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Seow J, Khan H, Rosa A, Calvaresi V, Graham C, Pickering S, Pye VE, Cronin NB, Huettner I, Malim MH, Politis A, Cherepanov P, Doores KJ. A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination. Cell Rep 2022; 40:111276. [PMID: 35981534 PMCID: PMC9365860 DOI: 10.1016/j.celrep.2022.111276] [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: 03/28/2022] [Revised: 07/25/2022] [Accepted: 08/05/2022] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization.
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Affiliation(s)
- Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | | | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Nora B Cronin
- LonCEM Facility, The Francis Crick Institute, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | | | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK; Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, UK.
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK.
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2
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El-Sayed Moustafa JS, Jackson AU, Brotman SM, Guan L, Villicaña S, Roberts AL, Zito A, Bonnycastle L, Erdos MR, Narisu N, Stringham HM, Welch R, Yan T, Lakka T, Parker S, Tuomilehto J, Seow J, Graham C, Huettner I, Acors S, Kouphou N, Wadge S, Duncan EL, Steves CJ, Doores KJ, Malim MH, Collins FS, Pajukanta P, Boehnke M, Koistinen HA, Laakso M, Falchi M, Bell JT, Scott LJ, Mohlke KL, Small KS. ACE2 expression in adipose tissue is associated with cardio-metabolic risk factors and cell type composition-implications for COVID-19. Int J Obes (Lond) 2022; 46:1478-1486. [PMID: 35589964 PMCID: PMC9119844 DOI: 10.1038/s41366-022-01136-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND COVID-19 severity varies widely. Although some demographic and cardio-metabolic factors, including age and obesity, are associated with increasing risk of severe illness, the underlying mechanism(s) are uncertain. SUBJECTS/METHODS In a meta-analysis of three independent studies of 1471 participants in total, we investigated phenotypic and genetic factors associated with subcutaneous adipose tissue expression of Angiotensin I Converting Enzyme 2 (ACE2), measured by RNA-Seq, which acts as a receptor for SARS-CoV-2 cellular entry. RESULTS Lower adipose tissue ACE2 expression was associated with multiple adverse cardio-metabolic health indices, including type 2 diabetes (T2D) (P = 9.14 × 10-6), obesity status (P = 4.81 × 10-5), higher serum fasting insulin (P = 5.32 × 10-4), BMI (P = 3.94 × 10-4), and lower serum HDL levels (P = 1.92 × 10-7). ACE2 expression was also associated with estimated proportions of cell types in adipose tissue: lower expression was associated with a lower proportion of microvascular endothelial cells (P = 4.25 × 10-4) and higher proportion of macrophages (P = 2.74 × 10-5). Despite an estimated heritability of 32%, we did not identify any proximal or distal expression quantitative trait loci (eQTLs) associated with adipose tissue ACE2 expression. CONCLUSIONS Our results demonstrate that individuals with cardio-metabolic features known to increase risk of severe COVID-19 have lower background ACE2 levels in this highly relevant tissue. Reduced adipose tissue ACE2 expression may contribute to the pathophysiology of cardio-metabolic diseases, as well as the associated increased risk of severe COVID-19.
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Affiliation(s)
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Sarah M Brotman
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Li Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Amy L Roberts
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Antonino Zito
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02114, USA
| | - Lori Bonnycastle
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Ryan Welch
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tingfen Yan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Timo Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Stephen Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jaakko Tuomilehto
- University of Helsinki and Department of Medicine, Helsinki University Hospital, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Samuel Wadge
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Päivi Pajukanta
- Department of Human Genetics and Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Heikki A Koistinen
- University of Helsinki and Department of Medicine, Helsinki University Hospital, Helsinki, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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3
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Fielding CA, Sabberwal P, Williamson JC, Greenwood EJD, Crozier TWM, Zelek W, Seow J, Graham C, Huettner I, Edgeworth JD, Price DA, Morgan PB, Ladell K, Eberl M, Humphreys IR, Merrick B, Doores K, Wilson SJ, Lehner PJ, Wang ECY, Stanton RJ. SARS-CoV-2 host-shutoff impacts innate NK cell functions, but antibody-dependent NK activity is strongly activated through non-spike antibodies. eLife 2022; 11:e74489. [PMID: 35587364 PMCID: PMC9239683 DOI: 10.7554/elife.74489] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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: 10/06/2021] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
The outcome of infection is dependent on the ability of viruses to manipulate the infected cell to evade immunity, and the ability of the immune response to overcome this evasion. Understanding this process is key to understanding pathogenesis, genetic risk factors, and both natural and vaccine-induced immunity. SARS-CoV-2 antagonises the innate interferon response, but whether it manipulates innate cellular immunity is unclear. An unbiased proteomic analysis determined how cell surface protein expression is altered on SARS-CoV-2-infected lung epithelial cells, showing downregulation of activating NK ligands B7-H6, MICA, ULBP2, and Nectin1, with minimal effects on MHC-I. This occurred at the level of protein synthesis, could be mediated by Nsp1 and Nsp14, and correlated with a reduction in NK cell activation. This identifies a novel mechanism by which SARS-CoV-2 host-shutoff antagonises innate immunity. Later in the disease process, strong antibody-dependent NK cell activation (ADNKA) developed. These responses were sustained for at least 6 months in most patients, and led to high levels of pro-inflammatory cytokine production. Depletion of spike-specific antibodies confirmed their dominant role in neutralisation, but these antibodies played only a minor role in ADNKA compared to antibodies to other proteins, including ORF3a, Membrane, and Nucleocapsid. In contrast, ADNKA induced following vaccination was focussed solely on spike, was weaker than ADNKA following natural infection, and was not boosted by the second dose. These insights have important implications for understanding disease progression, vaccine efficacy, and vaccine design.
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Affiliation(s)
- Ceri Alan Fielding
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Pragati Sabberwal
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - James C Williamson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Edward JD Greenwood
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Thomas WM Crozier
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Wioleta Zelek
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation TrustLondonUnited Kingdom
| | - David A Price
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Paul B Morgan
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Matthias Eberl
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Ian R Humphreys
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Blair Merrick
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation TrustLondonUnited Kingdom
| | - Katie Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Sam J Wilson
- MRC - University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Eddie CY Wang
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Richard J Stanton
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
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4
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Seow J, Graham C, Hallett SR, Lechmere T, Maguire TJA, Huettner I, Cox D, Khan H, Pickering S, Roberts R, Waters A, Ward CC, Mant C, Pitcher MJ, Spencer J, Fox J, Malim MH, Doores KJ. ChAdOx1 nCoV-19 vaccine elicits monoclonal antibodies with cross-neutralizing activity against SARS-CoV-2 viral variants. Cell Rep 2022; 39:110757. [PMID: 35477023 PMCID: PMC9010245 DOI: 10.1016/j.celrep.2022.110757] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 09/24/2021] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 11/29/2022] Open
Abstract
Although the antibody response to COVID-19 vaccination has been studied extensively at the polyclonal level using immune sera, little has been reported on the antibody response at the monoclonal level. Here, we isolate a panel of 44 anti-SARS-CoV-2 monoclonal antibodies (mAbs) from an individual who received two doses of the ChAdOx1 nCoV-19 (AZD1222) vaccine at a 12-week interval. We show that, despite a relatively low serum neutralization titer, Spike-reactive IgG+ B cells are still detectable 9 months post-boost. Furthermore, mAbs with potent neutralizing activity against the current SARS-CoV-2 variants of concern (Alpha, Gamma, Beta, Delta, and Omicron) are present. The vaccine-elicited neutralizing mAbs form eight distinct competition groups and bind epitopes overlapping with neutralizing mAbs elicited following SARS-CoV-2 infection. AZD1222-elicited mAbs are more mutated than mAbs isolated from convalescent donors 1-2 months post-infection. These findings provide molecular insights into the AZD1222 vaccine-elicited antibody response.
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Affiliation(s)
- Jeffrey Seow
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Sadie R Hallett
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Daniel Cox
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Anele Waters
- Harrison Wing, Guy's and St Thomas' NHS Trust, London, UK
| | - Christopher C Ward
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Christine Mant
- Infectious Diseases Biobank, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Michael J Pitcher
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jo Spencer
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Julie Fox
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK; Harrison Wing, Guy's and St Thomas' NHS Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
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5
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Huettner I, Krumm SA, Serna S, Brzezicka K, Monaco S, Walpole S, van Diepen A, Allan F, Hicks T, Kimuda S, Emery AM, Landais E, Hokke CH, Angulo J, Reichardt N, Doores KJ. Cross-reactivity of glycan-reactive HIV-1 broadly neutralizing antibodies with parasite glycans. Cell Rep 2022; 38:110611. [PMID: 35354052 PMCID: PMC10073069 DOI: 10.1016/j.celrep.2022.110611] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/26/2022] [Accepted: 03/11/2022] [Indexed: 11/03/2022] Open
Abstract
The HIV-1 Envelope glycoprotein (Env) is the sole target for broadly neutralizing antibodies (bnAbs). Env is heavily glycosylated with host-derived N-glycans, and many bnAbs bind to, or are dependent upon, Env glycans for neutralization. Although glycan-binding bnAbs are frequently detected in HIV-infected individuals, attempts to elicit them have been unsuccessful because of the poor immunogenicity of Env N-glycans. Here, we report cross-reactivity of glycan-binding bnAbs with self- and non-self N-glycans and glycoprotein antigens from different life-stages of Schistosoma mansoni. Using the IAVI Protocol C HIV infection cohort, we examine the relationship between S. mansoni seropositivity and development of bnAbs targeting glycan-dependent epitopes. We show that the unmutated common ancestor of the N332/V3-specific bnAb lineage PCDN76, isolated from an HIV-infected donor with S. mansoni seropositivity, binds to S. mansoni cercariae while lacking reactivity to gp120. Overall, these results present a strategy for elicitation of glycan-reactive bnAbs which could be exploited in HIV-1 vaccine development.
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Affiliation(s)
- Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Stefanie A Krumm
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sonia Serna
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Katarzyna Brzezicka
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Angela van Diepen
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Fiona Allan
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, UK
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Simon Kimuda
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Aidan M Emery
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, UK
| | - Elise Landais
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Cornelis H Hokke
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK; Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Niels Reichardt
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain; CIBER-BBN, Paseo Miramón 182, 20009 San Sebastian, Spain
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK.
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6
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Granger LA, Huettner I, Debeljak F, Kaleebu P, Schechter M, Tambussi G, Weber J, Miro JM, Phillips R, Babiker A, Cooper DA, Fisher M, Ramjee G, Fidler S, Frater J, Fox J, Doores KJ. Broadly neutralizing antibody responses in the longitudinal primary HIV-1 infection Short Pulse Anti-Retroviral Therapy at Seroconversion cohort. AIDS 2021; 35:2073-2084. [PMID: 34127581 PMCID: PMC8505148 DOI: 10.1097/qad.0000000000002988] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/11/2021] [Accepted: 03/02/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Development of immunogens that elicit an anti-HIV-1 broadly neutralizing antibody (bnAb) response will be a key step in the development of an effective HIV-1 vaccine. Although HIV-1 bnAb epitopes have been identified and mechanisms of action studied, current HIV-1 envelope-based immunogens do not elicit HIV-1 bnAbs in humans or animal models. A better understanding of how HIV-1 bnAbs arise during infection and the clinical factors associated with bnAb development may be critical for HIV-1 immunogen design efforts. DESIGN AND METHODS Longitudinal plasma samples from the treatment-naive control arm of the Short Pulse Anti-Retroviral Therapy at Seroconversion (SPARTAC) primary HIV-1 infection cohort were used in an HIV-1 pseudotype neutralization assay to measure the neutralization breadth, potency and specificity of bnAb responses over time. RESULTS In the SPARTAC cohort, development of plasma neutralization breadth and potency correlates with duration of HIV infection and high viral loads, and typically takes 3-4 years to arise. bnAb activity was mostly directed to one or two bnAb epitopes per donor and more than 60% of donors with the highest plasma neutralization having bnAbs targeted towards glycan-dependent epitopes. CONCLUSION This study highlights the SPARTAC cohort as an important resource for more in-depth analysis of bnAb developmental pathways.
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Affiliation(s)
- Luke A. Granger
- Department of Infectious Diseases, King's College London, Guy's Hospital, Great Maze Pond, London, UK
- Department of Infectious Disease, Imperial College London
| | - Isabella Huettner
- Department of Infectious Diseases, King's College London, Guy's Hospital, Great Maze Pond, London, UK
| | - Franka Debeljak
- Department of Infectious Diseases, King's College London, Guy's Hospital, Great Maze Pond, London, UK
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Entebbe, Uganda
| | - Mauro Schechter
- Projeto Praça Onze, Hospital Escola São Francisco de Assis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giuseppe Tambussi
- Department of Infectious Diseases, Ospedale San Raffaele, Milan, Italy
| | | | - Jose M. Miro
- Infectious Diseases Service. Hospital Clinic–Institut d’investigacions Biomèdiques August Pi I Sunyer, University of Barcelona, Barcelona, Spain
| | - Rodney Phillips
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, UK
| | - Abdel Babiker
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology
| | - David A. Cooper
- St Vincent's Centre for Applied Medical Research and The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | - Martin Fisher
- Brighton and Sussex University Hospitals, Brighton, UK
| | - Gita Ramjee
- HIV Prevention Research Unit, South African Medical Research Council, Durban, South Africa
| | - Sarah Fidler
- Department of Infectious Disease, Imperial College London
- NIHR Imperial Biomedical Research Centre, London
| | - John Frater
- Nuffield Department of Medicine, Oxford University
- Oxford NIHR Biomedical Research Centre, Oxford
| | - Julie Fox
- Department of Infectious Diseases, King's College London, Guy's Hospital, Great Maze Pond, London, UK
- King's College NIHR Research Biomedical Research Centre, London, UK
| | - Katie J. Doores
- Department of Infectious Diseases, King's College London, Guy's Hospital, Great Maze Pond, London, UK
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7
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Dupont L, Snell LB, Graham C, Seow J, Merrick B, Lechmere T, Maguire TJA, Hallett SR, Pickering S, Charalampous T, Alcolea-Medina A, Huettner I, Jimenez-Guardeño JM, Acors S, Almeida N, Cox D, Dickenson RE, Galao RP, Kouphou N, Lista MJ, Ortega-Prieto AM, Wilson H, Winstone H, Fairhead C, Su JZ, Nebbia G, Batra R, Neil S, Shankar-Hari M, Edgeworth JD, Malim MH, Doores KJ. Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern. Nat Microbiol 2021; 6:1433-1442. [PMID: 34654917 PMCID: PMC8556155 DOI: 10.1038/s41564-021-00974-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [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: 06/07/2021] [Accepted: 09/03/2021] [Indexed: 12/17/2022]
Abstract
COVID-19 vaccine design and vaccination rollout need to take into account a detailed understanding of antibody durability and cross-neutralizing potential against SARS-CoV-2 and emerging variants of concern (VOCs). Analyses of convalescent sera provide unique insights into antibody longevity and cross-neutralizing activity induced by variant spike proteins, which are putative vaccine candidates. Using sera from 38 individuals infected in wave 1, we show that cross-neutralizing activity can be detected up to 305 days pos onset of symptoms, although sera were less potent against B.1.1.7 (Alpha) and B1.351 (Beta). Over time, despite a reduction in overall neutralization activity, differences in sera neutralization potency against SARS-CoV-2 and the Alpha and Beta variants decreased, which suggests that continued antibody maturation improves tolerance to spike mutations. We also compared the cross-neutralizing activity of wave 1 sera with sera from individuals infected with the Alpha, the Beta or the B.1.617.2 (Delta) variants up to 79 days post onset of symptoms. While these sera neutralize the infecting VOC and parental virus to similar levels, cross-neutralization of different SARS-CoV-2 VOC lineages is reduced. These findings will inform the optimization of vaccines to protect against SARS-CoV-2 variants.
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Affiliation(s)
- Liane Dupont
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Sadie R Hallett
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Nathalia Almeida
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Daniel Cox
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Ruth E Dickenson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Marie Jose Lista
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Cassandra Fairhead
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jia Zhe Su
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
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8
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Dupont L, Snell LB, Graham C, Seow J, Merrick B, Lechmere T, Hallett SR, Charalampous T, Alcolea-Medina A, Huettner I, Maguire TJA, Acors S, Almeida N, Cox D, Dickenson RE, Galao RP, Jimenez-Guardeño JM, Kouphou N, Lista MJ, Pickering S, Ortega-Prieto AM, Wilson H, Winstone H, Fairhead C, Su J, Nebbia G, Batra R, Neil S, Shankar-Hari M, Edgeworth JD, Malim MH, Doores KJ. Antibody longevity and cross-neutralizing activity following SARS-CoV-2 wave 1 and B.1.1.7 infections. medRxiv 2021:2021.06.07.21258351. [PMID: 34127977 PMCID: PMC8202432 DOI: 10.1101/2021.06.07.21258351] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
As SARS-CoV-2 variants continue to emerge globally, a major challenge for COVID-19 vaccination is the generation of a durable antibody response with cross-neutralizing activity against both current and newly emerging viral variants. Cross-neutralizing activity against major variants of concern (B.1.1.7, P.1 and B.1.351) has been observed following vaccination, albeit at a reduced potency, but whether vaccines based on the Spike glycoprotein of these viral variants will produce a superior cross-neutralizing antibody response has not been fully investigated. Here, we used sera from individuals infected in wave 1 in the UK to study the long-term cross-neutralization up to 10 months post onset of symptoms (POS), as well as sera from individuals infected with the B.1.1.7 variant to compare cross-neutralizing activity profiles. We show that neutralizing antibodies with cross-neutralizing activity can be detected from wave 1 up to 10 months POS. Although neutralization of B.1.1.7 and B.1.351 is lower, the difference in neutralization potency decreases at later timepoints suggesting continued antibody maturation and improved tolerance to Spike mutations. Interestingly, we found that B.1.1.7 infection also generates a cross-neutralizing antibody response, which, although still less potent against B.1.351, can neutralize parental wave 1 virus to a similar degree as B.1.1.7. These findings have implications for the optimization of vaccines that protect against newly emerging viral variants.
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Affiliation(s)
- Liane Dupont
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sadie R Hallett
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Nathalia Almeida
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Daniel Cox
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ruth E Dickenson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Marie Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Cassandra Fairhead
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jia Su
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
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9
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Graham C, Seow J, Huettner I, Khan H, Kouphou N, Acors S, Winstone H, Pickering S, Galao RP, Dupont L, Lista MJ, Jimenez-Guardeño JM, Laing AG, Wu Y, Joseph M, Muir L, van Gils MJ, Ng WM, Duyvesteyn HME, Zhao Y, Bowden TA, Shankar-Hari M, Rosa A, Cherepanov P, McCoy LE, Hayday AC, Neil SJD, Malim MH, Doores KJ. Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant. Immunity 2021; 54:1276-1289.e6. [PMID: 33836142 PMCID: PMC8015430 DOI: 10.1016/j.immuni.2021.03.023] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [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: 02/03/2021] [Revised: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 01/21/2023]
Abstract
Interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the receptor ACE2 on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies, and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, N-terminal domain (NTD) and S2 subunits of Spike. To understand how these mutations affect Spike antigenicity, we isolated and characterized >100 monoclonal antibodies targeting epitopes on RBD, NTD, and S2 from SARS-CoV-2-infected individuals. Approximately 45% showed neutralizing activity, of which ∼20% were NTD specific. NTD-specific antibodies formed two distinct groups: the first was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Mutations present in B.1.1.7 Spike frequently conferred neutralization resistance to NTD-specific antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes should be considered when investigating antigenic drift in emerging variants.
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Affiliation(s)
- Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Liane Dupont
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Adam G Laing
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Yin Wu
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Magdalene Joseph
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Luke Muir
- Division of Infection and Immunity, University College London, London, UK
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands
| | - Weng M Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Adrian C Hayday
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium.
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10
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Graham C, Seow J, Huettner I, Khan H, Kouphou N, Acors S, Winstone H, Pickering S, Galao RP, Lista MJ, Jimenez-Guardeno JM, Laing AG, Wu Y, Joseph M, Muir L, Ng WM, Duyvesteyn HME, Zhao Y, Bowden TA, Shankar-Hari M, Rosa A, Cherepanov P, McCoy LE, Hayday AC, Neil SJ, Malim MH, Doores KJ. Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike. bioRxiv 2021:2021.02.03.429355. [PMID: 33564766 PMCID: PMC7872354 DOI: 10.1101/2021.02.03.429355] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the ACE2 receptor on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, the N-terminal domain (NTD) and S2 subunits of Spike. To fully understand how these mutations affect the antigenicity of Spike, we have isolated and characterized neutralizing antibodies targeting epitopes beyond the already identified RBD epitopes. Using recombinant Spike as a sorting bait, we isolated >100 Spike-reactive monoclonal antibodies from SARS-CoV-2 infected individuals. ≈45% showed neutralizing activity of which ≈20% were NTD-specific. None of the S2-specific antibodies showed neutralizing activity. Competition ELISA revealed that NTD-specific mAbs formed two distinct groups: the first group was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Importantly, mutations present in B.1.1.7 Spike frequently conferred resistance to neutralization by the NTD-specific neutralizing antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes need to be considered when investigating antigenic drift in emerging variants.
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Affiliation(s)
- Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Jose M Jimenez-Guardeno
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Adam G. Laing
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Yin Wu
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
- The Francis Crick Institute, UK
| | - Magdalene Joseph
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Luke Muir
- Division of Infection and Immunity, University College London, London, UK
| | - Weng M. Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M. E. Duyvesteyn
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | | | | | - Laura E. McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Adrian C. Hayday
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Stuart J.D. Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Genotype-to-Phenotype UK National Virology Consortium
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Genotype-to-Phenotype UK National Virology Consortium
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Genotype-to-Phenotype UK National Virology Consortium
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11
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Seow J, Graham C, Merrick B, Acors S, Pickering S, Steel KJA, Hemmings O, O'Byrne A, Kouphou N, Galao RP, Betancor G, Wilson HD, Signell AW, Winstone H, Kerridge C, Huettner I, Jimenez-Guardeño JM, Lista MJ, Temperton N, Snell LB, Bisnauthsing K, Moore A, Green A, Martinez L, Stokes B, Honey J, Izquierdo-Barras A, Arbane G, Patel A, Tan MKI, O'Connell L, O'Hara G, MacMahon E, Douthwaite S, Nebbia G, Batra R, Martinez-Nunez R, Shankar-Hari M, Edgeworth JD, Neil SJD, Malim MH, Doores KJ. Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans. Nat Microbiol 2020; 5:1598-1607. [PMID: 33106674 PMCID: PMC7610833 DOI: 10.1038/s41564-020-00813-8] [Citation(s) in RCA: 876] [Impact Index Per Article: 219.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023]
Abstract
Antibody responses to SARS-CoV-2 can be detected in most infected individuals 10-15 d after the onset of COVID-19 symptoms. However, due to the recent emergence of SARS-CoV-2 in the human population, it is not known how long antibody responses will be maintained or whether they will provide protection from reinfection. Using sequential serum samples collected up to 94 d post onset of symptoms (POS) from 65 individuals with real-time quantitative PCR-confirmed SARS-CoV-2 infection, we show seroconversion (immunoglobulin (Ig)M, IgA, IgG) in >95% of cases and neutralizing antibody responses when sampled beyond 8 d POS. We show that the kinetics of the neutralizing antibody response is typical of an acute viral infection, with declining neutralizing antibody titres observed after an initial peak, and that the magnitude of this peak is dependent on disease severity. Although some individuals with high peak infective dose (ID50 > 10,000) maintained neutralizing antibody titres >1,000 at >60 d POS, some with lower peak ID50 had neutralizing antibody titres approaching baseline within the follow-up period. A similar decline in neutralizing antibody titres was observed in a cohort of 31 seropositive healthcare workers. The present study has important implications when considering widespread serological testing and antibody protection against reinfection with SARS-CoV-2, and may suggest that vaccine boosters are required to provide long-lasting protection.
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Affiliation(s)
- Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Kathryn J A Steel
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Oliver Hemmings
- Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aoife O'Byrne
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Gilberto Betancor
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Harry D Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Adrian W Signell
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Claire Kerridge
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Karen Bisnauthsing
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Amelia Moore
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adrian Green
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Lauren Martinez
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Brielle Stokes
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Johanna Honey
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Alba Izquierdo-Barras
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gill Arbane
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mark Kia Ik Tan
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Lorcan O'Connell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Geraldine O'Hara
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Eithne MacMahon
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sam Douthwaite
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rocio Martinez-Nunez
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK.
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