1
|
Sun Y, Wang L. Development of Anti-HIV Therapeutics: From Conventional Drug Discovery to Cutting-Edge Technology. Pharmaceuticals (Basel) 2024; 17:887. [PMID: 39065738 DOI: 10.3390/ph17070887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
The efforts to discover HIV therapeutics have continued since the first human immunodeficiency virus (HIV) infected patient was confirmed in the 1980s. Ten years later, the first HIV drug, zidovudine (AZT), targeting HIV reverse transcriptase, was developed. Meanwhile, scientists were enlightened to discover new drugs that target different HIV genes, like integrase, protease, and host receptors. Combination antiretroviral therapy (cART) is the most feasible medical intervention to suppress the virus in people with HIV (PWH) and control the epidemic. ART treatment has made HIV a chronic infection rather than a fatal disease, but ART does not eliminate latent reservoirs of HIV-1 from the host cells; strict and life-long adherence to ART is required for the therapy to be effective in patients. In this review, we first discussed the scientific history of conventional HIV drug discovery since scientists need to develop more and more drugs to solve drug-resistant issues and release the side effects. Then, we summarized the novel research technologies, like gene editing, applied to HIV treatment and their contributions to eliminating HIV as a complementary therapy.
Collapse
Affiliation(s)
- Yaping Sun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Lingyun Wang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| |
Collapse
|
2
|
Sun M, Manson ML, Guo T, de Lange ECM. CNS Viral Infections-What to Consider for Improving Drug Treatment: A Plea for Using Mathematical Modeling Approaches. CNS Drugs 2024; 38:349-373. [PMID: 38580795 PMCID: PMC11026214 DOI: 10.1007/s40263-024-01082-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Neurotropic viruses may cause meningitis, myelitis, encephalitis, or meningoencephalitis. These inflammatory conditions of the central nervous system (CNS) may have serious and devastating consequences if not treated adequately. In this review, we first summarize how neurotropic viruses can enter the CNS by (1) crossing the blood-brain barrier or blood-cerebrospinal fluid barrier; (2) invading the nose via the olfactory route; or (3) invading the peripheral nervous system. Neurotropic viruses may then enter the intracellular space of brain cells via endocytosis and/or membrane fusion. Antiviral drugs are currently used for different viral CNS infections, even though their use and dosing regimens within the CNS, with the exception of acyclovir, are minimally supported by clinical evidence. We therefore provide considerations to optimize drug treatment(s) for these neurotropic viruses. Antiviral drugs should cross the blood-brain barrier/blood cerebrospinal fluid barrier and pass the brain cellular membrane to inhibit these viruses inside the brain cells. Some antiviral drugs may also require intracellular conversion into their active metabolite(s). This illustrates the need to better understand these mechanisms because these processes dictate drug exposure within the CNS that ultimately determine the success of antiviral drugs for CNS infections. Finally, we discuss mathematical model-based approaches for optimizing antiviral treatments. Thereby emphasizing the potential of CNS physiologically based pharmacokinetic models because direct measurement of brain intracellular exposure in living humans faces ethical restrictions. Existing physiologically based pharmacokinetic models combined with in vitro pharmacokinetic/pharmacodynamic information can be used to predict drug exposure and evaluate efficacy of antiviral drugs within the CNS, to ultimately optimize the treatments of CNS viral infections.
Collapse
Affiliation(s)
- Ming Sun
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Martijn L Manson
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Tingjie Guo
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Elizabeth C M de Lange
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Taylor IA, Fassati A. The capsid revolution. J Mol Cell Biol 2024; 15:mjad076. [PMID: 38037430 PMCID: PMC11193064 DOI: 10.1093/jmcb/mjad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023] Open
Abstract
Lenacapavir, targeting the human immunodeficiency virus type-1 (HIV-1) capsid, is the first-in-class antiretroviral drug recently approved for clinical use. The development of Lenacapavir is attributed to the remarkable progress in our understanding of the capsid protein made during the last few years. Considered little more than a component of the virus shell to be shed early during infection, the capsid has been found to be a key player in the HIV-1 life cycle by interacting with multiple host factors, entering the nucleus, and directing integration. Here, we describe the key advances that led to this 'capsid revolution'.
Collapse
Affiliation(s)
- Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ariberto Fassati
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, UK
| |
Collapse
|
5
|
Hurbans N, Naidoo P. Efficacy, safety, and tolerability of dolutegravir-based ART regimen in Durban, South Africa: a cohort study. BMC Infect Dis 2024; 24:343. [PMID: 38515041 PMCID: PMC10958909 DOI: 10.1186/s12879-024-09202-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Dolutegravir is an integrase strand transfer inhibitor that has been recommended for use in first-line antiretroviral regimens by the World Health Organisation and is currently being rolled out globally. There has been safety concerns with dolutegravir which has caused concern about its use in the general population. Dolutegravir first-line regimens have been used in South Africa since early 2020. Therefore, the aim of the present study was to assess the efficacy, safety, and tolerability of first-line dolutegravir-based antiretrovirals amongst adults living with HIV in Durban, South Africa. METHODS This was a mixed-methods study, which comprised a cross-sectional survey and longitudinal retrospective follow-up of medical records. The study was conducted between October 2020 and January 2022. Data were described using descriptive and summary statistics. Bivariate logistic regression was applied to socio-demographic and clinical variables and crude odds ratios with a 95% confidence interval was calculated. Pearson chi-square tests, paired sample T-tests, and cross-tabulations were performed on selected variables. RESULTS A total of 461 participants were enrolled in the study. There was a significant change in immunological outcomes (p < 0.001) after dolutegravir initiation. Furthermore, an assessment of laboratory parameters showed that there was a significant decrease in cholesterol (p < 0.001) and increase in creatinine (p < 0.001) levels. Increased weight was shown by 60.7% of the participants but was not associated with age, gender, CD4 counts, and previous antiretroviral usage. The study found that 43.6% of the participants experienced at least one side-effect. A total of 21.6% and 23.2% of the participants experienced neuropsychiatric and central nervous system side-effects, respectively. In the bivariate analyses, only gender was shown to be associated with side-effects, and only 1.7% of the participants discontinued the study due to side-effects. CONCLUSION Our results suggest that dolutegravir is effective, safe, and well tolerated in the study population.
Collapse
Affiliation(s)
- Nivriti Hurbans
- Discipline of Pharmaceutical Sciences, School of Health Sciences, College of Health Science, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.
- South African Medical Research Council, HIV and Other Infectious Diseases Research Unit, Durban, South Africa.
| | - Panjasaram Naidoo
- Discipline of Pharmaceutical Sciences, School of Health Sciences, College of Health Science, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| |
Collapse
|
6
|
Hall M, Golubchik T, Bonsall D, Abeler-Dörner L, Limbada M, Kosloff B, Schaap A, de Cesare M, MacIntyre-Cockett G, Otecko N, Probert W, Ratmann O, Bulas Cruz A, Piwowar-Manning E, Burns DN, Cohen MS, Donnell DJ, Eshleman SH, Simwinga M, Fidler S, Hayes R, Ayles H, Fraser C. Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study. THE LANCET. MICROBE 2024; 5:e62-e71. [PMID: 38081203 PMCID: PMC10789608 DOI: 10.1016/s2666-5247(23)00220-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND In the last decade, universally available antiretroviral therapy (ART) has led to greatly improved health and survival of people living with HIV in sub-Saharan Africa, but new infections continue to appear. The design of effective prevention strategies requires the demographic characterisation of individuals acting as sources of infection, which is the aim of this study. METHODS Between 2014 and 2018, the HPTN 071 PopART study was conducted to quantify the public health benefits of ART. Viral samples from 7124 study participants in Zambia were deep-sequenced as part of HPTN 071-02 PopART Phylogenetics, an ancillary study. We used these sequences to identify likely transmission pairs. After demographic weighting of the recipients in these pairs to match the overall HIV-positive population, we analysed the demographic characteristics of the sources to better understand transmission in the general population. FINDINGS We identified a total of 300 likely transmission pairs. 178 (59·4%) were male to female, with 130 (95% CI 110-150; 43·3%) from males aged 25-40 years. Overall, men transmitted 2·09-fold (2·06-2·29) more infections per capita than women, a ratio peaking at 5·87 (2·78-15·8) in the 35-39 years source age group. 40 (26-57; 13·2%) transmissions linked individuals from different communities in the trial. Of 288 sources with recorded information on drug resistance mutations, 52 (38-69; 18·1%) carried viruses resistant to first-line ART. INTERPRETATION HIV-1 transmission in the HPTN 071 study communities comes from a wide range of age and sex groups, and there is no outsized contribution to new infections from importation or drug resistance mutations. Men aged 25-39 years, underserved by current treatment and prevention services, should be prioritised for HIV testing and ART. FUNDING National Institute of Allergy and Infectious Diseases, US President's Emergency Plan for AIDS Relief, International Initiative for Impact Evaluation, Bill & Melinda Gates Foundation, National Institute on Drug Abuse, and National Institute of Mental Health.
Collapse
Affiliation(s)
- Matthew Hall
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Sydney Infectious Diseases Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - David Bonsall
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Barry Kosloff
- Zambart, University of Zambia, Lusaka, Zambia; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Ab Schaap
- Zambart, University of Zambia, Lusaka, Zambia
| | - Mariateresa de Cesare
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Newton Otecko
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - William Probert
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Ana Bulas Cruz
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - David N Burns
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Myron S Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Sarah Fidler
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Richard Hayes
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Helen Ayles
- Zambart, University of Zambia, Lusaka, Zambia; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Christophe Fraser
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
7
|
Ma J, Chen Z, Fu C, Wei S, Liu J, Yang X, Chen X, Zhao Q, Sun Y, Huo Y. Consistency of drug-resistant mutations in plasma and peripheral blood mononuclear cells of patients with treatment-naïve and treatment-experienced HIV-1 infection. Front Cell Infect Microbiol 2023; 13:1249837. [PMID: 38179423 PMCID: PMC10766352 DOI: 10.3389/fcimb.2023.1249837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction Genotypic drug resistance testing is cursrently recommended by the World Health Organization for all patients infected with human immunodeficiency virus type 1 (HIV-1) undergoing care or switching regimes due to failure with previous antiretroviral therapy (ART). Patients with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) who meet the criteria for free testing for genotypic drug resistance due to poor adherence in Henan Province may resume their previous regimens before resampling. Therefore, resistance testing based on plasma RNA can fail in a proportion of patients. Resistance testing based on peripheral blood mononuclear cells (PBMCs) is an alternative option. In this study, we investigated the differences in drug-resistant mutations (DRMs) between plasma HIV RNA and proviral DNA in treatment-experienced and treatment-naïve patients. Methods Matched plasma RNA and proviral DNA samples of 66 HIV-1 infected treatment-naïve and 78 treatment-experienced patients were selected for DRM analysis and comparison. Results DRMs were detected in 27.3% (18/66) of treatment-naïve and 80.8% (63/78) of treatment-experienced samples. Resistance to at least one drug was detected based on analysis of plasma RNA and proviral DNA in 7.6% (5/66) and 9.1% (6/66) of treatment-naïve patients and in 79.5% (62/78) and 78.2% (61/78) of treatment-experienced patients, respectively. Furthermore, 61/66 (92.4%) of treatment-naïve patients showed concordant RNA and DNA drug resistance. When drug resistance was defined as intermediate and high, the concordance of drug resistance profiles of paired RNA and proviral DNA samples derived from treatment-naïve patients were up to 97.0% compared with only 80.8% (63/78) in treatment-experienced patients. Discussion Our data indicate that drug resistance testing based on plasma RNA or proviral DNA might be interchangeable in treatment-naïve patients, whereas plasma RNA-based testing remains the best choice for drug resistance analysis in patients with ART failure in clinical practice.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Yan Sun
- Center for Translational Medicine, The Sixth People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Yuqi Huo
- Center for Translational Medicine, The Sixth People’s Hospital of Zhengzhou, Zhengzhou, China
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Schulz VE, Tuff JF, Tough RH, Lewis L, Chimukangara B, Garrett N, Abdool Karim Q, Abdool Karim SS, McKinnon LR, Kharsany ABM, McLaren PJ. Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population. J Virol 2023; 97:e0095423. [PMID: 37747237 PMCID: PMC10617395 DOI: 10.1128/jvi.00954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.
Collapse
Affiliation(s)
- Vanessa E. Schulz
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jeffrey F. Tuff
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Riley H. Tough
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Lyle R. McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Paul J. McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| |
Collapse
|
10
|
Kiros M, Biset S, Gebremariam B, Yalew GT, Abegaz WE, Geteneh A. Trends in HIV-1 pretreatment drug resistance and HIV-1 variant dynamics among antiretroviral therapy-naive Ethiopians from 2003 to 2018: a pooled sequence analysis. Virol J 2023; 20:243. [PMID: 37880705 PMCID: PMC10601210 DOI: 10.1186/s12985-023-02205-w] [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: 05/29/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Ethiopia is among the highly HIV-affected countries, with reported 12,000 and 12,000 AIDS-related deaths and incidents as per reports from 2021. Although the country has made a promising progress in antiretroviral therapy, recent studies have indicated that pretreatment drug resistance (PDR) is alarmingly increasing, which has become a challenge for the effectiveness of HIV treatment. Epidemiologic data on PDR is necessary to help establish ART regimens with good efficacy. Thus, this systematic review aimed to determine the trend analysis of PDR among ART-naïve individuals along with HIV variant dynamics in Ethiopia. METHOD HIV-1 pol sequences from studies conducted between 2003 and 2018 among ART-naïve Ethiopian individuals were retrieved from GenBank and analyzed for the presence of PDR mutations (PDRM) along with the analysis of HIV-1 variant dynamics. The Calibrated Population Resistance (CPR) tool Version 8.1 and the REGA HIV-1 Subtyping Tool Version 3 were used to determine the PDRM and HIV-1 genetic diversity, respectively. RESULT We identified nine studies and analyzed 1070 retrieved HIV-1 pol sequences in this systematic review. The pooled prevalence of PDR was 4.8% (51/1070), including 1.4% (15/1070), 2.8% (30/1070), and 0.8% (9/1070) for nucleoside reverse transcriptase inhibitor (NRTI), non-NRTI (NNRTI), and protease inhibitor (PI) resistance, respectively. NRTI and NNRTI concurrent PDRM were observed among 0.2% (2/799) of the analyzed sequences. The overall PDR prevalence has been increasing over the years. Though the prevalence of the NNRTI, NRTI, and PI PDR also increased over the years, the NNRTI increment was more pronounced than the others, reaching 7.84% in 2018 from 2.19% in 2003. The majority (97%; 1038/1070) of the genetic diversity was HIV-1 subtype C virus, followed by subtype C' (2%; 20/1038) and other subtypes (1%; 10/1038). CONCLUSIONS According to this systematic review, the overall pooled prevalence of PDR is low. Despite the low prevalence, there has been an increasing trend of PDR over the years, which implies the need for routine surveillance of PDRMs along with preventive measures. Hence, this supports the recently endorsed transition of ART regimens from NNRTI to integrase strand transfer inhibitor-based regimens recommended by the WHO. In addition, this finding underscores the need for routine baseline genotypic drug resistance testing for all newly diagnosed HIV-infected patients before initiating treatment to halt the upward trend of PDR.
Collapse
Affiliation(s)
- Mulugeta Kiros
- Department of Medical Laboratory Science, CollegeofMedicineandHealth Sciences, Aksum University, Aksum, Ethiopia.
| | - Sirak Biset
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Birhane Gebremariam
- Department of Medical Laboratory Science, CollegeofMedicineandHealth Sciences, Aksum University, Aksum, Ethiopia
| | - Gebrehiwet Tesfay Yalew
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Adigrat University, Adigrat, Ethiopia
| | - Woldaregay Erku Abegaz
- Department of Microbiology, Parasitology, and Immunology, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alene Geteneh
- Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia
| |
Collapse
|
11
|
Cilento ME, Wen X, Reeve AB, Ukah OB, Snyder AA, Carrillo CM, Smith CP, Edwards K, Wahoski CC, Kitzler DR, Kodama EN, Mitsuya H, Parniak MA, Tedbury PR, Sarafianos SG. HIV-1 Resistance to Islatravir/Tenofovir Combination Therapy in Wild-Type or NRTI-Resistant Strains of Diverse HIV-1 Subtypes. Viruses 2023; 15:1990. [PMID: 37896768 PMCID: PMC10612037 DOI: 10.3390/v15101990] [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: 08/09/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
Tenofovir disoproxil fumarate (TDF) and islatravir (ISL, 4'-ethynyl-2-fluoro-2'-deoxyadensine, or MK-8591) are highly potent nucleoside reverse transcriptase inhibitors. Resistance to TDF and ISL is conferred by K65R and M184V, respectively. Furthermore, K65R and M184V increase sensitivity to ISL and TDF, respectively. Therefore, these two nucleoside analogs have opposing resistance profiles and could present a high genetic barrier to resistance. To explore resistance to TDF and ISL in combination, we performed passaging experiments with HIV-1 WT, K65R, or M184V in the presence of ISL and TDF. We identified K65R, M184V, and S68G/N mutations. The mutant most resistant to ISL was S68N/M184V, yet it remained susceptible to TDF. To further confirm our cellular findings, we implemented an endogenous reverse transcriptase assay to verify in vitro potency. To better understand the impact of these resistance mutations in the context of global infection, we determined potency of ISL and TDF against HIV subtypes A, B, C, D, and circulating recombinant forms (CRF) 01_AE and 02_AG with and without resistance mutations. In all isolates studied, we found K65R imparted hypersensitivity to ISL whereas M184V conferred resistance. We demonstrated that the S68G polymorphism can enhance fitness of drug-resistant mutants in some genetic backgrounds. Collectively, the data suggest that the opposing resistance profiles of ISL and TDF suggest that a combination of the two drugs could be a promising drug regimen for the treatment of patients infected with any HIV-1 subtype, including those who have failed 3TC/FTC-based therapies.
Collapse
Affiliation(s)
- Maria E. Cilento
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xin Wen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Aaron B. Reeve
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Obiaara B. Ukah
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Alexa A. Snyder
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ciro M. Carrillo
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cole P. Smith
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kristin Edwards
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Claudia C. Wahoski
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Deborah R. Kitzler
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eiichi N. Kodama
- Division of Infectious Disease, International Institute of Disaster Science, Tohoku University, Sendai 980-8572, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health & Medicine Research Institute, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556, Japan
| | - Michael A. Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Philip R. Tedbury
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Eileen Delaney K, Ngobeni T, Woods CK, Gordijn C, Claassen M, Parikh U, Harrigan PR, van Zyl GU. Nano-RECall provides an integrated pipeline for HIV-1 drug resistance testing from Oxford Nanopore sequence data. Trop Med Int Health 2023; 28:186-193. [PMID: 36599816 PMCID: PMC10230441 DOI: 10.1111/tmi.13851] [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: 01/06/2023]
Abstract
OBJECTIVES Low-capital-layout sequencing options from Oxford Nanopore Technologies (ONT) could assist in expanding HIV drug resistance testing to resource-limited settings. HIV drug resistance mutations often occur as mixtures, but current ONT pipelines provide a consensus sequence only. Moreover, there is no integrated pipeline that provides a drug resistance report from an ONT sequence file without intervention from skilled bioinformaticists. We therefore investigated Nano-RECall, which provides seamless drug resistance interpretation while requiring low-read coverage ONT sequence data from affordable Flongle or MinION flow cells and which provides mutation mixtures similar to Sanger Sequencing. METHODS We compared Sanger sequencing to ONT sequencing of the same HIV-1 subtype C polymerase chain reaction (PCR) amplicons, respectively using RECall and the novel Nano-RECall bioinformatics pipelines. Amplicons were from separate assays: (a) Applied Biosystems HIV-1 Genotyping Kit (ThermoFisher) spanning protease (PR) to reverse transcriptase (RT) (PR-RT) (n = 46) and (b) homebrew integrase (IN) (n = 21). The agreement between Sanger sequences and ONT sequences was assessed at nucleotide level, and at codon level for Stanford HIV drug resistance database mutations at an optimal ONT read depth of 400 reads only. RESULTS The average sequence similarity between ONT and Sanger sequences was 99.3% (95% CI: 99.1%-99.4%) for PR-RT and 99.6% (95% CI: 99.4%-99.7%) for INT. Drug resistance mutations did not differ for 21 IN specimens; 8 mutations were detected by both ONT- and Sanger sequencing. For the 46 PR and RT specimens, 245 mutations were detected by either ONT or Sanger, of these 238 (97.1%) were detected by both. CONCLUSIONS The Nano-RECall pipeline, freely available as a downloadable application on a Windows computer, provides Sanger-equivalent HIV drug resistance interpretation. This novel pipeline combined with a simple workflow and multiplexing samples on ONT flow-cells would contribute to making HIV drug resistance sequencing feasible for resource-limited settings.
Collapse
Affiliation(s)
| | - Trevor Ngobeni
- Stellenbosch University, Division of Medical Virology, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Conan K. Woods
- Stellenbosch University, Division of Medical Virology, Cape Town, South Africa
| | - Carli Gordijn
- Stellenbosch University, Division of Medical Virology, Cape Town, South Africa
| | - Mathilda Claassen
- Stellenbosch University, Division of Medical Virology, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | | | | | - Gert Uves van Zyl
- Stellenbosch University, Division of Medical Virology, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| |
Collapse
|
14
|
van Zyl G, Jennings L, Kellermann T, Nkantsu Z, Cogill D, van Schalkwyk M, Spinelli M, Decloedt E, Orrell C, Gandhi M. Urine tenofovir-monitoring predicts HIV viremia in patients treated with high genetic-barrier regimens. AIDS 2022; 36:2057-2062. [PMID: 36305182 PMCID: PMC9623472 DOI: 10.1097/qad.0000000000003354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Access to viral load measurements is constrained in resource-limited settings. A lateral flow urine tenofovir (TFV) rapid assay (UTRA) for patients whose regimens include TFV offers an affordable approach to frequent adherence monitoring. DESIGN We conducted a cross-sectional study of patients to assess the utility of UTRA to predict virologic failure, defined as a viral load greater than 400 copies/ml. METHODS We assessed urine TFV among 113 participants at increased risk of viral failure (who had previous viral failure on this regimen or had previously been ≥30 days out of care), comparing low genetic-barrier efavirenz (EFV) regimens (n = 60) to dolutegravir (DTG)-boosted or ritonavir-boosted protease inhibitor (PI/r)-based high genetic-barrier regimens (n = 53). Dried blood spots (DBS) for TFV-diphosphate and plasma for TFV concentrations were collected, with drug resistance assessed if viral failure present. RESULTS Among 113 participants, 17 of 53 received DTG or PI/r had viral failure at the cross-sectional visit, with 11 (64.7%) demonstrating an undetectable urine TFV; the negative-predictive value (NPV) of undetectable UTRA for viral failure was 85% (34/40); none of the 16 sequenced had dual class drug resistance. In those treated with EFV regimens the sensitivity was lower, as only 1 (4.8%) of 21 with viral failure had an undetectable UTRA (P < 0.001). CONCLUSIONS Urine tenofovir-testing had a high negative-predictive value for viral failure in patients treated with DTG or ritonavir-boosted protease inhibitor regimens, where viral failure was largely explained by poor drug adherence. Frequent monitoring with inexpensive lateral flow urine TFV testing should be investigated prospectively in between viral load visits to improve viral load suppression on DTG-based first-line therapy in resource-limited settings.
Collapse
Affiliation(s)
- Gert van Zyl
- Division of Medical Virology, Department Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University
- National Health Laboratory Service, Tygerberg Business Unit
| | - Lauren Jennings
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town
| | | | - Zukisa Nkantsu
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town
| | - Dolphina Cogill
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town
| | - Marije van Schalkwyk
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Matthew Spinelli
- Division of HIV, Infectious Diseases, and Global Medicine at UCSF/San Francisco General Hospital, San Francisco, CA, USA
| | | | - Catherine Orrell
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine at UCSF/San Francisco General Hospital, San Francisco, CA, USA
| |
Collapse
|
15
|
Beesham I, Parikh UM, Mellors JW, Joseph Davey DL, Heffron R, Palanee-Phillips T, Bosman SL, Beksinska M, Smit J, Ahmed K, Makkan H, Selepe P, Louw C, Kotze P, Hofmeyr GJ, Singata‐Madliki M, Rees H, Baeten JM, Wallis C. High Levels of Pretreatment HIV-1 Drug Resistance Mutations Among South African Women Who Acquired HIV During a Prospective Study. J Acquir Immune Defic Syndr 2022; 91:130-137. [PMID: 36094478 PMCID: PMC9651927 DOI: 10.1097/qai.0000000000003027] [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: 10/21/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Pretreatment HIV drug resistance (PDR) undermines individual treatment success and threatens the achievement of UNAIDS 95-95-95 targets. In many African countries, limited data are available on PDR as detection of recent HIV infection is uncommon and access to resistance testing is limited. We describe the prevalence of PDR among South African women with recent HIV infection from the Evidence for Contraceptive Options and HIV Outcomes (ECHO) Trial. METHODS HIV-uninfected, sexually active women, aged 18-35 years, and seeking contraception were enrolled in the ECHO Trial at sites in South Africa, from 2015 to 2018. HIV testing was done at trial entry and repeated quarterly. We tested stored plasma samples collected at HIV diagnosis from women who seroconverted during follow-up and had a viral load >1000 copies/mL for antiretroviral resistant mutations using a validated laboratory-developed population genotyping assay, which sequences the full protease and reverse transcriptase regions. Mutation profiles were determined using the Stanford Drug Resistance Database. RESULTS We sequenced 275 samples. The median age was 23 years, and majority (98.9%, n = 272) were infected with HIV-1 subtype C. The prevalence of surveillance drug resistance mutations (SDRMs) was 13.5% (n = 37). Nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations were found in 12.4% of women (n = 34). Few women had NRTI (1.8%, n = 5) and protease inhibitor (1.1%, n = 3) mutations. Five women had multiple NRTI and NNRTI SDRMs. CONCLUSIONS The high levels of PDR, particularly to NNRTIs, strongly support the recent change to the South African national HIV treatment guidelines to transition to a first-line drug regimen that excludes NNRTIs.
Collapse
Affiliation(s)
- Ivana Beesham
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Urvi M. Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Dvora L. Joseph Davey
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA
| | - Renee Heffron
- Department of Global Health and Department of Epidemiology, University of Washington, Seattle, WA
| | - Thesla Palanee-Phillips
- Wits Reproductive Health and HIV Institute (Wits RHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shannon L. Bosman
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Mags Beksinska
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Jennifer Smit
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Khatija Ahmed
- Setshaba Research Centre, Soshanguve, South Africa
- Faculty of Health Sciences, Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Heeran Makkan
- The Aurum Institute, Klerksdorp, South Africa
- Department of Interdisciplinary Social Science, Public Health, Utrecht University, Utrecht, The Netherlands
| | | | - Cheryl Louw
- Madibeng Centre for Research, Brits, South Africa
- Department of Family Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Philip Kotze
- Qhakaza Mbokodo Research Clinic, Ladysmith, South Africa
| | - G. Justus Hofmeyr
- Effective Care Research Unit, Universities of the Witwatersrand, Walter Sisulu and Fort Hare and Eastern Cape Department of Health, East London, South Africa
- Department of Obstetrics and Gynaecology, University of Botswana, Gaborone, Botswana
| | - Mandisa Singata‐Madliki
- Effective Care Research Unit, Universities of the Witwatersrand, Walter Sisulu and Fort Hare and Eastern Cape Department of Health, East London, South Africa
- Effective Care Research Unit, Universities of the Witwatersrand and Fort Hare and Eastern Cape Department of Health, East London, South Africa
| | - Helen Rees
- Wits Reproductive Health and HIV Institute (Wits RHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jared M. Baeten
- Department of Global Health, Department of Epidemiology, Department of Medicine, University of Washington, Seattle, WA
- Currently, Gilead Sciences, Foster City, CA; and
| | - Carole Wallis
- BARC-SA and Lancet Laboratories, Johannesburg, South Africa
| |
Collapse
|
16
|
Ismael N, Wilkinson E, Mahumane I, Gemusse H, Giandhari J, Bauhofer A, Vubil A, Mambo P, Singh L, Mabunda N, Bila D, Engelbrecht S, Gudo E, Lessells R, de Oliveira T. Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999–2018. Viruses 2022; 14:v14091992. [PMID: 36146798 PMCID: PMC9505726 DOI: 10.3390/v14091992] [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: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
HIV drug resistance (HIVDR) can become a public health concern, especially in low- and middle-income countries where genotypic testing for people initiating antiretroviral therapy (ART) is not available. For first-line regimens to remain effective, levels of transmitted drug resistance (TDR) need to be monitored over time. To determine the temporal trends of TDR in Mozambique, a search for studies in PubMed and sequences in GenBank was performed. Only studies covering the pol region that described HIVDR and genetic diversity from treatment naïve patients were included. A dataset from seven published studies and one novel unpublished study conducted between 1999 and 2018 were included. The Calibrated Population Resistance tool (CPR) and REGA HIV-1 Subtyping Tool version 3 for sequences pooled by sampling year were used to determine resistance mutations and subtypes, respectively. The prevalence of HIVDR amongst treatment-naïve individuals increased over time, reaching 14.4% in 2018. The increase was most prominent for non-nucleoside reverse transcriptase inhibitors (NNRTIs), reaching 12.7% in 2018. Subtype C was predominant in all regions, but a higher genetic variability (19% non-subtype C) was observed in the north region of Mozambique. These findings confirm a higher diversity of HIV in the north of the country and an increased prevalence of NNRTI resistance among treatment naïve individuals over time.
Collapse
Affiliation(s)
- Nalia Ismael
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
- Correspondence: (N.I.); (T.d.O.)
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Isabel Mahumane
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Hernane Gemusse
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Adilson Bauhofer
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Adolfo Vubil
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Pirolita Mambo
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Dulce Bila
- Elizabeth Glaser Pediatric AIDS Foundation in Mozambique, Avenida Agostinho Neto, Maputo 620, Mozambique
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Eduardo Gudo
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Túlio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7602, South Africa
- Correspondence: (N.I.); (T.d.O.)
| |
Collapse
|
17
|
Werbel WA, Brown DM, Kusemiju OT, Doby BL, Seaman SM, Redd AD, Eby Y, Fernandez RE, Desai NM, Miller J, Bismut GA, Kirby CS, Schmidt HA, Clarke WA, Seisa M, Petropoulos CJ, Quinn TC, Florman SS, Huprikar S, Rana MM, Friedman-Moraco RJ, Mehta AK, Stock PG, Price JC, Stosor V, Mehta SG, Gilbert AJ, Elias N, Morris MI, Mehta SA, Small CB, Haidar G, Malinis M, Husson JS, Pereira MR, Gupta G, Hand J, Kirchner VA, Agarwal A, Aslam S, Blumberg EA, Wolfe CR, Myer K, Wood RP, Neidlinger N, Strell S, Shuck M, Wilkins H, Wadsworth M, Motter JD, Odim J, Segev DL, Durand CM, Tobian AAR. National Landscape of Human Immunodeficiency Virus-Positive Deceased Organ Donors in the United States. Clin Infect Dis 2022; 74:2010-2019. [PMID: 34453519 PMCID: PMC9187316 DOI: 10.1093/cid/ciab743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Organ transplantation from donors with human immunodeficiency virus (HIV) to recipients with HIV (HIV D+/R+) presents risks of donor-derived infections. Understanding clinical, immunologic, and virologic characteristics of HIV-positive donors is critical for safety. METHODS We performed a prospective study of donors with HIV-positive and HIV false-positive (FP) test results within the HIV Organ Policy Equity (HOPE) Act in Action studies of HIV D+/R+ transplantation (ClinicalTrials.gov NCT02602262, NCT03500315, and NCT03734393). We compared clinical characteristics in HIV-positive versus FP donors. We measured CD4 T cells, HIV viral load (VL), drug resistance mutations (DRMs), coreceptor tropism, and serum antiretroviral therapy (ART) detection, using mass spectrometry in HIV-positive donors. RESULTS Between March 2016 and March 2020, 92 donors (58 HIV positive, 34 FP), representing 98.9% of all US HOPE donors during this period, donated 177 organs (131 kidneys and 46 livers). Each year the number of donors increased. The prevalence of hepatitis B (16% vs 0%), syphilis (16% vs 0%), and cytomegalovirus (CMV; 91% vs 58%) was higher in HIV-positive versus FP donors; the prevalences of hepatitis C viremia were similar (2% vs 6%). Most HIV-positive donors (71%) had a known HIV diagnosis, of whom 90% were prescribed ART and 68% had a VL <400 copies/mL. The median CD4 T-cell count (interquartile range) was 194/µL (77-331/µL), and the median CD4 T-cell percentage was 27.0% (16.8%-36.1%). Major HIV DRMs were detected in 42%, including nonnucleoside reverse-transcriptase inhibitors (33%), integrase strand transfer inhibitors (4%), and multiclass (13%). Serum ART was detected in 46% and matched ART by history. CONCLUSION The use of HIV-positive donor organs is increasing. HIV DRMs are common, yet resistance that would compromise integrase strand transfer inhibitor-based regimens is rare, which is reassuring regarding safety.
Collapse
Affiliation(s)
- William A Werbel
- Correspondence: W. A. Werbel, Department of Medicine, Johns Hopkins School of Medicine, 725 N Wolfe St, PCTB/Second Floor, Baltimore, MD 21205 ()
| | - Diane M Brown
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Oyinkansola T Kusemiju
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brianna L Doby
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shanti M Seaman
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew D Redd
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yolanda Eby
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Reinaldo E Fernandez
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Niraj M Desai
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jernelle Miller
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gilad A Bismut
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles S Kirby
- Department of Biochemistry, Cellular, and Molecular Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Haley A Schmidt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William A Clarke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Seisa
- Laboratory Corporation of America (LabCorp), South San Francisco, California, USA
| | | | - Thomas C Quinn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sander S Florman
- Recanati/Miller Transplantation Institute, The Mount Sinai Hospital, New York City, New York, USA
| | - Shirish Huprikar
- Department of Medicine, Division of Infectious Diseases, The Mount Sinai Hospital, New York City, New York, USA
| | - Meenakshi M Rana
- Department of Medicine, Division of Infectious Diseases, The Mount Sinai Hospital, New York City, New York, USA
| | - Rachel J Friedman-Moraco
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Aneesh K Mehta
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Peter G Stock
- Department of Surgery, University of California San Francisco, San Francisco, California, USA
| | - Jennifer C Price
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Valentina Stosor
- Division of Infectious Disease and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shikha G Mehta
- Section of Transplant Nephrology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alexander J Gilbert
- MedStar Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, USA
| | - Nahel Elias
- Department of Surgery, Division of Transplant Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michele I Morris
- Department of Medicine, Division of Infectious Diseases, University of Miami, Miami, Florida, USA
| | - Sapna A Mehta
- New York University Langone Transplant Institute, New York University Grossman School of Medicine, New York, New York, USA
| | - Catherine B Small
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, New York, USA
| | - Ghady Haidar
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Maricar Malinis
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jennifer S Husson
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marcus R Pereira
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, New York, USA
| | - Gaurav Gupta
- Department of Medicine, Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jonathan Hand
- Department of Infectious Diseases, Ochsner Clinic Foundation, New Orleans, Louisiana, USA
| | - Varvara A Kirchner
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Avinash Agarwal
- Department of Surgery, Division of Transplantation, University of Virginia, Charlottesville, Virginia, USA
| | - Saima Aslam
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
| | - Emily A Blumberg
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cameron R Wolfe
- Department of Medicine, Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - R Patrick Wood
- Department of Surgery, Division of Transplantation, University of Wisconsin, Madison, Wisconsin, USA
| | - Nikole Neidlinger
- Department of Surgery, Division of Transplantation, University of Wisconsin, Madison, Wisconsin, USA
- UW Health Organ Procurement Organization, Madison, Wisconsin, USA
| | - Sara Strell
- UW Health Organ Procurement Organization, Madison, Wisconsin, USA
| | | | | | | | - Jennifer D Motter
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jonah Odim
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dorry L Segev
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - HOPE in Action Investigators
PiquantDominqueLinkKatherineRNHemmersbach-MillerMarionMD, PhDPearsonThomasMDTurgeonNicoleMDLyonG MarshallMD, MMScKitchensWilliamMD PhDHuckabyJerylMSCRA, CCRCLasseterA FrancieRNElbeinRivkaRN, BSNRobersonAprilRNFerryElizabethRNKlockEthanBSCochranWilla VCRNPMorrisonMichelleBSNRasmussenSarahBABollingerJuliMSSugarmanJeremyMDSmithAngela RMBAThomasMargaretBSCoakleyMargaretRNTimponeJosephMDStuckeAlyssaBSHaydelBrandyDieterRebeccaPharmDKleinElizabeth JBANeumannHenryMDGallonLorenzoMDGoudyLeahRNCallegariMichelleMarrazzoIliseRN, BSN, MPHJacksonTowandaPruettTimothyMDFarnsworthMaryCCRCLockeJayme EMD, MPH, FACS, FASTMompoint-WilliamsDarnellCRNP, DNPBasingerKatherineRN, CCRPMekeelKristinMDNguyenPhirumBSKwanJoanneSrisengfaTabChin-HongPeterMDRogersRodneySimkinsJacquesMDMunozCarlosCRCDunnTyMDSawinskiDierdreMDSilveiraFernandaMDHughesKaileyMPHPakstisDiana LynnRN, BSN, MBANagyJamieBABaldecchiMaryMuthukumarThangamaniMDEddieMelissa DMS, RNRobbKatharineRNSalsgiverElizabethMPHWittingBrittaBSAzarMarwan MVillanuevaMerceditasFormicaRichardTomlinRicardaBS, CCRP
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
18
|
Arimide DA, Amogne MD, Kebede Y, Balcha TT, Adugna F, Ramos A, DeVos J, Zeh C, Agardh A, Chang JCW, Björkman P, Medstrand P. High Level of HIV Drug Resistance and Virologic Nonsuppression Among Female Sex Workers in Ethiopia: A Nationwide Cross-Sectional Study. J Acquir Immune Defic Syndr 2022; 89:566-574. [PMID: 34966147 PMCID: PMC9058170 DOI: 10.1097/qai.0000000000002908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/20/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To determine viral load (VL) nonsuppression (VLN) rates, HIV drug resistance (HIVDR) prevalence, and associated factors among female sex workers (FSWs) in Ethiopia. METHODS A cross-sectional biobehavioral survey was conducted among FSWs in 11 cities in Ethiopia in 2014. Whole blood was collected, and HIVDR genotyping was performed. Logistic regression analysis was performed to identify factors associated with VLN and HIVDR. RESULTS Among 4900 participants, 1172 (23.9%) were HIV-positive and 1154 (98.5%) had a VL result. Participants were categorized into antiretroviral therapy (ART) (n = 239) and ART-naive (n = 915) groups based on self-report. From the 521 specimens (ART, 59; ART-naive, 462) with VL ≥1000 copies/mL, genotyping was successful for 420 (80.6%) and 92 (21.9%) had drug resistance mutations (DRMs). Pretreatment drug resistance (PDR) was detected in 16.5% (63/381) of the ART-naive participants. Nucleoside reverse transcriptase inhibitor (NRTI), non-NRTIs (NNRTIs), and dual-class DRMs were detected in 40 (10.5%), 55 (14.4%), and 35 (9.2%) of the participants, respectively. Among 239 participants on ART, 59 (24.7%) had VLN. Genotyping was successfully performed for 39 (66.1%). DRMs were detected in 29 (74.4%). All 29 had NNRTI, 23 (79.3%) had NRTI or dual-class DRMs. VLN was associated with age 35 years or older, CD4+ T-cell count <350 cells/mm3, and being forced into selling sex. PDR and acquired drug resistance were associated with CD4+ T-cell count <350 cells/mm3 (P < 0.001). CONCLUSIONS The high VLN and HIVDR rates among FSWs underscore the need for targeted interventions to improve ART access and virologic monitoring to maximize the benefit of ART and limit the spread of HIV and HIVDR.
Collapse
Affiliation(s)
- Dawit Assefa Arimide
- Department of Translational Medicine, Lund University, Malmo, Sweden
- TB/HIV Department, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Minilik Demissie Amogne
- TB/HIV Department, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Clinical Sciences, Lund University, Malmo, Sweden
| | - Yenew Kebede
- Africa Centre for Disease Prevention and Control, Africa Union Commission, Addis Ababa, Ethiopia
| | - Taye T. Balcha
- Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Fekadu Adugna
- NPO - HIV/AIDS, World Health Organization, Addis Ababa, Ethiopia
| | - Artur Ramos
- Division of Global HIV & TB, Center for Global Health, Center for Disease Control and Prevention, Atlanta, GA USA
| | - Joshua DeVos
- Division of Global HIV & TB, Center for Global Health, Center for Disease Control and Prevention, Atlanta, GA USA
| | - Clement Zeh
- Division of Global HIV & TB, Center for Global Health, Center for Disease Control and Prevention, Atlanta, GA USA
| | - Anette Agardh
- Department of Clinical Sciences, Lund University, Malmo, Sweden
| | - Joy Chih-Wei Chang
- Division of Global HIV & TB, Center for Global Health, Center for Disease Control and Prevention, Atlanta, GA USA
| | - Per Björkman
- Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmo, Sweden
| |
Collapse
|
19
|
Ogola B, Matume ND, Mavhandu-Ramarumo LG, Tebit DM, Bessong PO. Drug Resistance Mutations in a Population Before Antiretroviral Therapy Initiation in Northern South Africa. AIDS Res Hum Retroviruses 2022; 38:248-256. [PMID: 34107774 DOI: 10.1089/aid.2021.0026] [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
South Africa introduced the "diagnose and treat" universal HIV treatment program in September 2016. This program enables all identified HIV-positive patients to immediately start first-line antiretroviral therapy (ART). However, the presence of drug-resistant (DR) viruses in the drug-naive population complicates the choice of ART. We used next-generation sequencing (NGS) to determine the prevalence and diversity of HIV DR mutations in patients entering HIV treatment programs in northern South Africa. RNA was isolated from plasma of drug-naive HIV-1-infected patients. Using reverse transcriptase polymerase chain reaction, the HIV-1-pol gene comprising the complete protease (PR) and the first 900 bp of reverse transcriptase (RT) was amplified and sequenced on an Illumina MiniSeq platform. Consensus sequences were derived at >20% threshold and at >5% threshold using Geneious PRIME® software version 2020.1.2. HIV-1 surveillance drug resistance mutations (SDRM) were inferred using Calibrated Population Resistance tool in HIV Drug Resistance Database. Viral subtypes were determined using REGA and RIP genotyping tools. The HIV PR/RT region was successfully sequenced from 241 patients. From these, 23 (9.5%) had at least one SDRM detected at >20% threshold, with a prevalence of 9.5% (n = 18), 3% (n = 7), and 0.4% (n = 1) for non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors (NRTI), and protease inhibitors (PI), respectively. The number of patients with SDRM increased to 31 (12.9%) when minority variants were accounted for at >5% threshold. The most frequent SDRMs based on drug class were; K103N (7.9%-NNRTI), K65R (2.5%-NRTI), and D30N (0.8%-PI). Four cases of dual NRTI/NNRTI mutations were identified. All consensus sequences were subtype C, except three, which were C/A1, C/F1, and C/G recombinants. NGS analysis confirms that individuals entering HIV treatment programs in northern South Africa, habor moderate levels of SDRM, including cases of dual-class drug resistance. Further SDRM studies may be required to better understand resistance in the drug-naive population in the era of "diagnose and treat" in Limpopo Province, South Africa.
Collapse
Affiliation(s)
- Bixa Ogola
- HIV/AIDS & Global Health Research Program, University of Venda, Thohoyandou, South Africa
| | - Nontokozo D. Matume
- HIV/AIDS & Global Health Research Program, University of Venda, Thohoyandou, South Africa
| | | | - Denis M. Tebit
- HIV/AIDS & Global Health Research Program, University of Venda, Thohoyandou, South Africa
- Global Biomed Scientific LLC, PO Box 2368, Forest, VA 24551, USA
| | - Pascal O. Bessong
- HIV/AIDS & Global Health Research Program, University of Venda, Thohoyandou, South Africa
- Center for Global Health Equity, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
20
|
Kirichenko A, Kireev D, Lopatukhin A, Murzakova A, Lapovok I, Saleeva D, Ladnaya N, Gadirova A, Ibrahimova S, Safarova A, Grigoryan T, Petrosyan A, Sarhatyan T, Gasich E, Bunas A, Glinskaya I, Yurovsky P, Nurov R, Soliev A, Ismatova L, Musabaev E, Kazakova E, Rakhimova V, Pokrovsky V. Prevalence of HIV-1 drug resistance in Eastern European and Central Asian countries. PLoS One 2022; 17:e0257731. [PMID: 35061671 PMCID: PMC8782385 DOI: 10.1371/journal.pone.0257731] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/08/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Eastern Europe and Central Asia (EECA) is one of the regions where the HIV epidemic continues to grow at a concerning rate. Antiretroviral therapy (ART) coverage in EECA countries has significantly increased during the last decade, which can lead to an increase in the risk of emergence, transmission, and spread of HIV variants with drug resistance (DR) that cannot be controlled. Because HIV genotyping cannot be performed in these countries, data about HIV DR are limited or unavailable. OBJECTIVES To monitor circulating HIV-1 genetic variants, assess the prevalence of HIV DR among patients starting antiretroviral therapy, and reveal potential transmission clusters among patients in six EECA countries: Armenia, Azerbaijan, Belarus, Russia, Tajikistan, and Uzbekistan. MATERIALS AND METHODS We analyzed 1071 HIV-1 pol-gene fragment sequences (2253-3369 bp) from patients who were initiating or reinitiating first-line ART in six EECA counties, i.e., Armenia (n = 120), Azerbaijan (n = 96), Belarus (n = 158), Russia (n = 465), Tajikistan (n = 54), and Uzbekistan (n = 178), between 2017 and 2019. HIV Pretreatment DR (PDR) and drug resistance mutation (DRM) prevalence was estimated using the Stanford HIV Resistance Database. The PDR level was interpreted according to the WHO standard PDR survey protocols. HIV-1 subtypes were determined using the Stanford HIV Resistance Database and subsequently confirmed by phylogenetic analysis. Transmission clusters were determined using Cluster Picker. RESULTS Analyses of HIV subtypes showed that EECA, in general, has the same HIV genetic variants of sub-subtype A6, CRF63_02A1, and subtype B, with different frequencies and representation for each country. The prevalence of PDR to any drug class was 2.8% in Uzbekistan, 4.2% in Azerbaijan, 4.5% in Russia, 9.2% in Armenia, 13.9% in Belarus, and 16.7% in Tajikistan. PDR to protease inhibitors (PIs) was not detected in any country. PDR to nucleoside reverse-transcriptase inhibitors (NRTIs) was not detected among patients in Azerbaijan, and was relatively low in other countries, with the highest prevalence in Tajikistan (5.6%). The prevalence of PDR to nonnucleoside reverse-transcriptase inhibitors (NNRTIs) was the lowest in Uzbekistan (2.8%) and reached 11.1% and 11.4% in Tajikistan and Belarus, respectively. Genetic transmission network analyses identified 226/1071 (21.1%) linked individuals, forming 93 transmission clusters mainly containing two or three sequences. We found that the time since HIV diagnosis in clustered patients was significantly shorter than that in unclustered patients (1.26 years vs 2.74 years). Additionally, the K103N/S mutation was mainly observed in clustered sequences (6.2% vs 2.8%). CONCLUSIONS Our study demonstrated different PDR prevalence rates and DR dynamics in six EECA countries, with worrying levels of PDR in Tajikistan and Belarus, where prevalence exceeded the 10% threshold recommended by the WHO for immediate public health action. Because DR testing for clinical purposes is not common in EECA, it is currently extremely important to conduct surveillance of HIV DR in EECA due to the increased ART coverage in this region.
Collapse
Affiliation(s)
- Alina Kirichenko
- Central Research Institute of Epidemiology, Moscow, Russian Federation
| | - Dmitry Kireev
- Central Research Institute of Epidemiology, Moscow, Russian Federation
| | - Alexey Lopatukhin
- Central Research Institute of Epidemiology, Moscow, Russian Federation
| | | | - Ilya Lapovok
- Central Research Institute of Epidemiology, Moscow, Russian Federation
| | - Daria Saleeva
- Central Research Institute of Epidemiology, Moscow, Russian Federation
| | - Natalya Ladnaya
- Central Research Institute of Epidemiology, Moscow, Russian Federation
| | | | | | - Aygun Safarova
- Republic Center of the Struggle against AIDS, Baku, Azerbaijan
| | | | | | | | - Elena Gasich
- Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Anastasia Bunas
- Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Iryna Glinskaya
- Republican Center for Hygiene, Epidemiology and Public Health, Minsk, Belarus
| | - Pavel Yurovsky
- Republican Center for Hygiene, Epidemiology and Public Health, Minsk, Belarus
| | - Rustam Nurov
- Republican AIDS prevention center, Dushanbe, Tajikistan
| | - Alijon Soliev
- Republican AIDS prevention center, Dushanbe, Tajikistan
| | | | | | | | - Visola Rakhimova
- Center for development of profession qualification of medical workers, Tashkent, Uzbekistan
| | - Vadim Pokrovsky
- Central Research Institute of Epidemiology, Moscow, Russian Federation
| |
Collapse
|
21
|
Iwuji C, Osler M, Mazibuko L, Hounsome N, Ngwenya N, Chimukuche RS, Khoza T, Gareta D, Sunpath H, Boulle A, Herbst K. Optimised electronic patient records to improve clinical monitoring of HIV-positive patients in rural South Africa (MONART trial): study protocol for a cluster-randomised trial. BMC Infect Dis 2021; 21:1266. [PMID: 34930182 PMCID: PMC8686584 DOI: 10.1186/s12879-021-06952-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is poor viral load monitoring (VLM) and inadequate management of virological failure in HIV-positive individuals on antiretroviral therapy in rural KwaZulu-Natal, South Africa. This could be contributing to increasing HIV drug resistance in the setting. This study aims to investigate the clinical and process impediments in VLM within the health system and to evaluate a quality improvement package (QIP) to address the identified gaps. The QIP comprises (i) a designated viral load champion responsible for administrative management and triaging of viral load results (ii) technological enhancement of the routine clinic-based Three Interlinked Electronic Register (TIER.Net) to facilitate daily automatic import of viral load results from the National Health Service Laboratory to TIER.Net (iii) development of a dashboard system to support VLM. METHODS/DESIGN The study will evaluate the effectiveness of the QIP compared to current care for improving VLM and virological suppression using an effectiveness implementation hybrid type 3 design. This will use a cluster-randomised design with the primary healthcare clinics as the unit of randomisation with ten clinics randomised in a 1:1 ratio to either the intervention or control arm. We will enrol 150 HIV-positive individuals who had been on ART for ≥ 12 months from each of the ten clinics (750 in 5 intervention clinics vs. 750 in 5 control clinics) and follow them up for a period of 12 months. The primary outcome is the proportion of all patients who have a viral load (VL) measurement and are virally suppressed (composite outcome) after 12 months of follow up. Secondary outcomes during follow up include proportion of all patients with at least one documented VL in TIER.Net, proportion with VL ≥ 50 copies/mL, proportion with VL ≥ 1000 copies/mL (virological failure) and subsequent switch to second-line ART. DISCUSSION We aim to provide evidence that a staff-centred quality improvement package, designated viral load monitoring champion, and augmentation of TIER.Net with a dashboard system will improve viral load monitoring and lead to improved virological suppression. TRIAL REGISTRATION This trial is registered on ClinicalTrials.gov on 8 Oct 2021. Identifier: NCT05071573; https://clinicaltrials.gov/ct2/show/NCT05071573?term=NCT05071573&draw=2&rank=1.
Collapse
Affiliation(s)
- Collins Iwuji
- Department of Global Health Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, BN1 9PX, UK. .,Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa.
| | - Meg Osler
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Lusanda Mazibuko
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Natalia Hounsome
- Department of Global Health Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, BN1 9PX, UK
| | - Nothando Ngwenya
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
| | | | - Thandeka Khoza
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Dickman Gareta
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Henry Sunpath
- Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Andrew Boulle
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.,Department of Health, Provincial Government of the Western Cape, Cape Town, South Africa
| | - Kobus Herbst
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa.,DSI-MRC South African Population Research Infrastructure Network, Durban, South Africa
| |
Collapse
|
22
|
Parikh UM, Penrose KJ, Heaps AL, Halvas EK, Goetz BJ, Gordon KC, Hardesty R, Sethi R, Schwarzmann W, Szydlo DW, Husnik MJ, Chandran U, Palanee-Phillips T, Baeten JM, Mellors JW. HIV-1 drug resistance among individuals who seroconverted in the ASPIRE dapivirine ring trial. J Int AIDS Soc 2021; 24:e25833. [PMID: 34762770 PMCID: PMC8583424 DOI: 10.1002/jia2.25833] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/10/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction A potential concern with the use of dapivirine (DPV) for HIV prevention is the selection of a drug‐resistant virus that could spread and reduce the effectiveness of non‐nucleoside reverse transcriptase (NNRTI)‐based first‐line antiretroviral therapy. We evaluated HIV‐1 seroconversions in MTN‐020/ASPIRE for selection of drug resistance and evaluated the genetic basis for observed reductions in susceptibility to DPV. Methods MTN‐020/ASPIRE was a placebo‐controlled, Phase III safety and effectiveness study of DPV ring for HIV‐1 prevention conducted at 15 sites in South Africa, Zimbabwe, Malawi and Uganda between 2012 and 2015. Plasma from individuals who seroconverted in ASPIRE was analysed for HIV‐1 drug resistance using both population Sanger sequencing and next‐generation sequencing (NGS) with unique molecular identifiers to report mutations at ≥1% frequency. DPV susceptibility of plasma‐derived recombinant HIV‐1 containing bulk‐cloned full‐length reverse transcriptase sequences from MTN‐020/ASPIRE seroconversions was determined in TZM‐bl cells. Statistical significance was calculated using the Fisher's exact test. Results Plasma from all 168 HIV seroconversions were successfully tested by Sanger sequencing; 57 of 71 DPV arm and 82 of 97 placebo (PLB) arm participants had NGS results at 1% sensitivity. Overall, 18/168 (11%) had NNRTI mutations including K101E, K103N/S, V106M, V108I, E138A/G, V179D/I/T and H221Y. Five samples from both arms had low‐frequency NNRTI mutations that were not detected by Sanger sequencing. The frequency of NNRTI mutations from the DPV arm (11%) was not different from the PLB arm (10%; p = 0.80). The E138A mutation was detected in both the DPV (3 of 71 [4.2%]) and PLB arm (5 of 97 [5.2%]) and conferred modest reductions in DPV susceptibility in some reverse transcriptase backgrounds but not others. Conclusions HIV‐1 drug resistance including NNRTI resistance did not differ between the DPV and placebo arms of the MTN‐020/ASPIRE study, indicating that drug resistance was not preferentially acquired or selected by the DPV ring and that the preventive benefit of DPV ring outweighs resistance risk.
Collapse
Affiliation(s)
- Urvi M Parikh
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kerri J Penrose
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amy L Heaps
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Elias K Halvas
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - B Jay Goetz
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kelley C Gordon
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Russell Hardesty
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rahil Sethi
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William Schwarzmann
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel W Szydlo
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Marla J Husnik
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Uma Chandran
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Jared M Baeten
- Departments of Global Health, Medicine, Epidemiology, University of Washington, Seattle, Washington, USA
| | - John W Mellors
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | |
Collapse
|
23
|
Chimukangara B, Lessells RJ, Singh L, Grigalionyte I, Yende-Zuma N, Adams R, Dawood H, Dlamini L, Buthelezi S, Chetty S, Diallo K, Duffus WA, Mogashoa M, Hagen MB, Giandhari J, de Oliveira T, Moodley P, Padayatchi N, Naidoo K. Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa. AIDS Res Ther 2021; 18:74. [PMID: 34656129 PMCID: PMC8520607 DOI: 10.1186/s12981-021-00393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Background Introduction of tenofovir (TDF) plus lamivudine (3TC) and dolutegravir (DTG) in first- and second-line HIV treatment regimens in South Africa warrants characterization of acquired HIV-1 drug resistance (ADR) mutations that could impact DTG-based antiretroviral therapy (ART). In this study, we sought to determine prevalence of ADR mutations and their potential impact on susceptibility to drugs used in combination with DTG among HIV-positive adults (≥ 18 years) accessing routine care at a selected ART facility in KwaZulu-Natal, South Africa. Methods We enrolled adult participants in a cross-sectional study between May and September 2019. Eligible participants had a most recent documented viral load (VL) ≥ 1000 copies/mL after at least 6 months on ART. We genotyped HIV-1 reverse transcriptase and protease genes by Sanger sequencing and assessed ADR. We characterized the effect of ADR mutations on the predicted susceptibility to drugs used in combination with DTG. Results From 143 participants enrolled, we obtained sequence data for 115 (80%), and 92.2% (95% CI 85.7–96.4) had ADR. The proportion with ADR was similar for participants on first-line ART (65/70, 92.9%, 95% CI 84.1–97.6) and those on second-line ART (40/44, 90.9%, 95% CI 78.3–97.5), and was present for the single participant on third-line ART. Approximately 89% (62/70) of those on first-line ART had dual class NRTI and NNRTI resistance and only six (13.6%) of those on second-line ART had major PI mutations. Most participants (82%) with first-line viraemia maintained susceptibility to Zidovudine (AZT), and the majority of them had lost susceptibility to TDF (71%) and 3TC (84%). Approximately two in every five TDF-treated individuals had thymidine analogue mutations (TAMs). Conclusions Susceptibility to AZT among most participants with first-line viraemia suggests that a new second-line regimen of AZT + 3TC + DTG could be effective. However, atypical occurrence of TAMs in TDF-treated individuals suggests a less effective AZT + 3TC + DTG regimen in a subpopulation of patients. As most patients with first-line viraemia had at least low-level resistance to TDF and 3TC, identifying viraemia before switch to TDF + 3TC + DTG is important to avoid DTG functional monotherapy. These findings highlight a need for close monitoring of outcomes on new standardized treatment regimens. Supplementary Information The online version contains supplementary material available at 10.1186/s12981-021-00393-5.
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Park SY, Faraci G, Murphy G, Pilcher C, Busch MP, Lee HY. Microdrop Human Immunodeficiency Virus Sequencing for Incidence and Drug Resistance Surveillance. J Infect Dis 2021; 224:1048-1059. [PMID: 33517458 DOI: 10.1093/infdis/jiab060] [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: 12/01/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Precise and cost-efficient human immunodeficiency virus (HIV) incidence and drug resistance surveillances are in high demand for the advancement of the 90-90-90 "treatment for all" target. METHODS We developed microdrop HIV sequencing for the HIV incidence and drug resistance assay (HIDA), a single-blood-draw surveillance tool for incidence and drug resistance mutation (DRM) detection. We amplified full-length HIV envelope and pol gene sequences within microdroplets, and this compartmental amplification with long-read high-throughput sequencing enabled us to recover multiple unique sequences. RESULTS We achieved greater precision in determining the stage of infection than current incidence assays, with a 1.2% false recency rate (proportion of misclassified chronic infections) and a 262-day mean duration of recent infection (average time span of recent infection classification) from 83 recently infected and 81 chronically infected individuals. Microdrop HIV sequencing demonstrated an increased capacity to detect minority variants and linked DRMs. By screening all 93 World Health Organization surveillance DRMs, we detected 6 pretreatment drug resistance mutations with 2.6%-13.2% prevalence and cross-linked mutations. CONCLUSIONS HIDA with microdrop HIV sequencing may promote global HIV real-time surveillance by serving as a precise and high-throughput cross-sectional survey tool that can be generalized for surveillance of other pathogens.
Collapse
Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gary Murphy
- Public Health England, London, United Kingdom
| | - Christopher Pilcher
- Department of Medicine, University of California, San Francisco, California, USA
| | - Michael P Busch
- Research and Scientific Programs, Vitalant Research Institute, San Francisco, California, USA.,Deparment of Laboratory Medicine, University of California, California, San Francisco, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
26
|
Keene CM, Griesel R, Zhao Y, Gcwabe Z, Sayed K, Hill A, Cassidy T, Ngwenya O, Jackson A, Van Zyl G, Schutz C, Goliath R, Flowers T, Goemaere E, Wiesner L, Simmons B, Maartens G, Meintjes G. Virologic efficacy of tenofovir, lamivudine and dolutegravir as second-line antiretroviral therapy in adults failing a tenofovir-based first-line regimen. AIDS 2021; 35:1423-1432. [PMID: 33973876 PMCID: PMC7612028 DOI: 10.1097/qad.0000000000002936] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Recycling tenofovir and lamivudine/emtricitabine (XTC) with dolutegravir would provide a more tolerable, affordable, and scalable second-line regimen than dolutegravir with an optimized nucleoside reverse transcriptase inhibitor (NRTI) backbone. We evaluated efficacy of tenofovir/lamivudine/dolutegravir (TLD) in patients failing first-line tenofovir/XTC/efavirenz or nevirapine. DESIGN Single arm, prospective, interventional study. SETTING Two primary care clinics in Khayelitsha, South Africa. PARTICIPANTS Sixty adult patients with two viral loads greater than 1000 copies/ml. INTERVENTION Participants were switched to TLD with additional dolutegravir (50 mg) for 2 weeks to overcome efavirenz induction. PRIMARY OUTCOME Proportion achieving viral load less than 50 copies/ml at week 24 using the FDA snapshot algorithm. RESULTS Baseline median CD4+ cell count was 248 cells/μl, viral load 10 580 copies/ml and 48 of 54 (89%) had resistance (Stanford score ≥15) to one or both of tenofovir and XTC. No participants were lost to follow-up. At week 24, 51 of 60 [85%, 95% confidence interval (CI) 73-93%] were virologically suppressed, six had viral load 50-100 copies/ml, one had viral load 100-1000 copies/ml, one no viral load in window, and one switched because of tenofovir-related adverse event. No integrase mutations were detected in the one participant meeting criteria for resistance testing. Virological suppression was achieved by 29 of 35 (83%, 95% CI 66-93%) with resistance to tenofovir and XTC, 11 of 13 (85%, 95% CI 55-98%) with resistance to XTC, and six of six (100%, 95% CI 54-100%) with resistance to neither. CONCLUSION A high proportion of adults switching to second-line TLD achieved virologic suppression despite substantial baseline NRTI resistance and most not suppressed had low-level viraemia (≤100 copies/ml). This suggests recycling tenofovir and XTC with dolutegravir could provide an effective second-line option.
Collapse
Affiliation(s)
| | - Rulan Griesel
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ying Zhao
- University of Cape Town, Cape Town, South Africa
| | | | - Kaneez Sayed
- University of Cape Town, Cape Town, South Africa
| | - Andrew Hill
- University of Liverpool, Department of Pharmacology, Liverpool, United Kingdom
| | - Tali Cassidy
- Médecins Sans Frontières South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Gert Van Zyl
- University of Stellenbosch, Division of Medical Virology, Cape Town, South Africa
| | - Charlotte Schutz
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Rene Goliath
- University of Cape Town, Cape Town, South Africa
| | | | - Eric Goemaere
- Médecins Sans Frontières South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Bryony Simmons
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
27
|
Chimukangara B, Giandhari J, Lessells R, Yende-Zuma N, Sartorius B, Samuel R, Khanyile KS, Stray-Pedersen B, Moodley P, Metzner KJ, Padayatchi N, Naidoo K, De Oliveira T. Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals. J Antimicrob Chemother 2021; 75:3319-3326. [PMID: 32772079 PMCID: PMC7566390 DOI: 10.1093/jac/dkaa343] [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: 04/17/2020] [Accepted: 07/03/2020] [Indexed: 11/23/2022] Open
Abstract
Objectives To determine the impact of pretreatment low-abundance HIV-1 drug-resistant variants (LA-DRVs) on virological failure (VF) among HIV-1/TB-co-infected individuals treated with NNRTI first-line ART. Methods We conducted a case–control study of 170 adults with HIV-1/TB co-infection. Cases had at least one viral load (VL) ≥1000 RNA copies/mL after ≥6 months on NNRTI-based ART, and controls had sustained VLs <1000 copies/mL. We sequenced plasma viruses by Sanger and MiSeq next-generation sequencing (NGS). We assessed drug resistance mutations (DRMs) using the Stanford drug resistance database, and analysed NGS data for DRMs at ≥20%, 10%, 5% and 2% thresholds. We assessed the effect of pretreatment drug resistance (PDR) on VF. Results We analysed sequences from 45 cases and 125 controls. Overall prevalence of PDR detected at a ≥20% threshold was 4.7% (8/170) and was higher in cases than in controls (8.9% versus 3.2%), P = 0.210. Participants with PDR at ≥20% had almost 4-fold higher odds of VF (adjusted OR 3.7, 95% CI 0.8–18.3) compared with those without, P = 0.104. PDR prevalence increased to 18.2% (31/170) when LA-DRVs at ≥2% were included. Participants with pretreatment LA-DRVs only had 1.6-fold higher odds of VF (adjusted OR 1.6, 95% CI 0.6–4.3) compared with those without, P = 0.398. Conclusions Pretreatment DRMs and LA-DRVs increased the odds of developing VF on NNRTI-based ART, although without statistical significance. NGS increased detection of DRMs but provided no additional benefit in identifying participants at risk of VF at lower thresholds. More studies assessing mutation thresholds predictive of VF are required to inform use of NGS in treatment decisions.
Collapse
Affiliation(s)
- Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Benn Sartorius
- Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa.,Health Metrics Sciences, University of Washington, Seattle, USA
| | - Reshmi Samuel
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Khulekani S Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Babill Stray-Pedersen
- Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Pravi Moodley
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Tulio De Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
28
|
Nguyen H, Thorball CW, Fellay J, Böni J, Yerly S, Perreau M, Hirsch HH, Kusejko K, Thurnheer MC, Battegay M, Cavassini M, Kahlert CR, Bernasconi E, Günthard HF, Kouyos RD. Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link. eLife 2021; 10:67388. [PMID: 34061023 PMCID: PMC8169104 DOI: 10.7554/elife.67388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/18/2021] [Indexed: 11/26/2022] Open
Abstract
Background: Considering the remaining threat of drug-resistantmutations (DRMs) to antiretroviral treatment (ART) efficacy, we investigated how the selective pressure of human leukocyte antigen (HLA)-restricted cytotoxic T lymphocytes drives certain DRMs’ emergence and retention. Methods: We systematically screened DRM:HLA class I allele combinations in 3997 ART-naïve Swiss HIV Cohort Study (SHCS) patients. For each pair, a logistic regression model preliminarily tested for an association with the DRM as the outcome. The three HLA:DRM pairs remaining after multiple testing adjustment were analyzed in three ways: cross-sectional logistic regression models to determine any HLA/infection time interaction, survival analyses to examine if HLA type correlated with developing specific DRMs, and via NetMHCpan to find epitope binding evidence of immune escape. Results: Only one pair, RT-E138:HLA-B18, exhibited a significant interaction between infection duration and HLA. The survival analyses predicted two pairs with an increased hazard of developing DRMs: RT-E138:HLA-B18 and RT-V179:HLA-B35. RT-E138:HLA-B18 exhibited the greatest significance in both analyses (interaction term odds ratio [OR] 1.169 [95% confidence interval (CI) 1.075–1.273]; p-value<0.001; survival hazard ratio 12.211 [95% CI 3.523–42.318]; p-value<0.001). The same two pairs were also predicted by netMHCpan to have epitopic binding. Conclusions: We identified DRM:HLA pairs where HLA presence is associated with the presence or emergence of the DRM, indicating that the selective pressure for these mutations alternates direction depending on the presence of these HLA alleles. Funding: Funded by the Swiss National Science Foundation within the framework of the SHCS, and the University of Zurich, University Research Priority Program: Evolution in Action: From Genomes Ecosystems, in Switzerland.
Collapse
Affiliation(s)
- Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Christian Wandell Thorball
- School of Life Sciences, École Polytechnique, Fédérale de Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique, Fédérale de Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Hans H Hirsch
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,Infectious Diseases and Hospital Epidemiology, Department of Medicine, University Hospital Basel, Basel, Switzerland.,Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Maria Christine Thurnheer
- University Clinic of Infectious Diseases, University Hospital of Bern, University of Bern, Bern, Switzerland
| | - Manuel Battegay
- Infectious Diseases and Hospital Epidemiology, Department of Medicine, University Hospital Basel, Basel, Switzerland
| | - Matthias Cavassini
- Department of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital, Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | | |
Collapse
|
29
|
Anstey Watkins J, Griffiths F, Goudge J. Community health workers' efforts to build health system trust in marginalised communities: a qualitative study from South Africa. BMJ Open 2021; 11:e044065. [PMID: 34011590 PMCID: PMC8137175 DOI: 10.1136/bmjopen-2020-044065] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Community health workers (CHWs) enable marginalised communities, often experiencing structural poverty, to access healthcare. Trust, important in all patient-provider relationships, is difficult to build in such communities, particularly when stigma associated with HIV/AIDS, tuberculosis and now COVID-19, is widespread. CHWs, responsible for bringing people back into care, must repair trust. In South Africa, where a national CHW programme is being rolled out, marginalised communities have high levels of unemployment, domestic violence and injury. OBJECTIVES In this complex social environment, we explored CHW workplace trust, interpersonal trust between the patient and CHW, and the institutional trust patients place in the health system. DESIGN, PARTICIPANTS, SETTING Within the observation phase of a 3-year intervention study, we conducted interviews, focus groups and observations with patients, CHWs, their supervisors and, facility managers in Sedibeng. RESULTS CHWs had low levels of workplace trust. They had recently been on strike demanding better pay, employment conditions and recognition of their work. They did not have the equipment to perform their work safely, and some colleagues did not trust, or value, their contribution. There was considerable interpersonal trust between CHWs and patients, however, CHWs' efforts were hampered by structural poverty, alcohol abuse and no identification documents among long-term migrants. Those supervisors who understood the extent of the poverty supported CHW efforts to help the community. When patients had withdrawn from care, often due to nurses' insensitive behaviour, the CHWs' attempts to repair patients' institutional trust often failed due to the vulnerabilities of the community, and lack of support from the health system. CONCLUSION Strategies are needed to build workplace trust including supportive supervision for CHWs and better working conditions, and to build interpersonal and institutional trust by ensuring sensitivity to social inequalities and the effects of structural poverty among healthcare providers. Societies need to care for everyone.
Collapse
Affiliation(s)
- Jocelyn Anstey Watkins
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Frances Griffiths
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
- Centre for Health Policy, School of Public Health, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Jane Goudge
- Centre for Health Policy, School of Public Health, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| |
Collapse
|
30
|
Nanfuka M, Forrest JI, Zhang W, Okoboi S, Birungi J, Kaleebu P, Zhu J, Tibenganas S, Moore DM. Durability of non-nucleotide reverse transcriptase inhibitor-based first-line ART regimens after 7 years of treatment in rural Uganda: A prospective cohort study. Medicine (Baltimore) 2021; 100:e25763. [PMID: 34106606 PMCID: PMC8133171 DOI: 10.1097/md.0000000000025763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/14/2021] [Indexed: 11/26/2022] Open
Abstract
Most antiretroviral therapy (ART) programs in resource-limited settings have historically used non-nucleotide reverse transcriptase inhibitor (NNRTI)-based regimens with limited access to routine viral load (VL) testing. We examined the long-term success of these regimens in rural Uganda among participants with 1 measured suppressed VL.We conducted a prospective cohort study of participants who had been on NNRTI-based first-line regimens for ≥4 years and had a VL <1000 copies/mL at enrollment in Jinja, Uganda. We collected clinical and behavioral data every 6 months and measured VL again after 3 years. We quantified factors associated with virologic failure (VF) (VL ≥ 1000 copies/mL) using Wilcoxon Rank Sum, chi-square, and Fisher's Exact Tests.We enrolled 503 participants; 75.9% were female, the median age was 45 years, and the median duration of time on ART was 6.8 years (IQR = 6.0-7.6 years). Sixty-nine percent of participants were receiving nevirapine, lamivudine, and zidovudine regimens; 22.5% were receiving efavirenz, lamivudine, and zidovudine; and 8.6% were receiving other regimens. Of the 479 with complete follow-up data, 12 (2.5%) had VL ≥ 1000 copies/mL. VF was inversely associated with reporting never missing pills (41.7% of VFs vs 72.8% non-VFs, P = .034). There were differences in distribution of the previous ART regimens (P = .005), but no clear associations with specific regimens. There was no association between having a VL of 50 to 999 copies/mL at enrollment and later VF (P = .160).Incidence of VF among individuals receiving ART for nearly 7 years was very low in the subsequent 3 years. NNRTI-based regimens appear to be very durable among those with good initial adherence.
Collapse
Affiliation(s)
| | - Jamie I. Forrest
- British Columbia Centre for Excellence in HIV/AIDS
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Wendy Zhang
- British Columbia Centre for Excellence in HIV/AIDS
| | | | | | - Pontiano Kaleebu
- Uganda Virus Research Institute/London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Julia Zhu
- British Columbia Centre for Excellence in HIV/AIDS
| | | | - David M. Moore
- British Columbia Centre for Excellence in HIV/AIDS
- Uganda Virus Research Institute/London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| |
Collapse
|
31
|
Rhee SY, Kassaye SG, Barrow G, Sundaramurthi JC, Jordan MR, Shafer RW. HIV-1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates. J Int AIDS Soc 2021; 23:e25611. [PMID: 32936523 PMCID: PMC7507012 DOI: 10.1002/jia2.25611] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/01/2020] [Accepted: 08/02/2020] [Indexed: 11/10/2022] Open
Abstract
Introduction HIV‐1 transmitted drug resistance (TDR) prevalence increased during the initial years of the antiretroviral therapy (ART) global scale‐up. Few studies have examined recent trends in TDR prevalence using published genetic sequences and described the characteristics of ART‐naïve persons from whom these published sequences have been obtained. Methods We identified 125 studies published between 2014 and 2019 for which HIV‐1 reverse transcriptase (RT) with or without protease from ≥50 ART‐naïve adult persons were submitted to the GenBank sequence database. The population characteristics and TDR prevalence were compared to those in 122 studies published in the preceding five years between 2009 and 2013. TDR prevalence was analysed using median study‐level and person‐level data. Results and discussion The 2009 to 2013 and 2014 to 2019 studies reported sequence data from 32,866 and 41,724 ART‐naïve persons respectively. Studies from the low‐ and middle‐income country (LMIC) regions in sub‐Saharan Africa, South/Southeast Asia and Latin America/Caribbean accounted for approximately two‐thirds of the studies during each period. Between the two periods, the proportion of studies from sub‐Saharan Africa and from South/Southeast Asia countries other than China decreased from 43% to 32% and the proportion of studies performed at sentinel sites for recent HIV‐1 infection decreased from 33% to 22%. Between 2014 and 2019, median study‐level TDR prevalence was 4.1% in South/Southeast Asia, 6.0% in sub‐Saharan Africa, 9.1% in Latin America/Caribbean, 8.5% in Europe and 14.2% in North America. In the person‐level analysis, there was an increase in overall, NNRTI and two‐class NRTI/NNRTI resistance in sub‐Saharan Africa; an increase in NNRTI resistance in Latin America/Caribbean, and an increase in overall, NNRTI and PI resistance in North America. Conclusions Overall, NNRTI and dual NRTI/NNRTI‐associated TDR prevalence was significantly higher in sub‐Saharan Africa studies published between 2014 and 2019 compared with those published between 2009 and 2013. The decreasing proportion of studies from the hardest hit LMIC regions and the shift away from sentinel sites for recent infection suggests that global TDR surveillance efforts and publication of findings require renewed emphasis.
Collapse
Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Seble G Kassaye
- Department of Medicine, Georgetown University, Washington, DC, USA
| | - Geoffrey Barrow
- Department of Medicine, Faculty of Medical Science, University of the West Indies, Mona, Jamaica
| | | | - Michael R Jordan
- Division of Geographic Medicine, Tufts Medical Center, Boston, MA, USA.,Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA.,Tufts Center for Integrated Management of Antimicrobial Resistance (CIMAR), Boston, MA, USA
| | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|
32
|
Lockman S, Brummel SS, Ziemba L, Stranix-Chibanda L, McCarthy K, Coletti A, Jean-Philippe P, Johnston B, Krotje C, Fairlie L, Hoffman RM, Sax PE, Moyo S, Chakhtoura N, Stringer JS, Masheto G, Korutaro V, Cassim H, Mmbaga BT, João E, Hanley S, Purdue L, Holmes LB, Momper JD, Shapiro RL, Thoofer NK, Rooney JF, Frenkel LM, Amico KR, Chinula L, Currier J. Efficacy and safety of dolutegravir with emtricitabine and tenofovir alafenamide fumarate or tenofovir disoproxil fumarate, and efavirenz, emtricitabine, and tenofovir disoproxil fumarate HIV antiretroviral therapy regimens started in pregnancy (IMPAACT 2010/VESTED): a multicentre, open-label, randomised, controlled, phase 3 trial. Lancet 2021; 397:1276-1292. [PMID: 33812487 PMCID: PMC8132194 DOI: 10.1016/s0140-6736(21)00314-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Antiretroviral therapy (ART) during pregnancy is important for both maternal health and prevention of perinatal HIV-1 transmission; however adequate data on the safety and efficacy of different ART regimens that are likely to be used by pregnant women are scarce. In this trial we compared the safety and efficacy of three antiretroviral regimens started in pregnancy: dolutegravir, emtricitabine, and tenofovir alafenamide fumarate; dolutegravir, emtricitabine, and tenofovir disoproxil fumarate; and efavirenz, emtricitabine, and tenofovir disoproxil fumarate. METHODS This multicentre, open-label, randomised controlled, phase 3 trial was done at 22 clinical research sites in nine countries (Botswana, Brazil, India, South Africa, Tanzania, Thailand, Uganda, the USA, and Zimbabwe). Pregnant women (aged ≥18 years) with confirmed HIV-1 infection and at 14-28 weeks' gestation were eligible. Women who had previously taken antiretrovirals in the past were excluded (up to 14 days of ART during the current pregnancy was permitted), as were women known to be pregnant with multiple fetuses, or those with known fetal anomaly or a history of psychiatric illness. Participants were randomly assigned (1:1:1) using a central computerised randomisation system. Randomisation was done using permuted blocks (size six) stratified by gestational age (14-18, 19-23, and 24-28 weeks' gestation) and country. Participants were randomly assigned to receive either once-daily oral dolutegravir 50 mg, and once-daily oral fixed-dose combination emtricitabine 200 mg and tenofovir alafenamide fumarate 25 mg; once-daily oral dolutegravir 50 mg, and once-daily oral fixed-dose combination emtricitabine 200 mg and tenofovir disoproxil fumarate 300 mg; or once-daily oral fixed-dose combination of efavirenz 600 mg, emtricitabine 200 mg, and tenofovir disoproxil fumarate 300 mg. The primary efficacy outcome was the proportion of participants with viral suppression, defined as an HIV-1 RNA concentration of less than 200 copies per mL, at or within 14 days of delivery, assessed in all participants with an HIV-1 RNA result available from the delivery visit, with a prespecified non-inferiority margin of -10% in the combined dolutegravir-containing groups versus the efavirenz-containing group (superiority was tested in a pre-planned secondary analysis). Primary safety outcomes, compared pairwise among treatment groups, were the occurrence of a composite adverse pregnancy outcome (ie, either preterm delivery, the infant being born small for gestational age, stillbirth, or spontaneous abortion) in all participants with a pregnancy outcome, and the occurrence of grade 3 or higher maternal and infant adverse events in all randomised participants. This trial was registered with ClinicalTrials.gov, NCT03048422. FINDINGS Between Jan 19, 2018, and Feb 8, 2019, we enrolled and randomly assigned 643 pregnant women: 217 to the dolutegravir, emtricitabine, and tenofovir alafenamide fumarate group, 215 to the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group, and 211 to the efavirenz, emtricitabine, and tenofovir disoproxil fumarate group. At enrolment, median gestational age was 21·9 weeks (IQR 18·3-25·3), the median HIV-1 RNA concentration among participants was 902·5 copies per mL (152·0-5182·5; 181 [28%] of 643 participants had HIV-1 RNA concentrations of <200 copies per mL), and the median CD4 count was 466 cells per μL (308-624). HIV-1 RNA concentrations at delivery were available for 605 (94%) participants. Of these, 395 (98%) of 405 participants in the combined dolutegravir-containing groups had viral suppression at delivery compared with 182 (91%) of 200 participants in the efavirenz, emtricitabine, and tenofovir disoproxil fumarate group (estimated difference 6·5% [95% CI 2·0 to 10·7], p=0·0052; excluding the non-inferiority margin of -10%). Significantly fewer participants in the dolutegravir, emtricitabine, and tenofovir alafenamide fumarate group (52 [24%] of 216) had a composite adverse pregnancy outcome than those in the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group (70 [33%] of 213; estimated difference -8·8% [95% CI -17·3 to -0·3], p=0·043) or the efavirenz, emtricitabine, and tenofovir disoproxil fumarate group (69 [33%] of 211; -8·6% [-17·1 to -0·1], p=0·047). The proportion of participants or infants with grade 3 or higher adverse events did not differ among the three groups. The proportion of participants who had a preterm delivery was significantly lower in the dolutegravir, emtricitabine, and tenofovir alafenamide fumarate group (12 [6%] of 208) than in the efavirenz, emtricitabine, and tenofovir disoproxil fumarate group (25 [12%] of 207; -6·3% [-11·8 to -0·9], p=0·023). Neonatal mortality was significantly higher in the efavirenz, emtricitabine, and tenofovir disoproxil fumarate group (ten [5%] of 207 infants) than in the dolutegravir, emtricitabine, and tenofovir alafenamide fumarate group (two [1%] of 208; p=0·019) or the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group (three [2%] of 202; p=0·050). INTERPRETATION When started in pregnancy, dolutegravir-containing regimens had superior virological efficacy at delivery compared with the efavirenz, emtricitabine, and tenofovir disoproxil fumarate regimen. The dolutegravir, emtricitabine, and tenofovir alafenamide fumarate regimen had the lowest frequency of composite adverse pregnancy outcomes and of neonatal deaths. FUNDING National Institute of Allergy and Infectious Diseases, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, and the National Institute of Mental Health.
Collapse
Affiliation(s)
- Shahin Lockman
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA; Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
| | - Sean S Brummel
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Lauren Ziemba
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, MA, USA
| | | | | | | | - Patrick Jean-Philippe
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Lee Fairlie
- Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Risa M Hoffman
- David Geffen School of Medicine, Division of Infectious Diseases, University of California, Los Angeles, Los Angeles, CA, USA
| | - Paul E Sax
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA, USA
| | - Sikhulile Moyo
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA; Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Nahida Chakhtoura
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Sa Stringer
- Division of Global Women's Health, Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gaerolwe Masheto
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA; Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Violet Korutaro
- Baylor College of Medicine Children's Foundation, Kampala, Uganda
| | - Haseena Cassim
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre and Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Esau João
- Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil
| | - Sherika Hanley
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Umlazi, South Africa
| | - Lynette Purdue
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Jeremiah D Momper
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Roger L Shapiro
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA; Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | | | - Lisa M Frenkel
- Department of Pediatrics, Department of Laboratory Medicine, Department of Global Health, and Department of Medicine, University of Washington, and Seattle Children's Research Institute, Seattle, WA, USA
| | - K Rivet Amico
- Department of Health Behavior and Health Education, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lameck Chinula
- Division of Global Women's Health, Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; UNC Project Malawi, Lilongwe, Malawi
| | - Judith Currier
- David Geffen School of Medicine, Division of Infectious Diseases, University of California, Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
33
|
Bessong PO, Matume ND, Tebit DM. Potential challenges to sustained viral load suppression in the HIV treatment programme in South Africa: a narrative overview. AIDS Res Ther 2021; 18:1. [PMID: 33407664 PMCID: PMC7788882 DOI: 10.1186/s12981-020-00324-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
Background South Africa, with one of the highest HIV prevalences in the world, introduced the universal test and treat (UTT) programme in September 2016. Barriers to sustained viral suppression may include drug resistance in the pre-treated population, non-adherence, acquired resistance; pharmacokinetics and pharmacodynamics, and concurrent use of alternative treatments. Objective The purpose of this review is to highlight potential challenges to achieving sustained viral load suppression in South Africa (SA), a major expectation of the UTT initiative. Methodology Through the PRISMA approach, published articles from South Africa on transmitted drug resistance; adherence to ARV; host genetic factors in drug pharmacokinetics and pharmacodynamics, and interactions between ARV and herbal medicine were searched and reviewed. Results The level of drug resistance in the pre-treated population in South Africa has increased over the years, although it is heterogeneous across and within Provinces. At least one study has documented a pre-treated population with moderate (> 5%) or high (> 15%) levels of drug resistance in eight of the nine Provinces. The concurrent use of ARV and medicinal herbal preparation is fairly common in SA, and may be impacting negatively on adherence to ARV. Only few studies have investigated the association between the genetically diverse South African population and pharmacokinetics and pharmacodynamics of ARVs. Conclusion The increasing levels of drug resistant viruses in the pre-treated population poses a threat to viral load suppression and the sustainability of first line regimens. Drug resistance surveillance systems to track the emergence of resistant viruses, study the burden of prior exposure to ARV and the parallel use of alternative medicines, with the goal of minimizing resistance development and virologic failure are proposed for all the Provinces of South Africa. Optimal management of the different drivers of drug resistance in the pre-treated population, non-adherence, and acquired drug resistance will be beneficial in ensuring sustained viral suppression in at least 90% of those on treatment, a key component of the 90-90-90 strategy.
Collapse
|
34
|
Shah S, Hindley L, Hill A. Are New Antiretroviral Treatments Increasing the Risk of Weight Gain? Drugs 2021; 81:299-315. [PMID: 33400239 DOI: 10.1007/s40265-020-01457-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is a growing body of evidence from both observational and randomised trials implicating integrase inhibitors, particularly dolutegravir and bictegravir, with the development of weight gain and obesity in people living with HIV. Evidence with cabotegravir, the newest integrase inhibitor, is limited. Reasons for weight gain are currently unknown. Proposed mechanisms include improved tolerability, direct impact on adipogenesis, and gut microbiome disturbance. Clinical trials have found that weight gain with integrase inhibitors is greatest for women and people of Black ethnicity. Evidence suggests that the nucleoside reverse transcriptase backbone has additional effects on weight gain, with tenofovir alafenamide potentially enhancing the weight gain effect. Weight gain and obesity have long-term consequences, including metabolic syndrome, development of type 2 diabetes mellitus, cardiovascular disease and adverse birth outcomes. However, the current evidence for the medium and long-term effects of weight gain associated with integrase inhibitors is limited. There is an urgent need for clinical trials with longer follow-up periods and standardised endpoints to evaluate these effects. New thresholds for weight gain should be established as guidance for clinicians to stop treatment where weight gain is excessive. Novel treatments such as doravirine could offer a suitable therapy alternative, with current evidence showing efficacy with limited effect on weight gain.
Collapse
Affiliation(s)
- Shahini Shah
- Faculty of Medicine, Imperial College London, London, UK.
| | - Laura Hindley
- School of Public Health, Imperial College London, London, UK
| | - Andrew Hill
- Department of Translational Medicine, Liverpool University, Pharmacology, Liverpool, UK
| |
Collapse
|
35
|
Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase. Nat Commun 2020; 11:5922. [PMID: 33262331 PMCID: PMC7708638 DOI: 10.1038/s41467-020-19801-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/28/2020] [Indexed: 12/05/2022] Open
Abstract
Little is known about the impact of pretreatment drug resistance (PDR) on the efficacy of second generation integrase inhibitors. We sequenced pretreatment plasma specimens from the ADVANCE trial (NCT03122262). Our primary outcome was 96-week virologic success, defined as a sustained viral load <1000 copies/mL from 12 weeks onwards, <200 copies/mL from 24 weeks onwards, and <50 copies/mL after 48 weeks. Here we report how this outcome was impacted by PDR, defined by the World Health Organization (WHO) mutation list. Of 1053 trial participants, 874 (83%) have successful sequencing, including 289 (33%) randomized to EFV-based therapy and 585 (67%) randomized to DTG-based therapy. Fourteen percent (122/874) have ≥1 WHO-defined mutation, of which 98% (120/122) are NNRTI mutations. Rates of virologic suppression are lower in the total cohort among those with PDR 65% (73/112) compared to those without PDR (85% [605/713], P < 0.001), and for those on EFV-based treatment (60% [12/20] vs 86% [214/248], P = 0.002) and for those on DTG-based treatment (61/92 [66%] vs 84% [391/465] P < 0.001, P for interaction by regimen 0.49). Results are similar in multivariable models adjusted for clinical characteristics and adherence. NNRTI resistance prior to treatment is associated with long-term failure of integrase inhibitor-containing first-line regimens, and portends high rates of first-line failure in sub Saharan Africa. Here the authors combine next generation sequencing on plasma from participants of the ADVANCE clinical trial with virological and follow-up data to investigate the impact of pre-treatment drug resistance (PDR) to non-nucleoside reverse transcriptase inhibitors (NNRTIs) on the efficacy of second-generation integrase inhibitors and find an association between NNRTI resistance prior to treatment and long-term treatment.
Collapse
|
36
|
Hauser A, Kusejko K, Johnson LF, Günthard HF, Riou J, Wandeler G, Egger M, Kouyos RD. Impact of scaling up dolutegravir on antiretroviral resistance in South Africa: A modeling study. PLoS Med 2020; 17:e1003397. [PMID: 33315863 PMCID: PMC7735592 DOI: 10.1371/journal.pmed.1003397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/10/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Rising resistance of HIV-1 to non-nucleoside reverse transcriptase inhibitors (NNRTIs) threatens the success of the global scale-up of antiretroviral therapy (ART). The switch to WHO-recommended dolutegravir (DTG)-based regimens could reduce this threat due to DTG's high genetic barrier to resistance. We used mathematical modeling to predict the impact of the scale-up of DTG-based ART on NNRTI pretreatment drug resistance (PDR) in South Africa, 2020 to 2040. METHODS AND FINDINGS We adapted the Modeling Antiretroviral drug Resistance In South Africa (MARISA) model, an epidemiological model of the transmission of NNRTI resistance in South Africa. We modeled the introduction of DTG in 2020 under 2 scenarios: DTG as first-line regimen for ART initiators, or DTG for all patients, including patients on suppressive NNRTI-based ART. Given the safety concerns related to DTG during pregnancy, we assessed the impact of prescribing DTG to all men and in addition to (1) women beyond reproductive age; (2) women beyond reproductive age or using contraception; and (3) all women. The model projections show that, compared to the continuation of NNRTI-based ART, introducing DTG would lead to a reduction in NNRTI PDR in all scenarios if ART initiators are started on a DTG-based regimen, and those on NNRTI-based regimens are rapidly switched to DTG. NNRTI PDR would continue to increase if DTG-based ART was restricted to men. When given to all men and women, DTG-based ART could reduce the level of NNRTI PDR from 52.4% (without DTG) to 10.4% (with universal DTG) in 2040. If only men and women beyond reproductive age or on contraception are started on or switched to DTG-based ART, NNRTI PDR would reach 25.9% in 2040. Limitations include substantial uncertainty due to the long-term predictions and the current scarcity of knowledge about DTG efficacy in South Africa. CONCLUSIONS Our model shows the potential benefit of scaling up DTG-based regimens for halting the rise of NNRTI resistance. Starting or switching all men and women to DTG would lead to a sustained decline in resistance levels, whereas using DTG-based ART in all men, or in men and women beyond childbearing age, would only slow down the increase in levels of NNRTI PDR.
Collapse
Affiliation(s)
- Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Leigh F. Johnson
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, South Africa
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Gilles Wandeler
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, South Africa
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- * E-mail: (ME); (RDK)
| | - Roger D. Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- * E-mail: (ME); (RDK)
| |
Collapse
|
37
|
Venter WDF, Sokhela S, Simmons B, Moorhouse M, Fairlie L, Mashabane N, Serenata C, Akpomiemie G, Masenya M, Qavi A, Chandiwana N, McCann K, Norris S, Chersich M, Maartens G, Lalla-Edward S, Vos A, Clayden P, Abrams E, Arulappan N, Hill A. Dolutegravir with emtricitabine and tenofovir alafenamide or tenofovir disoproxil fumarate versus efavirenz, emtricitabine, and tenofovir disoproxil fumarate for initial treatment of HIV-1 infection (ADVANCE): week 96 results from a randomised, phase 3, non-inferiority trial. Lancet HIV 2020; 7:e666-e676. [PMID: 33010240 DOI: 10.1016/s2352-3018(20)30241-1] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/14/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND ADVANCE compared the efficacy and safety of two antiretroviral first-line combinations (dolutegravir combined with emtricitabine and either tenofovir disoproxil fumarate or tenofovir alafenamide), with a third regimen (efavirenz combined with emtricitabine and tenofovir disoproxil fumarate) previously recommended by WHO. Here, we report the 96-week data for the study. METHODS This randomised, open-label, non-inferiority phase 3 trial, was done at two research sites in Johannesburg, South Africa, after participant recruitment from 11 public health clinics also in Johannesburg. Eligible participants were aged 12 years or older with HIV-1 infection, who weighed at least 40 kg, had no antiretroviral exposure in the previous 6 months, with a creatinine clearance of more than 60 mL/min (>80 mL per min in individuals aged <19 years), and a plasma HIV-1 RNA concentration of 500 copies per mL or higher. Individuals who were pregnant or had tuberculosis were excluded. Participants were randomly assigned (1:1:1) by study staff using a computerised randomisation system. Randomisation was stratified by age (12 and <19 years and ≥19 years). Participants were randomly assigned to once-daily oral fixed-dose combination tenofovir alafenamide 25 mg and emtricitabine 200 mg, and once-daily oral dolutegravir 50 mg; once-daily oral fixed-dose combination tenofovir disoproxil fumarate 300 mg and emtricitabine 200 mg, and once-daily oral dolutegravir 50 mg; or once-daily oral fixed-dose combination of tenofovir disoproxil fumarate 300 mg, emtricitabine 200 mg, and efavirenz 600 mg. The primary efficacy endpoint was the proportion of participants who had a plasma HIV-1 RNA concentration of less than 50 copies per mL at week 48, which has been reported previously. Here, we report the key secondary efficacy endpoint of the proportion of participants who had a plasma HIV-1 RNA concentration of less than 50 copies per mL at the week 96 visit, assessed in all participants who received at least one dose of any study drug, with a prespecified non-inferiority margin of -10%. Safety data, including clinical, dual-energy X-ray absorptiometry and laboratory data, are also reported. This study was registered with ClinicalTrials.gov, NCT03122262. FINDINGS Between Jan 17, 2017, and May 14, 2018, we screened 1453 individuals, of whom 1053 were enrolled: 351 participants were randomly assigned to the tenofovir alafenamide, emtricitabine, and dolutegravir group, 351 to the tenofovir disoproxil fumarate, emtricitabine, and dolutegravir group, and 351 to the tenofovir disoproxil fumarate, emtricitabine, and efavirenz group. All participants received at least one dose of study medication and were included in the primary analysis. At week 96, 276 (79%) of 351 participants in the tenofovir alafenamide, emtricitabine, and dolutegravir group, 275 (78%) of 351 participants in the tenofovir disoproxil fumarate, emtricitabine, and dolutegravir group, and 258 (74%) of 351 participants in the tenofovir disoproxil fumarate, emtricitabine, and efavirenz group had achieved a plasma HIV-1 RNA concentration of less than 50 copies per mL. Non-inferiority was established in all three comparisons. The proportion of patients with protocol-defined virological failure at week 96 was low in all treatment groups. Participants in the tenofovir alafenamide, emtricitabine, and dolutegravir group had fewer changes in bone density than the two other treatment groups. Mean weight gain was substantial (7·1 kg [SD 7·4] in the tenofovir alafenamide, emtricitabine, and dolutegravir group; 4·3 kg [6·7] in the tenofovir disoproxil fumarate, emtricitabine, and dolutegravir group, and 2·3 kg [7·0] in the tenofovir disoproxil fumarate, emtricitabine, and efavirenz group), and was greater among women than men. Ten (3%) of 351 participants in the tenofovir disoproxil fumarate, emtricitabine, and efavirenz group discontinued due to treatment-related adverse events, of which liver dysfunction (n=4) and rash (n=4) were most common. INTERPRETATION Medium-term and long-term metabolic and clinical consequences of the considerable increase in bodyweight observed in participants given these antiretroviral regimens and the trajectory of this weight gain over time, especially among women, require further study. FUNDING USAID, Unitaid, South African Medical Research Council, ViiV Healthcare.
Collapse
Affiliation(s)
- Willem D F Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Simiso Sokhela
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bryony Simmons
- Department of Infectious Disease, Imperial College London, London, UK
| | - Michelle Moorhouse
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lee Fairlie
- Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Nkuli Mashabane
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Celicia Serenata
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Godspower Akpomiemie
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Masebole Masenya
- Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Ambar Qavi
- School of Public Health, Imperial College London, London, UK
| | - Nomathemba Chandiwana
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kaitlyn McCann
- School of Public Health, Imperial College London, London, UK
| | - Shane Norris
- South African Medical Research Council and Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, University of the Witwatersrand, Johannesburg, South Africa
| | - Matthew Chersich
- Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Samanta Lalla-Edward
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alinda Vos
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Elaine Abrams
- ICAP at Columbia University, Mailman School of Public Health, Columbia University, New York, NY, USA; Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Natasha Arulappan
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew Hill
- Department of Translational Medicine, Liverpool University, Liverpool, UK
| |
Collapse
|
38
|
Olum R, Baluku JB, Okidi R, Andia-Biraro I, Bongomin F. Prevalence of HIV-associated esophageal candidiasis in sub-Saharan Africa: a systematic review and meta-analysis. Trop Med Health 2020; 48:82. [PMID: 32982560 PMCID: PMC7510310 DOI: 10.1186/s41182-020-00268-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/14/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Esophageal candidiasis (OC) is a common AIDS-defining opportunistic infection. Antiretroviral therapy (ART) reduces the occurrence of OC and other opportunistic infections among persons living with HIV (PLHIV). We sought to determine and compare the prevalence of OC in the ART and pre-ART era among PLHIV in sub-Saharan Africa (SSA). METHODS We searched PubMed, Embase, Web of Science, and the African Journals Online databases to select studies in English and French reporting the prevalence of HIV-associated OC in SSA from January 1980 to June 2020. Reviews, single-case reports, and case series reporting < 10 patients were excluded. A random-effect cumulative meta-analysis was performed using STATA 16.0, and trend analysis performed using GraphPad Prism 8.0. RESULTS Thirteen eligible studies from 9 SSA countries including a total of 113,272 patients were qualitatively synthesized, and 9 studies were included in the meta-analysis. Overall pooled prevalence of HIV-associated OC was 12% (95% confidence interval (CI): 8 to 15%, I 2 = 98.61%, p <. 001). The prevalence was higher in the pre-ART era compared to the ART era, but not to statistical significance (34.1% vs. 8.7%, p = 0.095). In those diagnosed by endoscopy, the prevalence was higher compared to patients diagnosed by non-endoscopic approaches, but not to statistical significance (35.1% vs. 8.4%, p = .071). The prevalence of OC significantly decreased over the study period (24 to 16%, p < .025). CONCLUSION The prevalence of OC among PLHIV in the ART era in SSA is decreasing. However, OC remains a common problem. Active endoscopic surveillance of symptomatic patients and further empirical studies into the microbiology, optimal antifungal treatment, and impact of OC on quality of life of PLHIV in SSA are recommended.
Collapse
Affiliation(s)
- Ronald Olum
- School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Joseph Baruch Baluku
- Directorate of Programs, Mildmay Uganda, Wakiso, Uganda
- Division of Pulmonology, Mulago National Referral Hospital, Kampala, Uganda
| | - Ronald Okidi
- Department of General Surgery, St. Mary’s Hospital – Lacor, Gulu, Uganda
| | - Irene Andia-Biraro
- Department of Medicine, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Felix Bongomin
- Department of Medicine, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Gulu University, Gulu, Uganda
| |
Collapse
|
39
|
Nel J, Dlamini S, Meintjes G, Burton R, Black JM, Davies NECG, Hefer E, Maartens G, Mangena PM, Mathe MT, Moosa MY, Mulaudzi MB, Moorhouse M, Nash J, Nkonyane TC, Preiser W, Rassool MS, Stead D, van der Plas H, van Vuuren C, Venter WDF, Woods JF. Southern African HIV Clinicians Society guidelines for antiretroviral therapy in adults: 2020 update. South Afr J HIV Med 2020; 21:1115. [PMID: 33101723 PMCID: PMC7564911 DOI: 10.4102/sajhivmed.v21i1.1115] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 06/21/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Jeremy Nel
- Helen Joseph Hospital, Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - Sipho Dlamini
- Department of Infectious Diseases, Faculty of Medicine, University of Cape Town, Cape Town, South Africa
| | - Graeme Meintjes
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Rosie Burton
- Southern African Medical Unit, Médecins Sans Frontières (MSF), Cape Town, South Africa
| | - John M Black
- Department of Medicine, Division of Infectious Diseases, Livingstone Tertiary Hospital, Port Elizabeth, South Africa
| | | | - Eric Hefer
- Private Practice Medical Adviser, Johannesburg, South Africa
| | - Gary Maartens
- Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Cape Town, South Africa
| | - Phetho M Mangena
- Department of Internal Medicine, School of Medicine, Pietersburg Hospital, Polokwane, South Africa.,Department of Medicine, School of Medicine, University of Limpopo, Turfloop, South Africa
| | | | - Mahomed-Yunus Moosa
- Department of Infectious Diseases, Division of Internal Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Michelle Moorhouse
- Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jennifer Nash
- Specialist Family Physician, Amathole District Clinical Specialist Team, East London, South Africa
| | - Thandeka C Nkonyane
- Department of Infectious Diseases, Faculty of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa.,Department of Medicine, Dr George Mokhari Hospital, Pretoria, South Africa
| | - Wolfgang Preiser
- Department of Medical Virology, National Health Laboratory Service, Tygerberg, South Africa.,Department of Pathology, Faculty of Medicine and Health, Stellenbosch University, Cape Town, South Africa
| | - Mohammed S Rassool
- Clinical HIV Research Unit, Wits Health Consortium, Johannesburg, South Africa
| | - David Stead
- Department of Medicine, Faculty of Infectious Diseases, Frere and Cecilia Makiwane Hospitals, East London, South Africa.,Department of Medicine, Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa
| | - Helen van der Plas
- Department of Infectious Diseases, Faculty of Medicine, University of Cape Town, Cape Town, South Africa
| | - Cloete van Vuuren
- Department of Internal Medicine, Military Hospital, Bloemfontein, South Africa.,Department of Internal Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Willem D F Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Joana F Woods
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Krieger MS, Denison CE, Anderson TL, Nowak MA, Hill AL. Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections. PLoS Comput Biol 2020; 16:e1008010. [PMID: 32628660 PMCID: PMC7365476 DOI: 10.1371/journal.pcbi.1008010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/16/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
Antibiotic-resistant infections are a growing threat to human health, but basic features of the eco-evolutionary dynamics remain unexplained. Most prominently, there is no clear mechanism for the long-term coexistence of both drug-sensitive and resistant strains at intermediate levels, a ubiquitous pattern seen in surveillance data. Here we show that accounting for structured or spatially-heterogeneous host populations and variability in antibiotic consumption can lead to persistent coexistence over a wide range of treatment coverages, drug efficacies, costs of resistance, and mixing patterns. Moreover, this mechanism can explain other puzzling spatiotemporal features of drug-resistance epidemiology that have received less attention, such as large differences in the prevalence of resistance between geographical regions with similar antibiotic consumption or that neighbor one another. We find that the same amount of antibiotic use can lead to very different levels of resistance depending on how treatment is distributed in a transmission network. We also identify parameter regimes in which population structure alone cannot support coexistence, suggesting the need for other mechanisms to explain the epidemiology of antibiotic resistance. Our analysis identifies key features of host population structure that can be used to assess resistance risk and highlights the need to include spatial or demographic heterogeneity in models to guide resistance management.
Collapse
Affiliation(s)
- Madison S. Krieger
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Carson E. Denison
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Thayer L. Anderson
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Martin A. Nowak
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Alison L. Hill
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| |
Collapse
|
42
|
Neuhann F, de Forest A, Heger E, Nhlema A, Scheller C, Kaiser R, Steffen HM, Tweya H, Fätkenheuer G, Phiri S. Pretreatment resistance mutations and treatment outcomes in adults living with HIV-1: a cohort study in urban Malawi. AIDS Res Ther 2020; 17:22. [PMID: 32434561 PMCID: PMC7240935 DOI: 10.1186/s12981-020-00282-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Pre-treatment drug resistance (PDR) among antiretroviral drug-naïve people living with HIV (PLHIV) represents an important indicator for the risk of treatment failure and the spread of drug resistant HIV variants. We assessed the prevalence of PDR and treatment outcomes among adults living with HIV-1 in Lilongwe, Malawi. Methods We selected 200 participants at random from the Lighthouse Tenofovir Cohort Study (LighTen). Serum samples were drawn prior to treatment initiation in 2014 and 2015, frozen, and later analyzed for the presence of HIV-1 drug resistance mutations. Amplicons were sequenced and interpreted by Stanford HIVdb interpretation algorithm 8.4. We assessed treatment outcomes by evaluating clinical outcome and viral suppression at the end of the follow-up period in October 2019. Results PDR testing was successful in 197 of 200 samples. The overall NNRTI- PDR prevalence was 13.7% (27/197). The prevalence of intermediate or high level NNRTI- PDR was 11.2% (22/197). The most common mutation was K103N (5.6%, 11/197), followed by Y181C (3.6%, 7/197). In one case, we detected an NRTI resistance mutation (M184V), in combination with multiple NNRTI resistance mutations. All HIV-1 isolates analyzed were of subtype C. Of the 27 patients with NNRTI- PDR, 9 were still alive, on ART, and virally suppressed at the end of follow-up. Conclusion The prevalence of NNRTI- PDR was above the critical level of 10% suggested by the Global Action Plan on HIV Drug Resistance. The distribution of drug resistance mutations was similar to that seen in previous studies from the region, and further supports the introduction of integrase inhibitors in first-line treatment in Malawi. Furthermore, our findings underline the need for continued PDR surveillance and pharmacovigilance in Sub-Saharan Africa.
Collapse
|
43
|
Modulation of mTORC1 Signaling Pathway by HIV-1. Cells 2020; 9:cells9051090. [PMID: 32354054 PMCID: PMC7291251 DOI: 10.3390/cells9051090] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 02/06/2023] Open
Abstract
Mammalian target of rapamycin complex 1 (mTORC1) is a master regulator of cellular proliferation and survival which controls cellular response to different stresses, including viral infection. HIV-1 interferes with the mTORC1 pathway at every stage of infection. At the same time, the host cells rely on the mTORC1 pathway and autophagy to fight against virus replication and transmission. In this review, we will provide the most up-to-date picture of the role of the mTORC1 pathway in the HIV-1 life cycle, latency and HIV-related diseases. We will also provide an overview of recent trends in the targeting of the mTORC1 pathway as a promising strategy for HIV-1 eradication.
Collapse
|
44
|
Nakato R, Tumwine JK, Nanzigu S, Naluyima S, Buzibye A, Alinayitwe L, Makoha C, Mukonzo JK. Antiretroviral drugs found in pork on Ugandan market: Implications for HIV/AIDS treatment. One Health 2020; 9:100125. [PMID: 32195312 PMCID: PMC7076142 DOI: 10.1016/j.onehlt.2020.100125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Ritah Nakato
- Department of Pharmacology & Therapeutics, Makerere University College of Health Sciences, Uganda
| | - James K Tumwine
- Department of pediatrics, Makerere University College of Health Sciences, Uganda
| | - Sarah Nanzigu
- Department of Pharmacology & Therapeutics, Makerere University College of Health Sciences, Uganda
| | - Sandra Naluyima
- Department of Pharmacology & Therapeutics, Makerere University College of Health Sciences, Uganda
| | - Allan Buzibye
- Department of Pharmacology & Therapeutics, Makerere University College of Health Sciences, Uganda
| | | | - Carol Makoha
- Department of Clinical Epidemiology, Makerere University College of Health Sciences, Uganda
| | - Jackson K Mukonzo
- Department of Pharmacology & Therapeutics, Makerere University College of Health Sciences, Uganda
| |
Collapse
|
45
|
HIV viral load algorithm: what are the needs in the field?: authors' response. AIDS 2020; 34:160-162. [PMID: 31789891 DOI: 10.1097/qad.0000000000002383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
46
|
Pillay T, Cornell M, Fox MP, Euvrard J, Fatti G, Technau KG, Sipambo N, Prozesky H, Eley B, Tanser F, Johnson LF. Recording of HIV viral loads and viral suppression in South African patients receiving antiretroviral treatment: a multicentre cohort study. Antivir Ther 2020; 25:257-266. [PMID: 32960187 DOI: 10.3851/imp3371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Viral suppression in patients on antiretroviral treatment (ART) is critical to reducing HIV transmission and HIV-related mortality. Although many studies have evaluated factors associated with viral suppression, few have assessed the extent to which missing viral load data may bias results. METHODS We included data on all patients starting ART from 2005 to 2019 in eight South African cohorts participating in the International epidemiology Databases to Evaluate AIDS (IeDEA) collaboration. Multivariable logistic regression models were used to determine factors associated with having a viral load measurement within 2 months of a scheduled testing date and having a viral load <400 RNA copies/ml ('viral suppression'). In a sensitivity analysis, missing viral loads were imputed based on patients' clinical and demographic characteristics and outcomes. RESULTS Viral load tests were scheduled in 603,549 and 77,423 intervals in adults and children, respectively, but test results were recorded in only 40.7% and 41.2%, respectively. The proportion of recorded results suppressed was 85.7% in adults and 72.4% in children. After imputation of missing viral load measurements, viral suppression reduced slightly in adults (85.3%) and increased in children (73.2%). Predictors of virological suppression in adults, which included female sex, older age, higher baseline CD4+ T-cell count and recent testing year, were similar in the main analysis and after imputing missing viral loads. CONCLUSIONS Although viral load information was frequently missing in the South African setting, estimates of viral suppression and predictors of viral suppression did not change substantially after adjusting for missing data.
Collapse
Affiliation(s)
| | - Morna Cornell
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Matthew P Fox
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.,Department of Global Health, Boston University School of Public Health, Boston, MA, USA.,Health Economics and Epidemiology Research Office, University of the Witwatersrand, Johannesburg, South Africa
| | - Jonathan Euvrard
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Geoffrey Fatti
- Kheth'Impilo AIDS Free Living, Cape Town, South Africa.,Division of Epidemiology and Biostatistics, Department of Global Health, Stellenbosch University, Cape Town, South Africa
| | - Karl-Günter Technau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Nosisa Sipambo
- Harriet Shezi Children's Clinic, University of the Witwatersrand, Johannesburg, South Africa
| | - Hans Prozesky
- Division of Infectious Diseases, Tygerberg Academic Hospital, University of Stellenbosch, Cape Town, South Africa
| | - Brian Eley
- Red Cross War Memorial Children's Hospital and the Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Frank Tanser
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK.,Africa Health Research Institute, Somkhele, KwaZulu-Natal, South Africa.,School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Leigh F Johnson
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
47
|
Prevalence and Correlates of Pre-Treatment HIV Drug Resistance among HIV-Infected Children in Ethiopia. Viruses 2019; 11:v11090877. [PMID: 31546824 PMCID: PMC6784098 DOI: 10.3390/v11090877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 02/07/2023] Open
Abstract
Pediatric human immunodeficiency virus (HIV) care in resource-limited settings remains a major challenge to achieving global HIV treatment and virologic suppression targets, in part because the administration of combination antiretroviral therapies (cART) is inherently complex in this population and because viral load and drug resistance genotyping are not routinely available in these settings. Children may also be at elevated risk of transmission of drug-resistant HIV as a result of suboptimal antiretroviral administration for prevention of mother-to-child transmission. We investigated the prevalence and the correlates of pretreatment HIV drug resistance (PDR) among HIV-infected, cART-naive children in Ethiopia. We observed an overall PDR rate of 14%, where all cases featured resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs): ~9% of participants harbored resistance solely to NNRTIs while ~5% harbored resistance to both NNRTIs and nucleoside reverse transcriptase inhibitors (NRTIs). No resistance to protease inhibitors was observed. No sociodemographic or clinical parameters were significantly associated with PDR, though limited statistical power is noted. The relatively high (14%) rate of NNRTI resistance in cART-naive children supports the use of non-NNRTI-based regimens in first-line pediatric treatment in Ethiopia and underscores the urgent need for access to additional antiretroviral classes in resource-limited settings.
Collapse
|
48
|
Ndashimye E, Arts EJ. The urgent need for more potent antiretroviral therapy in low-income countries to achieve UNAIDS 90-90-90 and complete eradication of AIDS by 2030. Infect Dis Poverty 2019; 8:63. [PMID: 31370888 PMCID: PMC6676518 DOI: 10.1186/s40249-019-0573-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/28/2019] [Indexed: 12/17/2022] Open
Abstract
Background Over 90% of Human Immunodeficiency Virus (HIV) infected individuals will be on treatment by 2020 under UNAIDS 90–90-90 global targets. Under World Health Organisation (WHO) “Treat All” approach, this number will be approximately 36.4 million people with over 98% in low-income countries (LICs). Main body Pretreatment drug resistance (PDR) largely driven by frequently use of non-nucleoside reverse transcriptase inhibitors (NNRTIs), efavirenz and nevirapine, has been increasing with roll-out of combined antiretroviral therapy (cART) with 29% annual increase in some LICs countries. PDR has exceeded 10% in most LICs which warrants change of first line regimen to more robust classes under WHO recommendations. If no change in regimens is enforced in LICs, it’s estimated that over 16% of total deaths, 9% of new infections, and 8% of total cART costs will be contributed by HIV drug resistance by 2030. Less than optimal adherence, and adverse side effects associated with currently available drug regimens, all pose a great threat to achievement of 90% viral suppression and elimination of AIDS as a public health threat by 2030. This calls for urgent introduction of policies that advocate for voluntary and compulsory drug licensing of new more potent drugs which should also emphasize universal access of these drugs to all individuals worldwide. Conclusions The achievement of United Nations Programme on HIV and AIDS 2020 and 2030 targets in LICs depends on access to active cART with higher genetic barrier to drug resistance, better safety, and tolerability profiles. It’s also imperative to strengthen quality service delivery in terms of retention of patients to treatment, support for adherence to cART, patient follow up and adequate drug stocks to help achieve a free AIDS generation. Electronic supplementary material The online version of this article (10.1186/s40249-019-0573-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, 1151 Richmond St., DSB Rm.3007, London, ON, N6A5C1, Canada. .,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, 1151 Richmond St., DSB Rm.3007, London, ON, N6A5C1, Canada
| |
Collapse
|
49
|
Ngo-Giang-Huong N, Aghokeng AF. HIV Drug Resistance in Resource-limited Countries: Threat for HIV Elimination. EClinicalMedicine 2019; 9:3-4. [PMID: 31143873 PMCID: PMC6510715 DOI: 10.1016/j.eclinm.2019.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 11/30/2022] Open
Affiliation(s)
- Nicole Ngo-Giang-Huong
- IRD UMI 174-PHPT-Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Avelin F Aghokeng
- IRD UMR 224, CNRS 5290, MIVEGEC, Université de Montpellier, Montpellier, France
- Centre international de recherches médicales de Franceville (CIRMF), Département de virologie, Franceville, Gabon
| |
Collapse
|