledge correlated with adherence but not with lack of viral suppression at baseline. Socio-economic indicators did not correlate with viraemia. No instances of vertical transmission were observed at birth. CONCLUSIONS Approximately 20% of women receiving PCART may demonstrate viraemia. Half of these may be transient. Poor adherence is associated with viraemia, and efforts to encourage and monitor adherence are essential. The rate of unplanned pregnancies is high, and antiretroviral therapy programmes should focus on family planning needs of women in the reproductive age group to prevent viral non-suppression prior to pregnancy. KEYWORDS Preconception Antiretroviral Therapy; HIV; Viraemia; Antenatal Care; Adherence.
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Affiliation(s)
- Vuyokazi Ntlantsana
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J. Hift
- School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Wendy P. Mphatswe
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
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Derache A, Iwuji CC, Danaviah S, Giandhari J, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Pillay D, Gupta RK. Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART. J Antimicrob Chemother 2019; 74:473-479. [PMID: 30380053 PMCID: PMC6337894 DOI: 10.1093/jac/dky428] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023] Open
Abstract
Objectives The WHO recently recommended the use of a new first-line ART containing dolutegravir. We investigated the efficacy of NRTI backbones (tenofovir or abacavir with a cytosine analogue) in low- and middle-income countries where there is significant prior exposure to antiretrovirals and drug resistance to NRTIs. Methods Within the treatment-as-prevention study in South Africa, we selected participants with available next-generation sequencing (NGS) data for the HIV-1 pol gene at trial entry; they were either ART initiators (n = 1193) or already established on ART (n = 94). NGS of the HIV-1 pol gene was carried out using MiSeq technology; reverse transcriptase drug resistance mutations (DRMs) were detected at 5% (DRM5%) and 20% (DRM20%) for all 1287 participants. Genotypic susceptibility was assessed using the Stanford HIVDB resistance interpretation algorithm. Results NRTI DRM20% and DRM5% were detected among 5/1193 (0.4%) and 9/1193 (0.8%) of ART initiators, respectively. There was tenofovir exposure in 73/94 (77.7%) of those established on ART, with full susceptibility to abacavir in 57/94 (60.6%) and 56/94 (59.6%) for DRM20% and DRM5%, respectively, while 67/94 (71.3%) and 64/94 (68.1%) were fully susceptible to tenofovir, respectively. The differences between tenofovir and abacavir were not statistically significant at the 20% or 5% variant level (P = 0.16 and 0.29, respectively). NGS detection of variants at the 5% level increased detection of K65R in both naive and treated groups. One of 607 integrase sequences carried a DRM20% (Q148R). Conclusions Dolutegravir with a cytosine analogue plus tenofovir or abacavir appears to have similar efficacy in South Africans naive to ART. NGS should be considered in HIV drug resistance surveillance.
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Affiliation(s)
- Anne Derache
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Collins C Iwuji
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
- Institute for Global Health, University College London, London, UK
- Department of Global Health and Infection, Brighton and Sussex Medical School, Brighton, UK
| | - Siva Danaviah
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - François Dabis
- Université de Bordeaux, ISPED, Centre INSERM 1219, Bordeaux, France
| | - Deenan Pillay
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
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38
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Ahmed N, Flavell S, Ferns B, Frampton D, Edwards SG, Miller RF, Grant P, Nastouli E, Gupta RK. Development of the R263K Mutation to Dolutegravir in an HIV-1 Subtype D Virus Harboring 3 Class-Drug Resistance. Open Forum Infect Dis 2018; 6:ofy329. [PMID: 30648124 PMCID: PMC6329901 DOI: 10.1093/ofid/ofy329] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/09/2018] [Indexed: 11/14/2022] Open
Abstract
Dolutegravir (DTG), a second-generation integrase strand-transfer inhibitor (INSTI), is equivalent or superior to current non-nucleotide reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and first-generation INSTI-based antiretroviral regimens (ARVs). It has the potential to make big improvements in HIV control globally and within patients. This is perhaps the most "precious" HIV drug available. The integrase mutation R263K has been observed in tissue culture experiments and in patients treated with dolutegravir monotherapy in clinical trials. Globally, adherence and monitoring may be less than optimal and therefore DTG resistance more common. This is particularly important in low-middle-income countries, where patients may remain on failing regimens for longer periods of time and accumulate drug resistance. Data on this mutation in non-subtype B infections do not exist. We describe the first report of the R263K integrase mutation in a dolutegravir-exposed subtype D-infected individual with vertically acquired HIV. We have used deep sequencing of longitudinal samples to highlight the change in resistance over time while on a failing regimen. The case highlights that poorly adherent patients should not be offered dolutegravir even as part of a combination regimen and that protease inhibitors should be used preferentially.
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Affiliation(s)
- N Ahmed
- Mortimer Market Centre, Central and North West London NHS Foundation Trust, London, United Kingdom
| | - S Flavell
- Mortimer Market Centre, Central and North West London NHS Foundation Trust, London, United Kingdom
| | - B Ferns
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - D Frampton
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - S G Edwards
- Mortimer Market Centre, Central and North West London NHS Foundation Trust, London, United Kingdom
| | - R F Miller
- Mortimer Market Centre, Central and North West London NHS Foundation Trust, London, United Kingdom.,Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Centre for Clinical Research in Infection and Sexual Health, Institute for Global Health, University College London, London, United Kingdom
| | - P Grant
- Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - E Nastouli
- Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom.,Department of Population, Policy and Practice, UCL GOS Institute of Child Health, London, United Kingdom
| | - R K Gupta
- Mortimer Market Centre, Central and North West London NHS Foundation Trust, London, United Kingdom.,Division of Infection and Immunity, University College London, London, United Kingdom
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Drake TM, Knight SR, Harrison EM, Søreide K. Global Inequities in Precision Medicine and Molecular Cancer Research. Front Oncol 2018; 8:346. [PMID: 30234014 PMCID: PMC6131579 DOI: 10.3389/fonc.2018.00346] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022] Open
Abstract
Precision medicine based upon molecular testing is heralded as a revolution in how cancer is prevented, diagnosed, and treated. Large efforts across the world aim to conduct comprehensive molecular profiling of disease to inform preclinical models, translational research studies and clinical trials. However, most studies have only been performed in patients from high-income countries. As the burden on non-communicable diseases increases, cancer will become a pressing burden across the world, disproportionately affecting low-middle income settings. There is emerging evidence that the molecular landscape of disease differs geographically and by genetic ancestry, which cannot be explained by environmental factors alone. There is a lack of good quality evidence that characterises the molecular landscape of cancers found in low-middle income countries. As cancer medicine becomes increasingly driven by molecular alterations in high-income settings, low-income settings may become left behind. Further efforts on an international scale must be made by researchers, funders, and policymakers to ensure cancer research addresses disease across the world, so models are not limited to subtypes of disease found in high-income countries. In this review, we discuss differences found in the molecular profiles of tumours worldwide and the implication this has for the future of global cancer care. Finally, we identify several barriers currently limiting progress in this field and innovative solutions, which may address these shortcomings.
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Affiliation(s)
- Thomas M. Drake
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen R. Knight
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Ewen M. Harrison
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Kjetil Søreide
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
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40
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McCluskey SM, Lee GQ, Kamelian K, Kembabazi A, Musinguzi N, Bwana MB, Muzoora C, Haberer JE, Hunt PW, Martin JN, Boum Y, Bangsberg DR, Harrigan PR, Siedner MJ. Increasing Prevalence of HIV Pretreatment Drug Resistance in Women But Not Men in Rural Uganda During 2005-2013. AIDS Patient Care STDS 2018; 32:257-264. [PMID: 29985647 DOI: 10.1089/apc.2018.0020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The prevalence of HIV pretreatment drug resistance (PDR) is increasing in sub-Saharan Africa. We sought to describe correlates of PDR and evaluate effects of PDR on clinical outcomes in rural Uganda. We analyzed data from the Uganda AIDS Rural Treatment Outcomes study, a cohort of antiretroviral therapy (ART)-naive adults with HIV (2005-2015). We performed resistance testing on pre-ART specimens. We defined PDR as any World Health Organization (WHO) 2009 surveillance drug resistance mutation and classified PDR level using the Stanford algorithm. We fit unadjusted and sex-stratified log binomial regression and Cox proportional hazard models to identify correlates of PDR and the impact of PDR on viral suppression, loss to follow-up (LTFU), and death. We analyzed data from 738 participants (median age 33 years, 69% female). Overall, prevalence of PDR was 3.5% (n = 26), owing mostly to resistance to non-nucleoside reverse transcriptase inhibitors. PDR increased over time in women (1.8% in those enrolling in clinic in 2001-2006, vs. 7.0% in 2007-2013; p = 0.006), but not in men (1.15% vs. 0.72%, p = 0.737). Lower pre-ART log10 HIV RNA was also associated with higher prevalence of PDR. We identified longer time to viral suppression among those with PDR compared with without PDR (0.5 and 0.3 years, respectively, p = 0.023), but there was no significant relationship with mortality or LTFU (p = 0.139). We observed increasing rates of PDR in women in southwestern Uganda. Implications of this trend, particularly to prevention of mother-to-child transmission programs in the region, require attention due to delayed viral suppression among those with PDR.
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Affiliation(s)
- Suzanne M. McCluskey
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Guinevere Q. Lee
- Harvard Medical School, Boston, Massachusetts
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
- BC Center for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Kimia Kamelian
- BC Center for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Annet Kembabazi
- Mbarara University of Science and Technology, Mbarara, Uganda
| | | | | | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Jessica E. Haberer
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Peter W. Hunt
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Yap Boum
- Epicenter Mbarara Research Center, Mbarara, Uganda
| | - David R. Bangsberg
- Oregon Health Sciences University–Portland State University School of Public Health, Portland, Oregon
| | | | - Mark J. Siedner
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Mbarara University of Science and Technology, Mbarara, Uganda
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41
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Stockdale AJ, Saunders MJ, Boyd MA, Bonnett LJ, Johnston V, Wandeler G, Schoffelen AF, Ciaffi L, Stafford K, Collier AC, Paton NI, Geretti AM. Effectiveness of Protease Inhibitor/Nucleos(t)ide Reverse Transcriptase Inhibitor-Based Second-line Antiretroviral Therapy for the Treatment of Human Immunodeficiency Virus Type 1 Infection in Sub-Saharan Africa: A Systematic Review and Meta-analysis. Clin Infect Dis 2018; 66:1846-1857. [PMID: 29272346 PMCID: PMC5982734 DOI: 10.1093/cid/cix1108] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/18/2017] [Indexed: 02/02/2023] Open
Abstract
Background In sub-Saharan Africa, 25.5 million people are living with human immunodeficiency virus (HIV), representing 70% of the global total. The need for second-line antiretroviral therapy (ART) is projected to increase in the next decade in keeping with the expansion of treatment provision. Outcome data are required to inform policy. Methods We performed a systematic review and meta-analysis of studies reporting the virological outcomes of protease inhibitor (PI)-based second-line ART in sub-Saharan Africa. The primary outcome was virological suppression (HIV-1 RNA <400 copies/mL) after 48 and 96 weeks of treatment. The secondary outcome was the proportion of patients with PI resistance. Pooled aggregate data were analyzed using a DerSimonian-Laird random effects model. Results By intention-to-treat analysis, virological suppression occurred in 69.3% (95% confidence interval [CI], 58.2%-79.3%) of patients at week 48 (4558 participants, 14 studies), and in 61.5% (95% CI, 47.2%-74.9%) at week 96 (2145 participants, 8 studies). Preexisting resistance to nucleos(t)ide reverse transcriptase inhibitors (NRTIs) increased the likelihood of virological suppression. Major protease resistance mutations occurred in a median of 17% (interquartile range, 0-25%) of the virological failure population and increased with duration of second-line ART. Conclusions One-third of patients receiving PI-based second-line ART with continued NRTI use in sub-Saharan Africa did not achieve virological suppression, although among viremic patients, protease resistance was infrequent. Significant challenges remain in implementation of viral load monitoring. Optimizing definitions and strategies for management of second-line ART failure is a research priority. Prospero Registration CRD42016048985.
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Affiliation(s)
- Alexander J Stockdale
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre
- Institute of Infection and Global Health, University of Liverpool
| | - Matthew J Saunders
- Section of Infectious Diseases and Immunity and Wellcome Trust–Imperial College Centre for Global Health Research, Imperial College London, United Kingdom
| | - Mark A Boyd
- Kirby Institute for Infection and Immunity, University of New South Wales, Sydney
- Lyell McEwin Hospital, University of Adelaide, South Australia, Australia
| | | | | | - Gilles Wandeler
- Institute of Social and Preventative Medicine, University of Bern
- Department of Infectious Diseases, Bern University Hospital, Switzerland
| | - Annelot F Schoffelen
- Department of Infectious Diseases, University Medical Centre Utrecht, The Netherlands
| | - Laura Ciaffi
- Unité Mixte de Recherche de l’Institut de Rech (UMI), Institute de Recherche pour le Développement, Institute National de la Santé et de la Recherche Medicale, University of Montpellier, France
| | - Kristen Stafford
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore
| | - Ann C Collier
- University of Washington School of Medicine, Seattle
| | - Nicholas I Paton
- Yong Loo Lin School of Medicine, National University of Singapore
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Mayanja Y, Kamacooko O, Bagiire D, Namale G, Kaleebu P, Seeley J. 'Test and Treat' Among Women at High Risk for HIV-infection in Kampala, Uganda: Antiretroviral Therapy Initiation and Associated Factors. AIDS Behav 2018; 22:1053-1061. [PMID: 29127534 PMCID: PMC5847220 DOI: 10.1007/s10461-017-1973-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Data on implementation of 'Test and Treat' among key populations in sub-Saharan Africa are still limited. We examined factors associated with prompt antiretroviral therapy/ART (within 1 month of HIV-positive diagnosis or 1 week if pregnant) among 343 women at high risk for HIV infection in Kampala-Uganda, of whom 28% initiated prompt ART. Most (95%) reported paid sex within 3 months prior to enrolment. Multivariable logistic regression was used to determine baseline characteristics associated with prompt ART. Sex work as main job, younger age and being widowed/separated were associated with lower odds of prompt ART; being enrolled after 12 months of implementing the intervention was associated with higher odds of prompt ART. Younger women, widowed/separated and those reporting sex work as their main job need targeted interventions to start ART promptly after testing. Staff supervision and mentoring may need strengthening during the first year of implementing 'test and treat' interventions.
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Affiliation(s)
- Yunia Mayanja
- MRC/UVRI Uganda Research Unit on AIDS, Plot 51-59 Nakiwogo Road, Entebbe, Uganda.
| | - Onesmus Kamacooko
- MRC/UVRI Uganda Research Unit on AIDS, Plot 51-59 Nakiwogo Road, Entebbe, Uganda
| | - Daniel Bagiire
- MRC/UVRI Uganda Research Unit on AIDS, Plot 51-59 Nakiwogo Road, Entebbe, Uganda
| | - Gertrude Namale
- MRC/UVRI Uganda Research Unit on AIDS, Plot 51-59 Nakiwogo Road, Entebbe, Uganda
| | - Pontiano Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Plot 51-59 Nakiwogo Road, Entebbe, Uganda
| | - Janet Seeley
- MRC/UVRI Uganda Research Unit on AIDS, Plot 51-59 Nakiwogo Road, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
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43
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Chaplin B, Imade G, Onwuamah C, Odaibo G, Audu R, Okpokwu J, Olaleye D, Meloni S, Rawizza H, Muazu M, Musa AZ, Samuel J, Agbaji O, Ezechi O, Idigbe E, Kanki PJ. Distinct Pattern of Thymidine Analogue Mutations with K65R in Patients Failing Tenofovir-Based Antiretroviral Therapy. AIDS Res Hum Retroviruses 2018; 34:228-233. [PMID: 29084434 DOI: 10.1089/aid.2017.0198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Historically, in HIV patients, the K65R mutation and thymidine analogue mutations (TAMs) have been reported to rarely coexist. We retrospectively reviewed genotype data from paired samples in a cohort of HIV-1-infected Nigerian patients failing first-line antiretroviral therapies containing zidovudine (AZT) or tenofovir (TDF). Samples for each patient were taken at initial confirmed virological failure ≥1000 copies/ml (S1) and then at the latest available sample with viral load ≥1000 copies/ml before switch to second line (S2). Among 103 patients failing AZT, 19 (18.4%) had TAM-1s, 29 (28.2%) TAM-2s, and 21 (20.4%) mixed TAMs by S2. In contrast, in the 87 patients failing TDF, drug resistance mutations at S2 included K65R in 56 (64.4%), TAM-1s in 1 (1.1%), and TAM-2s in 25 patients (28.7%). Interestingly, 30.4% of patients with K65R in our study developed TAMs. These were exclusively K219E ± D67N and were not predicted to confer a resistance cost to future AZT-containing regimens.
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Affiliation(s)
- Beth Chaplin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | | | | | - Rosemary Audu
- Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | | | - Seema Meloni
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Holly Rawizza
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | - Jay Samuel
- AIDS Prevention Initiative Nigeria, Ltd./Gte., Abuja, Nigeria
| | - Oche Agbaji
- Jos University Teaching Hospital, Jos, Nigeria
| | - Oliver Ezechi
- Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | - Phyllis J. Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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Brenner BG, Ibanescu RI, Oliveira M, Roger M, Hardy I, Routy JP, Kyeyune F, Quiñones-Mateu ME, Wainberg MA. HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters. J Antimicrob Chemother 2018; 72:2171-2183. [PMID: 28472323 PMCID: PMC7263826 DOI: 10.1093/jac/dkx118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/22/2017] [Indexed: 12/20/2022] Open
Abstract
Objectives: Viral phylogenetics revealed two patterns of HIV-1 spread among
MSM in Quebec. While most HIV-1 strains (n = 2011) were
associated with singleton/small clusters (cluster size 1–4), 30 viral lineages formed
large networks (cluster size 20–140), contributing to 42% of diagnoses between 2011 and
2015. Herein, tissue culture selections ascertained if large cluster lineages possessed
higher replicative fitness than singleton/small cluster isolates, allowing for viral
escape from integrase inhibitors. Methods: Primary HIV-1 isolates from large 20+ cluster
(n = 11) or singleton/small cluster
(n = 6) networks were passagedin
vitro in escalating concentrations of dolutegravir, elvitegravir and lamivudine
for 24–36 weeks. Sanger and deep sequencing assessed genotypic changes under selective
drug pressure. Results: Large cluster HIV-1 isolates selected for resistance to
dolutegravir, elvitegravir and lamivudine faster than HIV-1 strains forming small
clusters. With dolutegravir, large cluster HIV-1 variants acquired solitary R263K
(n = 7), S153Y
(n = 1) or H51Y
(n = 1) mutations as the dominant quasi-species within
8–12 weeks as compared with small cluster lineages where R263K
(n = 1/6), S153Y (1/6) or WT species (4/6) were
observed after 24 weeks. Interestingly, dolutegravir-associated mutations compromised
viral replicative fitness, precluding escalations in concentrations beyond 5–10 nM. With
elvitegravir, large cluster variants more rapidly acquired first mutations (T66I, A92G,
N155H or S147G) by week 8 followed by sequential accumulation of multiple mutations
leading to viral escape (>10 μM) by week 24. Conclusions: Further studies are needed to understand virological features of
large cluster viruses that may favour their transmissibility, replicative competence and
potential to escape selective antiretroviral drug pressure.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Isabelle Hardy
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | | | - Fred Kyeyune
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,University Hospitals Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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45
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Goodall RL, Dunn DT, Nkurunziza P, Mugarura L, Pattery T, Munderi P, Kityo C, Gilks C, Kaleebu P, Pillay D, Gupta RK. Rapid accumulation of HIV-1 thymidine analogue mutations and phenotypic impact following prolonged viral failure on zidovudine-based first-line ART in sub-Saharan Africa. J Antimicrob Chemother 2018; 72:1450-1455. [PMID: 28160504 PMCID: PMC5400089 DOI: 10.1093/jac/dkw583] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023] Open
Abstract
Background: Lack of viral load monitoring of ART is known to be associated with slower switch from a failing regimen and thereby higher prevalence of MDR HIV-1. Many countries have continued to use thymidine analogue drugs despite recommendations to use tenofovir in combination with a cytosine analogue and NNRTI as first-line ART. The effect of accumulated thymidine analogue mutations (TAMs) on phenotypic resistance over time has been poorly characterized in the African setting. Patients and methods: A retrospective analysis of individuals with ongoing viral failure between weeks 48 and 96 in the NORA (Nevirapine OR Abacavir) study was conducted. We analysed 36 genotype pairs from weeks 48 and 96 of first-line ART (14 treated with zidovudine/lamivudine/nevirapine and 22 treated with zidovudine/lamivudine/abacavir). Phenotypic drug resistance was assessed using the Antivirogram assay (v. 2.5.01, Janssen Diagnostics). Results: At 96 weeks, extensive TAMs (≥3 mutations) were present in 50% and 73% of nevirapine- and abacavir-treated patients, respectively. The mean (SE) number of TAMs accumulating between week 48 and week 96 was 1.50 (0.37) in nevirapine-treated participants and 1.82 (0.26) in abacavir-treated participants. Overall, zidovudine susceptibility of viruses was reduced between week 48 [geometric mean fold change (FC) 1.3] and week 96 (3.4, P = 0.01). There was a small reduction in tenofovir susceptibility (FC 0.7 and 1.0, respectively, P = 0.18). Conclusions: Ongoing viral failure with zidovudine-containing first-line ART is associated with rapidly increasing drug resistance that could be mitigated with effective viral load monitoring.
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Affiliation(s)
| | | | | | | | - Theresa Pattery
- Janssen Diagnostics, a division of Janssen Pharmaceuticals NV, Beerse, Belgium
| | | | - Cissy Kityo
- Joint Clinical Research Centre, Kampala, Uganda
| | - Charles Gilks
- School of Population Health, University of Queensland, Brisbane, Australia
| | | | - Deenan Pillay
- Africa Health Research Institute, KwaZulu Natal, South Africa.,Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Africa Health Research Institute, KwaZulu Natal, South Africa.,Division of Infection and Immunity, University College London, London, UK
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46
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Chun HM, Obeng-Aduasare YF, Broyles LN, Ellenberger D. Expansion of Viral Load Testing and the Potential Impact on Human Immunodeficiency Virus Drug Resistance. J Infect Dis 2017; 216:S808-S811. [PMID: 29029178 DOI: 10.1093/infdis/jix404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increasing the volume, strengthening the quality, and proactively using data of human immunodeficiency virus (HIV) load testing are pivotal to limiting the threat of HIV drug resistance (HIVDR) accumulation,and allow for optimal case-based HIVDR surveillance. Triangulation of viral load (VL) and HIVDR testing data could be pursued to answer key questions and translate data and results for program and public policy. Identification of virologic failure and early management mitigates the greater risk of HIVDR. Routine VL monitoring and evaluation systems are necessary, and countries should consider reviewing system requirements, structural needs, and procedural and technical factors for the entire VL cascade, with special emphasis on post-test result use.
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Affiliation(s)
- Helen M Chun
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention
| | | | - Laura N Broyles
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention
| | - Dennis Ellenberger
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention
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47
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HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis. THE LANCET. INFECTIOUS DISEASES 2017; 18:346-355. [PMID: 29198909 PMCID: PMC5835664 DOI: 10.1016/s1473-3099(17)30702-8] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/13/2017] [Accepted: 11/14/2017] [Indexed: 11/27/2022]
Abstract
Background Pretreatment drug resistance in people initiating or re-initiating antiretroviral therapy (ART) containing non-nucleoside reverse transcriptase inhibitors (NNRTIs) might compromise HIV control in low-income and middle-income countries (LMICs). We aimed to assess the scale of this problem and whether it is associated with the intiation or re-initiation of ART in people who have had previous exposure to antiretroviral drugs. Methods This study was a systematic review and meta-regression analysis. We assessed regional prevalence of pretreatment drug resistance and risk of pretreatment drug resistance in people initiating ART who reported previous ART exposure. We systematically screened publications and unpublished datasets for pretreatment drug-resistance data in individuals in LMICs initiating or re-initiating first-line ART from LMICs. We searched for studies in PubMed and Embase and conference abstracts and presentations from the Conference on Retroviruses and Opportunistic Infections, the International AIDS Society Conference, and the International Drug Resistance Workshop for the period Jan 1, 2001, to Dec 31, 2016. To assess the prevalence of drug resistance within a specified region at any specific timepoint, we extracted study level data and pooled prevalence estimates within the region using an empty logistic regression model with a random effect at the study level. We used random effects meta-regression to relate sampling year to prevalence of pretreatment drug resistance within geographical regions. Findings We identified 358 datasets that contributed data to our analyses, representing 56 044 adults in 63 countries. Prevalence estimates of pretreatment NNRTI resistance in 2016 were 11·0% (7·5–15·9) in southern Africa, 10·1% (5·1–19·4) in eastern Africa, 7·2% (2·9–16·5) in western and central Africa, and 9·4% (6·6–13·2) in Latin America and the Caribbean. There were substantial increases in pretreatment NNRTI resistance per year in all regions. The yearly increases in the odds of pretreatment drug resistance were 23% (95% CI 16–29) in southern Africa, 17% (5–30) in eastern Africa, 17% (6–29) in western and central Africa, 11% (5–18) in Latin America and the Caribbean, and 11% (2–20) in Asia. Estimated increases in the absolute prevalence of pretreatment drug resistance between 2015 and 2016 ranged from 0·3% in Asia to 1·8% in southern Africa. Interpretation Pretreatment drug resistance is increasing at substantial rate in LMICs, especially in sub-Saharan Africa. In 2016, the prevalence of pretreatment NNRTI resistance was near WHO's 10% threshold for changing first-line ART in southern and eastern Africa and Latin America, underscoring the need for routine national HIV drug-resistance surveillance and review of national policies for first-line ART regimen composition. Funding Bill & Melinda Gates Foundation and World Health Organization.
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48
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Etta EM, Mavhandu L, Manhaeve C, McGonigle K, Jackson P, Rekosh D, Hammarskjold ML, Bessong PO, Tebit DM. High level of HIV-1 drug resistance mutations in patients with unsuppressed viral loads in rural northern South Africa. AIDS Res Ther 2017; 14:36. [PMID: 28750647 PMCID: PMC5531022 DOI: 10.1186/s12981-017-0161-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/19/2017] [Indexed: 02/07/2023] Open
Abstract
Background Combination antiretroviral therapy (cART) has significantly reduced HIV morbidity and mortality in both developed and developing countries. However, the sustainability of cART may be compromised by the emergence of viral drug resistance mutations (DRM) and the cellular persistence of proviruses carrying these DRM. This is potentially a more serious problem in resource limited settings. Methods DRM were evaluated in individuals with unsuppressed viral loads after first or multiple lines of cART at two sites in rural Limpopo, South Africa. Seventy-two patients with viral loads of >1000 copies/ml were recruited between March 2014 and December 2015. Complete protease (PR) and partial Reverse Transcriptase (RT) sequences were amplified from both plasma RNA and paired proviral DNA from 35 of these subjects. Amplicons were directly sequenced to determine subtype and DRM using the Stanford HIV Drug Resistance Interpretation algorithm. Results Among the 72 samples, 69 could be PCR amplified from RNA and 35 from both RNA and DNA. Sixty-five (94.2%) viruses were subtype C, while one was subtype B (1.4%), one recombinant K/C, one recombinant C/B and one unclassified. Fifty-eight (84%) sequences carried at least one DRM, while 11 (15.9%) displayed no DRM. DRM prevalence according to drug class was: NRTI 60.8% NNRTI 65.2%, and PI 5.8%. The most common DRMs were; M184V (51.7%), K103N (50%), V106M (20.6%), D67N (13.3%), K65R (12%). The frequency of the DRM tracked well with the frequency of use of medications to which the mutations were predicted to confer resistance. Interestingly, a significant number of subjects showed predicted resistance to the newer NNRTIs, etravirine (33%) and rilpivirine (42%), both of which are not yet available in this setting. The proportion of DRM in RNA and DNA were mostly similar with the exception of the thymidine analogue mutations (TAMs) D67N, K70R, K219QE; and K103N which were slightly more prevalent in DNA than RNA. Subjects who had received cART for at least 5 years were more likely to harbour >2 DRM (p < 0.05) compared to those treated for a shorter period. DRM were more prevalent in this rural setting compared to a neighbouring urban setting. Conclusion We found a very high prevalence of NRTI and NNRTI DRM in patients from rural Limpopo settings with different durations of treatment. The prevalence was significantly higher than those reported in urban settings in South Africa. The dominance of NNRTI based mutations late in treatment supports the use of PI based regimens for second line treatment in this setting. The slight dominance of TAMs in DNA from infected PBMCs compared to plasma virus requires further studies that should include cART subjects with suppressed virus. Such studies will improve our understanding of the pattern of drug resistance and dynamics of viral persistence in these rural settings.
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49
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Collier D, Iwuji C, Derache A, de Oliveira T, Okesola N, Calmy A, Dabis F, Pillay D, Gupta RK. Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis. Clin Infect Dis 2017; 64:1006-1016. [PMID: 28329393 PMCID: PMC5439490 DOI: 10.1093/cid/cix015] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/12/2017] [Indexed: 11/20/2022] Open
Abstract
Background Second-line antiretroviral therapy (ART) based on ritonavir-boosted protease inhibitors (bPIs) represents the only available option after first-line failure for the majority of individuals living with human immunodeficiency virus (HIV) worldwide. Maximizing their effectiveness is imperative. Methods This cohort study was nested within the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) cluster-randomized trial in rural KwaZulu-Natal, South Africa. We prospectively investigated risk factors for virological failure (VF) of bPI-based ART in the combined study arms. VF was defined by a plasma viral load >1000 copies/mL ≥6 months after initiating bPI-based ART. Cumulative incidence of VF was estimated and competing risk regression was used to derive the subdistribution hazard ratio (SHR) of the associations between VF and patient clinical and demographic factors, taking into account death and loss to follow-up. Results One hundred one participants contributed 178.7 person-years of follow-up. Sixty-five percent were female; the median age was 37.4 years. Second-line ART regimens were based on ritonavir-boosted lopinavir, combined with zidovudine or tenofovir plus lamivudine or emtricitabine. The incidence of VF on second-line ART was 12.9 per 100 person-years (n = 23), and prevalence of VF at censoring was 17.8%. Thirteen of these 23 (56.5%) virologic failures resuppressed after a median of 8.0 months (interquartile range, 2.8-16.8 months) in this setting where viral load monitoring was available. Tuberculosis treatment was associated with VF (SHR, 11.50 [95% confidence interval, 3.92-33.74]; P < .001). Conclusions Second-line VF was frequent in this setting. Resuppression occurred in more than half of failures, highlighting the value of viral load monitoring of second-line ART. Tuberculosis was associated with VF; therefore, novel approaches to optimize the effectiveness of PI-based ART in high-tuberculosis-burden settings are needed. Clinical Trials Registration NCT01509508.
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Affiliation(s)
- Dami Collier
- Department of Infection and Immunity, University College London, United Kingdom
| | - Collins Iwuji
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- Research Department of Infection and Population Health, University College London, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- Sorbonne Universités, University Pierre and Marie Curie Université Paris 06, Inserm, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Tulio de Oliveira
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- University of KwaZulu-Natal, Durban, South Africa
| | | | - Alexandra Calmy
- Geneva University Hospital, HIV Unit, Department of Internal Medicine, Switzerland
| | - Francois Dabis
- INSERM U1219-Centre Inserm Bordeaux Population Health, Université de Bordeaux, France
- Université de Bordeaux, ISPED, Centre INSERM U1219-Bordeaux Population Health, France
| | - Deenan Pillay
- Department of Infection and Immunity, University College London, United Kingdom
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Ravindra K Gupta
- Department of Infection and Immunity, University College London, United Kingdom
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
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50
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Rhee SY, Varghese V, Holmes SP, Van Zyl GU, Steegen K, Boyd MA, Cooper DA, Nsanzimana S, Saravanan S, Charpentier C, de Oliveira T, Etiebet MAA, Garcia F, Goedhals D, Gomes P, Günthard HF, Hamers RL, Hoffmann CJ, Hunt G, Jiamsakul A, Kaleebu P, Kanki P, Kantor R, Kerschberger B, Marconi VC, D'amour Ndahimana J, Ndembi N, Ngo-Giang-Huong N, Rokx C, Santoro MM, Schapiro JM, Schmidt D, Seu L, Sigaloff KCE, Sirivichayakul S, Skhosana L, Sunpath H, Tang M, Yang C, Carmona S, Gupta RK, Shafer RW. Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration. EBioMedicine 2017; 18:225-235. [PMID: 28365230 PMCID: PMC5405160 DOI: 10.1016/j.ebiom.2017.03.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/07/2017] [Accepted: 03/17/2017] [Indexed: 11/29/2022] Open
Abstract
Tenofovir disoproxil fumarate (TDF) genotypic resistance defined by K65R/N and/or K70E/Q/G occurs in 20% to 60% of individuals with virological failure (VF) on a WHO-recommended TDF-containing first-line regimen. However, the full spectrum of reverse transcriptase (RT) mutations selected in individuals with VF on such a regimen is not known. To identify TDF regimen-associated mutations (TRAMs), we compared the proportion of each RT mutation in 2873 individuals with VF on a WHO-recommended first-line TDF-containing regimen to its proportion in a cohort of 50,803 antiretroviral-naïve individuals. To identify TRAMs specifically associated with TDF-selection pressure, we compared the proportion of each TRAM to its proportion in a cohort of 5805 individuals with VF on a first-line thymidine analog-containing regimen. We identified 83 TRAMs including 33 NRTI-associated, 40 NNRTI-associated, and 10 uncommon mutations of uncertain provenance. Of the 33 NRTI-associated TRAMs, 12 - A62V, K65R/N, S68G/N/D, K70E/Q/T, L74I, V75L, and Y115F - were more common among individuals receiving a first-line TDF-containing compared to a first-line thymidine analog-containing regimen. These 12 TDF-selected TRAMs will be important for monitoring TDF-associated transmitted drug-resistance and for determining the extent of reduced TDF susceptibility in individuals with VF on a TDF-containing regimen.
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Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Vici Varghese
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Gert U Van Zyl
- Division of Medical Virology, Stellenbosch University, National Health Laboratory Service, Tygerberg 7505, South Africa
| | - Kim Steegen
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, WITS 2050, South Africa
| | - Mark A Boyd
- The Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | | | - Sabin Nsanzimana
- HIV/AIDS Division, Rwanda Biomedical Center, Kigali, P.O. Box 87, Rwanda
| | - Shanmugam Saravanan
- Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services, Taramani, Chennai 600113, India
| | - Charlotte Charpentier
- Univ Paris Diderot, Sorbonne Paris Cité, IAME, UMR 1137, INSERM, F-75018 Paris, France; AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - Tulio de Oliveira
- College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Mary-Ann A Etiebet
- Institute of Human Virology, University of Maryland School of Medicine, MD 21201, USA
| | | | - Dominique Goedhals
- Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301,South Africa
| | - Perpetua Gomes
- Laboratorio de Virologia, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon 1449-005, Portugal
| | - Huldrych F Günthard
- University Hospital Zurich, Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland
| | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam, P.O. Box 22700, The Netherlands
| | | | - Gillian Hunt
- National Institute for Communicable Diseases, Sandringham, Johannesburg 2131, South Africa
| | | | | | - Phyllis Kanki
- Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rami Kantor
- Division of Infectious Diseases, Alpert Medical School, Brown University, Providence, RI 02903, USA
| | | | - Vincent C Marconi
- Emory University School of Medicine, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | | | - Nicaise Ndembi
- Institute of Human Virology Nigeria, Abuja, Federal Capital Territory, P.O. Box 9396, Nigeria
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Developpement (IRD), UMI 174 - PHPT, 13572 Marseilles, France
| | - Casper Rokx
- Department of Internal Medicine and Infectious Diseases, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | | | | | - Daniel Schmidt
- Department of Infectious Disease Epidemiology, HIV/AIDS, STI and Blood Born Infections, Robert Koch-Institute, 13353 Berlin, Germany
| | - Lillian Seu
- School of Medicine, University of Alabama at Birmingham, AL 35210, USA
| | - Kim C E Sigaloff
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam, P.O. Box 22700, The Netherlands
| | | | - Lindiwe Skhosana
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, WITS 2050, South Africa
| | - Henry Sunpath
- School of Clinical Sciences, University of KwaZulu- Natal, Durban 4041, South Africa
| | - Michele Tang
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Chunfu Yang
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Port-au-Prince, Haiti
| | - Sergio Carmona
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, WITS 2050, South Africa
| | | | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
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