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Lindquist L, Kilembe W, Karita E, Price MA, Kamali A, Kaleebu P, Tang J, Allen S, Hunter E, Gilmour J, Rowland-Jones SL, Sanders EJ, Hassan AS, Esbjörnsson J. HLA-A*23 Is Associated With Lower Odds of Acute Retroviral Syndrome in Human Immunodeficiency Virus Type 1 Infection: A Multicenter Sub-Saharan African Study. Open Forum Infect Dis 2024; 11:ofae129. [PMID: 38560608 PMCID: PMC10977907 DOI: 10.1093/ofid/ofae129] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
The role of human leukocyte antigen (HLA) class I and killer immunoglobulin-like receptor molecules in mediating acute retroviral syndrome (ARS) during human immunodeficiency virus type 1 (HIV-1) infection is unclear. Among 72 sub-Saharan African adults, HLA-A*23 was associated with lower odds of ARS (adjusted odds ratio, 0.10 [95% confidence interval, .01-.48]; P = .009), which warrants further studies to explore its role on HIV-1-specific immunopathogenesis.
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Affiliation(s)
- Lovisa Lindquist
- Lund University Centre, Lund University, Lund, Sweden
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - William Kilembe
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - Etienne Karita
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - Matt A Price
- International AIDS Vaccine Initiative, New York, New York, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Centre Research Institute, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Susan Allen
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Eric Hunter
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, New York, New York, USA
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | - Sarah L Rowland-Jones
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Eduard J Sanders
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Aurum Institute, Johannesburg, South Africa
| | - Amin S Hassan
- Lund University Centre, Lund University, Lund, Sweden
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joakim Esbjörnsson
- Lund University Centre, Lund University, Lund, Sweden
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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2
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van Duijn J, Stieh D, Fernandez N, King D, Gilmour J, Tolboom J, Callewaert K, Willems W, Pau MG, De Rosa SC, McElrath MJ, Barouch DH, Hayes P. Mosaic HIV-1 vaccination induces anti-viral CD8 + T cell functionality in the phase 1/2a clinical trial APPROACH. J Virol 2023; 97:e0112623. [PMID: 37811993 PMCID: PMC10617392 DOI: 10.1128/jvi.01126-23] [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: 07/27/2023] [Accepted: 08/28/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE The functionality of CD8+ T cells against human immunodeficiency virus-1 (HIV-1) antigens is indicative of HIV-progression in both animal models and people living with HIV. It is, therefore, of interest to assess CD8+ T cell responses in a prophylactic vaccination setting, as this may be an important component of the immune system that inhibits HIV-1 replication. T cell responses induced by the adenovirus serotype 26 (Ad26) mosaic vaccine regimen were assessed previously by IFN-γ ELISpot and flow cytometric assays, yet these assays only measure cytokine production but not the capacity of CD8+ T cells to inhibit replication of HIV-1. In this study, we demonstrate direct anti-viral function of the clinical Ad26 mosaic vaccine regimen through ex vivo inhibition of replication of diverse clades of HIV-1 isolates in the participant's own CD4+ T cells.
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Affiliation(s)
| | - Daniel Stieh
- Janssen Vaccines & Prevention B.V., Leiden, the Netherlands
| | - Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Deborah King
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Jeroen Tolboom
- Janssen Vaccines & Prevention B.V., Leiden, the Netherlands
| | | | | | - Maria G. Pau
- Janssen Vaccines & Prevention B.V., Leiden, the Netherlands
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
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3
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Michelo CM, Fiore-Gartland A, Dalel JA, Hayes P, Tang J, McGowan E, Kilembe W, Fernandez N, Gilmour J, Hunter E. Cohort-Specific Peptide Reagents Broaden Depth and Breadth Estimates of the CD8 T Cell Response to HIV-1 Gag Potential T Cell Epitopes. Vaccines (Basel) 2023; 11:472. [PMID: 36851349 PMCID: PMC9961105 DOI: 10.3390/vaccines11020472] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
An effective HIV vaccine will need to stimulate immune responses against the sequence diversity presented in circulating virus strains. In this study, we evaluate breadth and depth estimates of potential T-cell epitopes (PTEs) in transmitted founder virus sequence-derived cohort-specific peptide reagents against reagents representative of consensus and global sequences. CD8 T-cells from twenty-six HIV-1+ PBMC donor samples, obtained at 1-year post estimated date of infection, were evaluated. ELISpot assays compared responses to 15mer consensus (n = 121), multivalent-global (n = 320), and 10mer multivalent cohort-specific (n = 300) PTE peptides, all mapping to the Gag antigen. Responses to 38 consensus, 71 global, and 62 cohort-specific PTEs were confirmed, with sixty percent of common global and cohort-specific PTEs corresponding to consensus sequences. Both global and cohort-specific peptides exhibited broader epitope coverage compared to commonly used consensus reagents, with mean breadth estimates of 3.2 (global), 3.4 (cohort) and 2.2 (consensus) epitopes. Global or cohort peptides each identified unique epitope responses that would not be detected if these peptide pools were used alone. A peptide set designed around specific virologic and immunogenetic characteristics of a target cohort can expand the detection of CD8 T-cell responses to epitopes in circulating viruses, providing a novel way to better define the host response to HIV-1 with implications for vaccine development.
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Affiliation(s)
- Clive M. Michelo
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jama A. Dalel
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - William Kilembe
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Eric Hunter
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
- Emory Vaccine Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
- Emory National Primate Research Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
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4
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Fernandez N, Hayes P, Makinde J, Hare J, King D, Xu R, Rehawi O, Mezzell AT, Kato L, Mugaba S, Serwanga J, Chemweno J, Nduati E, Price MA, Osier F, Ochsenbauer C, Yue L, Hunter E, Gilmour J. Assessment of a diverse panel of transmitted/founder HIV-1 infectious molecular clones in a luciferase based CD8 T-cell mediated viral inhibition assay. Front Immunol 2022; 13:1029029. [PMID: 36532063 PMCID: PMC9751811 DOI: 10.3389/fimmu.2022.1029029] [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: 08/26/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction Immunological protection against human immunodeficiency virus-1 (HIV-1) infection is likely to require both humoral and cell-mediated immune responses, the latter involving cytotoxic CD8 T-cells. Characterisation of CD8 T-cell mediated direct anti-viral activity would provide understanding of potential correlates of immune protection and identification of critical epitopes associated with HIV-1 control. Methods The present report describes a functional viral inhibition assay (VIA) to assess CD8 T-cell-mediated inhibition of replication of a large and diverse panel of 45 HIV-1 infectious molecular clones (IMC) engineered with a Renilla reniformis luciferase reporter gene (LucR), referred to as IMC-LucR. HIV-1 IMC replication in CD4 T-cells and CD8 T-cell mediated inhibition was characterised in both ART naive subjects living with HIV-1 covering a broad human leukocyte antigen (HLA) distribution and compared with uninfected subjects. Results & discussion CD4 and CD8 T-cell lines were established from subjects vaccinated with a candidate HIV-1 vaccine and provided standard positive controls for both assay quality control and facilitating training and technology transfer. The assay was successfully established across 3 clinical research centres in Kenya, Uganda and the United Kingdom and shown to be reproducible. This IMC-LucR VIA enables characterisation of functional CD8 T-cell responses providing a tool for rational T-cell immunogen design of HIV-1 vaccine candidates and evaluation of vaccine-induced T-cell responses in HIV-1 clinical trials.
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Affiliation(s)
- Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,*Correspondence: Natalia Fernandez, ; Peter Hayes,
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,*Correspondence: Natalia Fernandez, ; Peter Hayes,
| | - Julia Makinde
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,IAVI, New York, NY, United States
| | - Deborah King
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Ola Rehawi
- University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Laban Kato
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Susan Mugaba
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Jennifer Serwanga
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - James Chemweno
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Eunice Nduati
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Matt A. Price
- IAVI, New York, NY, United States,Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, United States
| | - Faith Osier
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | | | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Jill Gilmour
- Department of Infectious Diseases, Imperial College, London, United Kingdom
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5
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Kibirige CN, Manak M, King D, Abel B, Hack H, Wooding D, Liu Y, Fernandez N, Dalel J, Kaye S, Imami N, Jagodzinski L, Gilmour J. Author Correction: Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC. Sci Rep 2022; 12:11792. [PMID: 35821052 PMCID: PMC9276778 DOI: 10.1038/s41598-022-16308-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- C N Kibirige
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK.
| | - M Manak
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA.,Turesol Consulting, 314 S. Henderson Road, King of Prussia, PA, 19406, USA
| | - D King
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - B Abel
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - H Hack
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA.,Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - D Wooding
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - Y Liu
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA.,Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - N Fernandez
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - J Dalel
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - Steve Kaye
- Molecular Diagnostics Unit, Imperial College London, Jeferiss Trust Laboratory, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - N Imami
- Centre for Immunology and Vaccinology, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - L Jagodzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA.,Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - J Gilmour
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
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6
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Kapaata A, Balinda SN, Hare J, Leonova O, Kikaire B, Egesa M, Lubyayi L, Macharia GN, Kamali A, Gilmour J, Bagaya B, Salazar-Gonzalez JF, Kaleebu P. Infection with HIV-1 subtype D among acutely infected Ugandans is associated with higher median concentration of cytokines compared to subtype A. IJID Regions 2022; 3:89-95. [PMID: 35755471 PMCID: PMC9205166 DOI: 10.1016/j.ijregi.2022.03.007] [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] [Received: 12/21/2021] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 11/19/2022]
Abstract
HIV-1 subtype D exhibited significantly higher median concentrations of cytokines IL-12/23p40 and IL-1α were associated with faster CD4+T cell count decline bFGF was associated with maintenance of CD4+ counts above 350 cells/microliter
Objective The observation that HIV-1 subtype D progresses faster to disease than subtype A prompted us to examine cytokine levels early after infection within the predominant viral subtypes that circulate in Uganda and address the following research questions: (1) Do cytokine levels vary between subtypes A1 and D? (2) Do cytokine profiles correlate with disease outcomes? Methods To address these questions, HIV-1 subtypes were determined by population sequencing of the HIV-1 pol gene and 37 plasma cytokine concentrations were evaluated using V-Plex kits on Meso Scale Discovery platform in 65 recent sero-converters. Results HIV-1 subtype D (pol) infections exhibited significantly higher median plasma concentrations of IL-5, IL-16, IL-1α, IL-7, IL-17A, CCL11 (Eotaxin-1), CXCL10 (IP-10), CCL13 (MCP-4) and VEGF-D compared to subtype A1 (pol) infections. We also found that IL-12/23p40 and IL-1α were associated with faster CD4+T cell count decline, while bFGF was associated with maintenance of CD4+ counts above 350 cells/microliter. Conclusion Our results suggest that increased production of cytokines in early HIV infection may trigger a disruption of the immune environment and contribute to pathogenic mechanisms underlying the accelerated disease progression seen in individuals infected with HIV-1 subtype D in Uganda.
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Affiliation(s)
- Anne Kapaata
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Corresponding author:
| | - Sheila N. Balinda
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Jonathan Hare
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London, UK
| | - Olga Leonova
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London, UK
| | - Bernard Kikaire
- Uganda Virus Research Institute
- Department of Paediatrics, College of Health sciences, Makerere university
| | - Moses Egesa
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Lawrence Lubyayi
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Gladys N. Macharia
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London, UK
| | | | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London, UK
| | - Bernard Bagaya
- Department of Microbiology, College of Health Sciences, Makerere university
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
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7
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Balinda SN, Kapaata A, Xu R, Salazar MG, Mezzell AT, Qin Q, Herard K, Dilernia D, Kamali A, Ruzagira E, Kibengo FM, Song H, Ochsenbauer C, Salazar-Gonzalez JF, Gilmour J, Hunter E, Yue L, Kaleebu P. Characterization of Near Full-Length Transmitted/Founder HIV-1 Subtype D and A/D Recombinant Genomes in a Heterosexual Ugandan Population (2006–2011). Viruses 2022; 14:v14020334. [PMID: 35215928 PMCID: PMC8874453 DOI: 10.3390/v14020334] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 12/04/2022] Open
Abstract
Detailed characterization of transmitted HIV-1 variants in Uganda is fundamentally important to inform vaccine design, yet studies on the transmitted full-length strains of subtype D viruses are limited. Here, we amplified single genomes and characterized viruses, some of which were previously classified as subtype D by sub-genomic pol sequencing that were transmitted in Uganda between December 2006 to June 2011. Analysis of 5′ and 3′ half genome sequences showed 73% (19/26) of infections involved single virus transmissions, whereas 27% (7/26) of infections involved multiple variant transmissions based on predictions of a model of random virus evolution. Subtype analysis of inferred transmitted/founder viruses showed a high transmission rate of inter-subtype recombinants (69%, 20/29) involving mainly A1/D, while pure subtype D variants accounted for one-third of infections (31%, 9/29). Recombination patterns included a predominance of subtype D in the gag/pol region and a highly recombinogenic envelope gene. The signal peptide-C1 region and gp41 transmembrane domain (Tat2/Rev2 flanking region) were hotspots for A1/D recombination events. Analysis of a panel of 14 transmitted/founder molecular clones showed no difference in replication capacity between subtype D viruses (n = 3) and inter-subtype mosaic recombinants (n = 11). However, individuals infected with high replication capacity viruses had a faster CD4 T cell loss. The high transmission rate of unique inter-subtype recombinants is striking and emphasizes the extraordinary challenge for vaccine design and, in particular, for the highly variable and recombinogenic envelope gene, which is targeted by rational designs aimed to elicit broadly neutralizing antibodies.
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Affiliation(s)
- Sheila N. Balinda
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
- Correspondence: ; Tel.: +25-675-466-0098
| | - Anne Kapaata
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Rui Xu
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Maria G. Salazar
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Allison T. Mezzell
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, 3230, Eden Ave, Cincinnati, OH 45267, USA;
| | - Qianhong Qin
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Kimberly Herard
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Dario Dilernia
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Anatoli Kamali
- International AIDS Vaccine Initiative (IAVI), Nairobi 00202, Kenya;
| | - Eugene Ruzagira
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Freddie M. Kibengo
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Heeyah Song
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London SW10 9NH, UK;
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30329, USA
| | - Ling Yue
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Pontiano Kaleebu
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
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8
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Kibirige CN, Manak M, King D, Abel B, Hack H, Wooding D, Liu Y, Fernandez N, Dalel J, Kaye S, Imami N, Jagodzinski L, Gilmour J. Author Correction: Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC. Sci Rep 2022; 12:1980. [PMID: 35105930 PMCID: PMC8807713 DOI: 10.1038/s41598-022-06286-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- C. N. Kibirige
- grid.428062.a0000 0004 0497 2835IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH UK
| | - M. Manak
- grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA ,grid.507680.c0000 0001 2230 3166U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD 20910 USA ,Present Address: Turesol Consulting, 314 S. Henderson Road, King of Prussia, PA 19406 USA
| | - D. King
- grid.428062.a0000 0004 0497 2835IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH UK
| | - B. Abel
- grid.428062.a0000 0004 0497 2835IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH UK
| | - H. Hack
- grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA ,grid.507680.c0000 0001 2230 3166U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD 20910 USA ,grid.507680.c0000 0001 2230 3166Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD 20910 USA
| | - D. Wooding
- grid.428062.a0000 0004 0497 2835IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH UK
| | - Y. Liu
- grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA ,grid.507680.c0000 0001 2230 3166U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD 20910 USA ,grid.507680.c0000 0001 2230 3166Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD 20910 USA
| | - N. Fernandez
- grid.428062.a0000 0004 0497 2835IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH UK
| | - J. Dalel
- grid.428062.a0000 0004 0497 2835IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH UK
| | - Steve Kaye
- grid.7445.20000 0001 2113 8111Molecular Diagnostics Unit, Imperial College London, Jefferiss Trust Laboratory, St. Mary’s Campus, Norfolk Place, London, W2 1PG UK
| | - N. Imami
- grid.428062.a0000 0004 0497 2835Centre for Immunology and Vaccinology, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH UK
| | - L. Jagodzinski
- grid.507680.c0000 0001 2230 3166U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD 20910 USA ,grid.507680.c0000 0001 2230 3166Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD 20910 USA
| | - J. Gilmour
- grid.428062.a0000 0004 0497 2835IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH UK
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9
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Kibirige CN, Manak M, King D, Abel B, Hack H, Wooding D, Liu Y, Fernandez N, Dalel J, Kaye S, Imami N, Jagodzinski L, Gilmour J. Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC. Sci Rep 2022; 12:1550. [PMID: 35091568 PMCID: PMC8799642 DOI: 10.1038/s41598-021-03016-1] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022] Open
Abstract
An LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Inosine and mixed nucleotide bases were included at polymorphic sites. Real-time RT-qPCR and qPCR were performed on plasma viral RNA and cellular lysates. A step-up amplification approach to allow binding of primers across polymorphic regions showed improved sensitivity compared to universal cycling. Unlike a lead competing laboratory-developed assay, all major HIV-1 subtypes, and a wide range of recombinants from a 127-member diversity panel were detected and accurately quantified in spiked plasmas. Semi-nested PCR increased detection sensitivity even further. The assay was able to detect down to 88 copies/mL of HIV-1 in plasma with 95% efficiency or the equivalent of a single infected cell. The PCR assay will be valuable in studies that monitor very low viral levels including residual or break through HIV-1 in patients receiving antiretroviral therapy, in HIV-1 cure, and in other research studies.
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Affiliation(s)
- C N Kibirige
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK.
| | - M Manak
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD, 20910, USA
- Turesol Consulting, 314 S. Henderson Road, King of Prussia, PA, 19406, USA
| | - D King
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - B Abel
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - H Hack
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD, 20910, USA
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - D Wooding
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - Y Liu
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD, 20910, USA
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - N Fernandez
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - J Dalel
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - Steve Kaye
- Molecular Diagnostics Unit, Imperial College London, Jefferiss Trust Laboratory, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - N Imami
- Centre for Immunology and Vaccinology, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - L Jagodzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD, 20910, USA
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - J Gilmour
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
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10
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Umviligihozo G, Muok E, Nyirimihigo Gisa E, Xu R, Dilernia D, Herard K, Song H, Qin Q, Bizimana J, Farmer P, Hare J, Gilmour J, Allen S, Karita E, Hunter E, Yue L. Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts. Front Microbiol 2021; 12:734929. [PMID: 34690973 PMCID: PMC8529237 DOI: 10.3389/fmicb.2021.734929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022] Open
Abstract
Most studies of HIV-1 transmission have focused on subtypes B and C. In this study, we determined the genomic sequences of the transmitted founder (TF) viruses from acutely infected individuals enrolled between 2005 and 2011 into IAVI protocol C in Rwanda and have compared these isolates to viruses from more recent (2016–2019) acute/early infections in three at risk populations – MSM, high risk women (HRW), and discordant couples (DC). For the Protocol C samples, we utilized near full-length single genome (NFLG) amplification to generate 288 HIV-1 amplicons from 26 acutely infected seroconverters (SC), while for the 21 recent seroconverter samples (13 from HRW, two from DC, and six from MSM), we PCR amplified overlapping half-genomes. Using PacBio SMRT technology combined with the MDPseq workflow, we performed multiplex sequencing to obtain high accuracy sequences for each amplicon. Phylogenetic analyses indicated that the majority of recent transmitted viruses from DC and HRW clustered within those of the earlier Protocol C cohort. However, five of six sequences from the MSM cohort branched together and were greater than 97% identical. Recombination analyses revealed a high frequency (6/26; 23%) of unique inter-subtype recombination in Protocol C with 19% AC and 4% CD recombinant viruses, which contrasted with only 6.5% of recombinants defined by sequencing of the pol gene previously. The frequency of recombinants was significantly higher (12/21; 57%) in the more recent isolates, although, the five related viruses from the MSM cohort had identical recombination break points. While major drug resistance mutations were absent from Protocol C viruses, 4/21 of recent isolates exhibited transmitted nevirapine resistance. These results demonstrate the ongoing evolution and increased prevalence of recombinant and drug resistant transmitted viruses in Rwanda and highlight the importance of defining NFLG sequences to fully understand the nature of TF viruses and in particular the prevalence of unique recombinant forms (URFs) in transmission cohorts.
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Affiliation(s)
| | - Erick Muok
- Centre for Family Health Research, Kigali, Rwanda
| | | | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dario Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Kimberley Herard
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Heeyah Song
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Qianhong Qin
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Paul Farmer
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | | | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
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11
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Hebding J, Wingfield L, Negreskul Y, Gilmour J. 1369 Clinical Outcomes in Patients Undergoing Emergency General Surgery During the Covid-19 Pandemic Versus Control Patients: A Systematic Review and Meta-Analysis. Br J Surg 2021. [DOI: 10.1093/bjs/znab259.952] [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] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Introduction
Throughout the Covid-19 pandemic, the surgical community has attempted to address whether it is safe to continue surgery. The aim of this research was to review evidence on emergency general patients operated on during the pandemic compared to patients undergoing emergency surgery during non-pandemic times to determine if operating during the Covid-19 pandemic led to an increased risk of death, length of hospital stay and complications.
Method
A systematic review of the literature was performed. PubMed, Cochrane, MEDLINE, Science Direct, Springer Link, Elsevier, and reference lists were analysed for inclusion on 2 January 2021.
Results
Nine studies and 5,022 patients were included. There were no significant differences in the control group vs pandemic group in mean age (52.3yrs vs 51.9yrs, p = 0.67) or gender (44.4% females vs 49.3%, p = 0.173). Pooled analysis of control vs pandemic showed a mortality rate of 1.26% vs 3.06% (CI:-6.58–6.58, p = 1.00). Mean length of hospital stay was 7.9 vs 7.7 days in control v. pandemic (CI: -2.93-3.33, p = 0.87) and post-operative complication rate of 20.2% vs 25.7% (CI -6.4-25.0, p = 0.20), (control vs pandemic). The pandemic group had significantly more operative management (47.0% vs 40.0%, p = 0.03) with no significant difference in laparoscopic vs open technique (46.0% vs 43.6%, p = 0.20).
Conclusions
This meta-analysis shows there is no statistically significant difference in mortality rate, length of hospital stay and postoperative complication rate between the pandemic and control cohorts in emergency general surgery patients. This data suggests that general emergency surgery should continue in spite of the pandemic with appropriate precautions in place.
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Affiliation(s)
- J Hebding
- Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | - Y Negreskul
- John Radcliffe Hospital, Oxford, United Kingdom
| | - J Gilmour
- John Radcliffe Hospital, Oxford, United Kingdom
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12
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Negreskul Y, Wingfield L, Mandal I, Gilmour J. 1451 Early Experiences with Covid-19 In Surgical Patients at The Start of The Global Pandemic. Br J Surg 2021. [PMCID: PMC8524573 DOI: 10.1093/bjs/znab259.379] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Introduction
Covid-19 is a global threat which had emerged rapidly over the course of last year and is particularly deleterious to those with multiple co-morbidities. While limited data is available on the outcomes of emergency surgical patients infected with SARS-CoV-2, initial reports suggest prolonged post-operative course. Early Covid-19 diagnosis and understanding its impact on outcomes are essential for appropriate management of emergency surgical patients. We aim to report a tertiary hospital’s experiences with the first UK patients infected with Covid-19 at the time of surgery.
Method
A limited consecutive, case series (n = 4) was completed in March-April 2020 in a single tertiary centre with a review of case notes, image, and laboratory results.
Results
All patients presented with acute abdominal pathology (appendicitis, incarcerated umbilical hernia and small bowel obstruction). One patient had a laparoscopy whilst the rest underwent open procedures. All patients suffered from multiple co-morbidities and were on average 71 years-old (57-87). Initial SARS-CoV-2 PCR was negative in 3 patients. However, their clinical features, imaging findings and haematological profiles (raised inflammatory markers with lymphopenia) were in keeping with a diagnosis of Covid-19. All patients had a protracted hospital course with an average hospital stay of 22 days (15-30). 3 patients required unplanned ITU (ITU stay: 4-30 days). The length of ITU stay did not correlate with the procedure complexity.
Conclusions
These initial cases suggest that Covid-19 complicates post-operative recovery. Multimodal approach including PCR testing, imaging and haematological profiles is essential to identify patients at risk of post-operative deterioration and thus plan care accordingly.
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Affiliation(s)
- Y Negreskul
- John Radcliffe Hospital, Oxford, United Kingdom
| | - L Wingfield
- University of Oxford, Oxford, United Kingdom
| | - I Mandal
- John Radcliffe Hospital, Oxford, United Kingdom
| | - J Gilmour
- John Radcliffe Hospital, Oxford, United Kingdom
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13
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Hassan AS, Hare J, Gounder K, Nazziwa J, Karlson S, Olsson L, Streatfield C, Kamali A, Karita E, Kilembe W, Price MA, Borrow P, Björkman P, Kaleebu P, Allen S, Hunter E, Ndung'u T, Gilmour J, Rowland-Jones S, Esbjörnsson J, Sanders EJ. A Stronger Innate Immune Response During Hyperacute Human Immunodeficiency Virus Type 1 (HIV-1) Infection Is Associated With Acute Retroviral Syndrome. Clin Infect Dis 2021; 73:832-841. [PMID: 33588436 PMCID: PMC8423478 DOI: 10.1093/cid/ciab139] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Acute retroviral syndrome (ARS) is associated with human immunodeficiency virus type 1 (HIV-1) subtype and disease progression, but the underlying immunopathological pathways are poorly understood. We aimed to elucidate associations between innate immune responses during hyperacute HIV-1 infection (hAHI) and ARS. METHODS Plasma samples obtained from volunteers (≥18.0 years) before and during hAHI, defined as HIV-1 antibody negative and RNA or p24 antigen positive, from Kenya, Rwanda, Uganda, Zambia, and Sweden were analyzed. Forty soluble innate immune markers were measured using multiplexed assays. Immune responses were differentiated into volunteers with stronger and comparatively weaker responses using principal component analysis. Presence or absence of ARS was defined based on 11 symptoms using latent class analysis. Logistic regression was used to determine associations between immune responses and ARS. RESULTS Of 55 volunteers, 31 (56%) had ARS. Volunteers with stronger immune responses (n = 36 [65%]) had increased odds of ARS which was independent of HIV-1 subtype, age, and risk group (adjusted odds ratio, 7.1 [95% confidence interval {CI}: 1.7-28.8], P = .003). Interferon gamma-induced protein (IP)-10 was 14-fold higher during hAHI, elevated in 7 of the 11 symptoms and independently associated with ARS. IP-10 threshold >466.0 pg/mL differentiated stronger immune responses with a sensitivity of 84.2% (95% CI: 60.4-96.6) and specificity of 100.0% (95% CI]: 90.3-100.0). CONCLUSIONS A stronger innate immune response during hAHI was associated with ARS. Plasma IP-10 may be a candidate biomarker of stronger innate immunity. Our findings provide further insights on innate immune responses in regulating ARS and may inform the design of vaccine candidates harnessing innate immunity.
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Affiliation(s)
- Amin S Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Translational Medicine, Lund University, Sweden
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom.,IAVI, New York, New York, USA, and Nairobi, Kenya
| | - Kamini Gounder
- Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, Sweden
| | - Sara Karlson
- Department of Translational Medicine, Lund University, Sweden
| | - Linnéa Olsson
- Department of Internal Medicine, Helsingborg Hospital, Helsingborg, Sweden
| | | | | | - Etienne Karita
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - William Kilembe
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - Matt A Price
- IAVI, New York, New York, USA, and Nairobi, Kenya.,UCSF Department of Epidemiology and Biostatistics, San Francisco,California, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Per Björkman
- Department of Translational Medicine, Lund University, Sweden
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Uganda, and London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susan Allen
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia.,Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Eric Hunter
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia.,Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Max Planck Institute for Infection Biology, Berlin, Germany.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Sarah Rowland-Jones
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Sweden.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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14
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Hare J, Macharia G, Yue L, Streatfield CL, Hunter E, Purcell A, Ternette N, Gilmour J. Direct identification of HLA-presented CD8 T cell epitopes from transmitted founder HIV-1 variants. Proteomics 2021; 21:e2100142. [PMID: 34275180 DOI: 10.1002/pmic.202100142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 11/09/2022]
Abstract
Cytotoxic T lymphocytes (CTLs) are a critical arm of the immune response to viral infections. The activation and expansion of antigen specific CTL requires recognition of peptide antigens presented on class I major histocompatibility complex molecules (MHC-1) of infected cells. Methods to identify presented peptide antigens that do not rely on the pre-existence of antigen specific CTL are critical to the development of new vaccines. We infected activated CD4+ T cells with two HIV-1 transmitted founder (TF) isolates and used high-resolution mass spectrometry (MS) to identify HIV peptides bound on MHC-1. Using this approach, we identified 14 MHC-1 bound peptides from across the two TF isolates. Assessment of predicted binding thresholds revealed good association of the identified peptides to the shared HLA alleles between the HIV+ donors and the naïve PBMC sample with three peptides identified through peptide sequencing inducing a CD8 T-cell response (p < 0.05). Direct infection of naïve CD4 cells by HIV TF isolates and sequencing of MHC-I presented peptides by HPLC-MS/MS enables identification of novel peptides that may be missed by alternative epitope mapping strategies and can provide valuable insight in to the first peptides presented by an HIV-infected CD4 cell in the first few days post infection.
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Affiliation(s)
- Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,IAVI, New York, New York, USA
| | - Gladys Macharia
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
| | - Ling Yue
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Claire L Streatfield
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Anthony Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Jill Gilmour
- Department of Infectious Disease, Imperial College London, London, UK
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15
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Hare J, Fiore-Gartland A, McGowan E, Hunter E, Gilmour J, Nielsen M. Selective HLA restriction enables the evaluation and interpretation of immunogenic breadth at comparable levels to that observed with broader HLA distribution. Proteomics 2021; 21:e2100121. [PMID: 34275199 DOI: 10.1002/pmic.202100121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/06/2022]
Abstract
Existing approaches to identifying predictive T-cell epitopes have traditionally utilized either 2-digit HLA super-families or more commonly utilizing autologous HLA alleles to facilitate the predictions. However, the use of these criteria may not consider the HLA representation within any target population. Here we propose a modification to concept of utilizing autologous HLA whereby subsets of individuals are selected for their specific HLA allele profiles and the representation they provide within a given population. Using this selective approach to HLA selection and the linkages to specific individuals may enable the design of more targeted experimentalstrategies.
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Affiliation(s)
- Jonathan Hare
- International AIDS Vaccine Initiative, New York, New York, USA.,IAVI Human Immunology Laboratory, Imperial College, London, UK
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College, London, UK
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Jill Gilmour
- Department of Infectious Disease, Imperial College, London, UK
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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16
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Dalel J, Ung SK, Hayes P, Black SL, Joseph S, King DF, Makinde J, Gilmour J. HIV-1 infection and the lack of viral control are associated with greater expression of interleukin-21 receptor on CD8+ T cells. AIDS 2021; 35:1167-1177. [PMID: 33710028 PMCID: PMC8183476 DOI: 10.1097/qad.0000000000002864] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/29/2020] [Accepted: 02/06/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Interleukin-21 (IL-21) has been linked with the generation of virus-specific memory CD8+ T cells following acute infection with HIV-1 and reduced exhaustion of CD8+ T cells. IL-21 has also been implicated in the promotion of CD8+ T-cell effector functions during viral infection. Little is known about the expression of interleukin-21 receptor (IL-21R) during HIV-1 infection or its role in HIV-1-specific CD8+ T-cell maintenance and subsequent viral control. METHODS We compared levels of IL-21R expression on total and memory subsets of CD8+ T cells from HIV-1-negative and HIV-1-positive donors. We also measured IL-21R on antigen-specific CD8+ T cells in volunteers who were positive for HIV-1 and had cytomegalovirus-responding T cells. Finally, we quantified plasma IL-21 in treatment-naive HIV-1-positive individuals and compared this with IL-21R expression. RESULTS IL-21R expression was significantly higher on CD8+ T cells (P = 0.0256), and on central memory (P = 0.0055) and effector memory (P = 0.0487) CD8+ T-cell subsets from HIV-1-positive individuals relative to HIV-1-negative individuals. For those infected with HIV-1, the levels of IL-21R expression on HIV-1-specific CD8+ T cells correlated significantly with visit viral load (r = 0.6667, P = 0.0152, n = 13) and inversely correlated with plasma IL-21 (r = -0.6273, P = 0.0440, n = 11). Lastly, CD8+ T cells from individuals with lower set point viral load who demonstrated better viral control had the lowest levels of IL-21R expression and highest levels of plasma IL-21. CONCLUSION Our data demonstrates significant associations between IL-21R expression on peripheral CD8+ T cells and viral load, as well as disease trajectory. This suggests that the IL-21 receptor could be a novel marker of CD8+ T-cell dysfunction during HIV-1 infection.
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Affiliation(s)
- Jama Dalel
- IAVI Human Immunology Laboratory, Imperial College London, London, UK
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17
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Farinre O, Gounder K, Reddy T, Tongo M, Hare J, Chaplin B, Gilmour J, Kanki P, Mann JK, Ndung'u T. Subtype-specific differences in Gag-protease replication capacity of HIV-1 isolates from East and West Africa. Retrovirology 2021; 18:11. [PMID: 33952315 PMCID: PMC8097975 DOI: 10.1186/s12977-021-00554-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/12/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The HIV-1 epidemic in sub-Saharan Africa is heterogeneous with diverse unevenly distributed subtypes and regional differences in prevalence. Subtype-specific differences in disease progression rate and transmission efficiency have been reported, but the underlying biological mechanisms have not been fully characterized. Here, we tested the hypothesis that the subtypes prevalent in the East Africa, where adult prevalence rate is higher, have lower viral replication capacity (VRC) than their West African counterparts where adult prevalence rates are lower. RESULTS Gag-protease sequencing was performed on 213 and 160 antiretroviral-naïve chronically infected participants from West and East Africa respectively and bioinformatic tools were used to infer subtypes and recombination patterns. VRC of patient-derived gag-protease chimeric viruses from West (n = 178) and East (n = 114) Africa were determined using a green fluorescent protein reporter-based cell assay. Subtype and regional differences in VRC and amino acid variants impacting VRC were identified by statistical methods. CRF02_AG (65%, n = 139), other recombinants (14%, n = 30) and pure subtypes (21%, n = 44) were identified in West Africa. Subtypes A1 (64%, n = 103), D (22%, n = 35), or recombinants (14%, n = 22) were identified in East Africa. Viruses from West Africa had significantly higher VRC compared to those from East Africa (p < 0.0001), with subtype-specific differences found among strains within West and East Africa (p < 0.0001). Recombination patterns showed a preference for subtypes D, G or J rather than subtype A in the p6 region of gag, with evidence that subtype-specific differences in this region impact VRC. Furthermore, the Gag A83V polymorphism was associated with reduced VRC in CRF02_AG. HLA-A*23:01 (p = 0.0014) and HLA-C*07:01 (p = 0.002) were associated with lower VRC in subtype A infected individuals from East Africa. CONCLUSIONS Although prevalent viruses from West Africa displayed higher VRC than those from East Africa consistent with the hypothesis that lower VRC is associated with higher population prevalence, the predominant CRF02_AG strain in West Africa displayed higher VRC than other prevalent strains suggesting that VRC alone does not explain population prevalence. The study identified viral and host genetic determinants of virus replication capacity for HIV-1 CRF02_AG and subtype A respectively, which may have relevance for vaccine strategies.
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Affiliation(s)
- Omotayo Farinre
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Kamini Gounder
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, 4001, South Africa
| | - Tarylee Reddy
- Biostatistics Research Unit, South African Medical Research Council, Durban, South Africa
| | - Marcel Tongo
- Centre of Research for Emerging and Re-Emerging Diseases (CREMER), Yaoundé, Cameroon
| | - Jonathan Hare
- International AIDS Vaccine Initiative (IAVI) Human Immunology Laboratory (HIL), Imperial College, London, UK
- IAVI Global Headquarters, 125 Broad Street, 9th Floor,, New York, NY, USA
| | - Beth Chaplin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI) Human Immunology Laboratory (HIL), Imperial College, London, UK
- IAVI Global Headquarters, 125 Broad Street, 9th Floor,, New York, NY, USA
| | - Phyllis Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
- Africa Health Research Institute, Durban, 4001, South Africa.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Max Planck Institute for Infection Biology, Berlin, Germany.
- Division of Infection and Immunity, University College London, London, UK.
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18
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McInally S, Wall K, Yu T, Tirouvanziam R, Kilembe W, Gilmour J, Allen SA, Hunter E. Elevated levels of inflammatory plasma biomarkers are associated with risk of HIV infection. Retrovirology 2021; 18:8. [PMID: 33731158 PMCID: PMC7968240 DOI: 10.1186/s12977-021-00552-6] [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: 12/21/2020] [Accepted: 03/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To determine if individuals, from HIV-1 serodiscordant couple cohorts from Rwanda and Zambia, who become HIV-positive have a distinct inflammatory biomarker profile compared to individuals who remain HIV-negative, we compared levels of biomarkers in plasma of HIV-negative individuals who either seroconverted (pre-infection) and became HIV-positive or remained HIV-negative (uninfected). RESULTS We observed that individuals in the combined cohort, as well as those in the individual country cohorts, who later became HIV-1 infected had significantly higher baseline levels of multiple inflammatory cytokines/chemokines compared to individuals who remained HIV-negative. Genital inflammation/ulceration or schistosome infections were not associated with this elevated profile. Defined levels of ITAC and IL-7 were significant predictors of later HIV acquisition in ROC predictive analyses, whereas the classical Th1 and Th2 inflammatory cytokines such as IL-12 and interferon-γ or IL-4, IL-5 and Il-13 were not. CONCLUSIONS Overall, the data show a significant association between increased plasma biomarkers linked to inflammation and immune activation and HIV acquisition and suggests that pre-existing conditions that increase systemic biomarkers represent a factor for increased risk of HIV infection.
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Affiliation(s)
- Samantha McInally
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Kristin Wall
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Tianwei Yu
- School of Data Science, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong Province, China
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.,Center of CF and Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Susan A Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, USA. .,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.
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19
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Makinde J, Nduati EW, Freni-Sterrantino A, Streatfield C, Kibirige C, Dalel J, Black SL, Hayes P, Macharia G, Hare J, McGowan E, Abel B, King D, Joseph S, Hunter E, Sanders EJ, Price M, Gilmour J. A Novel Sample Selection Approach to Aid the Identification of Factors That Correlate With the Control of HIV-1 Infection. Front Immunol 2021; 12:634832. [PMID: 33777023 PMCID: PMC7991997 DOI: 10.3389/fimmu.2021.634832] [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: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Individuals infected with HIV display varying rates of viral control and disease progression, with a small percentage of individuals being able to spontaneously control infection in the absence of treatment. In attempting to define the correlates associated with natural protection against HIV, extreme heterogeneity in the datasets generated from systems methodologies can be further complicated by the inherent variability encountered at the population, individual, cellular and molecular levels. Furthermore, such studies have been limited by the paucity of well-characterised samples and linked epidemiological data, including duration of infection and clinical outcomes. To address this, we selected 10 volunteers who rapidly and persistently controlled HIV, and 10 volunteers each, from two control groups who failed to control (based on set point viral loads) from an acute and early HIV prospective cohort from East and Southern Africa. A propensity score matching approach was applied to control for the influence of five factors (age, risk group, virus subtype, gender, and country) known to influence disease progression on causal observations. Fifty-two plasma proteins were assessed at two timepoints in the 1st year of infection. We independently confirmed factors known to influence disease progression such as the B*57 HLA Class I allele, and infecting virus Subtype. We demonstrated associations between circulating levels of MIP-1α and IL-17C, and the ability to control infection. IL-17C has not been described previously within the context of HIV control, making it an interesting target for future studies to understand HIV infection and transmission. An in-depth systems analysis is now underway to fully characterise host, viral and immunological factors contributing to control.
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Affiliation(s)
- Julia Makinde
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Eunice W Nduati
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anna Freni-Sterrantino
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Claire Streatfield
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Catherine Kibirige
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Jama Dalel
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - S Lucas Black
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Gladys Macharia
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Brian Abel
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Deborah King
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Sarah Joseph
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | | | - Eric Hunter
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States.,Zambia-Emory HIV Research Project, Lusaka, Zambia
| | - Eduard J Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Matt Price
- IAVI, New York, NY, United States.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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McGowan E, Rosenthal R, Fiore-Gartland A, Macharia G, Balinda S, Kapaata A, Umviligihozo G, Muok E, Dalel J, Streatfield CL, Coutinho H, Dilernia D, Monaco DC, Morrison D, Yue L, Hunter E, Nielsen M, Gilmour J, Hare J. Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response. Front Immunol 2021; 12:609884. [PMID: 33679745 PMCID: PMC7930081 DOI: 10.3389/fimmu.2021.609884] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, diversity metric of the HLA profile of individuals within a population and consideration of sequence diversity in the context of an individual's CD8 T-cell immune repertoire to assess the HIV proteome for defined regions of immunogenicity. Using this approach, analysis of HLA adaptation and functional immunogenicity data enabled the identification of regions within the proteome that offer significant conservation, HLA recognition within a population, low prevalence of HLA adaptation and demonstrated immunogenicity. We believe this unique and novel approach to vaccine design as a supplement to vitro functional assays, offers a bespoke pipeline for expedited and rational CD8 T-cell vaccine design for HIV and potentially other pathogens with the potential for both global and local coverage.
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Affiliation(s)
- Ed McGowan
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, United Kingdom
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Gladys Macharia
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Sheila Balinda
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Health and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Anne Kapaata
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Health and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Gisele Umviligihozo
- Project San Francisco (PSF) Center for Family Health Research (CFHR), Kigali, Rwanda
| | - Erick Muok
- Project San Francisco (PSF) Center for Family Health Research (CFHR), Kigali, Rwanda
| | - Jama Dalel
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | | | - Helen Coutinho
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Dario Dilernia
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | | | | | - Ling Yue
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
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22
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Langat RK, Farah B, Indangasi J, Ogola S, Omosa-Manyonyi G, Anzala O, Bizimana J, Tekirya E, Ngetsa C, Silwamba M, Muyanja E, Chetty P, Jangano M, Hills N, Gilmour J, Dally L, Cox JH, Hayes P. Performance of International AIDS Vaccine Initiative African clinical research laboratories in standardised ELISpot and peripheral blood mononuclear cell processing in support of HIV vaccine clinical trials. Afr J Lab Med 2021; 10:1056. [PMID: 33833946 PMCID: PMC8014752 DOI: 10.4102/ajlm.v10i1.1056] [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: 06/06/2019] [Accepted: 09/23/2020] [Indexed: 11/28/2022] Open
Abstract
Background Standardisation of procedures for performing cellular functional assays across laboratories participating in multicentre clinical trials is key for generating comparable and reliable data. Objective This article describes the performance of accredited laboratories in Africa and Europe on testing done in support of clinical trials. Methods For enzyme-linked immunospot assay (ELISpot) proficiency, characterised peripheral blood mononuclear cells (PBMCs) obtained from 48 HIV-negative blood donors in Johannesburg, South Africa, were sent to participating laboratories between February 2010 and February 2014. The PBMCs were tested for responses against cytomegalovirus, Epstein Barr and influenza peptide pools in a total of 1751 assays. In a separate study, a total of 1297 PBMC samples isolated from healthy HIV-negative participants in clinical trials of two prophylactic HIV vaccine candidates in Kenya, Uganda, Rwanda and Zambia were analysed for cell viability, cell yield and cell recovery from frozen PBMCs. Results Most (99%) of the 1751 ELISpot proficiency assays had data within acceptable ranges with low responses to mock stimuli. No significant statistical difference were observed in ELISpot responses at the five laboratories actively conducting immunological analyses. Of the 1297 clinical trial PBMCs processed, 94% had cell viability above 90% and 96% had cell yield above 0.7 million per mL of blood in freshly isolated cells. All parameters were within the predefined acceptance criteria. Conclusion We demonstrate that multiple laboratories can generate reliable, accurate and comparable data by using standardised procedures, having regular training, having regular equipment maintenance and using centrally sourced reagents.
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Affiliation(s)
- Robert K Langat
- Kenya AIDS Vaccine Initiative, Institute of Clinical Research, University of Nairobi, Nairobi, Kenya.,International AIDS Vaccine Initiative (IAVI), Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Bashir Farah
- Kenya AIDS Vaccine Initiative, Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Jackton Indangasi
- Kenya AIDS Vaccine Initiative, Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Simon Ogola
- Kenya AIDS Vaccine Initiative, Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Gloria Omosa-Manyonyi
- Kenya AIDS Vaccine Initiative, Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative, Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | | | | | - Caroline Ngetsa
- Kenya Medical Research Institute Centre for Geographical Medicine Research Coast, Mombasa, Kenya
| | | | - Enoch Muyanja
- Ugandan Virus Research Institute-IAVI, Entebbe, Uganda
| | - Paramesh Chetty
- International AIDS Vaccine Initiative, Johannesburg, South Africa
| | | | - Nancy Hills
- School of Medicine, University of California, San Francisco, California, United States
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Len Dally
- Emmes Corporation, Rockville, Maryland, United States
| | - Josephine H Cox
- Clinical Trials Program, Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States
| | - Peter Hayes
- International AIDS Vaccine Initiative (IAVI), Human Immunology Laboratory, Imperial College, London, United Kingdom
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23
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Michelo CM, Dalel JA, Hayes P, Fernandez N, Fiore-Gartland A, Kilembe W, Tang J, Streatfield C, Gilmour J, Hunter E. Comprehensive epitope mapping using polyclonally expanded human CD8 T cells and a two-step ELISpot assay for testing large peptide libraries. J Immunol Methods 2021; 491:112970. [PMID: 33529681 DOI: 10.1016/j.jim.2021.112970] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 02/01/2023]
Abstract
The genetic diversity of circulating HIV-1 strains poses a major barrier to the design, development and evaluation of HIV-1 vaccines. The assessment of both vaccine- and natural infection-elicited T cell responses is commonly done with multivalent peptides that are designed to maximally capture the diversity of potential T cell epitopes (PTEs) observed in natural circulating sequences. However, depending on the sequence diversity of viral subtypes and number of the HIV immunogens under investigation, PTE estimates, including HLA-guided computational methods, can easily generate enormous peptide libraries. Evaluation of T cell epitope specificity using such extensive peptide libraries is usually limited by sample availability, even for high-throughput and robust epitope mapping techniques like ELISpot assays. Here we describe a novel, two-step protocol for in-vitro polyclonal expansion of CD8 T cells from a single vial of frozen PBMC, which facilitated the screening 441 HIV-1 Gag peptides for immune responses among 32 HIV-1 positive subjects and 40 HIV-1 negative subjects for peptide qualification. Using a pooled-peptide mapping strategy, epitopes were mapped in two sequential ELISpot assays; the first ELISpot screened 33 large peptide pools using CD8 T cells expanded for 7 days, while the second step tested pool-matrix peptides to identify individual peptides using CD8 T cells expanded for 10 days. This comprehensive epitope screening established the breadth and magnitude of HIV-1 Gag-specific CD8 T cells and further revealed the extent of immune responses to variable/polymorphic epitopes.
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Affiliation(s)
- Clive M Michelo
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia
| | - Jama A Dalel
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Peter Hayes
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Natalia Fernandez
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - William Kilembe
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Claire Streatfield
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Eric Hunter
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia; Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329, USA.
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24
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Kapaata A, Balinda SN, Xu R, Salazar MG, Herard K, Brooks K, Laban K, Hare J, Dilernia D, Kamali A, Ruzagira E, Mukasa F, Gilmour J, Salazar-Gonzalez JF, Yue L, Cotten M, Hunter E, Kaleebu P. HIV-1 Gag-Pol Sequences from Ugandan Early Infections Reveal Sequence Variants Associated with Elevated Replication Capacity. Viruses 2021; 13:v13020171. [PMID: 33498793 PMCID: PMC7912664 DOI: 10.3390/v13020171] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 01/05/2023] Open
Abstract
The ability to efficiently establish a new infection is a critical property for human immunodeficiency virus type 1 (HIV-1). Although the envelope protein of the virus plays an essential role in receptor binding and internalization of the infecting virus, the structural proteins, the polymerase and the assembly of new virions may also play a role in establishing and spreading viral infection in a new host. We examined Ugandan viruses from newly infected patients and focused on the contribution of the Gag-Pol genes to replication capacity. A panel of Gag-Pol sequences generated using single genome amplification from incident HIV-1 infections were cloned into a common HIV-1 NL4.3 pol/env backbone and the influence of Gag-Pol changes on replication capacity was monitored. Using a novel protein domain approach, we then documented diversity in the functional protein domains across the Gag-Pol region and identified differences in the Gag-p6 domain that were frequently associated with higher in vitro replication.
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Affiliation(s)
- Anne Kapaata
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Sheila N. Balinda
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Rui Xu
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Maria G. Salazar
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Kimberly Herard
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Kelsie Brooks
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Kato Laban
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Jonathan Hare
- Imperial College London, London SW7 2AZ, UK; (J.H.); (J.G.)
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Dario Dilernia
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | | | - Eugene Ruzagira
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Freddie Mukasa
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Jill Gilmour
- Imperial College London, London SW7 2AZ, UK; (J.H.); (J.G.)
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Ling Yue
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Matthew Cotten
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK
- Correspondence: ; Tel.: +25-6701-509-685
| | - Eric Hunter
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Pontiano Kaleebu
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
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25
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Macharia GN, Yue L, Staller E, Dilernia D, Wilkins D, Song H, McGowan E, King D, Fast P, Imami N, Price MA, Sanders EJ, Hunter E, Gilmour J. Infection with multiple HIV-1 founder variants is associated with lower viral replicative capacity, faster CD4+ T cell decline and increased immune activation during acute infection. PLoS Pathog 2020; 16:e1008853. [PMID: 32886726 PMCID: PMC7498102 DOI: 10.1371/journal.ppat.1008853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 04/17/2020] [Revised: 09/17/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023] Open
Abstract
HIV-1 transmission is associated with a severe bottleneck in which a limited number of variants from a pool of genetically diverse quasispecies establishes infection. The IAVI protocol C cohort of discordant couples, female sex workers, other heterosexuals and men who have sex with men (MSM) present varying risks of HIV infection, diverse HIV-1 subtypes and represent a unique opportunity to characterize transmitted/founder viruses (TF) where disease outcome is known. To identify the TF, the HIV-1 repertoire of 38 MSM participants' samples was sequenced close to transmission (median 21 days post infection, IQR 18-41) and assessment of multivariant infection done. Patient derived gag genes were cloned into an NL4.3 provirus to generate chimeric viruses which were characterized for replicative capacity (RC). Finally, an evaluation of how the TF virus predicted disease progression and modified the immune response at both acute and chronic HIV-1 infection was done. There was higher prevalence of multivariant infection compared with previously described heterosexual cohorts. A link was identified between multivariant infection and replicative capacity conferred by gag, whereby TF gag tended to be of lower replicative capacity in multivariant infection (p = 0.02) suggesting an overall lowering of fitness requirements during infection with multiple variants. Notwithstanding, multivariant infection was associated with rapid CD4+ T cell decline and perturbances in the CD4+ T cell and B cell compartments compared to single variant infection, which were reversible upon control of viremia. Strategies aimed at identifying and mitigating multivariant infection could contribute toward improving HIV-1 prognosis and this may involve strategies that tighten the stringency of the transmission bottleneck such as treatment of STI. Furthermore, the sequences and chimeric viruses help with TF based experimental vaccine immunogen design and can be used in functional assays to probe effective immune responses against TF.
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Affiliation(s)
- Gladys N. Macharia
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Ling Yue
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Ecco Staller
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Dario Dilernia
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Daniel Wilkins
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Heeyah Song
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Edward McGowan
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Deborah King
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Pat Fast
- IAVI, New York, NY, United States of America
| | - Nesrina Imami
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Matthew A. Price
- IAVI, New York, NY, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, United States of America
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, United Kingdom
| | - Eric Hunter
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States of America
| | - Jill Gilmour
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
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26
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El-Badry E, Macharia G, Claiborne D, Brooks K, Dilernia DA, Goepfert P, Kilembe W, Allen S, Gilmour J, Hunter E. Better Viral Control despite Higher CD4 + T Cell Activation during Acute HIV-1 Infection in Zambian Women Is Linked to the Sex Hormone Estradiol. J Virol 2020; 94:e00758-20. [PMID: 32461316 PMCID: PMC7394904 DOI: 10.1128/jvi.00758-20] [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: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 02/06/2023] Open
Abstract
The influence of biological sex on disease progression in HIV-1-infected individuals has been focused on the chronic stage of infection, but little is known about how sex differences influence acute HIV-1 infection. We observed profound differences in viral load and CD4+ T cell activation from the earliest time points in men and women in a Zambian heterosexual acute infection cohort. Women exhibited a >2-fold higher rate of CD4+ T cell loss despite significantly lower viral loads (VL) than men. The importance of studying acute infection was highlighted by the observation that very early in infection, women exhibited significantly higher levels of CD4+ T cell activation, a difference that was lost over the first 3 years of infection as activation in men increased. In women, activation of CD4+ T cells in the acute phase was significantly correlated with plasma levels of 17β-estradiol (E2). However, unlike in men, higher CD4+ T cell activation in women was not associated with higher VL. In contrast, a higher E2 level in early infection was associated with lower early and set-point VL in women. We attribute this to an inhibitory effect of estradiol on virus replication, which we were able to observe with relevant transmitted/founder viruses in vitro Thus, estradiol plays a key role in defining major differences between men and women during early HIV-1 infection by contributing to both viral control and CD4+ T cell loss, an effect that extends into the chronic phase of the disease.IMPORTANCE Previous studies have identified sex-specific differences during chronic HIV-1 infection, but little is known about sex differences in the acute phase, or how disparities in the initial response to the virus may affect disease. We demonstrate that restriction of viral load in women begins during acute infection and is maintained into chronic infection. Despite this, women exhibit more rapid CD4+ T cell loss than men. These profound differences are influenced by 17β-estradiol, which contributes both to T cell activation and to reduced viral replication. Thus, we conclude that estradiol plays a key role in shaping responses to early HIV-1 infection that influence the chronic phase of disease.
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Affiliation(s)
- Elina El-Badry
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Gladys Macharia
- Department of Medicine, Imperial College London, London, United Kingdom
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, United Kingdom
| | - Daniel Claiborne
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Kelsie Brooks
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Darío A Dilernia
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Jill Gilmour
- Department of Medicine, Imperial College London, London, United Kingdom
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, United Kingdom
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
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27
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Kasprowicz VO, Chopera D, Waddilove KD, Brockman MA, Gilmour J, Hunter E, Kilembe W, Karita E, Gaseitsiwe S, Sanders EJ, Ndung'u T. African-led health research and capacity building- is it working? BMC Public Health 2020; 20:1104. [PMID: 32664891 PMCID: PMC7359480 DOI: 10.1186/s12889-020-08875-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [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: 08/30/2019] [Accepted: 05/07/2020] [Indexed: 12/29/2022] Open
Abstract
Background Africa bears a disproportionately high burden of globally significant disease but has lagged in knowledge production to address its health challenges. In this contribution, we discuss the challenges and approaches to health research capacity strengthening in sub-Saharan Africa and propose that the recent shift to an African-led approach is the most optimal. Methods and findings We introduce several capacity building approaches and recent achievements, explore why African-led research on the continent is a potentially paradigm-shifting and innovative approach, and discuss the advantages and challenges thereof. We reflect on the approaches used by the African Academy of Sciences (AAS)-funded Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE) consortium as an example of an effective African-led science and capacity building programme. We recommend the following as crucial components of future efforts: 1. Directly empowering African-based researchers, 2. Offering quality training and career development opportunities to large numbers of junior African scientists and support staff, and 3. Effective information exchange and collaboration. Furthermore, we argue that long-term investment from international donors and increasing funding commitments from African governments and philanthropies will be needed to realise a critical mass of local capacity and to create and sustain world-class research hubs that will be conducive to address Africa’s intractable health challenges. Conclusions Our experiences so far suggest that African-led research has the potential to overcome the vicious cycle of brain-drain and may ultimately lead to improvement of health and science-led economic transformation of Africa into a prosperous continent.
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Affiliation(s)
- Victoria O Kasprowicz
- Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Denis Chopera
- Africa Health Research Institute, Durban, South Africa
| | | | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.,Rwanda Zambia Emory HIV Research Group, Zambia; Kigali, Rwanda and Emory University, Atlanta, USA
| | - William Kilembe
- Rwanda Zambia Emory HIV Research Group, Zambia; Kigali, Rwanda and Emory University, Atlanta, USA
| | - Etienne Karita
- Rwanda Zambia Emory HIV Research Group, Zambia; Kigali, Rwanda and Emory University, Atlanta, USA
| | - Simani Gaseitsiwe
- Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eduard J Sanders
- Kenyan Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa. .,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa. .,Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA. .,Max Planck Institute for Infection Biology, Berlin, Germany. .,Division of Infection and Immunity, University College London, London, UK.
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28
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Brooks K, Jones BR, Dilernia DA, Wilkins DJ, Claiborne DT, McInally S, Gilmour J, Kilembe W, Joy JB, Allen SA, Brumme ZL, Hunter E. HIV-1 variants are archived throughout infection and persist in the reservoir. PLoS Pathog 2020; 16:e1008378. [PMID: 32492044 PMCID: PMC7295247 DOI: 10.1371/journal.ppat.1008378] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 06/15/2020] [Accepted: 02/03/2020] [Indexed: 01/23/2023] Open
Abstract
The HIV-1 reservoir consists of latently infected cells that persist despite antiretroviral therapy (ART). Elucidating the proviral genetic composition of the reservoir, particularly in the context of pre-therapy viral diversity, is therefore important to understanding reservoir formation and the persistence of latently infected cells. Here we investigate reservoir proviral variants from 13 Zambian acutely-infected individuals with additional pre-therapy sampling for a unique comparison to the ART-naïve quasispecies. We identified complete transmitted/founder (TF) viruses from seroconversion plasma samples, and additionally amplified and sequenced HIV-1 from plasma obtained one year post-infection and just prior to ART initiation. While the majority of proviral variants in the reservoir were most closely related to viral variants from the latest pre-therapy time point, we also identified reservoir proviral variants dating to or near the time of infection, and to intermediate time points between infection and treatment initiation. Reservoir proviral variants differing by five or fewer nucleotide changes from the TF virus persisted during treatment in five individuals, including proviral variants that exactly matched the TF in two individuals, one of whom had remained ART-naïve for more than six years. Proviral variants during treatment were significantly less divergent from the TF virus than plasma variants present at the last ART-naïve time point. These findings indicate that reservoir proviral variants are archived throughout infection, recapitulating much of the viral diversity that arises throughout untreated HIV-1 infection, and strategies to target and reduce the reservoir must therefore permit for the clearance of proviruses encompassing this extensive diversity. Despite reducing viremia to levels below the limit of detection in standard assays, effective antiretroviral therapy (ART) does not eradicate cells latently infected with HIV-1. These cells serve as a reservoir for viral rebound if therapy is interrupted; thus, understanding the composition of the reservoir may yield further targets for HIV-1 cure strategies. We have taken a genetic approach to elucidating the reservoir in 13 Zambian subtype C seroconvertors who were followed longitudinally through ART initiation and virologic suppression. In five of the 13 individuals, provirus sequences identical to or differing by five or fewer nucleotides from the transmitted/founder virus were detected, indicating archiving and persistence of early infection variants for more than six years following infection. While the majority of proviral variants in latently infected cells were most closely related to plasma virus circulating immediately prior to treatment initiation, additional variants dating to intermediate time points in the infection were also observed. These findings demonstrate that virus is archived during all stages of ART-naïve infection, and these variants persist throughout ART. HIV-1 cure strategies to eliminate the reservoir must address the broad genetic diversity of a within-host proviral quasispecies including variants archived from acute through chronic infection.
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Affiliation(s)
- Kelsie Brooks
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Dario A. Dilernia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Daniel J. Wilkins
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Daniel T. Claiborne
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha McInally
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Jill Gilmour
- Human Immunology Lab, International AIDS Vaccine Initiative, London, England, United Kingdom
| | | | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Susan A. Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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29
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Munusamy Ponnan S, Hayes P, Fernandez N, Thiruvengadam K, Pattabiram S, Nesakumar M, Srinivasan A, Kathirvel S, Shankar J, Goyal R, Singla N, Mukherjee J, Chatrath S, Gilmour J, Subramanyam S, Prasad Tripathy S, Swaminathan S, Hanna LE. Evaluation of antiviral T cell responses and TSCM cells in volunteers enrolled in a phase I HIV-1 subtype C prophylactic vaccine trial in India. PLoS One 2020; 15:e0229461. [PMID: 32097435 PMCID: PMC7041807 DOI: 10.1371/journal.pone.0229461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/06/2019] [Accepted: 02/06/2020] [Indexed: 02/07/2023] Open
Abstract
T cells play an important role in controlling viral replication during HIV infection. An effective vaccine should, therefore, lead to the induction of a strong and early viral-specific CD8+ T cell response. While polyfunctional T cell responses are thought to be important contributors to the antiviral response, there is evidence to show that polyfunctional HIV- specific CD8+ T cells are just a small fraction of the total HIV-specific CD8+ T cells and may be absent in many individuals who control HIV replication, suggesting that other HIV-1 specific CD8+ effector T cell subsets may be key players in HIV control. Stem cell-like memory T cells (TSCM) are a subset of T cells with a long half-life and self-renewal capacity. They serve as key reservoirs for HIV and contribute a significant barrier to HIV eradication. The present study evaluated vaccine-induced antiviral responses and TSCM cells in volunteers vaccinated with a subtype C prophylactic HIV-1 vaccine candidate administered in a prime-boost regimen. We found that ADVAX DNA prime followed by MVA boost induced significantly more peripheral CD8+ TSCM cells and higher levels of CD8+ T cell-mediated inhibition of replication of different HIV-1 clades as compared to MVA alone and placebo. These findings are novel and provide encouraging evidence to demonstrate the induction of TSCM and cytotoxic immune responses by a subtype C HIV-1 prophylactic vaccine administered using a prime-boost strategy.
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Affiliation(s)
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London, England, United Kingdom
| | - Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London, England, United Kingdom
| | - Kannan Thiruvengadam
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Sathyamurthi Pattabiram
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Manohar Nesakumar
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Ashokkumar Srinivasan
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Sujitha Kathirvel
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Janani Shankar
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Rajat Goyal
- International AIDS Vaccine Initiative, New Delhi, India
| | - Nikhil Singla
- International AIDS Vaccine Initiative, New Delhi, India
| | | | | | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, England, United Kingdom
| | - Sudha Subramanyam
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Srikanth Prasad Tripathy
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Soumya Swaminathan
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Luke Elizabeth Hanna
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
- * E-mail:
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30
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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] [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: 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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Claiborne DT, Scully EP, Palmer CD, Prince JL, Macharia GN, Kopycinski J, Michelo CM, Wiener HW, Parker R, Nganou-Makamdop K, Douek D, Altfeld M, Gilmour J, Price MA, Tang J, Kilembe W, Allen SA, Hunter E. Protective HLA alleles are associated with reduced LPS levels in acute HIV infection with implications for immune activation and pathogenesis. PLoS Pathog 2019; 15:e1007981. [PMID: 31449552 PMCID: PMC6730937 DOI: 10.1371/journal.ppat.1007981] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 09/06/2019] [Accepted: 07/14/2019] [Indexed: 12/12/2022] Open
Abstract
Despite extensive research on the mechanisms of HLA-mediated immune control of HIV-1 pathogenesis, it is clear that much remains to be discovered, as exemplified by protective HLA alleles like HLA-B*81 which are associated with profound protection from CD4+ T cell decline without robust control of early plasma viremia. Here, we report on additional HLA class I (B*1401, B*57, B*5801, as well as B*81), and HLA class II (DQB1*02 and DRB1*15) alleles that display discordant virological and immunological phenotypes in a Zambian early infection cohort. HLA class I alleles of this nature were also associated with enhanced immune responses to conserved epitopes in Gag. Furthermore, these HLA class I alleles were associated with reduced levels of lipopolysaccharide (LPS) in the plasma during acute infection. Elevated LPS levels measured early in infection predicted accelerated CD4+ T cell decline, as well as immune activation and exhaustion. Taken together, these data suggest novel mechanisms for HLA-mediated immune control of HIV-1 pathogenesis that do not necessarily involve significant control of early viremia and point to microbial translocation as a direct driver of HIV-1 pathogenesis rather than simply a consequence. During acute HIV infection, there exists a complex interplay between the host immune response and the virus, and the balance of these interactions dramatically affects disease trajectory in infected individuals. Variations in Human Leukocyte Antigen (HLA) alleles dictate the potency of the cellular immune response to HIV, and certain well-studied alleles (HLA-B*57, B*27) are associated with control of HIV viremia. However, though plasma viral load is indicative of disease progression, the number of CD4+ T cells in the blood is a better measurement of disease severity. Through analysis of a large Zambian acute infection cohort, we identified HLA alleles that were associated with protection for CD4+ T cell loss, without dramatic affect on early plasma viremia. We further link these favorable HLA alleles to reduction in a well-known contributor to HIV pathogenesis, the presence of microbial products in the blood, which is indicative of damage to the gastrointestinal tract, a process which accelerates disease progression in HIV infected individuals. Ultimately, these results suggest a new mechanism by which the cellular immune response can combat HIV-associated pathogenesis, and further highlight the contribution of gut damage and microbial translocation to accelerating disease progression, even at early stages in HIV infection.
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Affiliation(s)
- Daniel T. Claiborne
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Eileen P. Scully
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christine D. Palmer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jessica L. Prince
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Gladys N. Macharia
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | - Jakub Kopycinski
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | | | - Howard W. Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rachel Parker
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Krystelle Nganou-Makamdop
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marcus Altfeld
- Virus Immunology Unit, Heinrich-Pette-Institut, Hamburg, Germany
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | - Matt A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | | | - Susan A. Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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32
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Priddy FH, Lewis DJM, Gelderblom HC, Hassanin H, Streatfield C, LaBranche C, Hare J, Cox JH, Dally L, Bendel D, Montefiori D, Sayeed E, Ackland J, Gilmour J, Schnepp BC, Wright JF, Johnson P. Adeno-associated virus vectored immunoprophylaxis to prevent HIV in healthy adults: a phase 1 randomised controlled trial. Lancet HIV 2019; 6:e230-e239. [PMID: 30885692 PMCID: PMC6443625 DOI: 10.1016/s2352-3018(19)30003-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [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: 10/01/2018] [Revised: 12/12/2018] [Accepted: 01/10/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND A preventive vaccine for HIV is a crucial public health need; adeno-associated virus (AAV)-mediated antibody gene delivery could be an alternative to immunisation to induce sustained expression of neutralising antibodies to prevent HIV. We assessed safety and tolerability of rAAV1-PG9DP, a recombinant AAV1 vector encoding the gene for PG9, a broadly neutralising antibody against HIV. METHODS This first-in-human, proof-of-concept, double-blind, phase 1, randomised, placebo-controlled, dose-escalation trial was done at one clinical research centre in the UK. Healthy men aged 18-45 years without HIV infection were randomly assigned to receive intramuscular injection with rAAV1-PG9DP or placebo in the deltoid or quadriceps in one of four dose-escalating cohorts (group A, 4 × 1012 vector genomes; group B, 4 × 1013 vector genomes; group C, 8 × 1013 vector genomes; and group D, 1·2 × 1014 vector genomes). Volunteers were followed up for 48 weeks. The primary objective was to assess safety and tolerability. A secondary objective was to assess PG9 expression in serum and related HIV neutralisation activity. All volunteers were included in primary and safety analyses. The trial is complete and is registered with ClinicalTrials.gov, number NCT01937455. FINDINGS Between Jan 30, 2014, and Feb 28, 2017, 111 volunteers were screened for eligibility. 21 volunteers were eligible and provided consent, and all 21 completed 48 weeks of follow-up. Reactogenicity was generally mild or moderate and resolved without intervention. No probably or definitely related adverse events or serious adverse events were recorded. We detected PG9 by HIV neutralisation in the serum of four volunteers, and by RT-PCR in muscle biopsy samples from four volunteers. We did not detect PG9 by ELISA in serum. PG9 anti-drug antibody was present in ten volunteers in the higher dose groups. Both anti-AAV1 antibodies and AAV1-specific T-cell responses were detected. INTERPRETATION Future studies should explore higher doses of AAV, alternative AAV serotypes and gene expression cassettes, or other broadly neutralising HIV antibodies. FUNDING International AIDS Vaccine Initiative, United States Agency for International Development, Bill & Melinda Gates Foundation, US National Institutes of Health.
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Affiliation(s)
| | - David J M Lewis
- NIHR Imperial Clinical Research Facility, Imperial College, London UK
| | | | - Hana Hassanin
- Surrey Clinical Research Centre, University of Surrey, Guildford, UK
| | | | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | | | - Len Dally
- The Emmes Company, LLC, Rockville, MD, USA
| | - Daryl Bendel
- Surrey Clinical Research Centre, University of Surrey, Guildford, UK
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Eddy Sayeed
- International AIDS Vaccine Initiative, New York, NY, USA
| | | | - Jill Gilmour
- International AIDS Vaccine Initiative, London, UK
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Hanke T, Fast P, Kaleebu P, Jaoko W, Sanders E, Kilembe W, Kuipers H, Okech B, Gilmour J. OC 8499 THE T-CELL VACCINE STRATEGY: GLOBALLY RELEVANT AIDS VACCINE EUROPE-AFRICA TRIALS PARTNERSHIP (GREAT). BMJ Glob Health 2019. [DOI: 10.1136/bmjgh-2019-edc.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundRemarkable progress has been achieved in decreasing AIDS-related deaths and HIV-1 transmission through ART. Nevertheless, an affordable, effective and durable HIV-1 vaccine protection remains the best solution for halting the AIDS epidemic.Our aim is to develop a vaccine inducing cytotoxic T lymphocytes (CTL), which effectively inhibit HIV-1 replication and complement bnAbs for prevention; such T cells are likely critical for a successful cure. Central to our strategy is to focus HIV-1-specific CTL on the most functionally conserved regions (not a string of epitopes and not full-length proteins) common to most HIV-1 variants, which HIV-1 typically cannot change without losing fitness. These conserved regions were defined by bioinformatics, and a bivalent mosaic was computationally designed to increase the vaccine perfect match of potential T-cell epitopes to 80% of global HIV-1 variants; if successful, the vaccine will be suitable for global deployment. Furthermore, we maximised the inclusion of protective epitopes associated with viral control in treatment-naive HIV-1-positive individuals defined on 4 continents. These immunogens are delivered by the non-replicating simian adenovirus ChAdOx1 prime and non-replicating poxvirus MVA boost regimen, clinically proven safe and potent.MethodsThe GREAT consortium has been established to build capacity for a future efficacy trial in Zambia, around Lake Victoria and in Kenya by engaging populations at documented high risk for HIV-1 infection, despite preventive interventions, by diverse clades. We will conduct a phase I/IIa clinical trial HIV-CORE 006 to assess the safety and immunogenicity of the conserved-region vaccines, in preparation for an efficacy trial in these at-risk populations.ConclusionThe aims of the GREAT consortium are to ensure that at the completion of the programme grant, the vaccine regimen will be proven safe and potent, and the sites will be prepared to launch an appropriately designed trial to prove vaccine efficacy.
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34
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Munusamy Ponnan S, Pattabiram S, Thiruvengadam K, Goyal R, Singla N, Mukherjee J, Chatrath S, Bergin P, T. Kopycinski J, Gilmour J, Kumar S, Muthu M, Subramaniam S, Swaminathan S, Prasad Tripathy S, Luke HE. Induction and maintenance of bi-functional (IFN-γ + IL-2+ and IL-2+ TNF-α+) T cell responses by DNA prime MVA boosted subtype C prophylactic vaccine tested in a Phase I trial in India. PLoS One 2019; 14:e0213911. [PMID: 30921340 PMCID: PMC6438518 DOI: 10.1371/journal.pone.0213911] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 03/04/2019] [Indexed: 01/09/2023] Open
Abstract
Effective vaccine design relies on accurate knowledge of protection against a pathogen, so as to be able to induce relevant and effective protective responses against it. An ideal Human Immunodeficiency virus (HIV) vaccine should induce humoral as well as cellular immune responses to prevent initial infection of host cells or limit early events of viral dissemination. A Phase I HIV-1 prophylactic vaccine trial sponsored by the International AIDS Vaccine Initiative (IAVI) was conducted in India in 2009.The trial tested a HIV-1 subtype C vaccine in a prime-boost regimen, comprising of a DNA prime (ADVAX) and Modified Vaccine Ankara (MVA) (TBC-M4) boost. The trial reported that the vaccine regimen was safe, well tolerated, and resulted in enhancement of HIV-specific immune responses. However, preliminary immunological studies were limited to vaccine-induced IFN-γ responses against the Env and Gag peptides. The present study is a retrospective study to characterize in detail the nature of the vaccine-induced cell mediated immune responses among volunteers, using Peripheral Blood Mononuclear Cells (PBMC) that were archived during the trial. ELISpot was used to measure IFN-γ responses and polyfunctional T cells were analyzed by intracellular multicolor flow cytometry. It was observed that DNA priming and MVA boosting induced Env and Gag specific bi-functional and multi-functional CD4+ and CD8+ T cells expressing IFN-γ, TNF-α and IL-2. The heterologous prime-boost regimen appeared to be slightly superior to the homologous prime-boost regimen in inducing favorable cell mediated immune responses. These results suggest that an in-depth analysis of vaccine-induced cellular immune response can aid in the identification of correlates of an effective immunogenic response, and inform future design of HIV vaccines.
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Affiliation(s)
- Sivasankaran Munusamy Ponnan
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Sathyamurthy Pattabiram
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Kannan Thiruvengadam
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Rajat Goyal
- International AIDS Vaccine Initiative, New Delhi, India
| | - Nikhil Singla
- International AIDS Vaccine Initiative, New Delhi, India
| | | | | | - Philip Bergin
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | | | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Sriram Kumar
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Malathy Muthu
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Sudha Subramaniam
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Soumya Swaminathan
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Srikanth Prasad Tripathy
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Hanna Elizabeth Luke
- Department of HIV, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
- * E-mail:
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35
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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36
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Peng BJ, Carlson JM, Liu MKP, Gao F, Goonetilleke N, McMichael AJ, Borrow P, Gilmour J, Heath SL, Hunter E, Bansal A, Goepfert PA. Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection. J Virol 2018; 92:e00711-18. [PMID: 30021907 PMCID: PMC6146806 DOI: 10.1128/jvi.00711-18] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/31/2023] Open
Abstract
While prior studies have demonstrated that CD8 T cell responses to cryptic epitopes (CE) are readily detectable during HIV-1 infection, their ability to drive escape mutations following acute infection is unknown. We predicted 66 CE in a Zambian acute infection cohort based on escape mutations occurring within or near the putatively predicted HLA-I-restricted epitopes. The CE were evaluated for CD8 T cell responses for patients with chronic and acute HIV infections. Of the 66 predicted CE, 10 were recognized in 8/32 and 4/11 patients with chronic and acute infections, respectively. The immunogenic CE were all derived from a single antisense reading frame within pol However, when these CE were tested using longitudinal study samples, CE-specific T cell responses were detected but did not consistently select for viral escape mutations. Thus, while we demonstrated that CE are immunogenic in acute infection, the immune responses to CE are not major drivers of viral escape in the initial stages of HIV infection. The latter finding may be due to either the subdominant nature of CE-specific responses, the low antigen sensitivity, or the magnitude of CE responses during acute infections.IMPORTANCE Although prior studies demonstrated that cryptic epitopes of HIV-1 induce CD8 T cell responses, evidence that targeting these epitopes drives HIV escape mutations has been substantially limited, and no studies have addressed this question following acute infection. In this comprehensive study, we utilized longitudinal viral sequencing data obtained from three separate acute infection cohorts to predict potential cryptic epitopes based on HLA-I-associated viral escape. Our data show that cryptic epitopes are immunogenic during acute infection and that many of the responses they elicit are toward translation products of HIV-1 antisense reading frames. However, despite cryptic epitope targeting, our study did not find any evidence of early CD8-mediated immune escape. Nevertheless, improving cryptic epitope-specific CD8 T cell responses may still be beneficial in both preventative and therapeutic HIV-1 vaccines.
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Affiliation(s)
- Binghao J Peng
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Michael K P Liu
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Feng Gao
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Nilu Goonetilleke
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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37
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Munusamy Ponnan S, Swaminathan S, Tiruvengadam K, K. K. V, Cheedarla N, Nesakumar M, Kathirvel S, Goyal R, Singla N, Mukherjee J, Bergin P, T. Kopycinski J, Gilmour J, Prasad Tripathy S, Luke HE. Induction of circulating T follicular helper cells and regulatory T cells correlating with HIV-1 gp120 variable loop antibodies by a subtype C prophylactic vaccine tested in a Phase I trial in India. PLoS One 2018; 13:e0203037. [PMID: 30157242 PMCID: PMC6114930 DOI: 10.1371/journal.pone.0203037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 03/20/2018] [Accepted: 08/07/2018] [Indexed: 01/12/2023] Open
Abstract
A Phase I HIV-1 vaccine trial sponsored by the International AIDS Vaccine Initiative (IAVI) was conducted in India in 2009 to test a subtype C prophylactic vaccine in a prime-boost regimen comprising of a DNA prime (ADVAX) and MVA (TBC-M4) boost. The trial demonstrated that the regimen was safe and well tolerated and resulted in enhancement of HIV-specific immune responses. Preliminary observations on vaccine-induced immune responses were limited to analysis of neutralizing antibodies and IFN-γ ELISPOT response. The present study involves a more detailed analysis of the nature of the vaccine-induced humoral immune response using specimens that were archived from the volunteers at the time of the trial. Interestingly, we found vaccine induced production of V1/V2 and V3 region-specific antibodies in a significant proportion of vaccinees. Variable region antibody levels correlated directly with the frequency of circulating T follicular helper cells (Tfh) and regulatory T cells (Treg). Our findings provide encouraging evidence to demonstrate the immunogenicity of the tested vaccine. Better insights into vaccine-induced immune responses can aid in informing future design of a successfulHIV-1 vaccine.
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Affiliation(s)
| | - Soumya Swaminathan
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Kannan Tiruvengadam
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Vidyavijayan K. K.
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Narayana Cheedarla
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Manohar Nesakumar
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Sujitha Kathirvel
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Rajat Goyal
- International AIDS Vaccine Initiative, New Delhi, India
| | - Nikhil Singla
- International AIDS Vaccine Initiative, New Delhi, India
| | | | - Philip Bergin
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | | | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Srikanth Prasad Tripathy
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Hanna Elizabeth Luke
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
- * E-mail:
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38
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Mónaco D, Dilernia D, Gartland A, Qin K, Dennis K, Tang J, Gilmour J, Bansal A, Allen S, Goepfert P, Hunter E. A12 Transmitted HLA pre-adapted polymorphisms in the GAG protein influences viral evolution in the new host. Virus Evol 2018. [PMCID: PMC5905476 DOI: 10.1093/ve/vey010.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- D Mónaco
- Emory University, Atlanta, GA, USA
| | | | - A Gartland
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - K Qin
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - K Dennis
- Emory University, Atlanta, GA, USA
| | - J Tang
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Gilmour
- International AIDS Vaccine Initiative (IAVI), London, UK
| | - A Bansal
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - S Allen
- Emory University, Atlanta, GA, USA
- Zambia-Emory HIV Research Project, Lusaka, Zambia
| | - P Goepfert
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - E Hunter
- Emory University, Atlanta, GA, USA
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39
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Powers KA, Price MA, Karita E, Kamali A, Kilembe W, Allen S, Hunter E, Bekker LG, Lakhi S, Inambao M, Anzala O, Latka MH, Fast PE, Gilmour J, Sanders EJ. Prediction of extended high viremia among newly HIV-1-infected persons in sub-Saharan Africa. PLoS One 2018; 13:e0192785. [PMID: 29614069 PMCID: PMC5882095 DOI: 10.1371/journal.pone.0192785] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/30/2018] [Indexed: 01/05/2023] Open
Abstract
Objective Prompt identification of newly HIV-infected persons, particularly those who are most at risk of extended high viremia (EHV), allows important clinical and transmission prevention benefits. We sought to determine whether EHV could be predicted during early HIV infection (EHI) from clinical, demographic, and laboratory indicators in a large HIV-1 incidence study in Africa. Design Adults acquiring HIV-1 infection were enrolled in an EHI study assessing acute retroviral syndrome (ARS) symptoms and viral dynamics. Methods Estimated date of infection (EDI) was based on a positive plasma viral load or p24 antigen test prior to seroconversion, or the mid-point between negative and positive serological tests. EHV was defined as mean untreated viral load ≥5 log10 copies/ml 130–330 days post-EDI. We used logistic regression to develop risk score algorithms for predicting EHV based on sex, age, number of ARS symptoms, and CD4 and viral load at diagnosis. Results Models based on the full set of five predictors had excellent performance both in the full population (c-statistic = 0.80) and when confined to persons with each of three HIV-1 subtypes (c-statistic = 0.80–0.83 within subtypes A, C, and D). Reduced models containing only 2–4 predictors performed similarly. In a risk score algorithm based on the final full-population model, predictor scores were one for male sex and enrollment CD4<350 cells/mm3, and two for having enrollment viral load >4.9 log10 copies/ml. With a risk score cut-point of two, this algorithm was 85% sensitive (95% CI: 76%-91%) and 61% specific (55%-68%) in predicting EHV. Conclusions Simple risk score algorithms can reliably identify persons with EHI in sub-Saharan Africa who are likely to sustain high viral loads if treatment is delayed. These algorithms may be useful for prioritizing intensified efforts around care linkage and retention, treatment initiation, adherence support, and partner services to optimize clinical and prevention outcomes.
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Affiliation(s)
- Kimberly A. Powers
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Matthew A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | | | - Anatoli Kamali
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Uganda Research Unit on AIDS, Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Shabir Lakhi
- Zambia-Emory Research Project, Lusaka & Copperbelt, Zambia
| | | | - Omu Anzala
- KAVI-ICR University of Nairobi, Nairobi, Kenya
| | | | - Patricia E. Fast
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Jill Gilmour
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Imperial College of Science, Technology and Medicine, London, United Kingdom
| | - Eduard J. Sanders
- Kenya Medical Research Institute, Kilifi, Kenya
- University of Oxford, Headington, United Kingdom
- University of Amsterdam, Amsterdam, The Netherlands
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40
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Kratochvil S, McKay PF, Chung AW, Kent SJ, Gilmour J, Shattock RJ. Corrigendum: Immunoglobulin G1 Allotype Influences Antibody Subclass Distribution in Response to HIV gp140 Vaccination. Front Immunol 2018; 9:342. [PMID: 29508861 PMCID: PMC5835318 DOI: 10.3389/fimmu.2018.00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Paul F McKay
- Imperial College London, Medicine, London, United Kingdom
| | - Amy W Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC, Australia.,Melbourne Sexual Health Centre, Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
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41
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Kratochvil S, McKay PF, Chung AW, Kent SJ, Gilmour J, Shattock RJ. Immunoglobulin G1 Allotype Influences Antibody Subclass Distribution in Response to HIV gp140 Vaccination. Front Immunol 2017; 8:1883. [PMID: 29326728 PMCID: PMC5742328 DOI: 10.3389/fimmu.2017.01883] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 10/15/2017] [Accepted: 12/11/2017] [Indexed: 01/13/2023] Open
Abstract
Antibody subclasses exhibit extensive polymorphisms (allotypes) that could potentially impact the quality of HIV-vaccine induced B cell responses. Allotypes of immunoglobulin (Ig) G1, the most abundant serum antibody, have been shown to display altered functional properties in regard to serum half-life, Fc-receptor binding and FcRn-mediated mucosal transcytosis. To investigate the potential link between allotypic IgG1-variants and vaccine-generated humoral responses in a cohort of 14 HIV vaccine recipients, we developed a novel protocol for rapid IgG1-allotyping. We combined PCR and ELISA assays in a dual approach to determine the IgG1 allotype identity (G1m3 and/or G1m1) of trial participants, using human plasma and RNA isolated from PBMC. The IgG1-allotype distribution of our participants mirrored previously reported results for caucasoid populations. We observed elevated levels of HIV gp140-specific IgG1 and decreased IgG2 levels associated with the G1m1-allele, in contrast to G1m3 carriers. These data suggest that vaccinees homozygous for G1m1 are predisposed to develop elevated Ag-specific IgG1:IgG2 ratios compared to G1m3-carriers. This elevated IgG1:IgG2 ratio was further associated with higher FcγR-dimer engagement, a surrogate for potential antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) function. Although preliminary, these results suggest that IgG1 allotype may have a significant impact on IgG subclass distribution in response to vaccination and associated Fc-mediated effector functions. These results have important implications for ongoing HIV vaccine efficacy studies predicated on engagement of FcγR-mediated cellular functions including ADCC and ADCP, and warrant further investigation. Our novel allotyping protocol provides new tools to determine the potential impact of IgG1 allotypes on vaccine efficacy.
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Affiliation(s)
| | - Paul F McKay
- Imperial College London, Medicine, London, United Kingdom
| | - Amy W Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC, Australia.,Melbourne Sexual Health Centre, Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
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42
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McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C, Gupta N, Gkrania-Klotsas E, Young EH, Bannert N, Del Amo J, Gill MJ, Gilmour J, Kellam P, Kelleher AD, Sönnerborg A, Wolinsky SM, Zangerle R, Post FA, Fisher M, Haas DW, Walker BD, Porter K, Goldstein DB, Sandhu MS, de Bakker PIW, Fellay J. Evaluating the Impact of Functional Genetic Variation on HIV-1 Control. J Infect Dis 2017; 216:1063-1069. [PMID: 28968755 PMCID: PMC5853944 DOI: 10.1093/infdis/jix470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022] Open
Abstract
Background Previous genetic association studies of human immunodeficiency virus-1 (HIV-1) progression have focused on common human genetic variation ascertained through genome-wide genotyping. Methods We sought to systematically assess the full spectrum of functional variation in protein coding gene regions on HIV-1 progression through exome sequencing of 1327 individuals. Genetic variants were tested individually and in aggregate across genes and gene sets for an influence on HIV-1 viral load. Results Multiple single variants within the major histocompatibility complex (MHC) region were observed to be strongly associated with HIV-1 outcome, consistent with the known impact of classical HLA alleles. However, no single variant or gene located outside of the MHC region was significantly associated with HIV progression. Set-based association testing focusing on genes identified as being essential for HIV replication in genome-wide small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR) studies did not reveal any novel associations. Conclusions These results suggest that exonic variants with large effect sizes are unlikely to have a major contribution to host control of HIV infection.
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Affiliation(s)
- Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Laboratory, Public Health Agency of Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Sara L Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
| | - Deepti Gurdasani
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Istvan Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York
| | - Cristina Pomilla
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Elizabeth H Young
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Julia Del Amo
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M John Gill
- Department of Medicine, University of Calgary, Canada
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, United Kingdom
| | - Paul Kellam
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Research Department of Infection, Division of Infection and Immunity, University College London, United Kingdom
| | - Anthony D Kelleher
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Anders Sönnerborg
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Steven M Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago
| | - Robert Zangerle
- Department of Dermatology and Venereology, Medical University Innsbruck, Austria
| | | | - Martin Fisher
- Royal Sussex County Hospital, Brighton, United Kingdom
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Boston
- Howard Hughes Medical Institute, Chevy Chase
| | | | | | - Manjinder S Sandhu
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Paul I W de Bakker
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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43
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Clark T, Jackson C, Bolkan H, Lewis C, Gilmour J. Adequacy of Informed Consent in Emergency General Surgery: An Audit to Investigate Current Practice in a Busy Surgical Emergency Unit. Int J Surg 2017. [DOI: 10.1016/j.ijsu.2017.08.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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44
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Hassan AS, Hare J, Kamini G, Yindom LM, Kamali A, Karita E, Kilemba W, Price MA, Borrow P, Bjorkman P, Albert J, Kaleebu P, Allan S, Fast P, Hunter E, Gilmour J, Ndung'u T, Rowland-Jones S, Sanders EJ, Esbjornsson J. A35 Viral evolution and innate immune responses during acute HIV-1 infection and their association with disease pathogenesis. Virus Evol 2017; 3:vew036.034. [PMID: 28845248 PMCID: PMC5565927 DOI: 10.1093/ve/vew036.034] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- A S Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - J Hare
- IAVI Human Immunology Laboratory, Lomndon, UK
| | - G Kamini
- Kwazulu-Natal Research Institute for Tuberculosis and HIV, Durban, South Africa
| | - L M Yindom
- Nuffield Department of Medicine, University of Oxford, UK
| | - A Kamali
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI), Uganda
| | - E Karita
- Rwanda and Lusaka, Rwanda/Zambia HIV Research Group (RZHRG) Kigali, Zambia
| | - W Kilemba
- Rwanda and Lusaka, Rwanda/Zambia HIV Research Group (RZHRG) Kigali, Zambia
| | | | - P Borrow
- Nuffield Department of Medicine, University of Oxford, UK
| | - P Bjorkman
- Department of laboratory medicine, Lund University, Sweden
| | - J Albert
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Sweden
| | - P Kaleebu
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI), Uganda
| | - S Allan
- Rwanda and Lusaka, Rwanda/Zambia HIV Research Group (RZHRG) Kigali, Zambia
| | | | - E Hunter
- Rwanda and Lusaka, Rwanda/Zambia HIV Research Group (RZHRG) Kigali, Zambia
| | - J Gilmour
- IAVI Human Immunology Laboratory, Lomndon, UK
| | - T Ndung'u
- Kwazulu-Natal Research Institute for Tuberculosis and HIV, Durban, South Africa
| | | | - E J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - J Esbjornsson
- Nuffield Department of Medicine, University of Oxford, UK
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45
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Abujaber R, Shea PR, McLaren PJ, Lakhi S, Gilmour J, Allen S, Fellay J, Hollox EJ. No Evidence for Association of β-Defensin Genomic Copy Number with HIV Susceptibility, HIV Load during Clinical Latency, or Progression to AIDS. Ann Hum Genet 2017; 81:27-34. [PMID: 28084001 DOI: 10.1111/ahg.12182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 10/03/2016] [Accepted: 11/30/2016] [Indexed: 11/28/2022]
Abstract
Common single-nucleotide variation in the host accounts for 25% of the variability in the plasma levels of HIV during the clinical latency stage (viral load set point). However, the role of rare variants and copy number variants remains relatively unexplored. Previous work has suggested copy number variation of a cluster of β-defensin genes affects HIV load in treatment-naïve sub-Saharan Africans and rate of response to antiretroviral treatment. Here we analyse a total of 1827 individuals from two cohorts of HIV-infected individuals from Europe and sub-Saharan Africa to investigate the role of β-defensin copy number variation on HIV load at set point. We find no evidence for association of copy number with viral load. We also compare distribution of β-defensin copy number between European cases and controls and find no differences, arguing against a role of β-defensin copy number in HIV acquisition. Taken together, our data argue against an effect of copy number variation of the β-defensin region in the spontaneous control of HIV infection.
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Affiliation(s)
- Razan Abujaber
- Department of Genetics, University of Leicester, Leicester, UK
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Paul J McLaren
- National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Shabir Lakhi
- International AIDS Vaccine Initiative (IAVI), New York, New York, USA.,Zambia-Emory HIV Research Project, Lusaka and Copperbelt, Zambia
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), New York, New York, USA.,IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Susan Allen
- International AIDS Vaccine Initiative (IAVI), New York, New York, USA.,School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
| | -
- Department of Genetics, University of Leicester, Leicester, UK
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46
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Kratochvil S, McKay PF, Kopycinski JT, Bishop C, Hayes PJ, Muir L, Pinder CL, Cizmeci D, King D, Aldon Y, Wines BD, Hogarth PM, Chung AW, Kent SJ, Held K, Geldmacher C, Dally L, Santos NS, Cole T, Gilmour J, Fidler S, Shattock RJ. A Phase 1 Human Immunodeficiency Virus Vaccine Trial for Cross-Profiling the Kinetics of Serum and Mucosal Antibody Responses to CN54gp140 Modulated by Two Homologous Prime-Boost Vaccine Regimens. Front Immunol 2017; 8:595. [PMID: 28596770 PMCID: PMC5442169 DOI: 10.3389/fimmu.2017.00595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 03/22/2017] [Accepted: 05/05/2017] [Indexed: 12/24/2022] Open
Abstract
A key aspect to finding an efficacious human immunodeficiency virus (HIV) vaccine is the optimization of vaccine schedules that can mediate the efficient maturation of protective immune responses. In the present study, we investigated the effect of alternate booster regimens on the immune responses to a candidate HIV-1 clade C CN54gp140 envelope protein, which was coadministered with the TLR4-agonist glucopyranosyl lipid A-aqueous formulation. Twelve study participants received a common three-dose intramuscular priming series followed by a final booster at either 6 or 12 months. The two homologous prime-boost regimens were well tolerated and induced CN54gp140-specific responses that were observed in both the systemic and mucosal compartments. Levels of vaccine-induced IgG-subclass antibodies correlated significantly with FcγR engagement, and both vaccine regimens were associated with strikingly similar patterns in antibody titer and FcγR-binding profiles. In both groups, identical changes in the antigen (Ag)-specific IgG-subclass fingerprint, leading to a decrease in IgG1 and an increase in IgG4 levels, were modulated by booster injections. Here, the dissection of immune profiles further supports the notion that prime-boost strategies are essential for the induction of diverse Ag-specific HIV-1 responses. The results reported here clearly demonstrate that identical responses were effectively and safely induced by both vaccine regimens, indicating that an accelerated 6-month regimen could be employed for the rapid induction of immune responses against CN54gp140 with no apparent impact on the overall quality of the induced immune response. (This study has been registered at http://ClinicalTrials.gov under registration no. NCT01966900.)
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Affiliation(s)
| | | | | | - Cynthia Bishop
- Flow Cytometry Core Facility, Biomedical Research Centre, Guy's Hospital, London, UK
| | | | - Luke Muir
- Imperial College London, Medicine, London, UK
| | | | | | | | - Yoann Aldon
- Imperial College London, Medicine, London, UK
| | | | | | - Amy W Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC, Australia.,Melbourne Sexual Health Centre, Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Len Dally
- Emmes Corporation, Rockville, MD, USA
| | - Nelson S Santos
- NIHR/Wellcome Trust Imperial Clinical Research Facility Hammersmith Hospital, Imperial College London, London, UK
| | - Tom Cole
- NIHR/Wellcome Trust Imperial Clinical Research Facility Hammersmith Hospital, Imperial College London, London, UK
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47
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Ford T, Wenden C, Mbekeani A, Dally L, Cox JH, Morin M, Winstone N, Hill AVS, Gilmour J, Ewer KJ. Cryopreservation-related loss of antigen-specific IFNγ producing CD4 + T-cells can skew immunogenicity data in vaccine trials: Lessons from a malaria vaccine trial substudy. Vaccine 2017; 35:1898-1906. [PMID: 28285985 PMCID: PMC5387668 DOI: 10.1016/j.vaccine.2017.02.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 09/16/2016] [Revised: 01/31/2017] [Accepted: 02/18/2017] [Indexed: 12/19/2022]
Abstract
Ex vivo functional immunoassays such as ELISpot and intracellular cytokine staining (ICS) by flow cytometry are crucial tools in vaccine development both in the identification of novel immunogenic targets and in the immunological assessment of samples from clinical trials. Cryopreservation and subsequent thawing of PBMCs via validated processes has become a mainstay of clinical trials due to processing restrictions inherent in the disparate location and capacity of trial centres, and also in the need to standardize biological assays at central testing facilities. Logistical and financial requirement to batch process samples from multiple study timepoints are also key. We used ELISpot and ICS assays to assess antigen-specific immunogenicity in blood samples taken from subjects enrolled in a phase II malaria heterologous prime-boost vaccine trial and showed that the freeze thaw process can result in a 3–5-fold reduction of malaria antigen-specific IFNγ-producing CD3+CD4+ effector populations from PBMC samples taken post vaccination. We have also demonstrated that peptide responsive CD8+ T cells are relatively unaffected, as well as CD4+ T cell populations that do not produce IFNγ. These findings contribute to a growing body of data that could be consolidated and synthesised as guidelines for clinical trials with the aim of increasing the efficiency of vaccine development pipelines.
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Affiliation(s)
- Tom Ford
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK.
| | - Claire Wenden
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK
| | - Alison Mbekeani
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK
| | - Len Dally
- EMMES Corporation, Rockville, MD, USA
| | - Josephine H Cox
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK
| | | | - Nicola Winstone
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK
| | - Adrian V S Hill
- Centre for Clinical Vaccinology and Tropical Medicine and the Jenner Institute Laboratories, University of Oxford, UK
| | - Jill Gilmour
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK
| | - Katie J Ewer
- Centre for Clinical Vaccinology and Tropical Medicine and the Jenner Institute Laboratories, University of Oxford, UK
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Joseph S, Quinn K, Greenwood A, Cope AV, McKay PF, Hayes PJ, Kopycinski JT, Gilmour J, Miller AN, Geldmacher C, Nadai Y, Ahmed MIM, Montefiori DC, Dally L, Bouliotis G, Lewis DJM, Tatoud R, Wagner R, Esteban M, Shattock RJ, McCormack S, Weber J. A Comparative Phase I Study of Combination, Homologous Subtype-C DNA, MVA, and Env gp140 Protein/Adjuvant HIV Vaccines in Two Immunization Regimes. Front Immunol 2017; 8:149. [PMID: 28275375 PMCID: PMC5319954 DOI: 10.3389/fimmu.2017.00149] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 11/24/2016] [Accepted: 01/30/2017] [Indexed: 01/11/2023] Open
Abstract
There remains an urgent need for a prophylactic HIV vaccine. We compared combined MVA and adjuvanted gp140 to sequential MVA/gp140 after DNA priming. We expected Env-specific CD4+ T-cells after DNA and MVA priming, and Env-binding antibodies in 100% individuals after boosting with gp140 and that combined vaccines would not compromise safety and might augment immunogenicity. Forty volunteers were primed three times with DNA plasmids encoding (CN54) env and (ZM96) gag-pol-nef at 0, 4 and 8 weeks then boosted with MVA-C (CN54 env and gag-pol-nef) and glucopyranosyl lipid adjuvant—aqueous formulation (GLA-AF) adjuvanted CN54gp140. They were randomised to receive them in combination at the same visit at 16 and 20 weeks (accelerated) or sequentially with MVA-C at 16, 20, and GLA-AF/gp140 at 24 and 28 weeks (standard). All vaccinations were intramuscular. Primary outcomes included ≥grade 3 safety events and the titer of CN54gp140-specific binding IgG. Other outcomes included neutralization, binding antibody specificity and T-cell responses. Two participants experienced asymptomatic ≥grade 3 transaminitis leading to discontinuation of vaccinations, and three had grade 3 solicited local or systemic reactions. A total of 100% made anti-CN54gp140 IgG and combining vaccines did not significantly alter the response; geometric mean titer 6424 (accelerated) and 6578 (standard); neutralization of MW965.2 Tier 1 pseudovirus was superior in the standard group (82 versus 45% responders, p = 0.04). T-cell ELISpot responses were CD4+ and Env-dominant; 85 and 82% responding in the accelerated and standard groups, respectively. Vaccine-induced IgG responses targeted multiple regions within gp120 with the V3 region most immunodominant and no differences between groups detected. Combining MVA and gp140 vaccines did not result in increased adverse events and did not significantly impact upon the titer of Env-specific binding antibodies, which were seen in 100% individuals. The approach did however affect other immune responses; neutralizing antibody responses, seen only to Tier 1 pseudoviruses, were poorer when the vaccines were combined and while T-cell responses were seen in >80% individuals in both groups and similarly CD4 and Env dominant, their breadth/polyfunctionality tended to be lower when the vaccines were combined, suggesting attenuation of immunogenicity and cautioning against this accelerated regimen.
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Affiliation(s)
- Sarah Joseph
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London , London , UK
| | - Killian Quinn
- Department of Medicine, Imperial College London , London , UK
| | | | - Alethea V Cope
- Department of Medicine, Imperial College London , London , UK
| | - Paul F McKay
- Department of Medicine, Imperial College London , London , UK
| | - Peter J Hayes
- IAVI Human Immunology Laboratory, Imperial College London , London , UK
| | | | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London , London , UK
| | - Aleisha N Miller
- ICTU, Department of Public Health, Imperial College London , London , UK
| | - Christof Geldmacher
- Department of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), Munich, Germany
| | - Yuka Nadai
- Department of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), Munich, Germany
| | - Mohamed I M Ahmed
- Department of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), Munich, Germany
| | | | - Len Dally
- The EMMES Corporation , Rockville, MD , USA
| | - George Bouliotis
- ICTU, Department of Public Health, Imperial College London , London , UK
| | - David J M Lewis
- Clinical Research Centre, University of Surrey, Guildford, UK; Clinical Research Facility, Imperial College Healthcare NHS Trust, London, UK
| | - Roger Tatoud
- Department of Medicine, Imperial College London , London , UK
| | - Ralf Wagner
- University of Regensburg and University Hospital Regensburg , Regensburg , Germany
| | | | | | - Sheena McCormack
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London , London , UK
| | - Jonathan Weber
- Department of Medicine, Imperial College London , London , UK
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49
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Kaleebu P, Levin J, Nanvubya A, Kibengo F, Jaoko W, Pala P, Perreau M, Namuniina A, Kitandwe P, Tapia G, Serwanga J, Yates N, Fast P, Mayer B, Montefiori D, Tomaras G, Robb M, Lee C, Wagner R, Sanders E, Kilembe W, Kiwanuka N, Gilmour J, Kuipers H, Vooij D, Chinyenze K, Priddy F, Ding S, Hanke T, Pantaleo G. THE RESULTS OF THE EV06 DNA-PROTEIN COMBINATION TRIAL AND PLANS FOR GREAT, AN EDCTP2-FUNDED CONSERVED-MOSAIC EPITOPE HIV VACCINE TRIAL. BMJ Glob Health 2017. [DOI: 10.1136/bmjgh-2016-000260.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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50
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Nyombayire J, Anzala O, Gazzard B, Karita E, Bergin P, Hayes P, Kopycinski J, Omosa-Manyonyi G, Jackson A, Bizimana J, Farah B, Sayeed E, Parks CL, Inoue M, Hironaka T, Hara H, Shu T, Matano T, Dally L, Barin B, Park H, Gilmour J, Lombardo A, Excler JL, Fast P, Laufer DS, Cox JH. First-in-Human Evaluation of the Safety and Immunogenicity of an Intranasally Administered Replication-Competent Sendai Virus-Vectored HIV Type 1 Gag Vaccine: Induction of Potent T-Cell or Antibody Responses in Prime-Boost Regimens. J Infect Dis 2016; 215:95-104. [PMID: 28077588 PMCID: PMC5225252 DOI: 10.1093/infdis/jiw500] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 06/30/2016] [Accepted: 10/13/2016] [Indexed: 11/22/2022] Open
Abstract
Background. We report the first-in-human safety and immunogenicity assessment of a prototype intranasally administered, replication-competent Sendai virus (SeV)–vectored, human immunodeficiency virus type 1 (HIV-1) vaccine. Methods. Sixty-five HIV-1–uninfected adults in Kenya, Rwanda, and the United Kingdom were assigned to receive 1 of 4 prime-boost regimens (administered at 0 and 4 months, respectively; ratio of vaccine to placebo recipients, 12:4): priming with a lower-dose SeV-Gag given intranasally, followed by boosting with an adenovirus 35–vectored vaccine encoding HIV-1 Gag, reverse transcriptase, integrase, and Nef (Ad35-GRIN) given intramuscularly (SLA); priming with a higher-dose SeV-Gag given intranasally, followed by boosting with Ad35-GRIN given intramuscularly (SHA); priming with Ad35-GRIN given intramuscularly, followed by boosting with a higher-dose SeV-Gag given intranasally (ASH); and priming and boosting with a higher-dose SeV-Gag given intranasally (SHSH). Results. All vaccine regimens were well tolerated. Gag-specific IFN-γ enzyme-linked immunospot–determined response rates and geometric mean responses were higher (96% and 248 spot-forming units, respectively) in groups primed with SeV-Gag and boosted with Ad35-GRIN (SLA and SHA) than those after a single dose of Ad35-GRIN (56% and 54 spot-forming units, respectively) or SeV-Gag (55% and 59 spot-forming units, respectively); responses persisted for ≥8 months after completion of the prime-boost regimen. Functional CD8+ T-cell responses with greater breadth, magnitude, and frequency in a viral inhibition assay were also seen in the SLA and SHA groups after Ad35-GRIN boost, compared with those who received either vaccine alone. SeV-Gag did not boost T-cell counts in the ASH group. In contrast, the highest Gag-specific antibody titers were seen in the ASH group. Mucosal antibody responses were sporadic. Conclusions. SeV-Gag primed functional, durable HIV-specific T-cell responses and boosted antibody responses. The prime-boost sequence appears to determine which arm of the immune response is stimulated. Clinical Trials Registration. NCT01705990.
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Affiliation(s)
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative Institute of Clinical Research, Nairobi
| | - Brian Gazzard
- Chelsea and Westminster Healthcare NHS Foundation Trust
| | | | - Philip Bergin
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | - Peter Hayes
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | - Jakub Kopycinski
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | | | - Akil Jackson
- Chelsea and Westminster Healthcare NHS Foundation Trust
| | | | - Bashir Farah
- Kenya AIDS Vaccine Initiative Institute of Clinical Research, Nairobi
| | - Eddy Sayeed
- International AIDS Vaccine Initiative, New York, New York
| | | | | | | | | | | | - Tetsuro Matano
- University of Tokyo.,National Institute of Infectious Diseases, Tokyo, Japan
| | - Len Dally
- Emmes Corporation, Rockville, Maryland
| | | | - Harriet Park
- International AIDS Vaccine Initiative, New York, New York
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | | | | | - Patricia Fast
- International AIDS Vaccine Initiative, New York, New York
| | - Dagna S Laufer
- International AIDS Vaccine Initiative, New York, New York
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