The antigenic anatomy of SARS-CoV-2 receptor binding domain

Wanwisa Dejnirattisai; Daming Zhou; Helen M Ginn; Helen M E Duyvesteyn; Piyada Supasa; James Brett Case; Yuguang Zhao; Thomas S Walter; Alexander J Mentzer; Chang Liu; Beibei Wang; Guido C Paesen; Jose Slon-Campos; César López-Camacho; Natasha M Kafai; Adam L Bailey; Rita E Chen; Baoling Ying; Craig Thompson; Jai Bolton; Alex Fyfe; Sunetra Gupta; Tiong Kit Tan; Javier Gilbert-Jaramillo; William James; Michael Knight; Miles W Carroll; Donal Skelly; Christina Dold; Yanchun Peng; Robert Levin; Tao Dong; Andrew J Pollard; Julian C Knight; Paul Klenerman; Nigel Temperton; David R Hall; Mark A Williams; Neil G Paterson; Felicity K R Bertram; C Alistair Siebert; Daniel K Clare; Andrew Howe; Julika Radecke; Yun Song; Alain R Townsend; Kuan-Ying A Huang; Elizabeth E Fry; Juthathip Mongkolsapaya; Michael S Diamond; Jingshan Ren; David I Stuart; Gavin R Screaton

doi:10.1016/j.cell.2021.02.032

The antigenic anatomy of SARS-CoV-2 receptor binding domain

Cell. 2021 Apr 15;184(8):2183-2200.e22. doi: 10.1016/j.cell.2021.02.032. Epub 2021 Feb 18.

Authors

Wanwisa Dejnirattisai¹, Daming Zhou², Helen M Ginn³, Helen M E Duyvesteyn², Piyada Supasa¹, James Brett Case⁴, Yuguang Zhao², Thomas S Walter², Alexander J Mentzer⁵, Chang Liu⁶, Beibei Wang¹, Guido C Paesen², Jose Slon-Campos¹, César López-Camacho¹, Natasha M Kafai⁷, Adam L Bailey⁸, Rita E Chen⁷, Baoling Ying⁴, Craig Thompson⁹, Jai Bolton¹⁰, Alex Fyfe⁹, Sunetra Gupta⁹, Tiong Kit Tan¹¹, Javier Gilbert-Jaramillo¹², William James¹², Michael Knight¹², Miles W Carroll¹³, Donal Skelly¹⁴, Christina Dold¹⁵, Yanchun Peng¹¹, Robert Levin¹⁶, Tao Dong¹⁷, Andrew J Pollard¹⁸, Julian C Knight⁵, Paul Klenerman¹⁹, Nigel Temperton²⁰, David R Hall³, Mark A Williams³, Neil G Paterson³, Felicity K R Bertram³, C Alistair Siebert³, Daniel K Clare³, Andrew Howe³, Julika Radecke³, Yun Song³, Alain R Townsend²¹, Kuan-Ying A Huang²², Elizabeth E Fry², Juthathip Mongkolsapaya²³, Michael S Diamond²⁴, Jingshan Ren²⁵, David I Stuart²⁶, Gavin R Screaton²⁷

Affiliations

¹ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.
² Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK.
³ Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK.
⁴ Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA.
⁵ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁶ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
⁷ Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA.
⁸ Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA.
⁹ Peter Medawar Building for Pathogen Research, Oxford OX1 3SY, UK; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.
¹⁰ Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.
¹¹ MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
¹² Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
¹³ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury SP4 0JG, UK.
¹⁴ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.
¹⁵ Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford OX3 7LE, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK.
¹⁶ Worthing Hospital, Worthing BN11 2DH, UK.
¹⁷ Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
¹⁸ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford OX3 7LE, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK.
¹⁹ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford OX1 3SY, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
²⁰ Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham ME4 4TB, UK.
²¹ Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
²² Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
²³ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand. Electronic address: jmongkol@well.ox.ac.uk.
²⁴ Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, St. Louis, MO 63110 USA. Electronic address: mdiamond@wustl.edu.
²⁵ Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK. Electronic address: ren@strubi.ox.ac.uk.
²⁶ Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK. Electronic address: dave@strubi.ox.ac.uk.
²⁷ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK. Electronic address: gavin.screaton@medsci.ox.ac.uk.

Abstract

Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC₅₀ < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.

Keywords: coronavirus, SARS-CoV-2, anti-RBD antibody, receptor binding domain, antibody, immune responses, virus structure.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Antibodies, Monoclonal / immunology*
Antibodies, Neutralizing / immunology*
Antibodies, Viral / immunology*
Binding Sites, Antibody
CHO Cells
COVID-19 / immunology*
Chlorocebus aethiops
Cricetulus
Epitopes
Female
HEK293 Cells
Humans
Male
Mice
Mice, Transgenic
Models, Molecular
Protein Binding
Protein Structure, Tertiary
SARS-CoV-2 / immunology
Spike Glycoprotein, Coronavirus / immunology*
Vero Cells

Substances

Antibodies, Monoclonal
Antibodies, Neutralizing
Antibodies, Viral
Epitopes
Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2

Abstract

Publication types

MeSH terms

Substances

Grants and funding