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Shalekoff S, Dias BDC, Loubser S, Strehlau R, Kuhn L, Tiemessen CT. Higher CCR5 density on CD4 + T-cells in mothers and infants is associated with increased risk of in-utero HIV-1 transmission. AIDS 2024; 38:945-954. [PMID: 38329228 PMCID: PMC11064911 DOI: 10.1097/qad.0000000000003857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
OBJECTIVE CCR5-tropic viruses are preferentially transmitted during perinatal HIV-1 infection. CCR5 density on CD4 + T-cells likely impacts susceptibility to HIV-1 infection. DESIGN Fifty-two mother-infant dyads were enrolled. All mothers were living with HIV-1, 27 of the infants acquired HIV-1 in utero and 25 infants remained uninfected. METHODS CCR5 density, together with frequencies of CD4 + and CD8 + T-cells expressing immune activation (CCR5, ICOS and HLA-DR) and immune checkpoint (TIGIT and PD-1) markers, were measured in whole blood from the dyads close to delivery. RESULTS Compared with mothers who did not transmit, mothers who transmitted HIV-1 had less exposure to ART during pregnancy ( P = 0.015) and higher plasma viral load close to delivery ( P = 0.0005). These mothers, additionally, had higher CCR5 density on CD4 + and CD8 + T-cells and higher frequencies of CCR5, ICOS and TIGIT-expressing CD8 + T-cells. Similarly, compared with infants without HIV-1, infants with HIV-1 had higher CCR5 density on CD4 + and CD8 + T-cells and higher frequencies of CCR5, TIGIT, and PD-1-expressing CD4 + and CD8 + T-cells as well as higher frequencies of HLA-DR-expressing CD8 + T-cells. CCR5 density on maternal CD4 + T-cells remained significantly associated with transmission after adjusting for maternal viral load and CD4 + T cell counts. Mother-infant dyads with shared high CCR5 density phenotypes had the highest risk of transmission/acquisition of infection compared with dyads with shared low-CCR5 density phenotypes. CONCLUSION This study provides strong evidence of a protective role for a combined mother-infant low CD4 + T-cell CCR5 density phenotype in in-utero transmission/acquisition of HIV-1.
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Affiliation(s)
- Sharon Shalekoff
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bianca Da Costa Dias
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Renate Strehlau
- VIDA Nkanyezi Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Ka'e AC, Santoro MM, Nanfack A, Ngoufack Jagni Semengue E, Yagai B, Nka AD, Ambada G, Mpouel ML, Sagnia B, Kenou L, Sanhanfo M, Togna Pabo WLR, Takou D, Chenwi CA, Sonela N, Sosso SM, Nkenfou C, Colizzi V, Halle-Ekane GE, Ndjolo A, Ceccherini-Silberstein F, Perno CF, Lewin S, Tiemessen CT, Fokam J. Characterization of HIV-1 Reservoirs in Children and Adolescents: A Systematic Review and Meta-Analysis Toward Pediatric HIV Cure. J Pediatr 2024; 267:113919. [PMID: 38237889 DOI: 10.1016/j.jpeds.2024.113919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/23/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
OBJECTIVE To conduct a comprehensive, systematic review of the profile of HIV-1 reservoirs in children and adolescents with perinatally acquired HIV infection. STUDY DESIGN Randomized and nonrandomized trials, cohort studies, and cross-sectional studies on HIV reservoirs in pediatric populations, published between 2002 and 2022, were included. Archived-drug resistance mutations (ADRMs) and the size of reservoirs were evaluated. Subgroup analyses were performed to characterize further the data, and the meta-analysis was done through random effect models. RESULTS Overall, 49 studies from 17 countries worldwide were included, encompassing 2356 perinatally infected participants (48.83% females). There are limited data on the quantitative characterization of viral reservoirs in sub-Saharan Africa, with sensitive methodologies such as droplet digital polymerase chain reaction rarely employed. The overall prevalence of ADRMs was 37.80% (95% CI 13.89-65.17), with 48.79% (95% CI 0-100) in Africa, 42.08% (95% CI 6.68-82.71) in America, 23.88% (95% CI 14.34-34.90) in Asia, and 20.00% (95% CI 10.72-31.17) in Europe, without any difference between infants and adolescents (P = .656). Starting antiretroviral therapy (ART) before 2 months of age limited the levels of HIV-1 DNA (P = .054). Participants with long-suppressed viremia (>5 years) had lower levels of HIV-1 DNA (P = .027). Pre- and post-ART CD4 ≤29% and pre-ART viremia ≥5Log were all found associated with greater levels of HIV-1 DNA (P = .038, P = .047, and P = .041, respectively). CONCLUSIONS The pooled prevalence of ADRMs is high in perinatally infected pediatric population, with larger proviral reservoir size driven by delayed ART initiation, a shorter period of viral suppression, and immunovirological failures. Thus, strategies for pediatric HIV functional cure should target children and adolescents with very early ART initiation, immunocompetence, and long-term viral suppression.
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Affiliation(s)
- Aude Christelle Ka'e
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon; Department of Experimental Medicine, PhD Course in Microbiology, Immunology, Infectious Diseases and Transplants (MIMIT), University of Rome "Tor Vergata", Rome, Italy
| | | | - Aubin Nanfack
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon; IAS Research Cure Academy, Geneva, Switzerland
| | - Ezechiel Ngoufack Jagni Semengue
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Bouba Yagai
- UniCamillus - Saint Camillus International University of Health Sciences, Rome, Italy
| | - Alex Durand Nka
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Georgia Ambada
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon; Department of Animal Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaounde, Cameroon
| | - Marie-Laure Mpouel
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Bertrand Sagnia
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Leslie Kenou
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Michelle Sanhanfo
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Willy Le Roi Togna Pabo
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon; Faculty of Sciences, Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - Desire Takou
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Collins Ambe Chenwi
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon; Department of Experimental Medicine, PhD Course in Microbiology, Immunology, Infectious Diseases and Transplants (MIMIT), University of Rome "Tor Vergata", Rome, Italy
| | - Nelson Sonela
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Samuel Martin Sosso
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Celine Nkenfou
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Vittorio Colizzi
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon; Chair of UNESCO, Department of Biotechnology, Immunology and Molecular Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Gregory Edie Halle-Ekane
- Faculty of Health Sciences, Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon
| | - Alexis Ndjolo
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | | | - Carlo-Federico Perno
- Laboratory of Microbiology and Virology, Bambino Gesu Pediatric Hospital, Rome, Italy
| | - Sharon Lewin
- Infectious Diseases, University of Melbourne, Melbourne, Australia
| | - Caroline T Tiemessen
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Joseph Fokam
- Departments of Virology and Immunology, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon; IAS Research Cure Academy, Geneva, Switzerland; Faculty of Health Sciences, Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon.
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Barrios-Tascon A, Strehlau R, Patel F, Burke M, Shiau S, Shen Y, Arpadi SM, Abrams EJ, Tiemessen CT, Kuhn L. Growth Trajectories Over the First Year of Life Among Early-Treated Infants with Human Immunodeficiency Virus and Infants Who are Human Immunodeficiency Virus-Exposed Uninfected. J Pediatr 2024; 270:114018. [PMID: 38508485 DOI: 10.1016/j.jpeds.2024.114018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/10/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
OBJECTIVE To investigate the role of early antiretroviral therapy (ART) on growth trajectories of infants with human immunodeficiency virus (IHIV) in the first year of life. STUDY DESIGN As part of a clinical trial of early ART in Johannesburg, South Africa (2015-2018), 116 IHIV diagnosed within 48 hours of birth were started on ART as soon as possible, and 80 uninfected infants born to mothers living with HIV (IHEU) were enrolled. Both groups were followed prospectively from birth through 48 weeks and growth parameters collected. The groups were compared and risk factors for poor growth investigated, in the full cohort and among IHIV separately. RESULTS IHIV had lower mean weight-for-age Z-scores (WAZ) than IHEU at 4 and 8 weeks (-1.17 [SE:0.14] vs -0.72 [0.14], P = .035 and -1.23 [0.15] vs -0.67 [0.14], P = .012). Although there was some closing of the gap over time, means remained lower in IHIV through 48 weeks. In length-for-age Z-scores (LAZ), differences widened over time and IHIV had lower Z-scores by 48 weeks (-1.41 [0.15] vs -0.80 [0.18], P = .011). Deficits in WAZ and LAZ in IHIV vs IHEU were most marked among girls. IHIV with pre-ART viral load ≥1000 copies/ml had significantly lower weight-for-length and mid-upper arm circumference Z-scores across all time points through 48 weeks. CONCLUSIONS IHIV on early ART had deficits in WAZ over the first 8 weeks of life and lower LAZ at 48 weeks than IHEU. Among IHIV, higher pre-ART viral load was associated with worse anthropometric indicators through 48 weeks.
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Affiliation(s)
- Ana Barrios-Tascon
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY.
| | - Renate Strehlau
- VIDA Nkanyezi Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Faeezah Patel
- Wits RHI, Shandukani Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Megan Burke
- VIDA Nkanyezi Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Stephen M Arpadi
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY; Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Elaine J Abrams
- Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY; ICAP, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institutes for Communicable Diseases, A Division of the National Health Laboratory Service, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY; Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
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4
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Maenetje P, Baik Y, Schramm DB, Vangu MDTW, Wallis RS, Mlotshwa M, Tiemessen CT, Li Y, Kornfeld H, Churchyard G, Auld SC, Bisson GP. Circulating Biomarkers, Fraction of Exhaled Nitric Oxide, and Lung Function in Patients With Human Immunodeficiency Virus and Tuberculosis. J Infect Dis 2024; 229:824-832. [PMID: 37386883 PMCID: PMC10938205 DOI: 10.1093/infdis/jiad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/12/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Identification of proinflammatory factors responding to Mycobacterium tuberculosis is important to reduce long-term sequelae of pulmonary tuberculosis (TB). METHODS We examined the association between plasma biomarkers, the fraction of exhaled nitric oxide (FeNO), and lung function among a prospective cohort of 105 adults newly diagnosed with TB/human immunodeficiency virus (HIV) in South Africa. Participants were followed for 48 weeks from antiretroviral therapy (ART) initiation with serial assessments of plasma biomarkers, FeNO, lung function, and respiratory symptoms. Linear regression and generalized estimating equations were used to examine the associations at baseline and over the course of TB treatment, respectively. RESULTS At baseline, higher FeNO levels were associated with preserved lung function, whereas greater respiratory symptoms and higher interleukin (IL)-6 plasma levels were associated with worse lung function. After ART and TB treatment initiation, improvements in lung function were associated with increases in FeNO (rate ratio [RR] = 86 mL, 95% confidence interval [CI] = 34-139) and decreases in IL-6 (RR = -118 mL, 95% CI = -193 to -43) and vascular endothelial growth factor ([VEGF] RR = -178 mL, 95% CI = -314 to -43). CONCLUSIONS Circulating IL-6, VEGF, and FeNO are associated with lung function in adults being treated for TB/HIV. These biomarkers may help identify individuals at higher risk for post-TB lung disease and elucidate targetable pathways to modify the risk of chronic lung impairment among TB survivors.
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Affiliation(s)
- Pholo Maenetje
- The Aurum Institute, Johannesburg, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Yeonsoo Baik
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Diana B Schramm
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mboyo Di-Tamba Willy Vangu
- Department of Nuclear Medicine, Charlotte Maxeke Johannesburg Academic Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yun Li
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, USA
| | - Gavin Churchyard
- The Aurum Institute, Johannesburg, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa
| | - Sara C Auld
- Departments of Medicine and Epidemiology, Emory University School of Medicine and Rollins School of Public Health, Atlanta, Georgia, USA
| | - Gregory P Bisson
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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5
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Tatoud R, Jones RB, Dong K, Ndung'u T, Deeks S, Tiemessen CT. Advancing HIV cure research in low- and middle-income countries requires empowerment of the next generation of scientists. J Virus Erad 2024; 10:100364. [PMID: 38559321 PMCID: PMC10979089 DOI: 10.1016/j.jve.2024.100364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
While low- and middle-income countries (LMICs), especially in Southern and Eastern Africa, bear the largest burden of the HIV globally, investigators working on the front lines in these regions are leading a limited number of research efforts, particularly related to HIV cure. Conducting HIV cure research in high-burden HIV LIMCs provides an unparalleled opportunity to formulate innovative research strategies, design trials tailored to the local context, evaluate clinical outcomes within key and vulnerable populations, meaningful involvement of stakeholders, and to shape policies in areas where HIV prevention and cure interventions can yield the most significant impact. Further, the high prevalence of infection, with varied HIV strains affecting large diverse populations, creates a unique environment for studies that would not be feasible in any other part of the world. This underscores the critical importance of addressing obstacles to unlock the full potential of research efforts in these regions. In this viewpoint, we identify significant challenges facing early career investigators in LMICs, particularly in Africa, that hinder their full engagement in HIV cure research. Drawing examples from the International AIDS Society's Research-for-Cure Academy, we provide practical recommendations to overcome barriers that include limited access to funding, effective mentors, educational and career development opportunities, coupled with inadequate investment in infrastructure that contribute towards the limited number of investigators from high-burden HIV LIMCs who are spearheading cutting-edge cure research. Addressing these challenges is crucial to empower investigators who possess unique insights and expertise, and who are well positioned to lead HIV cure-related research efforts. We acknowledge and welcome initiatives that promote capacity building and knowledge exchange between early-career investigators in LMICs and their peers and scientific leaders from high-income countries (HICs). Prioritizing investment in global collaboration and partnership will play a pivotal role in empowering the next generation of African scientists and clinicians. To expedite advancements of cure-related strategies that will be effective in high-burden HIV LMICs, we endorse the sustainable expansion of these pivotal initiatives in these regions, to enhance their effectiveness and hasten progress in the pursuit of a global HIV cure.
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Affiliation(s)
| | - R Brad Jones
- Weill Cornell Medicine Graduate School of Medical Sciences, New York, USA
| | - Krista Dong
- Ragon Institute of MGH, Harvard Medical School, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa
| | | | - Caroline T. Tiemessen
- National Institute for Communicable Diseases, University of the Witwatersrand, Johannesburg, South Africa
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6
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Twesigomwe D, Drögemöller BI, Wright GEB, Adebamowo C, Agongo G, Boua PR, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Lombard Z, Hazelhurst S. Characterization of CYP2B6 and CYP2A6 Pharmacogenetic Variation in Sub-Saharan African Populations. Clin Pharmacol Ther 2024; 115:576-594. [PMID: 38049200 DOI: 10.1002/cpt.3124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023]
Abstract
Genetic variation in CYP2B6 and CYP2A6 is known to impact interindividual response to antiretrovirals, nicotine, and bupropion, among other drugs. However, the full catalogue of clinically relevant pharmacogenetic variants in these genes is yet to be established, especially across African populations. This study therefore aimed to characterize the star allele (haplotype) distribution in CYP2B6 and CYP2A6 across diverse and understudied sub-Saharan African (SSA) populations. We called star alleles from 961 high-depth full genomes using StellarPGx, Aldy, and PyPGx. In addition, we performed CYP2B6 and CYP2A6 star allele frequency comparisons between SSA and other global biogeographical groups represented in the new 1000 Genomes Project high-coverage dataset (n = 2,000). This study presents frequency information for star alleles in CYP2B6 (e.g., *6 and *18; frequency of 21-47% and 2-19%, respectively) and CYP2A6 (e.g., *4, *9, and *17; frequency of 0-6%, 3-10%, and 6-20%, respectively), and predicted phenotypes (for CYP2B6), across various African populations. In addition, 50 potentially novel African-ancestry star alleles were computationally predicted by StellarPGx in CYP2B6 and CYP2A6 combined. For each of these genes, over 4% of the study participants had predicted novel star alleles. Three novel star alleles in CYP2A6 (*54, *55, and *56) and CYP2B6 apiece, and several suballeles were further validated via targeted Single-Molecule Real-Time resequencing. Our findings are important for informing the design of comprehensive pharmacogenetic testing platforms, and are highly relevant for personalized medicine strategies, especially relating to antiretroviral medication and smoking cessation treatment in Africa and the African diaspora. More broadly, this study highlights the importance of sampling diverse African ethnolinguistic groups for accurate characterization of the pharmacogene variation landscape across the continent.
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Affiliation(s)
- David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Galen E B Wright
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg Health Sciences Centre and Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Clement Adebamowo
- Institute for Human Virology, Abuja, Nigeria
- Division of Cancer Epidemiology, Department of Epidemiology and Public Health, and the Marlene and Stewart Greenebaum Comprehensive Cancer Centre, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Martin C Simuunza
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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7
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Ka'e AC, Santoro MM, Duca L, Chenwi CA, Ngoufack Jagni Semengue E, Nka AD, Etame NK, Togna Pabo WL, Beloumou G, Mpouel ML, Djupsa S, Takou D, Sosso SM, Tchidjou HK, Colizzi V, Halle-Ekane GE, Perno CF, Lewin S, Jones RB, Tiemessen CT, Ceccherini-Silberstein F, Fokam J. Evaluation of HIV-1 DNA levels among adolescents living with perinatally acquired HIV-1 in Yaounde, Cameroon: A contribution to paediatric HIV cure research in Sub-Saharan Africa. J Virus Erad 2024; 10:100367. [PMID: 38601701 PMCID: PMC11004643 DOI: 10.1016/j.jve.2024.100367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/17/2024] [Accepted: 03/24/2024] [Indexed: 04/12/2024] Open
Abstract
Background With the advent of antiretroviral therapy (ART), most children living with HIV in sub-Saharan Africa (SSA) are growing toward adolescence, with scarcity of evidence on the size of viral reservoirs to enhance paediatric cure research strategies. This study aims to compare HIV-1 proviral DNA levels according to virological response among adolescents living with perinatally acquired HIV-1 (ALPHIV) and identify associated-factors in the Cameroonian context. Methods In this observational cohort study, HIV-1 RNA viremia and CD4+ T-cell count were assessed through RT-PCR and flow cytometry respectively at three time-points over 18 months of observation. At the third time-point, 80 randomly-selected participants were classified as with viremia (≥50 HIV-1 copies/mL; n = 40) or without viremia (<50 HIV-1 copies/mL; n = 40); immune-competent (≥500 CD4+ T cells/mm3) or immunocompromised (<500 CD4+ T cells/mm3). Among these participants, total HIV-1 DNA load was quantified through droplet digital PCR using Bio-Rad QX200. Results Of the 80 randomly-selected adolescents, median [IQR] age was 15 (13-17) years, 56.2% were female, duration on ART was 9.3 [5.4-12.2] years. Among the 40 viremic ones (median viremia 7312 [283-71482]) HIV-1 copies/ml, 75.0% (30/40) were in virological failure (≥1000 HIV-1 copies/ml), while median of CD4 T cells were 494 [360-793] cell/mm3 with 48.8% (39/80) immunocompromised. No significant variation in HIV-1 RNA viremia and CD4 T cell count was observed between the three time-points, and 13.7% (11/80) adolescents remained aviremic and immune-competent throughout (stable adolescents). A positive and moderate correlation (r = 0.59; p < 0.001) was found between HIV-1 DNA levels and HIV- 1 RNA viremia. Regarding the CD4 T cell count, a negative and weak correlation (r = -0.28; p = 0.014) was found with HIV-1 DNA loads only among adolescents with viremia. Starting ART within the first year of life, ART for over 9 years and aviremia appear as predictors of low HIV-1 DNA loads. Conclusion Among ALPHIV, high HIV-1 RNA indicates an elevated viral reservoir size, representing a drawback to cure research. Interestingly, early ART initiation and longer ARTduration lead to sustained viral control and limited HIV-1 reservoir size. As limited size of viral reservoir appears consistent with viral control and immune competence, adolescents with sustained viral control (about 14% of this target population) would be candidates for analytical ART interruptions toward establishing paediatric post-treatment controllers in SSA.
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Affiliation(s)
- Aude Christelle Ka'e
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
- HIV Research for Cure Academy, International AIDS Society, Geneva, Switzerland
| | | | - Leonardo Duca
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Collins Ambe Chenwi
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Alex Durand Nka
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Naomi-Karell Etame
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Willy Leroi Togna Pabo
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- University of Antwerp, Antwerp, Belgium
| | - Grace Beloumou
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Marie Laure Mpouel
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- University of Yaounde I, Yaounde, Cameroon
| | - Sandrine Djupsa
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Desire Takou
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Samuel Martin Sosso
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | | | | | | | | | - Sharon Lewin
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - R Brad Jones
- HIV Research for Cure Academy, International AIDS Society, Geneva, Switzerland
- Weill Cornell Medicine Graduate School of Medical Sciences, New York, USA
| | - Caroline T. Tiemessen
- HIV Research for Cure Academy, International AIDS Society, Geneva, Switzerland
- Centre for HIV and STIs, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Joseph Fokam
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- HIV Research for Cure Academy, International AIDS Society, Geneva, Switzerland
- University of Yaounde I, Yaounde, Cameroon
- Central Technical Group, National AIDS Control Committee, Yaoundé, Cameroon
- National HIV Drug Resistance Working Group, Ministry of Public Health, Yaounde, Cameroon
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8
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Ka'e AC, Nanfack A, Santoro MM, Yagai B, Ambada G, Sagnia B, Nka AD, Ngoufack Jagni Semengue E, Pabo W, Takou D, Sonela N, Colizzi V, Perno CF, Ceccherini-Silberstein F, Lewin SR, Tiemessen CT, Fokam J. Characterisation of HIV-1 reservoirs in paediatric populations: protocol for a systematic review and meta-analysis. BMJ Open 2023; 13:e073672. [PMID: 37816567 PMCID: PMC10565271 DOI: 10.1136/bmjopen-2023-073672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
INTRODUCTION The success of antiretroviral therapy (ART) has changed HIV from a deadly to a chronic infection, thus increasing the transitioning from infancy toward adulthood. However, the virostatic nature of antiretrovirals maintains viruses in sanctuaries, with reactivation potentials. Because current ARTs are very limited for children, the emergence of new HIV epidemics driven by HIV drug-resistance mutations is favoured. Our systematic review aims to estimate the global burden of archived drug-resistance mutations (ADRMs) and the size of reservoir (HIV-1 DNA load), and their associated factors in children and adolescents. METHODS AND ANALYSIS Papers from the PubMed/MEDLINE, Google Scholar, ScienceDirect, African Journals Online and Academic Medical Education Databases will be systematically identified using the keywords: "HIV-1 reservoirs", "viral reservoirs", "HIV-1 DNA", infants, adolescents, child and children, linked by the following Boolean operators: 'OR' and 'AND'. Randomised and non-randomised trials, cohort studies and cross-sectional studies published in French or English from January 2002 will be included, while case reports, letters, comments, reviews, systematic reviews and meta-analyses, and editorials will be excluded. All studies describing data on ADRMs, HIV-1 DNA load and/or immunological markers among children/adolescents will be eligible. A random-effects model will be used to calculate the pooled prevalence of ADRMs. Data will be reported according to type of viral reservoir (peripheral blood mononuclear cells, CD4 cells), geographical location (country/continent), ethnicity/race, age (infants vs adolescents), gender, HIV-1 clades, ART exposure (naïve vs treated, drug class, type of regimen, age at ART initiation and treatment duration), WHO clinical staging (I, II, III, IV), immune status (immune compromised vs immune competent) and virological response (viraemic vs non-viraemic). Multivariate logistic regression will be performed to determine predictors of HIV reservoir profile in paediatric populations. The primary outcome will be to assess the genotypical and quantitative profile of HIV reservoirs, while the secondary outcomes will be to identify factors associated with ADRMs and reservoir size in paediatric populations. ETHICS AND DISSEMINATION Ethical approval is not applicable for this study as it will be based on published data. Results will be disseminated via a peer-reviewed scientific journal and relevant conferences. PROSPERO REGISTRATION NUMBER CRD42022327625.
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Affiliation(s)
- Aude Christelle Ka'e
- Laboratory of Virology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
- Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Aubin Nanfack
- Laboratory of Immunology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
| | | | - Bouba Yagai
- Central Technical Group, National AIDS Control Committee (NACC), Yaounde, Cameroon
| | - Georgia Ambada
- Laboratory of Immunology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
| | - Bertrand Sagnia
- Laboratory of Immunology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
| | - Alex Durand Nka
- Laboratory of Virology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
| | - Ezechiel Ngoufack Jagni Semengue
- Laboratory of Virology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
| | - Willy Pabo
- Faculty of Sciences, University of Buea, Buea, Cameroon
| | - Désiré Takou
- Laboratory of Virology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
| | - Nelson Sonela
- Laboratory of Immunology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
| | - Vittorio Colizzi
- Faculty of Sciences & Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
| | | | | | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Caroline T Tiemessen
- Cell Biology laboratory, National Institute for Communicable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Joseph Fokam
- Laboratory of Virology, Chantal Biya International Reference Centre for HIV/AIDS Research on Prevention and Treatment, Yaounde, Cameroon, Yaounde, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
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9
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Ka’e AC, Nanfack AJ, Ambada G, Santoro MM, Takou D, Semengue ENJ, Nka AD, Bala MLM, Endougou ON, Elong E, Beloumou G, Djupsa S, Gouissi DH, Fainguem N, Tchouaket MCT, Sosso SM, Kesseng D, Ndongo FA, Sonela N, Kamta ACL, Tchidjou HK, Ndomgue T, Ndiang STM, Nlend AEN, Nkenfou CN, Montesano C, Halle-Ekane GE, Cappelli G, Tiemessen CT, Colizzi V, Ceccherini-Silberstein F, Perno CF, Fokam J. Inflammatory profile of vertically HIV-1 infected adolescents receiving ART in Cameroon: a contribution toward optimal pediatric HIV control strategies. Front Immunol 2023; 14:1239877. [PMID: 37646023 PMCID: PMC10461471 DOI: 10.3389/fimmu.2023.1239877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/21/2023] [Indexed: 09/01/2023] Open
Abstract
Antiretroviral therapy (ART) has improved the lifespan of people living with HIV. However, their immune system remains in a state of sustained activation/inflammation, which favors viral replication and depletion of helper T-cells with varying profiles according to ART-response. We herein sought to ascertain the inflammatory profile of adolescents living with perinatal HIV-1 infection (ALPHI) receiving ART in an African context. In this cross-sectional and comparative study among ART-experienced ALPHI in Yaoundé-Cameroon, HIV-1 RNA was measured by Abbott Real-time PCR; CD4 cells were enumerated using flow cytometry; serum cytokines were measured by ELISA; HIV-1 proviral DNA was genotyped by Sanger-sequencing; and archived drug resistance mutations (ADRMs) were interpreted using Stanford HIVdb.v9.0.1. Overall, 73 adolescents were enrolled (60 ALPHI and 13 HIV-1 negative peers) aged 15 (13-18) years; 60.00% were female. ART median duration was 92 (46-123) months; median viral load was 3.99 (3.17-4.66) RNA Log10 (copies)/mL and median CD4 count was 326 (201-654) cells/mm3. As compared to HIV-negative adolescents, TNFα was highly expressed among ALPHI (p<0.01). Following a virological response, inflammatory cytokines (IFNγ and IL-12), anti-inflammatory cytokines (IL-4 and IL-10) and inflammation-related cytokines (IL-6 and IL-1β) were highly expressed with viral suppression (VS) vs. virological failure (VF), while the chemokine CCL3 was highly expressed with VF (p<0.01). Regarding the immune response, the inflammatory cytokine TNFα was highly expressed in those that are immunocompetent (CD4≥500 cell/mm3) vs. immunocompromised (CD4<500 cell/mm3), p ≤ 0.01; while chemokine CCL2 was highly expressed in the immunocompromised (p<0.05). In the presence of ADRMs, IL-4 and CCL3 were highly expressed (p=0.027 and p=0.043 respectively). Among ART-experienced ALPHI in Cameroon, the TNFα cytokine was found to be an inflammatory marker of HIV infection; IFNγ, IL-1β, IL-6, and IL-12 are potential immunological markers of VS and targeting these cytokines in addition to antiretroviral drugs may improve management. Moreover, CCL3 and CCL2 are possible predictors of VF and/or being immunocompromised and could serve as surrogates of poor ART response.
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Affiliation(s)
- Aude Christelle Ka’e
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Aubin Joseph Nanfack
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Georgia Ambada
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Faculty of Science, University of Yaounde 1, Yaounde, Cameroon
| | | | - Desire Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | | | - Alex Durand Nka
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Marie Laure Mpouel Bala
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Orphelie Ndoh Endougou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- School of Health Sciences, Catholic University of Central Africa, Yaounde, Cameroon
| | - Elise Elong
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Grace Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Sandrine Djupsa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Davy Hyacinthe Gouissi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Nadine Fainguem
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Michel Carlos Tommo Tchouaket
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- School of Health Sciences, Catholic University of Central Africa, Yaounde, Cameroon
| | - Samuel Martin Sosso
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Daniel Kesseng
- Mother and Child Centre, Chantal BIYA Foundation, Yaounde, Cameroon
| | - Francis Ateba Ndongo
- Mother and Child Centre, Chantal BIYA Foundation, Yaounde, Cameroon
- Division of Operational Health Research, Ministry of Public Health, Yaounde, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Garoua, Garoua, Cameroon
| | - Nelson Sonela
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Arnaud Cedric Lacmago Kamta
- Elisabeth Glaser Pediatric AIDS Foundation (EGPAF), Country-office, Yaoundé, Cameroon
- HIV Management Unit, Mfou District Hospital, Mfou, Cameroon
| | | | - Therese Ndomgue
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | | | | | - Celine Nguefeu Nkenfou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
| | - Carla Montesano
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Giulia Cappelli
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- National Research Council, Rome, Italy
| | - Caroline T. Tiemessen
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
- Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
| | | | - Carlo-Federico Perno
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Bambino Gesu Pediactric Hospital, Rome, Italy
| | - Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaounde, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
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Kuhn L, Wang T, Li F, Strehlau R, Tobin NH, Violari A, Brooker S, Patel F, Liberty A, Shiau S, Arpadi SM, Wadhwa S, Yin MT, Wang S, Tiemessen CT, Aldrovandi GM. Microbiota in the oral cavity of school-age children with HIV who started antiretroviral therapy at young ages in South Africa. AIDS 2023; 37:1583-1591. [PMID: 37199568 PMCID: PMC10524539 DOI: 10.1097/qad.0000000000003599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
BACKGROUND Infancy is an important developmental period when the microbiome is shaped. We hypothesized that earlier antiretroviral therapy (ART) initiation would attenuate HIV effects on microbiota in the mouth. METHODS Oral swabs were collected from 477 children with HIV (CWH) and 123 children without (controls) at two sites in Johannesburg, South Africa. CWH had started ART less than 3 years of age; 63% less than 6 months of age. Most were well controlled on ART at median age 11 years when the swab was collected. Controls were age-matched and recruited from the same communities. Sequencing of V4 amplicon of 16S rRNA was done. Differences in microbial diversity and relative abundances of taxa were compared between the groups. RESULTS CWH had lower alpha diversity than controls. Genus-level abundances of Granulicatella, Streptococcus, and Gemella were greater and Neisseria and Haemophilus less abundant among CWH than controls. Associations were stronger among boys. Associations were not attenuated with earlier ART initiation. Shifts in genus-level taxa abundances in CWH relative to controls were most marked in children on lopinavir/ritonavir regimens, with fewer shifts seen if on efavirenz ART regimens. CONCLUSION A distinct profile of less diverse oral bacterial taxa was observed in school-aged CWH on ART compared with uninfected controls suggesting modulation of microbiota in the mouth by HIV and/or its treatments. Earlier ART initiation was not associated with microbiota profile. Proximal factors, including current ART regimen, were associated with contemporaneous profile of oral microbiota and may have masked associations with distal factors such as age at ART initiation.
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Affiliation(s)
- Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons; and Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Tian Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Fan Li
- Department of Pediatrics, University of California Los Angeles, Los Angeles, CA
| | - Renate Strehlau
- VIDA Nkanyezi Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole H. Tobin
- Department of Pediatrics, University of California Los Angeles, Los Angeles, CA
| | - Avy Violari
- Perinatal HIV Research Unit, Chris Hani Baragwanath Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sarah Brooker
- Department of Pediatrics, University of California Los Angeles, Los Angeles, CA
| | - Faeezah Patel
- Wits RHI, Shandukani Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Afaaf Liberty
- Perinatal HIV Research Unit, Chris Hani Baragwanath Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
| | - Stephen M. Arpadi
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons; and Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Sunil Wadhwa
- College of Dental Medicine, Columbia University Irving Medical Center, New York, NY
| | - Michael T. Yin
- Division of Infectious Diseases, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Caroline T. Tiemessen
- National Institutes for Communicable Diseases, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Grace M. Aldrovandi
- Department of Pediatrics, University of California Los Angeles, Los Angeles, CA
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11
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Twesigomwe D, Drögemöller BI, Wright GE, Adebamowo C, Agongo G, Boua PR, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Lombard Z, Hazelhurst S. Characterization of CYP2D6 Pharmacogenetic Variation in Sub-Saharan African Populations. Clin Pharmacol Ther 2023; 113:643-659. [PMID: 36111505 PMCID: PMC9957841 DOI: 10.1002/cpt.2749] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/11/2022] [Indexed: 11/07/2022]
Abstract
Cytochrome P450 2D6 (CYP2D6) is a key enzyme in drug response owing to its involvement in the metabolism of ~ 25% of clinically prescribed medications. The encoding CYP2D6 gene is highly polymorphic, and many pharmacogenetics studies have been performed worldwide to investigate the distribution of CYP2D6 star alleles (haplotypes); however, African populations have been relatively understudied to date. In this study, the distributions of CYP2D6 star alleles and predicted drug metabolizer phenotypes-derived from activity scores-were examined across multiple sub-Saharan African populations based on bioinformatics analysis of 961 high-depth whole genome sequences. This was followed by characterization of novel star alleles and suballeles in a subset of the participants via targeted high-fidelity Single-Molecule Real-Time resequencing (Pacific Biosciences). This study revealed varying frequencies of known CYP2D6 alleles and predicted phenotypes across different African ethnolinguistic groups. Twenty-seven novel CYP2D6 star alleles were predicted computationally and two of them were further validated. This study highlights the importance of studying variation in key pharmacogenes such as CYP2D6 in the African context to better understand population-specific allele frequencies. This will aid in the development of better genotyping panels and star allele detection approaches with a view toward supporting effective implementation of precision medicine strategies in Africa and across the African diaspora.
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Affiliation(s)
- David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Britt I. Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Galen E.B. Wright
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg Health Sciences Centre and Max Rady College of MedicineUniversity of ManitobaWinnipegManitobaCanada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Clement Adebamowo
- Institute for Human VirologyAbujaNigeria
- Division of Cancer Epidemiology, Department of Epidemiology and Public Health, and the Marlene and Stewart Greenebaum Comprehensive Cancer CentreUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Godfred Agongo
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
- C.K. Tedam University of Technology and Applied SciencesNavrongoGhana
| | - Palwendé R. Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Clinical Research Unit of NanoroInstitut de Recherche en Sciences de la SantéNanoroBurkina Faso
| | - Mogomotsi Matshaba
- Botswana‐Baylor Children's Clinical Centre of ExcellenceGaboroneBotswana
- RetrovirologyDepartment of Pediatrics, Baylor College of MedicineHoustonTexasUSA
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of ScienceUniversity of DschangDschangCameroon
| | - Martin C. Simuunza
- Department of Disease Control, School of Veterinary MedicineUniversity of ZambiaLusakaZambia
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- School of Electrical and Information EngineeringUniversity of the WitwatersrandJohannesburgSouth Africa
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12
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Yoon H, Wake RM, Nakouzi AS, Wang T, Agalliu I, Tiemessen CT, Govender NP, Jarvis JN, Harrison TS, Pirofski LA. Association of Antibody Immunity With Cryptococcal Antigenemia and Mortality in a South African Cohort With Advanced Human Immunodeficiency Virus Disease. Clin Infect Dis 2023; 76:649-657. [PMID: 35915964 PMCID: PMC10226730 DOI: 10.1093/cid/ciac633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/06/2022] [Accepted: 07/29/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Asymptomatic cryptococcal antigenemia (positive blood cryptococcal antigen [CrAg]) is associated with increased mortality in individuals with human immunodeficiency virus (HIV) even after adjusting for CD4 count and despite receiving antifungal treatment. The association of antibody immunity with mortality in adults with HIV with cryptococcal antigenemia is unknown. METHODS Cryptococcal capsular glucuronoxylomannan (GXM)- and naturally occurring β-glucans (laminarin, curdlan)-binding antibodies were measured in blood samples of 197 South Africans with HIV who underwent CrAg screening and were followed up to 6 months. Associations between antibody titers, CrAg status, and all-cause mortality were sought using logistic and Cox regression, respectively. RESULTS Compared with CrAg-negative individuals (n = 130), CrAg-positive individuals (n = 67) had significantly higher IgG1 (median, 6672; interquartile range [IQR], 4696-10 414 vs 5343, 3808-7722 μg/mL; P = .007), IgG2 (1467, 813-2607 vs 1036, 519-2012 μg/mL; P = .01), and GXM-IgG (1:170, 61-412 vs 1:117, 47-176; P = .0009) and lower curdlan-IgG (1:47, 11-133 vs 1:93, 40-206; P = .01) titers. GXM-IgG was associated directly with cryptococcal antigenemia adjusted for CD4 count and antiretroviral therapy use (odds ratio, 1.64; 95% confidence interval [CI], 1.21 to 2.22). Among CrAg-positive individuals, GXM-IgG was inversely associated with mortality at 6 months adjusted for CD4 count and tuberculosis (hazard ratio, 0.50; 95% CI, .33 to .77). CONCLUSIONS The inverse association of GXM-IgG with mortality in CrAg-positive individuals suggests that GXM-IgG titer may have prognostic value in those individuals. Prospective longitudinal studies to investigate this hypothesis and identify mechanisms by which antibody may protect against mortality are warranted.
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Affiliation(s)
- Hyunah Yoon
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Rachel M Wake
- Institute for Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, United Kingdom
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Clinical Academic Group in Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, United Kingdom
| | - Antonio S Nakouzi
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
- Department of Urology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Caroline T Tiemessen
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV & STIs, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nelesh P Govender
- Institute for Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, United Kingdom
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- MRC Center for Medical Mycology, University of Exeter, Exeter, United Kingdom
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Joseph N Jarvis
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Botswana Harvard AIDS Institute Partnership, Botswana, Southern Africa
| | - Thomas S Harrison
- Institute for Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, United Kingdom
- Clinical Academic Group in Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, United Kingdom
- MRC Center for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Liise-anne Pirofski
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
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13
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Lassaunière R, Tiemessen CT. SARS-CoV-2 vaccine-induced antibody levels: what lies beneath. The Lancet Rheumatology 2022; 4:e579-e581. [PMID: 35966646 PMCID: PMC9363038 DOI: 10.1016/s2665-9913(22)00225-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ria Lassaunière
- Department of Virus and Microbiological Special Diagnostic, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Caroline T Tiemessen
- Centre for HIV & STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of The Witwatersrand, Johannesburg, South Africa
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14
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Morris SE, Strehlau R, Shiau S, Abrams EJ, Tiemessen CT, Kuhn L, Yates AJ. Healthy dynamics of CD4 T cells may drive HIV resurgence in perinatally-infected infants on antiretroviral therapy. PLoS Pathog 2022; 18:e1010751. [PMID: 35969641 PMCID: PMC9410541 DOI: 10.1371/journal.ppat.1010751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/25/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022] Open
Abstract
In 2019 there were 490,000 children under five living with HIV. Understanding the dynamics of HIV suppression and rebound in this age group is crucial to optimizing treatment strategies and increasing the likelihood of infants achieving and sustaining viral suppression. Here we studied data from a cohort of 122 perinatally-infected infants who initiated antiretroviral treatment (ART) early after birth and were followed for up to four years. These data included longitudinal measurements of viral load (VL) and CD4 T cell numbers, together with information regarding treatment adherence. We previously showed that the dynamics of HIV decline in 53 of these infants who suppressed VL within one year were similar to those in adults. However, in extending our analysis to all 122 infants, we find that a deterministic model of HIV infection in adults cannot explain the full diversity in infant trajectories. We therefore adapt this model to include imperfect ART adherence and natural CD4 T cell decline and reconstitution processes in infants. We find that individual variation in both processes must be included to obtain the best fits. We also find that infants with faster rates of CD4 reconstitution on ART were more likely to experience resurgences in VL. Overall, our findings highlight the importance of combining mathematical modeling with clinical data to disentangle the role of natural immune processes and viral dynamics during HIV infection. For infants infected with HIV at or near birth, early and continued treatment with antiretroviral therapy (ART) can lead to sustained suppression of virus and a healthy immune system. However many treated infants experience viral rebound and associated depletion of CD4 T cells. Mathematical models can successfully capture the dynamics of HIV infection in treated adults, but many of the assumptions encoded in these models do not apply early in life. Here we study data from a cohort of HIV-positive infants exhibiting diverse trajectories in response to ART. We show that wide-ranging outcomes can be explained by a modified, but still remarkably simple, model that includes both the natural dynamics of their developing immune systems and variation in treatment adherence. Strikingly, we show that infants with strong rates of recovery of CD4 T cells while on ART may be most at risk of virus resurgence.
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Affiliation(s)
- Sinead E. Morris
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, United States of America
| | - Elaine J. Abrams
- Department of Epidemiology, Mailman School of Public Health, Columbia University Medical Center, New York, New York, United States of America
- ICAP at Columbia University, Mailman School of Public Health, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University Medical Center, New York, New York, United States of America
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Louise Kuhn
- Department of Epidemiology, Mailman School of Public Health, Columbia University Medical Center, New York, New York, United States of America
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, United States of America
| | - Andrew J. Yates
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
- * E-mail:
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15
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Nkone P, Loubser S, Quinn TC, Redd AD, Ismail A, Tiemessen CT, Mayaphi SH. Correction to: Deep sequencing of the HIV-1 polymerase gene for characterisation of cytotoxic T-lymphocyte epitopes during early and chronic disease stages. Virol J 2022; 19:78. [PMID: 35513827 PMCID: PMC9069713 DOI: 10.1186/s12985-022-01803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Paballo Nkone
- Department of Medical Virology, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa
| | - Shayne Loubser
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Arshad Ismail
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simnikiwe H Mayaphi
- Department of Medical Virology, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa. .,National Health Laboratory Service-Tshwane Academic Division (NHLS-TAD), Tshwane, South Africa.
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16
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Wake RM, Govender NP, Omar SV, Ismail F, Tiemessen CT, Harrison TS, Jarvis JN. Rapid urine-based screening tests increase the yield of same-day tuberculosis diagnoses among patients living with advanced HIV disease. AIDS 2022; 36:839-844. [PMID: 35075041 DOI: 10.1097/qad.0000000000003177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Investigation of the diagnostic yield of urine-based tuberculosis (TB) screening in patients with advanced HIV disease. DESIGN A cross-sectional screening study. SETTING HIV outpatient clinics and wards at two hospitals in Johannesburg, South Africa, between June 2015 and October 2017. PARTICIPANTS Two hundred and one patients living with advanced HIV disease (CD4+ T-lymphocytes <100 cells/μl) attending healthcare facilities following cryptococcal antigen (CrAg) screening. INTERVENTION Screening for TB using sputum for microscopy, culture, and Xpert MTB/Rif and urine for lipoarabinomannan (LAM) and Xpert Ultra. MAIN OUTCOME MEASURES Proportion of positive results using each testing modality, sensitivity, and specificity of urine-based testing compared with culture, and survival outcomes during 6 months follow up. RESULTS Urine was obtained from 177 of 181 (98%) participants and sputum from 91 (50%). Urine-based screening increased same-day diagnostic yield from 7 (4%) to 31 (17%). A positive urine test with either LAM or Xpert Ultra had 100% sensitivity (95% confidence interval, 59-100%) for detecting culture-positive TB at any site. Patients with newly diagnosed TB on urine-based screening were initiated on treatment and did not have excess mortality compared with the remainder of the cohort. CONCLUSION Urine is an easily obtainable sample with utility for detecting TB in patients with advanced HIV disease. Combining urine and sputum-based screening in this population facilitates additional same-day TB diagnoses and early treatment initiation, potentially reducing the risk of TB-related mortality. Urine-based as well as sputum-based screening for TB should be integrated with CrAg screening in patients living with advanced HIV disease.
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Affiliation(s)
- Rachel M Wake
- Institute for Infection and Immunity, St George's University of London
- Clinical Academic Group in Infection and Immunity, St George's University Hospital NHS Foundation Trust, London, UK
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases, a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Nelesh P Govender
- Institute for Infection and Immunity, St George's University of London
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases, a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
- Faculty of Health Sciences, University of the Witwatersrand, Witwatersrand
- Division of Medical Microbiology, University of Cape Town, Cape Town
| | - Shaheed V Omar
- Faculty of Health Sciences, University of the Witwatersrand, Witwatersrand
- Department of Medical Microbiology, University of Pretoria, Pretoria
- Centre for Tuberculosis
| | - Farzana Ismail
- Department of Medical Microbiology, University of Pretoria, Pretoria
- Centre for Tuberculosis
| | - Caroline T Tiemessen
- Faculty of Health Sciences, University of the Witwatersrand, Witwatersrand
- Centre for HIV & STIs, National Institute for Communicable Diseases, a Division of the NHLS, Johannesburg, South Africa
| | - Thomas S Harrison
- Institute for Infection and Immunity, St George's University of London
- Clinical Academic Group in Infection and Immunity, St George's University Hospital NHS Foundation Trust, London, UK
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Joseph N Jarvis
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Botswana Harvard AIDS Institute Partnership, Gabarone, Botswana
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17
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Wake RM, Ismail NA, Omar SV, Ismail F, Tiemessen CT, Harrison TS, Jarvis JN, Govender NP. Prior Pulmonary Tuberculosis is a Risk Factor for Asymptomatic Cryptococcal Antigenemia in a Cohort of Adults living with Advanced HIV Disease. Open Forum Infect Dis 2022; 9:ofac202. [PMID: 35794929 PMCID: PMC9251663 DOI: 10.1093/ofid/ofac202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The greater mortality risk among people with advanced HIV disease and cryptococcal antigenemia, despite treatment, indicates an increased susceptibility to other infections. We found that prior TB was an independent risk factor for cryptococcal antigenemia (aOR 2.72, 95% CI 1.13 – 6.52, p=0.03) among patients with CD4 counts <100 cells/µL.
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Affiliation(s)
- Rachel M Wake
- Institute for Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, UK
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases, a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Clinical Academic Group in Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, UK
| | - Nazir A Ismail
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Centre for Tuberculosis, National Institute for Communicable Diseases, a Division of the NHLS, Johannesburg, South Africa
| | - Shaheed V Omar
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Centre for Tuberculosis, National Institute for Communicable Diseases, a Division of the NHLS, Johannesburg, South Africa
| | - Farzana Ismail
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Centre for Tuberculosis, National Institute for Communicable Diseases, a Division of the NHLS, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV & STIs, National Institute for Communicable Diseases, a Division of the NHLS, Johannesburg, South Africa
| | - Thomas S Harrison
- Institute for Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, UK
- Clinical Academic Group in Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, UK
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Joseph N Jarvis
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Botswana Harvard AIDS Institute Partnership, Gabarone, Botswana
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nelesh P Govender
- Institute for Infection and Immunity, St George’s University Hospital NHS Foundation Trust, London, UK
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases, a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
- Division of Medical Microbiology, University of Cape Town, South Africa; University of Cape Town, South Africa
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18
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Nkone P, Loubser S, Quinn TC, Redd AD, Ismail A, Tiemessen CT, Mayaphi SH. Deep sequencing of the HIV-1 polymerase gene for characterisation of cytotoxic T-lymphocyte epitopes during early and chronic disease stages. Virol J 2022; 19:56. [PMID: 35346259 PMCID: PMC8959563 DOI: 10.1186/s12985-022-01772-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/07/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Despite multiple attempts, there is still no effective HIV-1 vaccine available. The HIV-1 polymerase (pol) gene is highly conserved and encodes cytotoxic T-lymphocyte (CTL) epitopes. The aim of the study was to characterise HIV-1 Pol CTL epitopes in mostly sample pairs obtained during early and chronic stages of infection. METHODS Illumina deep sequencing was performed for all samples while Sanger sequencing was only performed on baseline samples. Codons under immune selection pressure were assessed by computing nonsynonymous to synonymous mutation ratios using MEGA. Minority CTL epitope variants occurring at [Formula: see text] 5% were detected using low-frequency variant tool in CLC Genomics. Los Alamos HIV database was used for mapping mutations to known HIV-1 CTL epitopes. RESULTS Fifty-two participants were enrolled in the study. Their median age was 28 years (interquartile range: 24-32 years) and majority of participants (92.3%) were female. Illumina minority variant analysis identified a significantly higher number of CTL epitopes (n = 65) compared to epitopes (n = 8) identified through Sanger sequencing. Most of the identified epitopes mapped to reverse transcriptase (RT) and integrase (IN) regardless of sequencing method. There was a significantly higher proportion of minority variant epitopes in RT (n = 39, 60.0%) compared to IN (n = 17, 26.2%) and PR (n = 9, 13.8%), p = 0.002 and < 0.0001, respectively. However, no significant difference was observed between the proportion of minority variant epitopes in IN versus PR, p = 0.06. Some epitopes were detected in either early or chronic HIV-1 infection whereas others were detected in both stages. Different distribution patterns of minority variant epitopes were observed in sample pairs; with some increasing or decreasing over time, while others remained constant. Some of the identified epitopes have not been previously reported for HIV-1 subtype C. There were also variants that could not be mapped to reported CTL epitopes in the Los Alamos HIV database. CONCLUSION Deep sequencing revealed many Pol CTL epitopes, including some not previously reported for HIV-1 subtype C. The findings of this study support the inclusion of RT and IN epitopes in HIV-1 vaccine candidates as these proteins harbour many CTL epitopes.
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Affiliation(s)
- Paballo Nkone
- Department of Medical Virology, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa
| | - Shayne Loubser
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Arshad Ismail
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simnikiwe H Mayaphi
- Department of Medical Virology, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa. .,National Health Laboratory Service-Tshwane Academic Division (NHLS-TAD), Tshwane, South Africa.
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19
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Suchard MS, Martinson N, Malfeld S, de Assis Rosa D, Mackelprang RD, Lingappa J, Hou X, Rees H, Delany-Moretlwe S, Goldfein H, Ranchod H, Coetzee D, Otwombe K, Morris L, Tiemessen CT, Savulescu DM. Alloimmunity to Class 2 Human Leucocyte Antigens May Reduce HIV-1 Acquisition – A Nested Case-Control Study in HIV-1 Serodiscordant Couples. Front Immunol 2022; 13:813412. [PMID: 35401581 PMCID: PMC8987441 DOI: 10.3389/fimmu.2022.813412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Enveloped viruses, including the Human Immunodeficiency Virus-1 (HIV), incorporate host proteins such as human leucocyte antigens (HLA) into their envelope. Pre-existing antibodies against HLA, termed HLA antibodies, may bind to these surface proteins and reduce viral infectivity. Related evidence includes macaque studies which suggest that xenoimmunization with HLA antigens may protect against simian immunodeficiency virus infection. Since HIV gp120 shows homology with class 2 HLA, including shared affinity for binding to CD4, class 2 HLA antibodies may influence HIV acquisition via binding to gp120 on the viral envelope. We conducted a nested case-control study on HIV serodiscordant couples, comparing the frequency of HLA antibodies among highly exposed persistently seronegative controls with those who went on to acquire HIV (HIV-seroconverters). We first performed low resolution HLA typing on 143 individuals who were HIV-infected at enrollment (index partners) and their corresponding sexual partners (115 highly exposed persistently seronegative individuals and 28 HIV-seroconverters). We then measured HLA class 1 and 2 antibodies in the highly exposed persistently seronegative individuals and HIV-seroconverters at early and late timepoints. We analyzed whether such antibodies were directed at HLA specificities of their HIV-infected index partners, and whether autoantibodies or complement-fixing class 2 HLA antibodies were present. Seventy-nine percent of highly exposed persistently seronegative individuals had HLA antibodies; 56% against class 1 and 50% against class 2 alleles. Half of the group of highly exposed persistently seronegative individuals, prior to seroconversion, expressed class 2 HLA antibodies, compared with only 29% of controls (p=0.05). HIV infection was a sensitizing event leading to de novo development of antibodies against HLA-A and HLA-B loci, but not against class 2 loci. HLA autoantibodies were present in 27% of highly exposed persistently seronegative individuals. Complement-fixing class 2 HLA antibodies did not differ significantly between highly exposed persistently seronegative individuals and seroconverters. In multivariable regression, presence of class 2 HLA antibodies at early timepoints was associated with reduced odds of HIV acquisition (odds ratio 0.330, confidence interval 0.112-0.976, p=0.045). These epidemiological data suggest that pre-existing class 2 HLA antibodies were associated with reduced odds of HIV acquisition.
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Affiliation(s)
- Melinda S. Suchard
- National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
- Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- *Correspondence: Melinda S. Suchard,
| | - Neil Martinson
- Perinatal Health Research Unit (PHRU), University of The Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Centre for TB Research, Baltimore, MD, United States
| | - Susan Malfeld
- National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Debbie de Assis Rosa
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Romel D. Mackelprang
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, United States
| | - Jairam Lingappa
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Medicine and Department of Paediatrics, University of Washington, Seattle, WA, United States
| | - Xuanlin Hou
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Helen Rees
- Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Sinead Delany-Moretlwe
- Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Hadassa Goldfein
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Heena Ranchod
- National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
- Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - David Coetzee
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Johannesburg, South Africa
| | - Kennedy Otwombe
- Perinatal Health Research Unit (PHRU), University of The Witwatersrand, Johannesburg, South Africa
- Epidemiology and Biostatistics Department, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lynn Morris
- National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
- Virology Department, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T. Tiemessen
- National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
- Virology Department, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dana M. Savulescu
- National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
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Picton ACP, Paximadis M, Koor GW, Bharuthram A, Shalekoff S, Lassauniere R, Ive P, Tiemessen CT. Reduced CCR5 Expression and Immune Quiescence in Black South African HIV-1 Controllers. Front Immunol 2021; 12:781263. [PMID: 34987508 PMCID: PMC8720782 DOI: 10.3389/fimmu.2021.781263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Unique Individuals who exhibit either suppressive HIV-1 control, or the ability to maintain low viral load set-points and preserve their CD4+ T cell counts for extended time periods in the absence of antiretroviral therapy, are broadly termed HIV-1 controllers. We assessed the extent to which black South African controllers (n=9), differ from uninfected healthy controls (HCs, n=22) in terms of lymphocyte and monocyte CCR5 expression (density and frequency of CCR5-expressing cells), immune activation as well as peripheral blood mononuclear cell (PBMC) mitogen-induced chemokine/cytokine production. In addition, relative CD4+ T cell CCR5 mRNA expression was assessed in a larger group of controllers (n=20) compared to HCs (n=10) and HIV-1 progressors (n=12). Despite controllers having significantly higher frequencies of activated CD4+ and CD8+ T cells (HLA-DR+) compared to HCs, CCR5 density was significantly lower in these T cell populations (P=0.039 and P=0.064, respectively). This lower CCR5 density was largely attributable to controllers with higher VLs (>400 RNA copies/ml). Significantly lower CD4+ T cell CCR5 density in controllers was maintained (P=0.036) when HCs (n=12) and controllers (n=9) were matched for age. CD4+ T cell CCR5 mRNA expression was significantly less in controllers compared to HCs (P=0.007) and progressors (P=0.002), whereas HCs and progressors were similar (P=0.223). The levels of soluble CD14 in plasma did not differ between controllers and HCs, suggesting no demonstrable monocyte activation. While controllers had lower monocyte CCR5 density compared to the HCs (P=0.02), significance was lost when groups were age-matched (P=0.804). However, when groups were matched for both CCR5 promoter haplotype and age (n=6 for both) reduced CCR5 density on monocytes in controllers relative to HCs was highly significant (P=0.009). Phytohemagglutinin-stimulated PBMCs from the controllers produced significantly less CCL3 (P=0.029), CCL4 (P=0.008) and IL-10 (P=0.028) compared to the HCs, which was largely attributable to the controllers with lower VLs (<400 RNA copies/ml). Our findings support a hypothesis of an inherent (genetic) predisposition to lower CCR5 expression in individuals who naturally control HIV-1, as has been suggested for Caucasian controllers, and thus, likely involves a mechanism shared between ethnically divergent population groups.
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Affiliation(s)
- Anabela C. P. Picton
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- *Correspondence: Maria Paximadis,
| | - Gemma W. Koor
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Avani Bharuthram
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sharon Shalekoff
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ria Lassauniere
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Prudence Ive
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Clinical HIV Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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21
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Ebonwu J, Lassaunière R, Paximadis M, Goosen M, Strehlau R, Gray GE, Kuhn L, Tiemessen CT. An HIV Vaccine Protective Allele in FCGR2C Associates With Increased Odds of Perinatal HIV Acquisition. Front Immunol 2021; 12:760571. [PMID: 34917081 PMCID: PMC8668943 DOI: 10.3389/fimmu.2021.760571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
In the Thai RV144 HIV-1 vaccine trial, a three-variant haplotype within the Fc gamma receptor 2C gene (FCGR2C) reduced the risk of HIV-1 acquisition. A follow-on trial, HVTN702, of a similar vaccine candidate found no efficacy in South Africa, where the predominant population is polymorphic for only a single variant in the haplotype, c.134-96C>T (rs114945036). To investigate a role for this variant in HIV-1 acquisition in South Africans, we used the model of maternal-infant HIV-1 transmission. A nested case-control study was conducted of infants born to mothers living with HIV-1, comparing children with perinatally-acquired HIV-1 (cases, n = 176) to HIV-1-exposed uninfected children (controls, n = 349). All had received nevirapine for prevention of mother-to-child transmission. The FCGR2C copy number and expression variants (c.-386G>C, c.-120A>T c.169T>C, and c.798+1A>G) were determined using a multiplex ligation-dependent probe amplification assay and the c.134-96C>T genotype with Sanger sequencing. The copy number, genotype and allele carriage were compared between groups using univariate and multivariate logistic regression. The FCGR2C c.134-96C>T genotype distribution and copy number differed significantly between HIV-1 cases and exposed-uninfected controls (P = 0.002, P Bonf = 0.032 and P = 0.010, P Bonf = > 0.05, respectively). The FCGR2C c.134-96T allele was overrepresented in the cases compared to the controls (58% vs 42%; P = 0.001, P Bonf = 0.016). Adjusting for birthweight and FCGR2C copy number, perinatal HIV-1 acquisition was associated with the c.134-96C>T (AOR = 1.89; 95% CI 1.25-2.87; P = 0.003, P Bonf = 0.048) and c.169C>T (AOR = 2.39; 95% CI 1.45-3.95; P = 0.001, P Bonf = 0.016) minor alleles but not the promoter variant at position c.-386G>C. The c.134-96C>T variant was in strong linkage disequilibrium with the c.169C>T variant, but remained significantly associated with perinatal acquisition when adjusted for c.169C>T in multivariate analysis. In contrast to the protective effect observed in the Thai RV144 trial, we found the FCGR2C variant c.134-96T-allele associated with increased odds of perinatal HIV-1 acquisition in South African children. These findings, taken together with a similar deleterious association found with HIV-1 disease progression in South African adults, highlight the importance of elucidating the functional relevance of this variant in different populations and vaccination/disease contexts.
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Affiliation(s)
- Joy Ebonwu
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ria Lassaunière
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Maria Paximadis
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for HIV & STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Mark Goosen
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for HIV & STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Johannesburg, South Africa.,Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,South African Medical Research Council, Cape Town, South Africa
| | - Louise Kuhn
- Gertrude H. Sergievsky Centre, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Caroline T Tiemessen
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for HIV & STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
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22
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Abstract
Receptors for the crystallisable fragment (Fc) of immunoglobulin (Ig) G, Fcγ receptors (FcγRs), link the humoral and cellular arms of the immune response, providing a diverse armamentarium of antimicrobial effector functions. Findings from HIV-1 vaccine efficacy trials highlight the need for further study of Fc-FcR interactions in understanding what may constitute vaccine-induced protective immunity. These include host genetic correlates identified within the low affinity Fcγ-receptor locus in three HIV-1 efficacy trials – VAX004, RV144, and HVTN 505. This perspective summarizes our present knowledge of FcγR genetics in the context of findings from HIV-1 efficacy trials, and draws on genetic variation described in other contexts, such as mother-to-child HIV-1 transmission and HIV-1 disease progression, to explore the potential contribution of FcγR variability in modulating different HIV-1 vaccine efficacy outcomes. Appreciating the complexity and the importance of the collective contribution of variation within the FCGR gene locus is important for understanding the role of FcγRs in protection against HIV-1 acquisition.
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Affiliation(s)
- Ria Lassaunière
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- *Correspondence: Caroline T. Tiemessen, ; Ria Lassaunière,
| | - Caroline T. Tiemessen
- Centre for HIV and STI’s, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- *Correspondence: Caroline T. Tiemessen, ; Ria Lassaunière,
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23
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Deeks SG, Archin N, Cannon P, Collins S, Jones RB, de Jong MAWP, Lambotte O, Lamplough R, Ndung'u T, Sugarman J, Tiemessen CT, Vandekerckhove L, Lewin SR. Research priorities for an HIV cure: International AIDS Society Global Scientific Strategy 2021. Nat Med 2021; 27:2085-2098. [PMID: 34848888 DOI: 10.1038/s41591-021-01590-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/27/2021] [Indexed: 12/21/2022]
Abstract
Despite the success of antiretroviral therapy (ART) for people living with HIV, lifelong treatment is required and there is no cure. HIV can integrate in the host genome and persist for the life span of the infected cell. These latently infected cells are not recognized as foreign because they are largely transcriptionally silent, but contain replication-competent virus that drives resurgence of the infection once ART is stopped. With a combination of immune activators, neutralizing antibodies, and therapeutic vaccines, some nonhuman primate models have been cured, providing optimism for these approaches now being evaluated in human clinical trials. In vivo delivery of gene-editing tools to either target the virus, boost immunity or protect cells from infection, also holds promise for future HIV cure strategies. In this Review, we discuss advances related to HIV cure in the last 5 years, highlight remaining knowledge gaps and identify priority areas for research for the next 5 years.
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Affiliation(s)
- Steven G Deeks
- University of California San Francisco, San Fransisco, CA, USA.
| | - Nancie Archin
- UNC HIV Cure Center, Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Paula Cannon
- University of Southern California, Los Angeles, CA, USA
| | | | - R Brad Jones
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - Olivier Lambotte
- University Paris Saclay, AP-HP, Bicêtre Hospital, UMR1184 INSERM CEA, Le Kremlin Bicêtre, Paris, France
| | | | - Thumbi Ndung'u
- Africa Health Research Institute and University of KwaZulu-Natal, Durban, South Africa
- University College London, London, UK
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Jeremy Sugarman
- Berman Institute of Bioethics and Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Caroline T Tiemessen
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Sharon R Lewin
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia.
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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24
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Mukendi A, Kufa T, Murray T, Burke M, Strehlau R, Technau KG, Tiemessen CT, Sherman GG, Mazanderani AH. Evaluating the performance of the GeneXpert HIV-1 qualitative assay as a consecutive test for a new early infant diagnosis algorithm in South Africa. S Afr Med J 2021; 111:857-861. [PMID: 34949250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND The proportion of HIV-exposed infants and young children infected with HIV in South Africa (SA) has declined markedly over the past decade as a result of the country's comprehensive prevention of mother-to-child transmission programme. This decrease has in turn reduced the positive predictive value (PPV) of diagnostic assays, necessitating review of early infant diagnosis (EID) algorithms to ensure improved accuracy. OBJECTIVES To evaluate the performance of the GeneXpert HIV-1 qualitative assay (Xpert EID) as a consecutive test for infants with an 'HIV-detected' polymerase chain reaction screening test at birth. METHODS We retrospectively analysed a longitudinal cohort of HIV-exposed infants on whom birth testing was performed, using whole-blood ethylenediaminetetra-acetic acid samples, from four tertiary sites in Gauteng Province between June 2014 and December 2019. Birth samples from all infants with a Cobas AmpliPrep/Cobas TaqMan HIV-1 Qualitative Test v2.0 (CAP/CTM v2.0) HIV-detected screening test, a concurrent Xpert EID test and a subsequent confirmatory CAP/CTM v2.0 test on a separate specimen were included. Performance of the Xpert EID in predicting final HIV status was determined as proportions with 95% confidence intervals (CIs). A comparison of indeterminate CAP/CTM v2.0 results, as per National Health Laboratory Service resulting practice, with discordant CAP/CTM v2.0 v. Xpert EID results was performed. RESULTS Of 150 infants who met the inclusion criteria, 6 (3.9%) had an Xpert EID result discordant with final HIV status: 5 (3.3%) were false negatives and 1 (0.7%) was false positive. As a consecutive test, the Xpert EID yielded a sensitivity of 96.5% (95% CI 92 - 98.9), specificity of 85.7% (95% CI 42.1 - 99.6), PPV of 99.3% (95% CI 95.7 - 99.9), negative predictive value of 54.5% (95% CI 32.5 - 74.9) and overall accuracy of 96.1% (95% CI 91.5 - 98.5). Using discordant CAP/CTM v2.0/Xpert EID results as criteria to verify indeterminate results instead of current practice would have reduced the number of indeterminate screening results by 42.1%, from 18 (12.6%) to 11 (7.2%), without increasing the false-positive rate. CONCLUSIONS Addition of the Xpert EID as a consecutive test for specimens with an HIV-detected PCR screening result has the potential to improve the PPV and reduce the indeterminate rate, thereby reducing diagnostic challenges and time to final status, in SA's EID programme.
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Affiliation(s)
- A Mukendi
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
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25
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Govender Y, Shalekoff S, Ebrahim O, Waja Z, Chaisson RE, Martinson N, Tiemessen CT. Systemic DPP4/CD26 is associated with natural HIV-1 control: Implications for COVID-19 susceptibility. Clin Immunol 2021; 230:108824. [PMID: 34391936 PMCID: PMC8360992 DOI: 10.1016/j.clim.2021.108824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/18/2021] [Accepted: 08/10/2021] [Indexed: 01/20/2023]
Abstract
The current intersection of the COVID-19 and HIV-1 pandemics, has raised concerns about the risk for poor COVID-19 outcomes particularly in regions like sub-Saharan Africa, disproportionally affected by HIV. DPP4/CD26 has been suggested to be a potential therapeutic target and a biomarker for risk in COVID-19 patients with high risk co-morbidities. We therefore evaluated soluble DPP4 (sDPP4) levels and activity in plasma of 131 HIV-infected and 20 HIV-uninfected South African individuals. Flow cytometry was performed to compare cell surface expression of DPP4/CD26 and activation markers on peripheral blood mononuclear cells of extreme clinical phenotypes. Progressors had lower specific DPP4 activity and lower frequency of CD3+ T-cells expressing CD26 than HIV-1 controllers, but more activated CD3+CD26+ T-cells. The frequency of CD26-expressing T-cells negatively correlated with HLA-DR+ and CD38+ T-cells. Divergent DPP4/CD26 expression between HIV-1 controllers and progressors may have implications for risk and treatment of COVID-19 in people living with HIV.
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Affiliation(s)
- Yashini Govender
- Centre for HIV & STIs, National Institute for Communicable Diseases, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sharon Shalekoff
- Centre for HIV & STIs, National Institute for Communicable Diseases, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Osman Ebrahim
- Department of Therapeutic Sciences, Division of Pharmacology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Ziyaad Waja
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Medical Research Council Soweto Matlosana Centre for HIV/AIDS and TB Research, South Africa
| | - Richard E Chaisson
- Johns Hopkins University Centre for AIDS Research, Baltimore, MD, United States
| | - Neil Martinson
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Medical Research Council Soweto Matlosana Centre for HIV/AIDS and TB Research, South Africa
| | - Caroline T Tiemessen
- Centre for HIV & STIs, National Institute for Communicable Diseases, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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26
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Kuhn L, Paximadis M, Da Costa Dias B, Shen Y, Mncube S, Strehlau R, Shiau S, Patel F, Burke M, Technau KG, Sherman G, Loubser S, Abrams EJ, Tiemessen CT. Predictors of cell-associated HIV-1 DNA over one year in very early treated infants. Clin Infect Dis 2021; 74:1047-1054. [PMID: 34185838 DOI: 10.1093/cid/ciab586] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Younger age of antiretroviral therapy (ART) initiation is associated with a smaller viral reservoir size in perinatally-acquired HIV-1 infection, but there is wide variability among early-treated infants. Predictors of this variability are not fully described. METHODS Sixty-three neonates diagnosed with HIV-1 <48 hours after birth in Johannesburg, South Africa were started on ART as soon as possible. Fifty-nine (94%) infants received daily nevirapine prophylaxis from birth until ART start. Viably-preserved peripheral blood mononuclear cells (PBMC) collected at regular intervals to 48 weeks, and from respective mothers at enrolment, were tested using integrase-targeted, semi-nested, real-time quantitative hydrolysis probe (TaqMan) PCR assays to quantify total HIV-1 subtype C viral DNA (vDNA). Predictors were investigated using Generalized Estimating Equation (GEE) regression models. RESULTS Thirty-one (49.2%) infants initiated ART <48 hours, 24 (38.1%) <14 days and 8 (12.7%) >14 days of birth. Three-quarters were infected despite maternal antenatal ART (however, only 9.5% of women had undetectable viral load closest to delivery) and 86% were breastfed. Higher infant CD4+ T-cell percentage and viral load <100,000 copies/ml pre-ART were associated with lower levels of vDNA copies/10 6 PBMC equivalents in the first 48 weeks after ART start. No antenatal maternal ART and breastfeeding were also associated with lower vDNA. Older age at ART initiation had a discernible negative impact when initiated >14 days. CONCLUSIONS Among very early treated infants, higher CD4+ T-cell percentage and viral load <100,000 copies/ml pre-ART, infection occurring in the absence of maternal antenatal ART and breastfeeding were associated with lower levels of HIV-1 DNA in the first 48 weeks of treatment.
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Affiliation(s)
- Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.,Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, USA
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bianca Da Costa Dias
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Sizanani Mncube
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
| | - Faeezah Patel
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Wits Reproductive Health and HIV Institute (WRHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Megan Burke
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Karl-Günter Technau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gayle Sherman
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Elaine J Abrams
- ICAP at Columbia University, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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27
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Shiau S, Strehlau R, Shen Y, He Y, Patel F, Burke M, Abrams EJ, Tiemessen CT, Wang S, Kuhn L. Virologic Response to Very Early HIV Treatment in Neonates. J Clin Med 2021; 10:jcm10102074. [PMID: 34066021 PMCID: PMC8151270 DOI: 10.3390/jcm10102074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022] Open
Abstract
Factors that influence viral response when antiretroviral therapy (ART) is initiated in neonates are not well characterized. We assessed if there is consistency in predictive factors when operationalizing viral response using different methods. Data were collected from a clinical study in South Africa that started ART in neonates within 14 days of birth (2013–2018). Among 61 infants followed for ≥48 weeks after ART initiation, viral response through 72 weeks was defined by three methods: (1) clinical endpoints (virologic success, rebound, and failure); (2) time to viral suppression, i.e., any viral load (VL: copies/mL) <400, <50, or target not detected (TND) using time-to-event methods; and (3) latent class growth analysis (LCGA) to empirically estimate discrete groups with shared patterns of VL trajectories over time. We investigated the following factors: age at ART initiation, sex, birthweight, preterm birth, mode of delivery, breastfeeding, pre-treatment VL and CD4, maternal ART during pregnancy, and maternal VL and CD4 count. ART was initiated 0–48 h of birth among 57.4% of the infants, 48 h–7 days in 29.5% and 8–14 days in 13.1%. By Method 1, infants were categorized into ‘success’ (54.1%), ‘rebound’ (21.3%), and ‘failure’ (24.6%) for viral response. For Method 2, median time to achieving a VL <400, <50, or TND was 58, 123, and 331 days, respectively. For Method 3, infants were categorized into three trajectories: ‘rapid decline’ (29.5%), ‘slow decline’ (47.5%), and ‘persistently high’ (23.0%). All methods found that higher pre-treatment VL, particularly >100,000, was associated with less favorable viral outcomes. No exposure to maternal ART was associated with a better viral response, while a higher maternal VL was associated with less favorable viral response and higher maternal CD4 was associated with better viral response across all three methods. The LCGA method found that infants who initiated ART 8–14 days had less favorable viral response than those who initiated ART earlier. The other two methods trended in a similar direction. Across three methods to operationalize viral response in the context of early infant treatment, findings of factors associated with viral response were largely consistent, including infant pre-treatment VL, maternal VL, and maternal CD4 count.
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Affiliation(s)
- Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ 08854, USA
- Correspondence: ; Tel.: +1-732-235-9104
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2112, South Africa; (R.S.); (F.P.); (M.B.)
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Y.S.); (L.K.)
| | - Yun He
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (Y.H.); (S.W.)
| | - Faeezah Patel
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2112, South Africa; (R.S.); (F.P.); (M.B.)
| | - Megan Burke
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2112, South Africa; (R.S.); (F.P.); (M.B.)
| | - Elaine J. Abrams
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA;
- ICAP at Columbia University, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
- Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa;
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (Y.H.); (S.W.)
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Y.S.); (L.K.)
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA;
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Shalekoff S, Loubser S, Dias BDC, Strehlau R, Shiau S, Wang S, He Y, Abrams EJ, Kuhn L, Tiemessen CT. Normalization of B Cell Subsets but Not T Follicular Helper Phenotypes in Infants With Very Early Antiretroviral Treatment. Front Pediatr 2021; 9:618191. [PMID: 33996678 PMCID: PMC8118125 DOI: 10.3389/fped.2021.618191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: Infant HIV-1-infection is associated with high morbidity and mortality if antiretroviral treatment (ART) is not initiated promptly. We characterized development of circulating T follicular helper cells (cTfh) and their relationship to naïve/memory B cell subsets in a cohort of neonates initiating ART within the first week of life. Methods: Infants were diagnosed within 48 hours of birth and started ART as soon as possible. The frequency and phenotype of cTfh and B cells were analyzed at enrollment (birth -19 days) and at 4, 12, and 72 weeks of age in blood of 27 HIV-1-intrauterine-infected and 25 HIV-1 exposed uninfected (HEU) infants as part of a study in Johannesburg, South Africa. cTfh cells were divided into Tfh1, Tfh2, and Tfh17 subsets. B cell phenotypes were defined as naïve, resting memory, activated memory and tissue-like memory cells. Results: HIV-1-infected infants had higher frequencies of cTfh cells than HEU infants up to 12 weeks of age and these cTfh cells were polarized toward the Tfh1 subset. Higher frequencies of Tfh1 and lower frequencies of Tfh2 and Tfh17 correlated with lower CD4+ T cell percentages. Lower frequencies of resting memory, with corresponding higher frequencies of activated memory B cells, were observed with HIV-1 infection. Importantly, dysregulations in B cell, but not cTfh cell, subsets were normalized by 72 weeks. Conclusion: Very early ART initiation in HIV-1-infected infants normalizes B cell subsets but does not fully normalize perturbations in cTfh cell subsets which remain Tfh1 polarized at 72 weeks. It remains to be determined if very early ART improves vaccine antibody responses despite the cTfh and B cell perturbations observed over the time course of this study.
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Affiliation(s)
- Sharon Shalekoff
- Centre for HIV & STIs, National Institute for Communicable Diseases and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shayne Loubser
- Centre for HIV & STIs, National Institute for Communicable Diseases and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bianca Da Costa Dias
- Centre for HIV & STIs, National Institute for Communicable Diseases and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, United States
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York City, NY, United States
| | - Yun He
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York City, NY, United States
| | - Elaine J. Abrams
- ICAP at Columbia University, Mailman School of Public Health, and Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York City, NY, United States
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York City, NY, United States
| | - Caroline T. Tiemessen
- Centre for HIV & STIs, National Institute for Communicable Diseases and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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da Rocha JEB, Othman H, Botha G, Cottino L, Twesigomwe D, Ahmed S, Drögemöller BI, Fadlelmola FM, Machanick P, Mbiyavanga M, Panji S, Wright GEB, Adebamowo C, Matshaba M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Baldwin S, Chiano M, Cox C, Gross AS, Thomas P, Gamo FJ, Hazelhurst S. The Extent and Impact of Variation in ADME Genes in Sub-Saharan African Populations. Front Pharmacol 2021; 12:634016. [PMID: 34721006 PMCID: PMC8549571 DOI: 10.3389/fphar.2021.634016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/10/2021] [Indexed: 01/13/2023] Open
Abstract
Introduction: Investigating variation in genes involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs are key to characterizing pharmacogenomic (PGx) relationships. ADME gene variation is relatively well characterized in European and Asian populations, but data from African populations are under-studied-which has implications for drug safety and effective use in Africa. Results: We identified significant ADME gene variation in African populations using data from 458 high-coverage whole genome sequences, 412 of which are novel, and from previously available African sequences from the 1,000 Genomes Project. ADME variation was not uniform across African populations, particularly within high impact coding variation. Copy number variation was detected in 116 ADME genes, with equal ratios of duplications/deletions. We identified 930 potential high impact coding variants, of which most are discrete to a single African population cluster. Large frequency differences (i.e., >10%) were seen in common high impact variants between clusters. Several novel variants are predicted to have a significant impact on protein structure, but additional functional work is needed to confirm the outcome of these for PGx use. Most variants of known clinical outcome are rare in Africa compared to European populations, potentially reflecting a clinical PGx research bias to European populations. Discussion: The genetic diversity of ADME genes across sub-Saharan African populations is large. The Southern African population cluster is most distinct from that of far West Africa. PGx strategies based on European variants will be of limited use in African populations. Although established variants are important, PGx must take into account the full range of African variation. This work urges further characterization of variants in African populations including in vitro and in silico studies, and to consider the unique African ADME landscape when developing precision medicine guidelines and tools for African populations.
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Affiliation(s)
- Jorge E. B. da Rocha
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Laura Cottino
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Samah Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Britt I. Drögemöller
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Faisal M. Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Philip Machanick
- Department of Computer Science, Rhodes University, Makhanda, South Africa
| | - Mamana Mbiyavanga
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Sumir Panji
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Galen E. B. Wright
- Neuroscience Research Program, Winnipeg Health Sciences Centre and Max Rady College of Medicine, Kleysen for Advanced Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Clement Adebamowo
- Institute for Human Virology, Abuja, Nigeria
- Institute of Human Virology and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Center of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, TX, United States
| | - Michéle Ramsay
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Martin C. Simuunza
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sandra Baldwin
- Drug Metabolism and Pharmacokinetics, GlaxoSmithKline R&D, Ware, United Kingdom
| | - Mathias Chiano
- Human Genetics, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Charles Cox
- Human Genetics, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Annette S. Gross
- Clinical Pharmacology Modelling and Simulation, GlaxoSmithKline R&D, Sydney, NSW, Australia
| | - Pamela Thomas
- Data and Computational Sciences, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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30
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Loubser S, Da Costa Dias B, Shalekoff S, Gentle NL, Tiemessen CT. Lack of association of KIR2DL1-R 245 and KIR2DL1-C 245 with HIV-1 control in black South Africans with HLA-C2. Hum Immunol 2021; 82:600-607. [PMID: 33906789 DOI: 10.1016/j.humimm.2021.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 11/30/2022]
Abstract
Activating/inhibitory Killer-cell Immunoglobulin-like Receptors (KIRs) partly regulate Natural Killer (NK) cells. KIR2DL1 allotypes with cysteine at position-245 (KIR2DL1-C245) express at lower levels and demonstrate weaker inhibitory signaling compared to allotypes with arginine at position-245 (KIR2DL1-R245). The functional consequence of either allotype in infectious diseases is unknown. Since NK cells mediate antiviral immunity, we investigated KIR2DL1-R245 and KIR2DL1-C245 in association with HIV-1 virological control in untreated immunocompetent black South Africans. Allotype carriage, determined by KIR2DL1 sequencing, was similar between uninfected South Africans (n = 104) and other black African populations, but differed significantly from Europeans, while no significant differences were noted between uninfected and HIV-1-infected individuals (n = 52). KIR2DL1 expression, measured by flow cytometry, in uninfected individuals showed higher KIR2DL1-R245 expression compared to KIR2DL1-C245 in white donors (n = 27), while black donors (n = 21) generally expressed lower levels of both allotypes. KIR2DL1 expression was reduced in HLA-C2 carriers, most evident in black HLA-C2/C2 donors. KIR2DL1-R245 and KIR2DL1-C245 did not associate with viral load when HLA-C2 ligands were present, however in HLA-C1 homozygotes, individuals with only KIR2DL1-R245, showed lower viral loads compared to carriers of both allotypes. The lack of association of KIR2DL1-R245 or KIR2DL1-C245 with HIV-1 control in HLA-C2 carriers may relate to lower KIR2DL1 expression levels in a population with high HLA-C2 prevalence.
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Affiliation(s)
- Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Bianca Da Costa Dias
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Sharon Shalekoff
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Nikki L Gentle
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa.
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31
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Paximadis M, Picton ACP, Sengupta D, Ramsay M, Puren A, Tiemessen CT. Interleukin-8 genetic diversity, haplotype structure and production differ in two ethnically distinct South African populations. Cytokine 2021; 143:155489. [PMID: 33814271 DOI: 10.1016/j.cyto.2021.155489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/14/2020] [Accepted: 02/28/2021] [Indexed: 11/16/2022]
Abstract
A single nucleotide polymorphism (SNP), 251 bases upstream from the IL-8 transcription start (-251A>T, rs4073), has been extensively investigated in cancers and inflammatory and infectious diseases in predominantly European and Asian populations. We sequenced the IL-8 gene of 109 black and 32 white South African (SA) individuals and conducted detailed characterization of gene variation and haplotype structure. IL-8 production in phytohaemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) of a subset (black: N = 22; white: N = 32) of these individuals was measured using ELISA. Select variants were genotyped for additional black individuals (N = 141), and data from the 1000 Genomes Project were used for haplotype analysis and comparative purposes. In white individuals, the -251A>T SNP formed part of a prevalent six-variant haplotype [haplotype frequency (HF): 61%], Hap-1C, involving the following variants: -251A>T; +394T>G (rs2227307); +780C>T (rs2227306); +1240->A (rs2227541); +1635C>T (rs2227543) and +2770A>T (rs2227543). Hap-1C (-251T+394T+780C+1240+A+1635C+2770A) was composed of two three-variant sub-haplotypes [Hap-1Ca: -251T+394T+1240+A; Hap-1Cb: +780C+1635C+2770A) sharing similarities with haplotypes identified in the black population. Hap-1C was found to be present in European, East and South Asian populations. Four haplotypes were identified in the black population with the two prevalent haplotypes each comprised of two variants: Hap-1B [-251A>T and +1240->A; -251T+1240+A; HF: 14%] and Hap-2B [-743T>C (rs2227532) and +2452A>C (rs2227545); -743C+2452C; HF: 13%]. Populations did not differ in unstimulated PBMC IL-8 production. Upon PHA stimulation, PBMCs from white individuals produced more IL-8 (P = 0.04), suggesting the -251T allele is responsible for higher production, however further analysis revealed that Hap-1C (and constituent sub-haplotypes), did not associate with IL-8 production. Populations did however differ in monocyte number with the white population having significantly more monocytes compared to the black population (P = 0.025), and furthermore monocyte number strongly correlated with IL-8 production in both population groups (black: p = 0.0002, r = 0.71; white: P = 0.0005, r = 0.59). Hap-1B, Hap-2B, and a SNP located one base pair upstream of the IL-8 ATG start codon, +100C>T SNP (rs2227538), all associated with higher IL-8 production in the black population - individuals harbouring at least one of these haplotypes/variant associated with higher IL-8 production (P = 0.003) compared to individuals without. The black population was enriched for individuals harbouring Hap-1B and/or Hap-2B compared to the 1000 Genomes project sub-Saharan African population (P = 0.006), suggesting that SA black individuals may be high IL-8 producers. Given the paucity of IL-8-related studies that have been conducted in populations from sub-Saharan Africa, this study has significantly increased our understanding of this important chemokine in the South African population.
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Affiliation(s)
- Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Anabela C P Picton
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adrian Puren
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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32
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Affiliation(s)
- Caroline T Tiemessen
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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33
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Glanzmann B, Jooste T, Ghoor S, Gordon R, Mia R, Mao J, Li H, Charls P, Douman C, Kotze MJ, Peeters AV, Loots G, Esser M, Tiemessen CT, Wilkinson RJ, Louw J, Gray G, Warren RM, Möller M, Kinnear C. Human whole genome sequencing in South Africa. Sci Rep 2021; 11:606. [PMID: 33436733 PMCID: PMC7803990 DOI: 10.1038/s41598-020-79794-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/08/2020] [Indexed: 12/26/2022] Open
Abstract
The advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council’s Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.
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Affiliation(s)
- Brigitte Glanzmann
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Tracey Jooste
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town, South Africa.,Division of Medical Physiology Faculty of Medicine and Health Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Samira Ghoor
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Richard Gordon
- Grants, Innovation and Product Development, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Rizwana Mia
- Grants, Innovation and Product Development, South African Medical Research Council, Tygerberg, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Jun Mao
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Yantian District, Shenzhen, 518083, China.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Hao Li
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Yantian District, Shenzhen, 518083, China
| | - Patrick Charls
- Information Technology Services Division, South African Medical Research Council, Cape Town, South Africa
| | - Craig Douman
- Information Technology Services Division, South African Medical Research Council, Cape Town, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Armand V Peeters
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Glaudina Loots
- South African National Department of Science and Innovation, Pretoria, South Africa
| | - Monika Esser
- Department of Pathology, Division Medical Microbiology and Immunology, Faculty of Medicine and Health Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, South Africa.,Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK.,The Francis Crick Institute, London, NW1 1AT, UK
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Glenda Gray
- Office of the President, South African Medical Research Council, Cape Town, South Africa.,Perinatal HIV Research Unit, Faculty of Clinical Medicine, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - Robin M Warren
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa
| | - Craig Kinnear
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa. .,Genomics Centre, South African Medical Research Council, Tygerberg, Cape Town, South Africa.
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Patel F, Shiau S, Strehlau R, Shen Y, Burke M, Paximadis M, Shalekoff S, Schramm D, Technau KG, Sherman GG, Coovadia A, Tiemessen CT, Abrams EJ, Kuhn L. Low Pretreatment Viral Loads in Infants With HIV in an Era of High-maternal Antiretroviral Therapy Coverage. Pediatr Infect Dis J 2021; 40:55-59. [PMID: 32925542 PMCID: PMC7722046 DOI: 10.1097/inf.0000000000002897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND With expansion of antiretroviral therapy (ART) programs, transmission rates are low but new infant infections still occur. We investigated predictors of pre-ART viral load (VL) and CD4+ T-cell counts and percentages in infants diagnosed with HIV at birth in a setting with high coverage of maternal ART and infant prophylaxis. METHODS As part of an early treatment study, 97 infants with confirmed HIV-infection were identified at a hospital in Johannesburg, South Africa. Infant VL and CD4+ T-cell parameters were measured before ART initiation. Data were collected on maternal characteristics, including VL, CD4+ T-cell counts and ART, and infant characteristics, including sex, birth weight, and mode of delivery. RESULTS Pre-ART, median infant VL was 28,405 copies/mL [interquartile range (IQR): 2515-218,150], CD4+ T-cell count 1914 cells/mm (IQR: 1474-2639) and percentage 40.8% (IQR: 32.2-51.2). Most (80.4%) infants were born to mothers who received ART during pregnancy and 97.9% of infants received daily nevirapine prophylaxis until ART initiation at median of 2 days of age (IQR: 1-7). Infant pre-ART VL was more likely to be ≥1000 copies/mL when their mothers had VL ≥1000 copies/mL [Odds Ratio (OR): 6.88, 95% confidence interval (CI): 2.32-20.41] and was higher in boys than girls (OR: 3.29, 95% CI: 1.07-9.95). Lower maternal CD4+ T-cell count (<350 cells/mm) was associated with lower infant CD4+ T-cell count (<1500 cells/mm) (OR: 3.59, 95% CI: 1.24-10.43). CONCLUSIONS Pre-ART VL and CD4+ T-cell parameters of intrauterine-infected infants were associated with VL and CD4+ T-cell counts of their mothers. Maternal ART during pregnancy may begin treatment of intrauterine infection and may mask the severity of disease in infected infants identified in the current era with high-maternal ART coverage.
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Affiliation(s)
- Faeezah Patel
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Megan Burke
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sharon Shalekoff
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Diana Schramm
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Karl-Günter Technau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gayle G. Sherman
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ashraf Coovadia
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Elaine J. Abrams
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- ICAP at Columbia University, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Louise Kuhn
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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Seedat F, James I, Loubser S, Waja Z, Mallal SA, Hoffmann C, Tiemessen CT, Chaisson RE, Martinson NA. Human leukocyte antigen associations with protection against tuberculosis infection and disease in human immunodeficiency virus-1 infected individuals, despite household tuberculosis exposure and immune suppression. Tuberculosis (Edinb) 2021; 126:102023. [PMID: 33249336 DOI: 10.1016/j.tube.2020.102023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/04/2020] [Accepted: 11/15/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND To determine the association of human leukocyte antigen (HLA) alleles as correlates of risk for and protection against tuberculin skin test (TST) positivity and active TB disease amongst HIV-infected adults. METHODS Genomic DNA was extracted from 754 HIV-infected adults whole-blood. HLA-A, -B, -C and -DRB1 loci were genotyped by next generation sequencing methods. HLA alleles were analysed by the presence/absence of TST immune conversion and active TB disease and further stratified by exposure to a household TB contact, CD4+ T-cell count and, for active TB disease, TST-positivity. RESULTS HLA-A*29:11 and - B*45:01/07 were associated with TST-positivity, while HLA-A*24:02, -A*29:02 and -B*15:16 with TST-negativity. In participants with a household TB contact, HLA-A*66:01, -A*68:02 and -B*49:01 were associated with TST-negativity. For TB disease, HLA-B*41:01, -C*06:02, -DRB1*04:01 and -DRB1*15:01 were associated with susceptibility, while HLA-B*07:02 and -DRB1*11:01 were protective, even for CD4+ T-cell count <350 cells/mm3. For initial TST-positivity and subsequent TB disease, HLA-A*01:01 and -DRB1*11:01 conveyed protection including for those with CD4+ T-cell count <350 cells/mm3. CONCLUSION Several HLA alleles are noted as correlates of TB infection, risk and natural protection in HIV-infected individuals. HLA associations may enable risk stratification of those with HIV infection. Protective alleles may assist in future TB vaccine development.
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Affiliation(s)
- Faheem Seedat
- Department of Internal Medicine, Klerksdorp Tshepong Hospital Complex, Benji Oliphant Road, North West Province Department of Health, University of the Witwatersrand, South Africa.
| | - Ian James
- Institute for Immunology and Infectious Diseases, 90 South Street, Murdoch University, Western Australia, Australia
| | - Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road and Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg, South Africa
| | - Ziyaad Waja
- Perinatal HIV Research Unit (PHRU), MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, Chris Hani Road, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, South Africa
| | - Simon A Mallal
- Department of Pathology, Microbiology and Immunology, 2201, West End Avenue, Vanderbilt University, Nashville, TN, USA
| | - Christopher Hoffmann
- Johns Hopkins University Centre for TB Research, Charles Street, John Hopkins University, Baltimore, MD, USA
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road and Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg, South Africa
| | - Richard E Chaisson
- Johns Hopkins University Centre for TB Research, Charles Street, John Hopkins University, Baltimore, MD, USA
| | - Neil A Martinson
- Perinatal HIV Research Unit (PHRU), MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, Chris Hani Road, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, South Africa
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Kannambath S, Jarvis JN, Wake RM, Longley N, Loyse A, Matzaraki V, Aguirre-Gamboa R, Wijmenga C, Doyle R, Paximadis M, Tiemessen CT, Kumar V, Pittman A, Meintjes G, Harrison TS, Netea MG, Bicanic T. Genome-Wide Association Study Identifies Novel Colony Stimulating Factor 1 Locus Conferring Susceptibility to Cryptococcosis in Human Immunodeficiency Virus-Infected South Africans. Open Forum Infect Dis 2020; 7:ofaa489. [PMID: 33269293 PMCID: PMC7686661 DOI: 10.1093/ofid/ofaa489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/12/2020] [Indexed: 12/31/2022] Open
Abstract
Background Cryptococcus is the most common cause of meningitis in human immunodeficiency virus (HIV)-infected Africans. Despite universal exposure, only 5%-10% of patients with HIV/acquired immune deficiency syndrome and profound CD4+ T-cell depletion develop disseminated cryptococcosis: host genetic factors may play a role. Prior targeted immunogenetic studies in cryptococcosis have comprised few Africans. Methods We analyzed genome-wide single-nucleotide polymorphism (SNP) genotype data from 524 patients of African descent: 243 cases (advanced HIV with cryptococcal antigenemia and/or cryptococcal meningitis) and 281 controls (advanced HIV, no history of cryptococcosis, negative serum cryptococcal antigen). Results Six loci upstream of the colony-stimulating factor 1 (CSF1) gene, encoding macrophage colony-stimulating factor (M-CSF) were associated with susceptibility to cryptococcosis at P < 10-6 and remained significantly associated in a second South African cohort (83 cases; 128 controls). Meta-analysis of the genotyped CSF1 SNP rs1999713 showed an odds ratio for cryptococcosis susceptibility of 0.53 (95% confidence interval, 0.42-0.66; P = 5.96 × 10-8). Ex vivo functional validation and transcriptomic studies confirmed the importance of macrophage activation by M-CSF in host defence against Cryptococcus in HIV-infected patients and healthy, ethnically matched controls. Conclusions This first genome-wide association study of susceptibility to cryptococcosis has identified novel and immunologically relevant susceptibility loci, which may help define novel strategies for prevention or immunotherapy of HIV-associated cryptococcal meningitis.
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Affiliation(s)
- Shichina Kannambath
- Institute of Infection and Immunity, St George's University of London, London, United Kingdom.,National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Joseph N Jarvis
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Rachel M Wake
- Institute of Infection and Immunity, St George's University of London, London, United Kingdom.,Clinical Academic Group in Infection, St George's Hospital NHS Trust, London, United Kingdom
| | - Nicky Longley
- Institute of Infection and Immunity, St George's University of London, London, United Kingdom
| | - Angela Loyse
- Institute of Infection and Immunity, St George's University of London, London, United Kingdom
| | - Vicky Matzaraki
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Raúl Aguirre-Gamboa
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Ronan Doyle
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vinod Kumar
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University, Nijmegen, the Netherlands
| | - Alan Pittman
- Institute of Infection and Immunity, St George's University of London, London, United Kingdom
| | - Graeme Meintjes
- Department of Medicine and Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Thomas S Harrison
- Institute of Infection and Immunity, St George's University of London, London, United Kingdom.,Clinical Academic Group in Infection, St George's Hospital NHS Trust, London, United Kingdom.,Department of Medicine and Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University, Nijmegen, the Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Tihana Bicanic
- Institute of Infection and Immunity, St George's University of London, London, United Kingdom.,Clinical Academic Group in Infection, St George's Hospital NHS Trust, London, United Kingdom
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Ravimohan S, Maenetje P, Auld SC, Ncube I, Mlotshwa M, Chase W, Tiemessen CT, Vangu MDT, Wallis RS, Churchyard G, Weissman D, Kornfeld H, Bisson GP. A Common NLRC4 Gene Variant Associates With Inflammation and Pulmonary Function in Human Immunodeficiency Virus and Tuberculosis. Clin Infect Dis 2020; 71:924-932. [PMID: 31751447 PMCID: PMC7428399 DOI: 10.1093/cid/ciz898] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/27/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Inflammasomes mediate inflammation in adults living with both human immunodeficiency virus (HIV) and tuberculosis (TB), but the relevance of inflammasome gene polymorphisms in TB-associated pulmonary damage is unknown. We hypothesized that functional single-nucleotide polymorphisms (SNPs) in inflammasome pathway genes modify systemic and pulmonary inflammation, contributing to respiratory impairment in adults living with HIV/pulmonary TB. METHODS This was a prospective cohort study set in South Africa following individuals living with HIV/TB up to 48 weeks post-antiretroviral therapy (ART) initiation. Ten functional SNPs in 5 inflammasome pathway genes were related to circulating inflammatory biomarkers and lung function assessed by spirometry pre- and post-ART initiation. Analyses used 2-sided t tests, Wilcoxon rank sum tests, Spearman correlation coefficients, linear regression, and generalized estimating equation models. RESULTS Among 102 patients with baseline samples, the minor allele (T) in NLRC4 rs385076 was independently associated with lower levels of interleukin (IL)-18 and IL-6 before and up to 12 weeks post-ART initiation (Benjamini-Hochberg corrected P values < .02). Patients with the CT/TT genotypes also had improved lung function vs CC patients up to 48 weeks post-ART initiation (forced vital capacity, 206 mL higher; 95% confidence interval [CI], 67-345 mL; P = .004 and forced expiratory volume in 1 second, 143 mL higher; 95% CI, 11-274 mL; P = .034). CONCLUSIONS A common SNP in the NLRC4 inflammasome may modify TB-associated inflammation in clinically relevant ways. This SNP may identify high-risk groups for lung damage in TB. Inhibition of NLRC4 activity may be an important approach for TB host-directed therapy.
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Affiliation(s)
- Shruthi Ravimohan
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Sara C Auld
- Department of Medicine, Emory University Rollins School of Public Health and School of Medicine, Atlanta, Georgia, USA, Johannesburg, South Africa
| | - Itai Ncube
- The Aurum Institute, Johannesburg, South Africa
| | | | - William Chase
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Caroline T Tiemessen
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mboyo-Di-Tamba Vangu
- Nuclear Medicine, CM Johannesburg Academic Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Gavin Churchyard
- The Aurum Institute, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Drew Weissman
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Gregory P Bisson
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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da Rocha J, Othman H, Tiemessen CT, Botha G, Ramsay M, Masimirembwa C, Adebamowo C, Choudhury A, Brandenburg JT, Matshaba M, Simo G, Gamo FJ, Hazelhurst S. G6PD variant distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19. medRxiv 2020:2020.05.27.20114066. [PMID: 32577690 PMCID: PMC7302299 DOI: 10.1101/2020.05.27.20114066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chloroquine/hydroxychloroquine have been proposed as potential treatments for COVID-19. These drugs have warning labels for use in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Analysis of whole-genome sequence data of 458 individuals from sub-Saharan Africa showed significant G6PD variation across the continent. We identified nine variants, of which four are potentially deleterious to G6PD function, and one (rs1050828) that is known to cause G6PD deficiency. We supplemented data for the rs1050828 variant with genotype array data from over 11,000 Africans. Although this variant is common in Africans overall, large allele frequency differences exist between sub-populations. African sub-populations in the same country can show significant differences in allele frequency (e.g. 16.0% in Tsonga vs 0.8% in Xhosa, both in South Africa, ρ=2.4×10 -3 ). The high prevalence of variants in the G6PD gene found in this analysis suggests that it may be a significant interaction factor in clinical trials of chloroquine and hydrochloroquine for treatment of COVID-19 in Africans.
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Affiliation(s)
- Jorge da Rocha
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg South Africa
| | - Gerrit Botha
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Collen Masimirembwa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clement Adebamowo
- Institute for Human Virology, Abuja, Nigeria
- Institute of Human Virology and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Center of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, United States
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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Wake RM, Govender NP, Omar T, Nel C, Mazanderani AH, Karat AS, Ismail NA, Tiemessen CT, Jarvis JN, Harrison TS. Cryptococcal-related Mortality Despite Fluconazole Preemptive Treatment in a Cryptococcal Antigen Screen-and-Treat Program. Clin Infect Dis 2020; 70:1683-1690. [PMID: 31179488 PMCID: PMC7346756 DOI: 10.1093/cid/ciz485] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/07/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cryptococcal antigen (CrAg) screening and treatment with preemptive fluconazole reduces the incidence of clinically evident cryptococcal meningitis in individuals living with advanced human immunodeficiency virus (HIV) disease. However, mortality remains higher in CrAg-positive than in CrAg-negative patients with similar CD4+ T-lymphocyte counts. METHODS We conducted a cohort study to investigate causes of morbidity and mortality during 6 months of follow-up among asymptomatic CrAg-positive and CrAg-negative (ratio of 1:2) patients living with HIV with CD4 counts <100 cells/µL attending 2 hospitals in Johannesburg, South Africa. When possible, minimally invasive autopsy (MIA) was performed on participants who died. RESULTS Sixty-seven CrAg-positive and 134 CrAg-negative patients were enrolled. Death occurred in 17/67 (25%) CrAg-positive and 12/134 (9%) CrAg-negative participants (hazard ratio for death, adjusted for CD4 count, 3.0; 95% confidence interval, 1.4-6.7; P = .006). Cryptococcal disease was an immediate or contributing cause of death in 12/17 (71%) CrAg-positive participants. Postmortem cryptococcal meningitis and pulmonary cryptococcosis were identified at MIA in all 4 CrAg-positive participants, 3 of whom had negative cerebrospinal fluid CrAg tests from lumbar punctures (LPs) at the time of CrAg screening. CONCLUSIONS Cryptococcal disease was an important cause of mortality among asymptomatic CrAg-positive participants despite LPs to identify and treat those with subclinical cryptococcal meningitis and preemptive fluconazole for those without meningitis. Thorough investigation for cryptococcal disease with LPs and blood cultures, prompt ART initiation, and more intensive antifungals may reduce mortality among asymptomatic CrAg-positive patients identified through screening.
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Affiliation(s)
- Rachel M Wake
- Centre for Healthcare-associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Johannesburg, South Africa
- Institute of Infection & Immunity, St George’s University of London, United Kingdom
| | - Nelesh P Govender
- Centre for Healthcare-associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Division of Medical Microbiology, University of Cape Town, South Africa
| | - Tanvier Omar
- Department of Anatomical Pathology, University of the Witwatersrand, South Africa
- Department of Pathology, National Health Laboratory Services, South Africa
| | - Carolina Nel
- Department of Anatomical Pathology, University of the Witwatersrand, South Africa
- Department of Pathology, National Health Laboratory Services, South Africa
| | - Ahmad Haeri Mazanderani
- Centre for HIV & STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Medical Virology, University of Pretoria, South Africa
| | - Aaron S Karat
- Tuberculosis Centre, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Nazir A Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV & STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Joseph N Jarvis
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
- Botswana-UPenn Partnership, Gaborone
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Thomas S Harrison
- Institute of Infection & Immunity, St George’s University of London, United Kingdom
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Dias BDC, Paximadis M, Martinson N, Chaisson RE, Ebrahim O, Tiemessen CT. The impact of bone marrow stromal antigen-2 (BST2) gene variants on HIV-1 control in black South African individuals. Infect Genet Evol 2020; 80:104216. [PMID: 32006707 DOI: 10.1016/j.meegid.2020.104216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/24/2022]
Abstract
Bone marrow stromal cell antigen 2 (BST2 or tetherin) is a host-encoded, interferon-inducible antiviral restriction factor which blocks the release of enveloped viruses. Few studies have assessed the role of BST2 polymorphisms on HIV-1 acquisition or disease progression in sub-Saharan Africa. This study investigated the frequency of four HIV-1-associated BST2 variants rs3217318, rs12609479, rs10415893 and rs113189798 in uninfected and HIV-1 infected black South Africans. Homozygosity for the rs12609479-A minor allele, previously associated with decreased HIV-1 acquisition risk, was underrepresented in HIV-1 uninfected black South Africans (2%) compared to reference African (9%) and in particular European populations (61%) (p = .047 and p < .0001, respectively). To determine if any of these gene variants influenced HIV-1 control in the absence of antiretroviral treatment (ART), we compared HIV-1 infected ART-naïve progressors [n = 72] and controllers [n = 71], the latter includes elite controllers [EC: n = 23; VL < 50 RNA copies/ml]. Heterozygosity for the rs12609479 SNP (G/A) was enriched in progressors compared to ECs (47.2% vs 21.7%, OR = 3.50 [1.16-10.59], p = .03), while rs113189798 heterozygosity (A/G) showed a strong trend of overrepresentation in ECs compared to progressors (47.8% vs 26.4%, OR = 0.39 [0.14-1.04], p = .07). Heterozygosity for the promoter indel rs3217318 (i19/Δ19) was associated with a faster rate of CD4+ T-cell decline in progressors (p = .0134). Carriage of the rs3217318 (i19/Δ19), rs12609479 (G/G), rs10415893(G/A) and rs113189798 (A/G) combined genotype, denoted as i19Δ19 GG GA AG, was associated with significantly higher CD4+ T-cell counts in progressors (p = .03), a finding predominantly driven by the _GG_AG combination. Our data suggest that the possession of select BST2 genotype combinations may be implicated in HIV-1 disease progression and natural spontaneous control.
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Affiliation(s)
- Bianca Da Costa Dias
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Neil Martinson
- Perinatal HIV Research Unit (PHRU), SA MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa; Centre for TB Research, Johns Hopkins University, Baltimore, USA
| | | | - Osman Ebrahim
- School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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41
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Kuhn L, Strehlau R, Shiau S, Patel F, Shen Y, Technau KG, Burke M, Sherman G, Coovadia A, Aldrovandi GM, Hazra R, Tsai WY, Tiemessen CT, Abrams EJ. Early antiretroviral treatment of infants to attain HIV remission. EClinicalMedicine 2020; 18:100241. [PMID: 31993578 PMCID: PMC6978195 DOI: 10.1016/j.eclinm.2019.100241] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 11/27/2019] [Accepted: 12/11/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Studies in adults and children suggested that starting antiretroviral therapy (ART) soon after infection positively influences early events in HIV infection raising the possibility that remission may be achieved in some. METHODS We designed an analytic treatment interruption (ATI) trial to test the hypothesis that a sizable minority of HIV-infected neonates who initiated ART <14 days of birth and maintained on ART would be able to maintain viral suppression when ART was withdrawn. To yield the target cohort for this trial, 73 HIV-infected neonates identified at one hospital in Johannesburg, South Africa, were initiated on ART <14 days of birth and maintained on ART tracking viral load (VL) decline and immune recovery (clinicaltrials.gov # NCT02431975). FINDINGS Three HIV-infected infants (4.1%) died and nine (12.3%) were lost to follow-up before 48 weeks of age. Of those surviving on study, 52.5% attained and sustained VL <50 copies/ml and half of these sustained CD4+ T-cell percentage >30% which were the primary entry criteria for the ATI trial. Proportions achieving ATI eligibility criteria were similar in the 46 infants starting ART <48 h (19.6%) to 27 infants starting 2-14 days (25.9%) (p = 0.567). INTERPRETATION Very early ART on its own, using regimens available when the trial was designed, is insufficient to attain minimum entry criteria needed to justify our trial of ART interruption. Decisions about how quickly to start ART should be based on optimizing standard clinical outcomes rather than with the expectation that remission can be attained. FUNDING NICHD/NIAID (U01HD080441), South African Research Chairs Initiative of DST and NRF (South Africa).
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Affiliation(s)
- Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY 10032, United States
- Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, United States
- Corresponding author at: Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY 10032 United States.
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY 10032, United States
- Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, United States
| | - Faeezah Patel
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY 10032, United States
| | - Karl-Günter Technau
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Megan Burke
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gayle Sherman
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ashraf Coovadia
- Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Rohan Hazra
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Wei-Yann Tsai
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, United States
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Elaine J. Abrams
- Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, United States
- ICAP at Columbia University, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, United States
- Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY, United States
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Abstract
PURPOSE OF REVIEW We review the international evolution of HIV and solid organ transplantation over 30 years. We emphasise recent developments in solid organ transplantation from HIV-infected to HIV-uninfected individuals, and their implications. RECENT FINDINGS In 2017, Johannesburg, South Africa, a life-saving partial liver transplant from an HIV-infected mother to her HIV-uninfected child was performed. This procedure laid the foundation not only for consideration of HIV-infected individuals as living donors, but also for the possibility that HIV-uninfected individuals could receive organs from HIV-infected donors. Recent advances in this field are inclusion of HIV-infected individuals as living organ donors and the possibility of offering HIV-uninfected individuals organs from HIV-infected donors who are well-controlled on combination antiretroviral therapy (cART). The large number of HIV-infected individuals on cART is an unutilised source of otherwise eligible living organ donors. HIV-positive-to-HIV-negative organ transplantation has become a reality, providing possible new therapeutic options to address extreme organ shortages.
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Affiliation(s)
- Jean Botha
- Wits Donald Gordon Medical Centre, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Rd, Parktown, Johannesburg, 2193, South Africa
| | - June Fabian
- Wits Donald Gordon Medical Centre, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Rd, Parktown, Johannesburg, 2193, South Africa
| | - Harriet Etheredge
- Wits Donald Gordon Medical Centre, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Rd, Parktown, Johannesburg, 2193, South Africa
| | - Francesca Conradie
- Clinical HIV Research Unit, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Rd, Parktown, Johannesburg, 2193, South Africa
| | - Caroline T Tiemessen
- Centre for HIV & STIs, National Institute for Communicable Diseases, 1 Modderfontein Road, Sandringham, 2131, Private Bag X4, Sandringham, Johannesburg, 2131, South Africa.
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Rd, Parktown, Johannesburg, 2193, South Africa.
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Mzingwane ML, Hunt G, Lassauniere R, Kalimashe M, Bongwe A, Ledwaba J, Chaisson RE, Martinson N, Richter K, Bowyer SM, Tiemessen CT. Detection and molecular characterization of urinary tract HIV-1 populations. Ann Clin Microbiol Antimicrob 2019; 18:27. [PMID: 31551072 PMCID: PMC6760049 DOI: 10.1186/s12941-019-0326-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/16/2019] [Indexed: 11/20/2022] Open
Abstract
Background Identification of all possible HIV reservoirs is an important aspect in HIV eradication efforts. The urinary tract has however not been well studied as a potential HIV reservoir. In this pilot study we molecularly characterized HIV-1 viruses in urine and plasma samples to investigate HIV-1 replication, compartmentalization and persistence in the urinary tract. Methods Prospectively collected urine and blood samples collected over 12–36 months from 20 HIV-1 infected individuals were analysed including sampling points from prior to and after ART initiation. HIV-1 pol gene RNA and DNA from urine supernatant and urine pellets respectively were analysed and compared to plasma RNA viruses from the same individual. Results HIV-1 nucleic acid was detected in urine samples from at least one time point in 8/20 (40%) treatment-naïve subjects compared to 1/13 (7.7%) individuals on antiretroviral treatment (ART) during periods of plasma viral suppression and 1/7 (14.3%) individuals with virological failure. HIV-1 RNA was undetectable in urine samples after ART initiation but HIV-1 DNA was detectable in one patient more than 6 months after treatment initiation. There was co-clustering of urine-derived pol sequences but some urine-derived sequences were interspersed among the plasma-derived sequences. Conclusions Suppressive ART reduces HIV-1 replication in the urinary tract but HIV-1 DNA may persist in these cells despite treatment. A larger number of sequences would be required to confirm HIV compartmentalization in the urinary tract.
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Affiliation(s)
- M L Mzingwane
- Department of Pathology, Faculty of Medicine, National University of Science & Technology, Ascot, P. O Box AC 939, Bulawayo, Zimbabwe. .,Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
| | - G Hunt
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R Lassauniere
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa.,Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - M Kalimashe
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - A Bongwe
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - J Ledwaba
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - R E Chaisson
- Johns Hopkins University Center for AIDS Research, Baltimore, MD, USA
| | - N Martinson
- Perinatal HIV Research Unit (PHRU), SA MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | - K Richter
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Services Tshwane Academic Division, Pretoria, South Africa
| | - S M Bowyer
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - C T Tiemessen
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Loubser S, Kwenda S, Sengupta D, Tiemessen CT. Identification of a novel allele, HLA-DPB1*34:01:01:03, in Black South African individuals. HLA 2019; 94:547-549. [PMID: 31464043 DOI: 10.1111/tan.13681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 12/01/2022]
Abstract
Genetic characterisation of a non-coding region allelic variant, HLA-DPB1*34:01:01:03, in Black South African individuals.
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Affiliation(s)
- Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
| | - Stanford Kwenda
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa.,Sequencing Core Facility, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, Republic of South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
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45
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Loubser S, Kwenda S, Sengupta D, Tiemessen CT. Identification of a novel recombinant allele, HLA-DPB1*835:01:01:02, in Black South African individuals. HLA 2019; 94:549-551. [PMID: 31478356 DOI: 10.1111/tan.13680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 11/27/2022]
Abstract
Genetic characterisation of a novel intra-locus recombinant allele, HLA-DPB1*835:01:01:02, in Black South African individuals.
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Affiliation(s)
- Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, Republic of South Africa.,National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
| | - Stanford Kwenda
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, Republic of South Africa.,Sequencing Core Facility, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, Republic of South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, Republic of South Africa.,National Health Laboratory Service (NHLS), Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg, Republic of South Africa
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46
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Koor GW, Paximadis M, Picton ACP, Karatas F, Loubser SA, He W, Ahuja SK, Chaisson RE, Martinson N, Ebrahim O, Tiemessen CT. Cis-regulatory genetic variants in the CCR5 gene and natural HIV-1 control in black South Africans. Clin Immunol 2019; 205:16-24. [PMID: 31100442 DOI: 10.1016/j.clim.2019.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/24/2019] [Accepted: 05/13/2019] [Indexed: 12/15/2022]
Abstract
Studies have investigated CCR5 haplotypes (HHA, HHB, HHC, HHD, HHE, HHF*1, HHF*2, HHG*1, HHG*2), defined by seven 5'UTR single nucleotide polymorphisms (SNPs), CCR2-V64I and CCR5Δ32, in HIV-1 disease. CCR5 cis-regulatory regions were sequenced, CCR2-V64I and CCR5Δ32 genotyped, and compared in HIV-1-infected black South Africans: 71 HIV-1 controllers (23 elite controllers, 37 viraemic controllers (VCs), 11 high viral load long-term non-progressors) and 74 progressors. The HHE haplotype and 3'UTR +2919 T > G SNP heterozygosity were underrepresented in total controllers and VCs vs. progressors (p = .004; p = .007 and p = .002, pbonferroni = 0.032; p = .004, respectively). Possession of the +2919 T > G SNP (dominant mode) was associated with HIV-1 progression (controllers vs. progressors: p = .001, pbonferroni = 0.016). The +2919 T > G SNP is in linkage disequilibrium (LD; r2 = 0.73) with two 5'UTR SNPs (-2459G > A and -2135 T > C; r2 = 1: 5'UTR-2SNP-hap). The 5'UTR-2SNP-hap was lower in total controllers and VCs vs. progressors (p = .003, pbonferroni = 0.048; p = .01, respectively). Results suggest -2459G > A, -2135 T > C, and + 2919 T > G as key CCR5 variants in HIV-1 control.
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Affiliation(s)
- Gemma W Koor
- Centre for HIV & STIs, National Institute for Communicable Diseases, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV & STIs, National Institute for Communicable Diseases, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Anabela C P Picton
- Centre for HIV & STIs, National Institute for Communicable Diseases, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Fidan Karatas
- Centre for HIV & STIs, National Institute for Communicable Diseases, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shayne A Loubser
- Centre for HIV & STIs, National Institute for Communicable Diseases, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Weijing He
- Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System, San Antonio, TX, United States of America; Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, United States of America; Department of Medicine, University of Texas Health Science Center, San Antonio, TX, United States of America
| | - Sunil K Ahuja
- Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System, San Antonio, TX, United States of America; Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, United States of America; Department of Medicine, University of Texas Health Science Center, San Antonio, TX, United States of America; Department of Microbiology, University of Texas Health Science Center, San Antonio, TX, United States of America
| | - Richard E Chaisson
- Johns Hopkins University Center for AIDS Research, Baltimore, MD, United States of America
| | - Neil Martinson
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Medical Research Council Soweto Matlosana Centre for HIV/AIDS and TB Research, Johannesburg, South Africa
| | - Osman Ebrahim
- School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV & STIs, National Institute for Communicable Diseases, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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47
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Phaahla NG, Lassaunière R, Da Costa Dias B, Waja Z, Martinson NA, Tiemessen CT. Chronic HIV-1 Infection Alters the Cellular Distribution of FcγRIIIa and the Functional Consequence of the FcγRIIIa-F158V Variant. Front Immunol 2019; 10:735. [PMID: 31024562 PMCID: PMC6467939 DOI: 10.3389/fimmu.2019.00735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/19/2019] [Indexed: 11/21/2022] Open
Abstract
Chronic HIV-infection modulates the expression of Fc gamma receptors (FcγRs) on immune cells and their antibody-dependent effector function capability. Given the increasingly recognized importance of antibody-dependent cellular cytotoxicity (ADCC) in HIV-specific immunity, we investigated the cellular distribution of FcγRIIIa on cytotoxic lymphocytes—natural killer cells and CD8+ T cells—and the effect of the FcγRIIIa-F158V variant on ADCC capacity in HIV-infected individuals (n = 23) and healthy controls (n = 23). Study participants were matched for F158V genotypes, carried two copies of the FCGR3A gene and were negative for FcγRIIb expression on NK cells. The distribution of CD56dimFcγRIIIabright and CD56negFcγRIIIabright NK cell subsets, but not FcγRIIIa surface expression, differed significantly between HIV-1 negative and HIV-1 positive donors. NK cell-mediated ADCC responses negatively correlated with the proportion of the immunoregulatory CD56brightFcγRIIIadim/neg cells and were lower in the HIV-1 positive group. Intriguingly, the FcγRIIIa-F158V variant differentially affected the NK-mediated ADCC responses for HIV-1 negative and HIV-1 positive donors. Healthy donors bearing at least one 158V allele had higher ADCC responses compared to those homozygous for the 158F allele (48.1 vs. 34.1%), whereas the opposite was observed for the HIV-infected group (26.4 vs. 34.6%), although not statistically significantly different. Furthermore, FcγRIIIa+CD8bright and FcγRIIIa+CD8dim T cell subsets were observed in both HIV-1 negative and HIV-1 positive donors, with median proportions that were significantly higher in HIV-1 positive donors compared to healthy controls (15.7 vs. 8.3%; P = 0.016 and 18.2 vs. 14.1%; P = 0.038, respectively). Using an HIV-1-specific GranToxiLux assay, we demonstrate that CD8+ T cells mediate ADCC through the delivery of granzyme B, which was overall lower compared to that of autologous NK cells. In conclusion, our findings demonstrate that in the presence of an HIV-1 infection, the cellular distribution of FcγRIIIa is altered and that the functional consequence of FcγRIIIa variant is affected. Importantly, it underscores the need to characterize FcγR expression, cellular distribution and functional consequences of FcγR genetic variants within a specific environment or disease state.
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Affiliation(s)
- Ntando G. Phaahla
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ria Lassaunière
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Bianca Da Costa Dias
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ziyaad Waja
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- MRC Soweto Matlosana Centre for HIV/AIDS and TB Research, Johannesburg, South Africa
| | - Neil A. Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- MRC Soweto Matlosana Centre for HIV/AIDS and TB Research, Johannesburg, South Africa
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- *Correspondence: Caroline T. Tiemessen
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48
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Julg B, Dee L, Ananworanich J, Barouch DH, Bar K, Caskey M, Colby DJ, Dawson L, Dong KL, Dubé K, Eron J, Frater J, Gandhi RT, Geleziunas R, Goulder P, Hanna GJ, Jefferys R, Johnston R, Kuritzkes D, Li JZ, Likhitwonnawut U, van Lunzen J, Martinez-Picado J, Miller V, Montaner LJ, Nixon DF, Palm D, Pantaleo G, Peay H, Persaud D, Salzwedel J, Salzwedel K, Schacker T, Sheikh V, Søgaard OS, Spudich S, Stephenson K, Sugarman J, Taylor J, Tebas P, Tiemessen CT, Tressler R, Weiss CD, Zheng L, Robb ML, Michael NL, Mellors JW, Deeks SG, Walker BD. Recommendations for analytical antiretroviral treatment interruptions in HIV research trials-report of a consensus meeting. Lancet HIV 2019; 6:e259-e268. [PMID: 30885693 PMCID: PMC6688772 DOI: 10.1016/s2352-3018(19)30052-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/11/2019] [Accepted: 02/12/2019] [Indexed: 04/16/2023]
Abstract
Analytical antiretroviral treatment interruption (ATI) is an important feature of HIV research, seeking to achieve sustained viral suppression in the absence of antiretroviral therapy (ART) when the goal is to measure effects of novel therapeutic interventions on time to viral load rebound or altered viral setpoint. Trials with ATIs also intend to determine host, virological, and immunological markers that are predictive of sustained viral control off ART. Although ATI is increasingly incorporated into proof-of-concept trials, no consensus has been reached on strategies to maximise its utility and minimise its risks. In addition, differences in ATI trial designs hinder the ability to compare efficacy and safety of interventions across trials. Therefore, we held a meeting of stakeholders from many interest groups, including scientists, clinicians, ethicists, social scientists, regulators, people living with HIV, and advocacy groups, to discuss the main challenges concerning ATI studies and to formulate recommendations with an emphasis on strategies for risk mitigation and monitoring, ART resumption criteria, and ethical considerations. In this Review, we present the major points of discussion and consensus views achieved with the goal of informing the conduct of ATIs to maximise the knowledge gained and minimise the risk to participants in clinical HIV research.
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Affiliation(s)
- Boris Julg
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA.
| | - Lynda Dee
- AIDS Action Baltimore, Baltimore, MD, USA
| | | | - Dan H Barouch
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katharine Bar
- Department of Medicine, University of Pennsylvania, Pennsylvania, PA, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY, USA
| | - Donn J Colby
- Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - Liza Dawson
- National Institute of Allergy and Infectious Diseases, Fishers ln Rockville, MD, USA
| | - Krista L Dong
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; University of KwaZulu Natal, Durban, South Africa
| | - Karine Dubé
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Joseph Eron
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford National Institute of Health Research Biomedical Research Centre, Oxford, UK
| | - Rajesh T Gandhi
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | | | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | | | | | - Daniel Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Cambridge, MA, USA
| | | | | | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Barcelona, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, Spain; University of Vic-Central University of Catalonia, Barcelona, Spain
| | | | - Luis J Montaner
- The Montaner Laboratory, The Wistar Institute, Philadelphia, PA, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York City, NY, USA
| | - David Palm
- Global HIV Prevention, and Treatment Clinical Trials Unit, University of North Carolina, Chapel Hill, NC, USA
| | - Giuseppe Pantaleo
- Service Immunology and Allergy, and Swiss Vaccine Research Institute, Centre Hospitalier Universitaire, Lausanne, Switzerland
| | - Holly Peay
- Research Triangle Institute, Research Triangle Park, NC, USA
| | - Deborah Persaud
- Pediatrics Infectious Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | | | - Karl Salzwedel
- National Institute of Allergy and Infectious Diseases, Fishers ln Rockville, MD, USA
| | - Timothy Schacker
- Division of Infectious Disease and International Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Virginia Sheikh
- Division of Antiviral Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Ole S Søgaard
- Department of Infectious Diseases, Aarhus University, Aarhus, Denmark
| | - Serena Spudich
- Department of Neurology, Yale University, New Haven, CT, USA
| | - Kathryn Stephenson
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jeremy Sugarman
- Berman Institute of Bioethics, University of North Carolina, Chapel Hill, NC, USA
| | - Jeff Taylor
- Collaboratory for AIDS Researchers for Eradication, University of North Carolina, Chapel Hill, NC, USA
| | - Pablo Tebas
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Caroline T Tiemessen
- Cell Biology Research Laboratory, Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Randall Tressler
- National Institute of Allergy and Infectious Diseases, Fishers ln Rockville, MD, USA
| | - Carol D Weiss
- Division of Antiviral Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Lu Zheng
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Merlin L Robb
- US Military HIV Research Program, Henry Jackson Foundation, Bethesda, MD, USA
| | - Nelson L Michael
- US Military HIV Research Program, Henry Jackson Foundation, Bethesda, MD, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven G Deeks
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
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49
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Lassaunière R, Paximadis M, Ebrahim O, Chaisson RE, Martinson NA, Tiemessen CT. The FCGR2C allele that modulated the risk of HIV-1 infection in the Thai RV144 vaccine trial is implicated in HIV-1 disease progression. Genes Immun 2018; 20:651-659. [PMID: 30563969 PMCID: PMC6881233 DOI: 10.1038/s41435-018-0053-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 11/10/2022]
Abstract
In the HIV-1 Thai RV144 vaccine trial—the only trial to demonstrate any
vaccine efficacy to date—a three-variant haplotype within the Fc gamma receptor 2C
gene (FCGR2C) modified the risk of HIV-1
acquisition. A similar vaccine regimen is currently being evaluated in South Africa
in the HVTN702 trial, where the predominant population is polymorphic for only a
single variant in the haplotype, c.134-96C>T. To investigate the significance of
c.134-96C>T in HIV-specific immunity in South Africans, this study assessed its
role in HIV-1 disease progression. In a cohort of HIV-1-infected South African
controllers (n = 71) and progressors (n = 73), the c.134-96C>T minor allele significantly
associated with increased odds of HIV-1 disease progression (odds ratio 3.80, 95%
confidence interval 1.90–7.62; P = 2.0 × 10–4, PBonf = 2.4 × 10–3).
It is unlikely that the underlying mechanism involves wild-type FcγRIIc function,
since only a single study participant was predicted to express wild-type FcγRIIc as
determined by the FCGR2C c.798+1A>G
splice-site variant. Conversely, in silico analysis revealed a potential role for
c.134-96C> T in modulating mRNA transcription. In conclusion, these data provide
additional evidence towards a role for FCGR2C
c.134-96C>T in the context of HIV-1 and underscore the need to investigate its
significance in the HVTN702 efficacy trial in South Africa.
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Affiliation(s)
- Ria Lassaunière
- National Institute for Communicable Diseases, Centre for HIV and STI's, Johannesburg, South Africa.,University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.,Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Maria Paximadis
- National Institute for Communicable Diseases, Centre for HIV and STI's, Johannesburg, South Africa.,University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
| | - Osman Ebrahim
- University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.,Brenthurst Clinic, Johannesburg, South Africa
| | | | - Neil A Martinson
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa.,MRC Soweto Matlosana Centre for HIV/AIDS and TB Research, Johannesburg, South Africa
| | - Caroline T Tiemessen
- National Institute for Communicable Diseases, Centre for HIV and STI's, Johannesburg, South Africa. .,University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.
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50
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Harris L, van Zyl LJ, Kirby-McCullough BM, Damelin LH, Tiemessen CT, Trindade M. Identification and sequence analysis of two novel cryptic plasmids isolated from the vaginal mucosa of South African women. Plasmid 2018; 98:56-62. [PMID: 30240699 DOI: 10.1016/j.plasmid.2018.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/13/2018] [Accepted: 09/16/2018] [Indexed: 10/28/2022]
Abstract
The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy- and bacterial vaginosis (BV)-infected women Lactobacillus crispatus and Lactobacillus jensenii have been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. In the present study two plasmids, pLc4 and pLc17, isolated from vaginal Lactobacillus strains of both healthy and BV-infected women were characterized. The smaller plasmid, pLc4 (4224 bp), was detected in both L. crispatus and L. jensenii strains, while pLc17 was only detected in L. crispatus. Based on its nucleotide sequence pLc4 appears highly novel, with its replication protein having 44% identity to the replication initiation protein of pSMQ173b_03. Phylogenetic analysis with other Rolling Circle Replication plasmids confirmed that pLc4 shows a low degree of similarity to these plasmids. Plasmid pLc17 (16,663 bp) appears to carry both a RCR replicon and a theta replicon, which is rare in naturally occurring plasmids. pLc4 was maintained at a high copy number of 29, while pLc17 appears to be a medium copy number plasmid maintained at 11 copies per chromosome. While sequence analysis is a valuable tool to study cryptic plasmids, further function-based analysis will be required in order to fully elucidate the role of these plasmids within the vaginal milieu.
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Affiliation(s)
- Lyle Harris
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
| | - Leonardo J van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
| | - Bronwyn M Kirby-McCullough
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
| | - Leonard H Damelin
- Centre for HIV & STIs, National Institute of Communicable Diseases, Sandringham, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, South Africa
| | - Caroline T Tiemessen
- Centre for HIV & STIs, National Institute of Communicable Diseases, Sandringham, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa.
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