­­­The Antigenic Anatomy of SARS-CoV-2 Receptor Binding Domain

Abstract

Antibodies are crucial to immune protection against SARS-CoV-2 with some in emergency use as therapeutics. Here we identified 377 human monoclonal antibodies (mAbs) recognizing the viral spike, and focused on 80 which bind the receptor binding domain (RBD). By mapping antigenic sites using a unique computational methodology and comparing with inhibitory activity, we show that binding sites are widely dispersed, but neutralizing epitopes highly focused. Nearly all highly potent neutralizing mAbs (IC50< 0.1mg/ml) block receptor interaction, although one binds a unique epitope in the N-terminal domain. Many mAbs use public V-genes and are close to germline, boding well for vaccine responses. 19 Fab-antigen structures, some as RBD complexed with two Fabs, reveal two novel modes of engagement for potently inhibitory mAbs. Several Fabs are glycosylated, enhancing neutralisation for three, for two of which the sugar contacts the antigen. The most potent mAbs protect, prophylactically or therapeutically, in animal models. Ethical Approval: Patients were recruited into the Sepsis Immunomics project [Oxford REC C, reference:19/SC/0296] ISARIC/WHO Clinical Characterisation Protocol for Severe Emerging Infections [Oxford REC C, reference 13/SC/0149]. Animal studies were carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocols were approved by the Institutional Animal Care and Use Committee at the Washington University School of Medicine (assurance number A3381–01). Funding: The Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Science (CIFMS), China (ID: 2018-I2M-2-002); Medical Research Council, UK. National Institute for Health Research Biomedical Research Centre Funding Scheme (to G.R.S.), the Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Science (CIFMS), China (grant number: 2018-I2M-2-002) to D.I.S. and G.R.S., and G.R.S. is supported as a Wellcome Trust Senior Investigator (grant 095541/A/11/Z). H.M.E.D. and J.Ren are supported by the Wellcome Trust (101122/Z/13/Z), Y.Z. by Cancer Research UK (C375/A17721) and D.I.S. by the UK Medical Research Council (MR/N00065X/1). D.I.S. and GRS are Jenner Investigators. N.M.K is supported by T32AI007172. The National Institute for Health Research Biomedical Research Centre Funding Scheme supports G.R.S. We are also grateful for a Fast Grant from Fast Grants, Mercatus Center to support the isolation of human monoclonal antibodies to SARS-2 and Schmidt Futures for support of this work. G.R.S. is also supported as a Wellcome Trust Senior Investigator (grant 095541/A/11/Z). This is a contribution from the UK Instruct-ERIC Centre. The Wellcome Centre for Human Genetics is supported by the Wellcome Trust (grant 090532/Z/09/Z). We acknowledge Diamond Light Source for time on Beamline I03 under Proposal lb27009 and for electron microscope time at the UK national electron bio-imaging centre (eBIC), Proposal BI26983. Computational aspects were supported by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z and the NIHR Oxford BRC. This study was supported by grants from NIH (R01 AI157155) and the Defense Advanced Research Project Agency (HR001117S0019). J.B.C. is supported by a Helen Hay Whitney Foundation postdoctoral fellowship. Competing Interest: M.S.D. is a consultant for Inbios, Vir Biotechnology, NGM Biopharmaceuticals, Carnival Corporation and on the Scientific Advisory Boards of Moderna and Immunome. The M.S.D. laboratory has received unrelated funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions. GRS sits on the GSK Vaccines Scientific Advisory Board.