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Neufeld B, Munyuza C, Reimer A, Capiña R, Lee ER, Becker M, Sandstrom P, Ji H, Cholette F. A validated in-house assay for HIV drug resistance mutation surveillance from dried blood spot specimens. J Virol Methods 2024; 327:114939. [PMID: 38604585 DOI: 10.1016/j.jviromet.2024.114939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
Despite increasing scale-up of antiretroviral therapy (ART) coverage, challenges related to adherence and HIV drug resistance (HIVDR) remain. The high cost of HIVDR surveillance is a persistent challenge with implementation in resource-constrained settings. Dried blood spot (DBS) specimens have been demonstrated to be a feasible alternative to plasma or serum for HIVDR genotyping and are more suitable for lower resource settings. There is a need for affordable HIVDR genotyping assays which can amplify HIV-1 sequences from DBS specimens, particularly those with low viral loads, at a low cost. Here, we present an in-house assay capable of reliably amplifying HIV-1 protease and partial reverse transcriptase genes from DBS specimens, which covers the complete World Health Organization 2009 list of drug resistance mutations under surveillance. DBS specimens were prepared using whole blood spiked with HIV-1 at concentrations of 10,000, 5000, 1000, and 500 copies/mL (n=30 for each concentration). Specimens were tested in triplicate. A two-step approach was used consisting of cDNA synthesis followed by nested PCR. The limit of detection of the assay was calculated to be approximately 5000 (95% CI: 3200-10,700) copies/mL for the protease gene and 3600 (95% CI: 2200-10,000) copies/mL for reverse transcriptase. The assay was observed to be most sensitive with higher viral load specimens (97.8% [95% CI: 92.2-99.7]) for both protease and reverse transcriptase at 10,000 copies/mL with performance decreasing with the use of specimens with lower viral loads (46.7% [36.1-57.5] and 60.0% [49.1-70.2] at 500 copies/mL for protease and reverse transcriptase, respectively). Ultimately, this assay presents a promising opportunity for use in resource-constrained settings. Future work should involve validation under field conditions including sub-optimal storage conditions and preparation of DBS with fingerprick blood in order to accurately reflect real-world collection scenarios.
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Affiliation(s)
- Bronwyn Neufeld
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.
| | - Chantal Munyuza
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Alexandria Reimer
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Rupert Capiña
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Emma R Lee
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Marissa Becker
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Paul Sandstrom
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - François Cholette
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
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2
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van Paassen PM, van Pul L, van der Straten K, Buchholtz NV, Grobben M, van Nuenen AC, van Dort KA, Boeser-Nunnink BD, van den Essenburg MD, Burger JA, van Luin M, Jurriaans S, Sanders RW, Swelsen WT, Symons J, Klouwens MJ, Nijhuis M, van Gils MJ, Prins JM, de Bree GJ, Kootstra NA. Virological and immunological correlates of HIV posttreatment control after temporal antiretroviral therapy during acute HIV infection. AIDS 2023; 37:2297-2304. [PMID: 37702421 PMCID: PMC10653294 DOI: 10.1097/qad.0000000000003722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/14/2023]
Abstract
OBJECTIVE People with HIV rarely control viral replication after cessation of antiretroviral therapy (ART). We present a person with HIV with extraordinary posttreatment control (PTC) for over 23 years after temporary ART during acute HIV infection (AHI) leading to a new insight in factors contributing to PTC. DESIGN/METHODS Viral reservoir was determined by HIV qPCR, Intact Proviral DNA Assay, and quantitative viral outgrowth assay. Viral replication kinetics were determined in autologous and donor PBMC. IgG levels directed against HIV envelope and neutralizing antibodies were measured. Immune phenotyping of T cells and HIV-specific T-cell responses were analyzed by flow cytometry. RESULTS The case presented with AHI and a plasma viral load of 2.7 million copies/ml. ART was initiated 2 weeks after diagnosis and interrupted after 26 months. Replicating virus was isolated shortly after start ART. At 18 years after treatment interruption, HIV-DNA in CD4 + T cells and low levels of HIV-RNA in plasma (<5 copies/ml) were detectable. Stable HIV envelope glycoprotein-directed IgG was present during follow-up, but lacked neutralizing activity. Strong antiviral CD8 + T-cell responses, in particular targeting HIV-gag, were detected during 25 years follow-up. Moreover, we found a P255A mutation in an HLA-B∗44 : 02 restricted gag-epitope, which was associated with decreased replication. CONCLUSION We describe an exceptional case of PTC, which is likely associated with sustained potent gag-specific CD8 + T-cell responses in combination with a replication attenuating escape mutation in gag. Understanding the initiation and preservation of the HIV-specific T-cell responses could guide the development of strategies to induce HIV control.
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Affiliation(s)
- Pien M. van Paassen
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | - Lisa van Pul
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | - Karlijn van der Straten
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Ninée V.J.E. Buchholtz
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht
| | - Marloes Grobben
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Ad C. van Nuenen
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | - Karel A. van Dort
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | - Brigitte D. Boeser-Nunnink
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | | | - Judith A. Burger
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Matthijs van Luin
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht
| | - Suzanne Jurriaans
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Rogier W. Sanders
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Wendy T. Swelsen
- Department of Immunogenetics, Sanquin Diagnostic Services, Amsterdam, the Netherlands
| | - Jori Symons
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht
| | - Michelle J. Klouwens
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, The Netherlands
| | - Monique Nijhuis
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht
| | - Marit J. van Gils
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Jan M. Prins
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, The Netherlands
| | - Godelieve J. de Bree
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
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3
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Tang J. Immunogenetic determinants of heterosexual HIV-1 transmission: key findings and lessons from two distinct African cohorts. Genes Immun 2021; 22:65-74. [PMID: 33934119 PMCID: PMC8225584 DOI: 10.1038/s41435-021-00130-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/05/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023]
Abstract
Immunogenetic studies in the past three decades have uncovered a broad range of human genetic factors that seem to influence heterosexual HIV-1 transmission in one way or another. In our own work that jointly evaluated both genetic and nongenetic factors in two African cohorts of cohabiting, HIV-1-discordant couples (donor and recipient pairs) at risk of transmission during quarterly follow-up intervals, relatively consistent findings have been seen with three loci (IL19, HLA-A, and HLA-B), although the effect size (i.e., odds ratio or hazards ratio) of each specific variant was quite modest. These studies offered two critical lessons that should benefit future research on sexually transmitted infections. First, in donor partners, immunogenetic factors (e.g., HLA-B*57 and HLA-A*36:01) that operate directly through HIV-1 viral load or indirectly through genital coinfections are equally important. Second, thousands of single-nucleotide polymorphisms previously recognized as "causal" factors for human autoimmune disorders did not appear to make much difference, which is somewhat puzzling as these variants are predicted or known to influence the expression of many immune response genes. Replicating these observations in additional cohorts is no longer feasible as the field has shifted its focus to early diagnosis, universal treatment, and active management of comorbidities.
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Affiliation(s)
- Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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4
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Price MA, Kilembe W, Ruzagira E, Karita E, Inambao M, Sanders EJ, Anzala O, Allen S, Edward VA, Kaleebu P, Fast PE, Rida W, Kamali A, Hunter E, Tang J, Lakhi S, Mutua G, Bekker LG, Abu-Baker G, Tichacek A, Chetty P, Latka MH, Maenetje P, Makkan H, Hare J, Kibengo F, Priddy F, Landais E, Chinyenze K, Gilmour J. Cohort Profile: IAVI's HIV epidemiology and early infection cohort studies in Africa to support vaccine discovery. Int J Epidemiol 2021; 50:29-30. [PMID: 32879950 PMCID: PMC7938500 DOI: 10.1093/ije/dyaa100] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Affiliation(s)
- Matt A Price
- IAVI, New York, USA & Nairobi, Kenya
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
| | - William Kilembe
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
| | - Eugene Ruzagira
- Medical Research Council, Uganda Virus Research Institute, and London School of Hygiene and Tropical Medicine Uganda Research Unit (MULS), Entebbe & Masaka, Uganda
| | - Etienne Karita
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
| | - Mubiana Inambao
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
| | - Eduard J Sanders
- Kenyan Medical Research Institute-Wellcome Trust, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Omu Anzala
- KAVI-Institute of Clinical Research, Nairobi, Kenya
| | - Susan Allen
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Vinodh A Edward
- The Aurum Institute, Johannesburg and Rustenburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Advancing Care and Treatment for TB/HIV, A Collaborating Centre of the South African Medical Research Council, Cape Town, South Africa
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Pontiano Kaleebu
- Medical Research Council, Uganda Virus Research Institute, and London School of Hygiene and Tropical Medicine Uganda Research Unit (MULS), Entebbe & Masaka, Uganda
| | - Patricia E Fast
- IAVI, New York, USA & Nairobi, Kenya
- Pediatric Infectious Diseases, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Wasima Rida
- Biostatistics Consultant, Arlington, VA, USA
| | | | - Eric Hunter
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shabir Lakhi
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
| | | | - Linda Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Ggayi Abu-Baker
- Medical Research Council, Uganda Virus Research Institute, and London School of Hygiene and Tropical Medicine Uganda Research Unit (MULS), Entebbe & Masaka, Uganda
| | - Amanda Tichacek
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
- Department of Epidemiology, Emory University, Atlanta, GA, USA
| | | | - Mary H Latka
- The Aurum Institute, Johannesburg and Rustenburg, South Africa
| | - Pholo Maenetje
- The Aurum Institute, Johannesburg and Rustenburg, South Africa
| | - Heeran Makkan
- The Aurum Institute, Johannesburg and Rustenburg, South Africa
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, UK
| | - Freddie Kibengo
- Medical Research Council, Uganda Virus Research Institute, and London School of Hygiene and Tropical Medicine Uganda Research Unit (MULS), Entebbe & Masaka, Uganda
| | | | - Elise Landais
- IAVI, New York, USA & Nairobi, Kenya
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, UK
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5
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Price MA, Rida W, Kilembe W, Karita E, Inambao M, Ruzagira E, Kamali A, Sanders EJ, Anzala O, Hunter E, Allen S, Edward VA, Wall KM, Tang J, Fast PE, Kaleebu P, Lakhi S, Mutua G, Bekker LG, Abu-Baker G, Tichacek A, Chetty P, Latka MH, Maenetje P, Makkan H, Kibengo F, Priddy F, Gilmour J. Control of the HIV-1 Load Varies by Viral Subtype in a Large Cohort of African Adults With Incident HIV-1 Infection. J Infect Dis 2020; 220:432-441. [PMID: 30938435 PMCID: PMC6603968 DOI: 10.1093/infdis/jiz127] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Few human immunodeficiency virus (HIV)–infected persons can maintain low viral levels without therapeutic intervention. We evaluate predictors of spontaneous control of the viral load (hereafter, “viral control”) in a prospective cohort of African adults shortly after HIV infection. Viral control was defined as ≥2 consecutively measured viral loads (VLs) of ≤10 000 copies/mL after the estimated date of infection, followed by at least 4 subsequent measurements for which the VL in at least 75% was ≤10 000 copies/mL in the absence of ART. Multivariable logistic regression characterized predictors of viral control. Of 590 eligible volunteers, 107 (18.1%) experienced viral control, of whom 25 (4.2%) maintained a VL of 51–2000 copies/mL, and 5 (0.8%) sustained a VL of ≤50 copies/mL. The median ART-free follow-up time was 3.3 years (range, 0.3–9.7 years). Factors independently associated with control were HIV-1 subtype A (reference, subtype C; adjusted odds ratio [aOR], 2.1 [95% confidence interval {CI}, 1.3–3.5]), female sex (reference, male sex; aOR, 1.8 [95% CI, 1.1–2.8]), and having HLA class I variant allele B*57 (reference, not having this allele; aOR, 1.9 [95% CI, 1.0–3.6]) in a multivariable model that also controlled for age at the time of infection and baseline CD4+ T-cell count. We observed strong associations between infecting HIV-1 subtype, HLA type, and sex on viral control in this cohort. HIV-1 subtype is important to consider when testing and designing new therapeutic and prevention technologies, including vaccines.
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Affiliation(s)
- Matt A Price
- International AIDS Vaccine Initiative, New York, New York.,Department of Epidemiology and Biostatistics, University of California-San Francisco
| | | | - William Kilembe
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda
| | - Etienne Karita
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda
| | - Mubiana Inambao
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda
| | | | - Anatoli Kamali
- International AIDS Vaccine Initiative, New York, New York
| | - Eduard J Sanders
- Kenyan Medical Research Institute-Wellcome Trust, Kilifi, Nairobi, Kenya.,Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, London, United Kingdom
| | - Omu Anzala
- KAVI Institute of Clinical Research, Nairobi, Kenya
| | - Eric Hunter
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Susan Allen
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Vinodh A Edward
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut.,The Aurum Institute, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, South Africa.,Advancing Care and Treatment for TB/HIV, South African Medical Research Council, Johannesburg, South Africa
| | - Kristin M Wall
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda.,Department of Epidemiology, Emory University, Atlanta, Georgia
| | - Jianming Tang
- Department of Medicine, University of Alabama-Birmingham
| | | | | | - Shabir Lakhi
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda
| | | | | | | | - Amanda Tichacek
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda.,Department of Epidemiology, Emory University, Atlanta, Georgia
| | - Paramesh Chetty
- International AIDS Vaccine Initiative, New York, New York.,International AIDS Vaccine Initiative Human Immunology Laboratory, London, United Kingdom
| | | | | | | | | | - Fran Priddy
- International AIDS Vaccine Initiative, New York, New York
| | - Jill Gilmour
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, United Kingdom
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6
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Boelen L, Debebe B, Silveira M, Salam A, Makinde J, Roberts CH, Wang ECY, Frater J, Gilmour J, Twigger K, Ladell K, Miners KL, Jayaraman J, Traherne JA, Price DA, Qi Y, Martin MP, Macallan DC, Thio CL, Astemborski J, Kirk G, Donfield SM, Buchbinder S, Khakoo SI, Goedert JJ, Trowsdale J, Carrington M, Kollnberger S, Asquith B. Inhibitory killer cell immunoglobulin-like receptors strengthen CD8 + T cell-mediated control of HIV-1, HCV, and HTLV-1. Sci Immunol 2018; 3:eaao2892. [PMID: 30413420 PMCID: PMC6277004 DOI: 10.1126/sciimmunol.aao2892] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 06/06/2018] [Accepted: 10/09/2018] [Indexed: 01/05/2023]
Abstract
Killer cell immunoglobulin-like receptors (KIRs) are expressed predominantly on natural killer cells, where they play a key role in the regulation of innate immune responses. Recent studies show that inhibitory KIRs can also affect adaptive T cell-mediated immunity. In mice and in human T cells in vitro, inhibitory KIR ligation enhanced CD8+ T cell survival. To investigate the clinical relevance of these observations, we conducted an extensive immunogenetic analysis of multiple independent cohorts of HIV-1-, hepatitis C virus (HCV)-, and human T cell leukemia virus type 1 (HTLV-1)-infected individuals in conjunction with in vitro assays of T cell survival, analysis of ex vivo KIR expression, and mathematical modeling of host-virus dynamics. Our data suggest that functional engagement of inhibitory KIRs enhances the CD8+ T cell response against HIV-1, HCV, and HTLV-1 and is a significant determinant of clinical outcome in all three viral infections.
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Affiliation(s)
- Lies Boelen
- Department of Medicine, Imperial College London, London, UK
| | - Bisrat Debebe
- Department of Medicine, Imperial College London, London, UK
| | - Marcos Silveira
- Department of Medicine, Imperial College London, London, UK
- Faculty of Engineering, São Paulo State University-UNESP, São Paulo, Brazil
| | - Arafa Salam
- Institute for Infection and Immunity, St. George's, University of London, London, UK
| | - Julia Makinde
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, UK
| | - Chrissy H Roberts
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Eddie C Y Wang
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Jill Gilmour
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, UK
| | - Katie Twigger
- Department of Medicine, Imperial College London, London, UK
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Jyothi Jayaraman
- Immunology Division, Department of Pathology, University of Cambridge, Cambridge, UK
| | - James A Traherne
- Immunology Division, Department of Pathology, University of Cambridge, Cambridge, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maureen P Martin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Derek C Macallan
- Institute for Infection and Immunity, St. George's, University of London, London, UK
| | | | | | | | | | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Salim I Khakoo
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - John Trowsdale
- Immunology Division, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Simon Kollnberger
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Becca Asquith
- Department of Medicine, Imperial College London, London, UK.
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7
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Eccleston RC, Coveney PV, Dalchau N. Host genotype and time dependent antigen presentation of viral peptides: predictions from theory. Sci Rep 2017; 7:14367. [PMID: 29084996 PMCID: PMC5662608 DOI: 10.1038/s41598-017-14415-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/11/2017] [Indexed: 01/20/2023] Open
Abstract
The rate of progression of HIV infected individuals to AIDS is known to vary with the genotype of the host, and is linked to their allele of human leukocyte antigen (HLA) proteins, which present protein degradation products at the cell surface to circulating T-cells. HLA alleles are associated with Gag-specific T-cell responses that are protective against progression of the disease. While Pol is the most conserved HIV sequence, its association with immune control is not as strong. To gain a more thorough quantitative understanding of the factors that contribute to immunodominance, we have constructed a model of the recognition of HIV infection by the MHC class I pathway. Our model predicts surface presentation of HIV peptides over time, demonstrates the importance of viral protein kinetics, and provides evidence of the importance of Gag peptides in the long-term control of HIV infection. Furthermore, short-term dynamics are also predicted, with simulation of virion-derived peptides suggesting that efficient processing of Gag can lead to a 50% probability of presentation within 3 hours post-infection, as observed experimentally. In conjunction with epitope prediction algorithms, this modelling approach could be used to refine experimental targets for potential T-cell vaccines, both for HIV and other viruses.
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Affiliation(s)
- R Charlotte Eccleston
- Centre for Computational Science, Department of Chemistry, University College London, London, WC1H 0AJ, UK.,CoMPLEX, University College London, London, WC1E 6BT, UK
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London, WC1H 0AJ, UK.,CoMPLEX, University College London, London, WC1E 6BT, UK
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8
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Roff SR, Sanou MP, Rathore MH, Levy JA, Yamamoto JK. Conserved epitopes on HIV-1, FIV and SIV p24 proteins are recognized by HIV-1 infected subjects. Hum Vaccin Immunother 2016; 11:1540-56. [PMID: 25844718 DOI: 10.1080/21645515.2015.1026500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cross-reactive peptides on HIV-1 and FIV p24 protein sequences were studied using peripheral blood mononuclear cells (PBMC) from untreated HIV-1-infected long-term survivors (LTS; >10 y of infection without antiretroviral therapy, ART), short-term HIV-1 infected subjects not on ART, and ART-treated HIV-1 infected subjects. IFNγ-ELISpot and CFSE-proliferation analyses were performed with PBMC using overlapping HIV-1 and FIV p24 peptides. Over half of the HIV-1 infected subjects tested (22/31 or 71%) responded to one or more FIV p24 peptide pools by either IFNγ or T-cell proliferation analysis. PBMC and T cells from infected subjects in all 3 HIV(+) groups predominantly recognized one FIV p24 peptide pool (Fp14) by IFNγ production and one additional FIV p24 peptide pool (Fp9) by T-cell proliferation analysis. Furthermore, evaluation of overlapping SIV p24 peptide sequences identified conserved epitope(s) on the Fp14/Hp15-counterpart of SIV, Sp14, but none on Fp9-counterpart of SIV, Sp9. The responses to these FIV peptide pools were highly reproducible and persisted throughout 2-4 y of monitoring. Intracellular staining analysis for cytotoxins and phenotyping for CD107a determined that peptide epitopes from Fp9 and Fp14 pools induced cytotoxic T lymphocyte-associated molecules including perforin, granzyme B, granzyme A, and/or expression of CD107a. Selected FIV and corresponding SIV epitopes recognized by HIV-1 infected patients indicate that these protein sequences are evolutionarily conserved on both SIV and HIV-1 (e.g., Hp15:Fp14:Sp14). These studies demonstrate that comparative immunogenicity analysis of HIV-1, FIV, and SIV can identify evolutionarily-conserved T cell-associated lentiviral epitopes, which could be used as a vaccine for prophylaxis or immunotherapy.
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Key Words
- AIDS, acquired immune deficiency syndrome
- ART, anti-retroviral therapy
- CFSE, Carboxyfluorescein succinimidyl ester
- CMI, cell mediated immunity
- CTL epitopes
- CTL, cytotoxic T cell
- FIV p24
- FIV, feline immunodeficiency virus
- GrzA, granzyme A
- GrzB, granzyme B
- HERV, human endogenous retrovirus
- HIV p24
- HIV, human immunodeficiency virus
- HLA, human leukocyte antigen
- ICS, intracellular staining
- LANL, Los Alamos National Laboratory
- LTS, Long term survivors
- Nab, broadly neutralizing antibody
- PHA, phytohaemagglutinin
- SFU, spot forming units
- SIV p24
- SIV, simian immunodeficiency virus
- ST, short term survivors
- aa, amino acid
- feline immunodeficiency virus
- vaccine epitopes
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Affiliation(s)
- Shannon R Roff
- a Department of Infectious Diseases and Pathology; College of Veterinary Medicine; University of Florida ; Gainesville , FL , USA
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9
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Tang J, Li X, Price MA, Sanders EJ, Anzala O, Karita E, Kamali A, Lakhi S, Allen S, Hunter E, Kaslow RA, Gilmour J. CD4:CD8 lymphocyte ratio as a quantitative measure of immunologic health in HIV-1 infection: findings from an African cohort with prospective data. Front Microbiol 2015; 6:670. [PMID: 26191056 PMCID: PMC4486831 DOI: 10.3389/fmicb.2015.00670] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/19/2015] [Indexed: 01/06/2023] Open
Abstract
In individuals with human immunodeficiency virus type 1 (HIV-1) infection, CD4:CD8 lymphocyte ratio is often recognized as a quantitative outcome that reflects the critical role of both CD4(+) and CD8(+) T-cells in HIV-1 pathogenesis or disease progression. Our work aimed to first establish the dynamics and clinical relevance of CD4:CD8 ratio in a cohort of native Africans and then to examine its association with viral and host factors, including: (i) length of infection, (ii) demographics, (iii) HIV-1 viral load (VL), (iv) change in CD4(+) T-lymphocyte count (CD4 slope), (v) HIV-1 subtype, and (vi) host genetics, especially human leukocyte antigen (HLA) variants. Data from 499 HIV-1 seroconverters with frequent (monthly to quarterly) follow-up revealed that CD4:CD8 ratio was stable in the first 3 years of infection, with a modest correlation with VL and CD4 slope. A relatively normal CD4:CD8 ratio (>1.0) in early infection was associated with a substantial delay in disease progression to severe immunodeficiency (<350 CD4 cells/μl), regardless of other correlates of HIV-1 pathogenesis (adjusted hazards ratio (HR) = 0.43, 95% confidence interval (CI) = 0.29-0.63, P < 0.0001). Low VL (<10,000 copies/ml) and HLA-A*74:01 were the main predictors of CD4:CD8 ratio >1.0, but HLA variants (e.g., HLA-B*57 and HLA-B*81) previously associated with VL and/or CD4 trajectories in eastern and southern Africans had no obvious impact on CD4:CD8 ratio. Collectively, these findings suggest that CD4:CD8 ratio is a robust measure of immunologic health with both clinical and epidemiological implications.
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Affiliation(s)
- Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Xuelin Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York, NY USA ; Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA USA
| | - Eduard J Sanders
- Centre for Geographic Medicine Research, Kenya Medical Research Institute, Kilifi Kenya ; Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford UK
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative, Nairobi Kenya
| | | | - Anatoli Kamali
- Uganda Virus Research Unit on AIDS, Medical Research Council/Uganda Virus Research Institute, Masaka Uganda
| | - Shabir Lakhi
- Zambia-Emory HIV Research Project, Lusaka Zambia
| | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka Zambia ; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA USA
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA USA
| | - Richard A Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London UK
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10
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Adland E, Paioni P, Thobakgale C, Laker L, Mori L, Muenchhoff M, Csala A, Clapson M, Flynn J, Novelli V, Hurst J, Naidoo V, Shapiro R, Huang KHG, Frater J, Prendergast A, Prado JG, Ndung’u T, Walker BD, Carrington M, Jooste P, Goulder PJR. Discordant Impact of HLA on Viral Replicative Capacity and Disease Progression in Pediatric and Adult HIV Infection. PLoS Pathog 2015; 11:e1004954. [PMID: 26076345 PMCID: PMC4468173 DOI: 10.1371/journal.ppat.1004954] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/13/2015] [Indexed: 11/18/2022] Open
Abstract
HLA class I polymorphism has a major influence on adult HIV disease progression. An important mechanism mediating this effect is the impact on viral replicative capacity (VRC) of the escape mutations selected in response to HLA-restricted CD8+ T-cell responses. Factors that contribute to slow progression in pediatric HIV infection are less well understood. We here investigate the relationship between VRC and disease progression in pediatric infection, and the effect of HLA on VRC and on disease outcome in adult and pediatric infection. Studying a South African cohort of >350 ART-naïve, HIV-infected children and their mothers, we first observed that pediatric disease progression is significantly correlated with VRC. As expected, VRCs in mother-child pairs were strongly correlated (p = 0.004). The impact of the protective HLA alleles, HLA-B*57, HLA-B*58:01 and HLA-B*81:01, resulted in significantly lower VRCs in adults (p<0.0001), but not in children. Similarly, in adults, but not in children, VRCs were significantly higher in subjects expressing the disease-susceptible alleles HLA-B*18:01/45:01/58:02 (p = 0.007). Irrespective of the subject, VRCs were strongly correlated with the number of Gag CD8+ T-cell escape mutants driven by HLA-B*57/58:01/81:01 present in each virus (p = 0.0002). In contrast to the impact of VRC common to progression in adults and children, the HLA effects on disease outcome, that are substantial in adults, are small and statistically insignificant in infected children. These data further highlight the important role that VRC plays both in adult and pediatric progression, and demonstrate that HLA-independent factors, yet to be fully defined, are predominantly responsible for pediatric non-progression.
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Affiliation(s)
- Emily Adland
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Paolo Paioni
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Christina Thobakgale
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Leana Laker
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Luisa Mori
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Maximilian Muenchhoff
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Anna Csala
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Margaret Clapson
- Department of Paediatric Infectious Diseases, Great Ormond St Hospital for Children, London, United Kingdom
| | - Jacquie Flynn
- Department of Paediatric Infectious Diseases, Great Ormond St Hospital for Children, London, United Kingdom
| | - Vas Novelli
- Department of Paediatric Infectious Diseases, Great Ormond St Hospital for Children, London, United Kingdom
| | - Jacob Hurst
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Oxford National Institute of Health Research, Biomedical Research Centre, Oxford, United Kingdom
| | - Vanessa Naidoo
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Kuan-Hsiang Gary Huang
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - John Frater
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Oxford National Institute of Health Research, Biomedical Research Centre, Oxford, United Kingdom
| | - Andrew Prendergast
- Centre for Paediatrics, Blizard Institute, Queen Mary University of London, London, United Kingdom
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Julia G. Prado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- The Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Boston, Massachusetts, United States of America
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Bruce D. Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- The Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Boston, Massachusetts, United States of America
| | - Mary Carrington
- The Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Boston, Massachusetts, United States of America
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Pieter Jooste
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Philip J. R. Goulder
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Paediatric Infectious Diseases, Great Ormond St Hospital for Children, London, United Kingdom
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11
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Shrestha S, Wiener HW, Aissani B, Shendre A, Tang J, Portman MA. Imputation of class I and II HLA loci using high-density SNPs from ImmunoChip and their associations with Kawasaki disease in family-based study. Int J Immunogenet 2015; 42:140-6. [PMID: 25809546 DOI: 10.1111/iji.12190] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/28/2015] [Accepted: 02/19/2015] [Indexed: 02/03/2023]
Abstract
Kawasaki disease (KD) is the leading cause of acquired heart disease in children in most developed countries including the United States. The etiology of KD is not known; however, epidemiological and immunological data suggest infectious or immune-related factors in the manifestation of the disease. Further, KD has several hereditary features that strongly suggest a genetic component to disease pathogenesis. Human leucocyte antigen (HLA) loci have also been reported to be associated with KD, but results have been inconsistent, in part, because of small study samples and varying linkage disequilibrium (LD) patterns observed across different ethnic groups. To maximize the informativeness of single nucleotide polymorphism (SNP) genotypes in the major histocompatibility (MHC) region, we imputed classical HLA I (A, B, C) and HLA II (DRB1, DQA1, DQB1) alleles using SNP2HLA method from genotypes of 6700 SNPs within the extended MHC region contained in the ImmunoChip among 112 White patients with KD and their biological parents from North America and tested their association with KD susceptibility using the transmission disequilibrium test. Mendelian consistency in the trios suggested high accuracy and reliability of the imputed alleles (class I = 97.5%, class II = 96.6%). While several SNPs in the MHC region were individually associated with KD susceptibility, we report over-transmission of HLA-C*15 (z = +2.19, P = 0.03) and under-transmission of HLA-B*44 (z = -2.49, P = 0.01) alleles from parents to patients with KD. HLA-B*44 has been associated with KD in other smaller studies, and both HLA-C*15 and HLA-B*44 have biological mechanisms that could potentially be involved in KD pathogenesis. Overall, inferring HLA loci within the same ethnic group, using family-based information is a powerful approach. However, studies with larger sample sizes are warranted to evaluate the correlations of the strength and directions between the SNPs in MHC region and the imputed HLA alleles with KD.
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Affiliation(s)
- S Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - H W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - B Aissani
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - A Shendre
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - M A Portman
- Department of Pediatrics, University of Washington, Seattle Children's Research Institute, Seattle, WA, USA
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12
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Kagoné TS, Bisseye C, Méda N, Testa J, Pietra V, Kania D, Yonli AT, Compaoré TR, Nikiéma JB, de Souza C, Simpore J. A variant of DC-SIGN gene promoter associated with resistance to HIV-1 in serodiscordant couples in Burkina Faso. ASIAN PAC J TROP MED 2014; 7S1:S93-6. [PMID: 25312200 DOI: 10.1016/s1995-7645(14)60211-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/09/2014] [Accepted: 06/18/2014] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE To study the involvement of variations in 4 genes associated with susceptibility and/or protection against HIV-1 in serodiscordant couples in Burkina Faso, namely, genes encoding HLA-B57, interferon regulatory factor 1 (IRF1), dendritic cell-specific ICAM3-grabbing nonintegrin (DC-SIGN) and CCR5 delta 32 (CCR5Δ32). METHODS Two DC-SIGN and two IRF1 single nucleotide polymorphisms (SNPs) as well as HLA-B57*01 and CCR5Δ32 alleles were genotyped in 51 serodiscordant couples in Burkina Faso. DC-SIGN, IRF1 and HLA-B57*01 genotyping was carried out by real time PCR using TaqMan assays (Applied Biosystems, USA and Sacace Biotechnologies, Italy). CCR5Δ32 deletion was investigated by PCR. RESULTS The two SNPs of DC-SIGN promoter showed a significant genotypic difference in serodiscordant couples. After multivariate analysis, only the association between DC-SIGN rs2287886 and HIV-1 remained significant (P<0.01). No association was found between IRF1 SNPs and HIV-1 infection. CCR5Δ32 wild type allele was found in 100% of serodiscordant couples. A high frequency of HLA-B57*01 allele was found in the HIV-positive (78%) compared with HIV-negative group (51%), however this difference was no longer significant after the correction of the sex confounding effect in the logistic regression model. CONCLUSIONS Our study suggests a protective role of a variation of DC-SIGN promoter and genetic resistance to HIV-1 in serodiscordant couples in Burkina Faso.
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Affiliation(s)
- Thérèse Samdapawindé Kagoné
- Biomolecular Research Center Pietro Annigoni CERBA/Labiogene University of Ouagadougou, Burkina Faso; Centre MURAZ Bobo-Dioulasso, Burkina Faso
| | - Cyrille Bisseye
- Biomolecular Research Center Pietro Annigoni CERBA/Labiogene University of Ouagadougou, Burkina Faso; Laboratory of Molecular and Cellular Biology, University of Science and Technique of Masuku (USTM), Franceville, Gabon.
| | | | - Jean Testa
- Centre MURAZ Bobo-Dioulasso, Burkina Faso
| | | | | | - Albert Théophane Yonli
- Biomolecular Research Center Pietro Annigoni CERBA/Labiogene University of Ouagadougou, Burkina Faso
| | - Tegwindé Rebeca Compaoré
- Biomolecular Research Center Pietro Annigoni CERBA/Labiogene University of Ouagadougou, Burkina Faso
| | - Jean Baptiste Nikiéma
- Biomolecular Research Center Pietro Annigoni CERBA/Labiogene University of Ouagadougou, Burkina Faso
| | | | - Jacques Simpore
- Biomolecular Research Center Pietro Annigoni CERBA/Labiogene University of Ouagadougou, Burkina Faso
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13
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Li X, Price MA, He D, Kamali A, Karita E, Lakhi S, Sanders EJ, Anzala O, Amornkul PN, Allen S, Hunter E, Kaslow RA, Gilmour J, Tang J. Host genetics and viral load in primary HIV-1 infection: clear evidence for gene by sex interactions. Hum Genet 2014; 133:1187-97. [PMID: 24969460 PMCID: PMC4127002 DOI: 10.1007/s00439-014-1465-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/16/2014] [Indexed: 01/09/2023]
Abstract
Research in the past two decades has generated unequivocal evidence that host genetic variations substantially account for the heterogeneous outcomes following human immunodeficiency virus type 1 (HIV-1) infection. In particular, genes encoding human leukocyte antigens (HLA) have various alleles, haplotypes, or specific motifs that can dictate the set-point (a relatively steady state) of plasma viral load (VL), although rapid viral evolution driven by innate and acquired immune responses can obscure the long-term relationships between HLA genotypes and HIV-1-related outcomes. In our analyses of VL data from 521 recent HIV-1 seroconverters enrolled from eastern and southern Africa, HLA-A*03:01 was strongly and persistently associated with low VL in women (frequency = 11.3 %, P < 0.0001) but not in men (frequency = 7.7 %, P = 0.66). This novel sex by HLA interaction (P = 0.003, q = 0.090) did not extend to other frequent HLA class I alleles (n = 34), although HLA-C*18:01 also showed a weak association with low VL in women only (frequency = 9.3 %, P = 0.042, q > 0.50). In a reduced multivariable model, age, sex, geography (clinical sites), previously identified HLA factors (HLA-B*18, B*45, B*53, and B*57), and the interaction term for female sex and HLA-A*03:01 collectively explained 17.0 % of the overall variance in geometric mean VL over a 3-year follow-up period (P < 0.0001). Multiple sensitivity analyses of longitudinal and cross-sectional VL data yielded consistent results. These findings can serve as a proof of principle that the gap of "missing heritability" in quantitative genetics can be partially bridged by a systematic evaluation of sex-specific associations.
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Affiliation(s)
- Xuelin Li
- Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294 USA
| | - Matthew A. Price
- International AIDS Vaccine Initiative, New York City, NY USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA USA
| | - Dongning He
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Anatoli Kamali
- MRC/UVRI Uganda Virus Research Unit on AIDS, Masaka Site, Masaka, Uganda
| | | | - Shabir Lakhi
- Zambia-Emory HIV-1 Research Project, Lusaka, Zambia
| | - Eduard J. Sanders
- Centre for Geographic Medicine Research, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative (KAVI), Nairobi, Kenya
| | - Pauli N. Amornkul
- International AIDS Vaccine Initiative, New York City, NY USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA USA
| | - Susan Allen
- Projet San Francisco, Kigali, Rwanda
- Zambia-Emory HIV-1 Research Project, Lusaka, Zambia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA USA
| | - Eric Hunter
- Vaccine Research Center, Emory University, Atlanta, GA USA
| | - Richard A. Kaslow
- International AIDS Vaccine Initiative, New York City, NY USA
- Present Address: Department of Veterans Affairs, Washington, DC, 20420 USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, UK
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294 USA
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
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14
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Prentice HA, Pajewski NM, He D, Zhang K, Brown EE, Kilembe W, Allen S, Hunter E, Kaslow RA, Tang J. Host genetics and immune control of HIV-1 infection: fine mapping for the extended human MHC region in an African cohort. Genes Immun 2014; 15:275-81. [PMID: 24784026 PMCID: PMC4111776 DOI: 10.1038/gene.2014.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 03/28/2014] [Accepted: 03/28/2014] [Indexed: 12/31/2022]
Abstract
Multiple MHC loci encoding human leukocyte antigens (HLA) have allelic variants unequivocally associated with differential immune control of HIV-1 infection. Fine mapping based on single nucleotide polymorphisms (SNPs) in the extended MHC (xMHC) region is expected to reveal causal or novel factors and to justify a search for functional mechanisms. We have tested the utility of a custom fine-mapping platform (the ImmunoChip) for 172 HIV-1 seroconverters (SCs) and 449 seroprevalent individuals (SPs) from Lusaka, Zambia, with a focus on more than 6,400 informative xMHC SNPs. When conditioned on HLA and non-genetic factors previously associated with HIV-1 viral load (VL) in the study cohort, penalized approaches (HyperLasso models) identified an intergenic SNP (rs3094626 between RPP21 and HLA-E) and an intronic SNP (rs3134931 in NOTCH4) as novel correlates of early set-point VL in SCs. The minor allele of rs2857114 (downstream from HLA-DOB) was an unfavorable factor in SPs. Joint models based on demographic features, HLA alleles and the newly identified SNP variants could explain 29% and 15% of VL variance in SCs and SPs, respectively. These findings and bioinformatics strongly suggest that both classic and non-classic MHC genes deserve further investigation, especially in Africans with relatively short haplotype blocks.
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Affiliation(s)
- H A Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - N M Pajewski
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - D He
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - K Zhang
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - E E Brown
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - W Kilembe
- Zambia-Emory HIV-1 Research Project, Lusaka, Zambia
| | - S Allen
- 1] Zambia-Emory HIV-1 Research Project, Lusaka, Zambia [2] Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - E Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - R A Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Tang
- 1] Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA [2] Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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15
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Sanchez AM, DeMarco CT, Hora B, Keinonen S, Chen Y, Brinkley C, Stone M, Tobler L, Keating S, Schito M, Busch MP, Gao F, Denny TN. Development of a contemporary globally diverse HIV viral panel by the EQAPOL program. J Immunol Methods 2014; 409:117-30. [PMID: 24447533 DOI: 10.1016/j.jim.2014.01.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/07/2013] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
The significant diversity among HIV-1 variants poses serious challenges for vaccine development and for developing sensitive assays for screening, surveillance, diagnosis, and clinical management. Recognizing a need to develop a panel of HIV representing the current genetic and geographic diversity NIH/NIAID contracted the External Quality Assurance Program Oversight Laboratory (EQAPOL) to isolate, characterize and establish panels of HIV-1 strains representing global diverse subtypes and circulating recombinant forms (CRFs), and to make them available to the research community. HIV-positive plasma specimens and previously established isolates were collected through a variety of collaborations with a preference for samples from acutely/recently infected persons. Source specimens were cultured to high-titer/high-volume using well-characterized cryopreserved PBMCs from National y donors. Panel samples were stored as neat culture supernatant or diluted into defibrinated plasma. Characterization for the final expanded virus stocks included viral load, p24 antigen, infectivity (TCID), sterility, coreceptor usage, and near full-length genome sequencing. Viruses are made available to approved, interested laboratories using an online ordering application. The current EQAPOL Viral Diversity panel includes 100 viral specimens representing 6 subtypes (A, B, C, D, F, and G), 2 sub-subtypes (F1 and F2), 7 CRFs (01, 02, 04, 14, 22, 24, and 47), 19 URFs and 3 group O viruses from 22 countries. The EQAPOL Viral Diversity panel is an invaluable collection of well-characterized reagents that are available to the scientific community, including researchers, epidemiologists, and commercial manufacturers of diagnostics and pharmaceuticals to support HIV research, as well as diagnostic and vaccine development.
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Affiliation(s)
| | | | - Bhavna Hora
- Duke University Medical Center, Durham, NC, USA
| | | | - Yue Chen
- Duke University Medical Center, Durham, NC, USA
| | | | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Leslie Tobler
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Sheila Keating
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Marco Schito
- HJF-DAIDS, A Division of The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | | | - Feng Gao
- Duke University Medical Center, Durham, NC, USA.
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16
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Prentice HA, Price MA, Porter TR, Cormier E, Mugavero MJ, Kamali A, Karita E, Lakhi S, Sanders EJ, Anzala O, Amornkul PN, Allen S, Hunter E, Kaslow RA, Gilmour J, Tang J. Dynamics of viremia in primary HIV-1 infection in Africans: insights from analyses of host and viral correlates. Virology 2013; 449:254-62. [PMID: 24418560 DOI: 10.1016/j.virol.2013.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/11/2013] [Accepted: 11/14/2013] [Indexed: 12/15/2022]
Abstract
In HIV-1 infection, plasma viral load (VL) has dual implications for pathogenesis and public health. Based on well-known patterns of HIV-1 evolution and immune escape, we hypothesized that VL is an evolving quantitative trait that depends heavily on duration of infection (DOI), demographic features, human leukocyte antigen (HLA) genotypes and viral characteristics. Prospective data from 421 African seroconverters with at least four eligible visits did show relatively steady VL beyond 3 months of untreated infection, but host and viral factors independently associated with cross-sectional and longitudinal VL often varied by analytical approaches and sliding time windows. Specifically, the effects of age, HLA-B(⁎)53 and infecting HIV-1 subtypes (A1, C and others) on VL were either sporadic or highly sensitive to time windows. These observations were strengthened by the addition of 111 seroconverters with 2-3 eligible VL results, suggesting that DOI should be a critical parameter in epidemiological and clinical studies.
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Affiliation(s)
- Heather A Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York City, NY, USA; Department of Epidemiology & Biostatistics, UCSF, San Francisco, CA, USA
| | - Travis R Porter
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Emmanuel Cormier
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, UK
| | - Michael J Mugavero
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anatoli Kamali
- MRC/UVRI Uganda Virus Research Unit on AIDS, Masaka Site, Masaka, Uganda
| | | | - Shabir Lakhi
- Zambia-Emory HIV Research Project, Lusaka, Zambia
| | - Eduard J Sanders
- Centre for Geographic Medicine Research, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya; Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative (KAVI), Nairobi, Kenya
| | | | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Eric Hunter
- Vaccine Research Center, Emory University, Atlanta, GA, USA
| | - Richard A Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, UK
| | - Jianming Tang
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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17
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Abstract
Objective: To describe immunologic, virologic, and clinical HIV disease progression by HIV-1 subtype among Africans with well documented estimated dates of HIV infection (EDIs). Design: Prospective cohort. Methods: Adults and youth with documented HIV-1 infection in the past 12 months were recruited from seroincidence cohorts in East and Southern Africa and followed at 3–6 month intervals. Blood for lymphocyte subset and viral load determination was collected at each visit. Pol was sequenced from the first positive specimen to ascertain subtype. Preantiretroviral therapy disease progression was measured by three time-to-event endpoints: CD4+ cell count 350 cells/μl or less, viral load measurement at least 1 × 105 copies/ml, and clinical AIDS. Results: From 2006 to 2011, 615 participants were enrolled at nine research centers in Kenya, Rwanda, South Africa, Uganda, and Zambia; 579 (94.1%) had viral subtyping completed. Predominant subtypes were C (256, 44.2%), A (209, 36.1%), and D (84, 14.5%). After adjustment for age, sex, and human leukocyte antigen alleles in Cox regression analyses, subtype C-infected participants progressed faster than subtype A to all three endpoints [CD4+ hazard ratio 1.60, 95% (confidence interval) CI 1.16, 2.20; viral load hazard ratio 1.59, 95% CI 1.12, 2.25; and AIDS hazard ratio 1.60, 95% CI 1.11, 2.31). Subtype D-infected participants reached high viral load more rapidly (hazard ratio 1.61, 95% CI 1.01, 2.57) and progressed nearly twice as fast to AIDS compared to subtype A (hazard ratio 1.93, 95% CI 1.21, 3.09). Conclusion: Subtype-specific differences in HIV disease progression suggest that the local subtype distribution be considered when planning HIV programs and designing and defining clinical endpoints for HIV prevention trials.
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18
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Munier CML, Kelleher AD, Kent SJ, De Rose R. The role of T cell immunity in HIV-1 infection. Curr Opin Virol 2013; 3:438-46. [PMID: 23747036 DOI: 10.1016/j.coviro.2013.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/07/2013] [Accepted: 05/07/2013] [Indexed: 12/11/2022]
Abstract
The interplay between the T cell immune response and human immunodeficiency virus (HIV)-1 largely determines the outcome of infection. Typically, the virus overcomes the immune defences leading to a gradual decline in function that permits the development of disease. In recent years, a concerted effort in comparing T cell responses between 'controllers' and 'progressors' is beginning to identify the T cell subsets and factors that affect disease progression related to the effector functions of both CD4 and CD8 T cells. These efforts are providing opportunities for development of novel therapies and vaccines.
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Affiliation(s)
- C Mee Ling Munier
- The Kirby Institute for Infection and Immunity in Society, University of NSW, Sydney, NSW, Australia
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19
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HLA-B*44 is associated with a lower viral set point and slow CD4 decline in a cohort of Chinese homosexual men acutely infected with HIV-1. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 20:1048-54. [PMID: 23677320 DOI: 10.1128/cvi.00015-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
HLA class I alleles have been shown to have differential impacts on the viral load and the outcome of HIV-1 disease progression. In this study, HLA class I types from residents of China with acute HIV-1 infection, diagnosed between 2006 and 2011, were identified and the association between expression of individual HLA alleles and the level of the set point viral load was analyzed. A lower level of set point viral load was found to be associated with the Bw4 homozygote on HLA-B alleles. B*44 and B*57 alleles have also been found to be associated with lower set point viral load. The set point viral load of B*44-positive individuals homozygous for Bw4 was significantly lower than that of B*44-negative individuals homozygous for Bw4 (P = 0.030). The CD4 count declined to <350 in fewer B*44-positive individuals than B*44-negative individuals (X(2) = 7.295, P = 0.026). B*44-positive individuals had a lower magnitude of p24 pool-specific T cell responses than B*44-negative individuals homozygous for Bw4, though this was not statistically significant. The p24 pool-specific T cell responses were also inversely correlated with lower viral load (rs = -0.88, P = 0.033). Six peptides within p24 were recognized to induce the specific-T cell response in B*44-positive individuals, and the peptide breadth of response was same as that in B*44-negative individuals homozygous for Bw4, but the median magnitude of specific-T cell responses to the recognized peptides in B*44-positive individuals was lower than that in B*44-negative individuals homozygous for Bw4 (P = 0.049). These findings imply that weak p24-specific CD8(+) T cell responses might play an important role in the control of HIV viremia in B*44 allele-positive individuals. Such studies might contribute to the development of future therapeutic strategies that take into account the genetic background of the patients.
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20
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Prentice HA, Porter TR, Price MA, Cormier E, He D, Farmer PK, Kamali A, Karita E, Lakhi S, Sanders EJ, Anzala O, Amornkul PN, Allen S, Hunter E, Kaslow RA, Gilmour J, Tang J. HLA-B*57 versus HLA-B*81 in HIV-1 infection: slow and steady wins the race? J Virol 2013; 87:4043-51. [PMID: 23365442 PMCID: PMC3624227 DOI: 10.1128/jvi.03302-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 01/23/2013] [Indexed: 11/20/2022] Open
Abstract
Two human leukocyte antigen (HLA) variants, HLA-B*57 and -B*81, are consistently known as favorable host factors in human immunodeficiency virus type 1 (HIV-1)-infected Africans and African-Americans. In our analyses of prospective data from 538 recent HIV-1 seroconverters and cross-sectional data from 292 subjects with unknown duration of infection, HLA-B*57 (mostly B*57:03) and -B*81 (exclusively B*81:01) had mostly discordant associations with virologic and immunologic manifestations before antiretroviral therapy. Specifically, relatively low viral load (VL) in HLA-B*57-positive subjects (P ≤ 0.03 in various models) did not translate to early advantage in CD4(+) T-cell (CD4) counts (P ≥ 0.37). In contrast, individuals with HLA-B*81 showed little deviation from the normal set point VL (P > 0.18) while maintaining high CD4 count during early and chronic infection (P = 0.01). These observations suggest that discordance between VL and CD4 count can occur in the presence of certain HLA alleles and that effective control of HIV-1 viremia is not always a prerequisite for favorable prognosis (delayed immunodeficiency). Of note, steady CD4 count associated with HLA-B*81 in HIV-1-infected Africans may depend on the country of origin, as observations differed slightly between subgroups enrolled in southern Africa (Zambia) and eastern Africa (Kenya, Rwanda, and Uganda).
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Affiliation(s)
| | | | - Matthew A. Price
- International AIDS Vaccine Initiative (IAVI), New York City, New York, USA
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, USA
| | - Emmanuel Cormier
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, United Kingdom
| | | | | | - Anatoli Kamali
- MRC/UVRI Uganda Virus Research Unit on AIDS, Masaka Site, Masaka, Uganda
| | | | - Shabir Lakhi
- Zambia-Emory HIV Research Project, Lusaka, Zambia
| | - Eduard J. Sanders
- Centre for Geographic Medicine Research, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, United Kingdom
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative (KAVI), Nairobi, Kenya
| | - Pauli N. Amornkul
- International AIDS Vaccine Initiative (IAVI), New York City, New York, USA
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
- Project San Francisco, Kigali, Rwanda
- Zambia-Emory HIV Research Project, Lusaka, Zambia
| | | | - Richard A. Kaslow
- Department of Epidemiology
- Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, United Kingdom
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
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21
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Haaland RE, Johnson JA, Tang J. Recent advances in research of HIV infection: implications of viral and host genetics on treatment and prevention. Public Health Genomics 2013; 16:31-6. [PMID: 23548715 DOI: 10.1159/000345935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The genetic diversity among human immunodeficiency virus (HIV) subtypes as well as the variability of viral sequences found in HIV-infected individuals presents a number of difficult obstacles for the development of universally effective HIV treatment and prevention methods. Here, we present a brief summary of recent developments in the analysis of viral genetics and human genomics to provide insight into future methods for HIV treatment and prevention. Recent studies have mined viral sequences found in newly infected individuals to identify common features of all transmitted viruses that could provide potential targets for HIV vaccine development. Analysis of human immunogenetics has identified specific alleles associated with reduced virus loads in HIV-infected individuals providing valuable information that may influence individual responses to treatment and prevention methods. Increased sensitivity of antiretroviral drug resistance testing has improved the detection of hidden drug resistant virus but also highlighted the potential for drug resistant viruses to reduce the effectiveness of clinical treatment regimens. The rapidly expanding amount of data generated by studies of viral genetics and human immunogenetics will provide valuable information to guide the design of new strategies to improve clinical treatment and enhance HIV vaccine development.
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Affiliation(s)
- R E Haaland
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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22
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Baalwa J, Wang S, Parrish NF, Decker JM, Keele BF, Learn GH, Yue L, Ruzagira E, Ssemwanga D, Kamali A, Amornkul PN, Price MA, Kappes JC, Karita E, Kaleebu P, Sanders E, Gilmour J, Allen S, Hunter E, Montefiori DC, Haynes BF, Cormier E, Hahn BH, Shaw GM. Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones. Virology 2012; 436:33-48. [PMID: 23123038 DOI: 10.1016/j.virol.2012.10.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 09/25/2012] [Accepted: 10/05/2012] [Indexed: 11/18/2022]
Abstract
We report the molecular identification, cloning and initial biological characterization of 12 full-length HIV-1 subtype A, D and A/D recombinant transmitted/founder (T/F) genomes. T/F genomes contained intact canonical open reading frames and all T/F viruses were replication competent in primary human T-cells, although subtype D virus replication was more efficient (p<0.05). All 12 viruses utilized CCR5 but not CXCR4 as a co-receptor for entry and exhibited a neutralization profile typical of tier 2 primary virus strains, with significant differences observed between subtype A and D viruses with respect to sensitivity to monoclonal antibodies VRC01, PG9 and PG16 and polyclonal subtype C anti-HIV IgG (p<0.05 for each). The present report doubles the number of T/F HIV-1 clones available for pathogenesis and vaccine research and extends their representation to include subtypes A, B, C and D.
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Affiliation(s)
- Joshua Baalwa
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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23
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Abstract
The dynamics of HIV-1 viremia is a complex and evolving landscape with clinical and epidemiological (public health) implications. Most studies have relied on the use of set-point viral load (VL) as a readily available proxy of viral dynamics to assess host and viral correlates. This review highlights recent findings from population-based studies of set-point VL, focusing primarily on robust data related to host genetics. A comprehensive understanding of viral dynamics will clearly need to consider both host and viral characteristics, with close attention to (i) the timing of VL measurements, (ii) the biology of viral evolution, (iii) compartments of active viral replication, (iv) the transmission source partner as the immediate past microenvironment, and (v) proper application of statistical models.
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Affiliation(s)
- Heather A. Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama;
- Author to whom correspondence should be addressed; ; Tel.: +1-720-352-3432
| | - Jianming Tang
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama;
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama;
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24
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Prevalence of seroconversion symptoms and relationship to set-point viral load: findings from a subtype C epidemic, 1995-2009. AIDS 2012; 26:175-84. [PMID: 22089380 DOI: 10.1097/qad.0b013e32834ed8c8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To describe symptoms, physical examination findings, and set-point viral load associated with acute HIV seroconversion in a heterosexual cohort of HIV-discordant couples in Zambia. DESIGN We followed HIV serodiscordant couples in Lusaka, Zambia from 1995 to 2009 with HIV testing of negative partners and symptom inventories 3 monthly, and physical examinations annually. METHODS We compared prevalence of self-reported or treated symptoms (malaria syndrome, chronic diarrhea, asthenia, night sweats, and oral candidiasis) and annual physical examination findings (unilateral or bilateral neck, axillary, or inguinal adenopathy; and dermatosis) in seroconverting vs. HIV-negative or HIV-positive intervals, controlling for repeated observations, age, and sex. A composite score comprised of significant symptoms and physical examination findings predictive of seroconversion vs. HIV-negative intervals was constructed. We modeled the relationship between number of symptoms and physical examination findings at seroconversion and log set-point viral load using linear regression. RESULTS Two thousand, three hundred and eighty-eight HIV-negative partners were followed for a median of 18 months; 429 seroconversions occurred. Neither symptoms nor physical examination findings were reported for most seroconverters. Seroconversion was significantly associated with malaria syndrome among nondiarrheic patients [adjusted odds ratio (aOR) = 4.0], night sweats (aOR = 1.4), and bilateral axillary (aOR = 1.6), inguinal (aOR = 2.2), and neck (aOR = 2.2) adenopathy relative to HIV-negative intervals. Median number of symptoms and findings was positively associated with set-point viral load (P < 0.001). CONCLUSION Although most acute and early infections were asymptomatic, malaria syndrome was more common and more severe during seroconversion. When present, symptoms and physical examination findings were nonspecific and associated with higher set-point viremia.
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