Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations

Creators: Muecksch, Frauke; Weisblum, Yiska; Barnes, Christopher O.; Schmidt, Fabian; Schaefer-Babajew, Dennis; Wang, Zijun; C. Lorenzi, Julio C.; Flyak, Andrew I.; DeLaitsch, Andrew T.; Huey-Tubman, Kathryn E.; Hou, Shurong; Schiffer, Celia A.; Gaebler, Christian; Da Silva, Justin; Poston, Daniel; Finkin, Shlomo; Cho, Alice; Cipolla, Melissa; Oliveira, Thiago Y.; Millard, Katrina G.; Ramos, Victor; Gazumyan, Anna; Rutkowska, Magdalena; Caskey, Marina; Nussenzweig, Michel C.; Bjorkman, Pamela J.; Hatziioannou, Theodora; Bieniasz, Paul D.

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Abstract

Antibodies elicited by infection accumulate somatic mutations in germinal centers that can increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) Spike receptor-binding domain (RBD)-specific antibodies from 5 individuals shortly after infection and later in convalescence to determine the impact of maturation over months. In addition to increased affinity and neutralization potency, antibody evolution changed the mutational pathways for the acquisition of viral resistance and restricted neutralization escape options. For some antibodies, maturation imposed a requirement for multiple substitutions to enable escape. For certain antibodies, affinity maturation enabled the neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.

Additional Information

© 2021 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Received 15 March 2021, Revised 26 May 2021, Accepted 12 July 2021, Available online 30 July 2021. We thank all of the study participants and clinical staff. We thank members of the Bjorkman, Nussenzweig, and Bieniasz laboratories for helpful discussions; and Dr. Jost Vielmetter, Pauline Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance. Electron microscopy was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy with assistance from Dr. Songye Chen. We thank the Gordon and Betty Moore Foundation and the Beckman Foundation for gifts to Caltech to support the Molecular Observatory (Dr. Jens Kaiser, director), and Drs. Silvia Russi, Aina Cohen, and Clyde Smith and the beamline staff at SSRL for data collection assistance. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-c76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P41GM103393). This work was supported by NIH grants R37-AI64003 (to P.D.B.), R01AI78788 (to T.H.), P01-AI138938-S1 (to P.J.B. and M.C.N.), K99 AI153465 (to A.I.F.), and 2U19AI111825 (to M.C.N.). This work was also supported by a George Mason University Fast Grant (to P.J.B.), NSF grant no. GRFP DGE-1745301 (to A.T.D.), and by the Caltech Merkin Institute for Translational Research (to P.J.B.). C.O.B was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. F.M. was supported by the Bulgari Women & Science Fellowship in COVID-19 Research. C.G. was supported by the Robert S. Wennett Post-Doctoral Fellowship, in part by the National Center for Advancing Translational Sciences (National Institutes of Health Clinical and Translational Science Award program, grant no. UL1 TR001866), and by the Shapiro-Silverberg Fund for the Advancement of Translational Research. M.C.N. and P.D.B. are Howard Hughes Medical Institute investigators. The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS, NIAID, or NIH. Author contributions: F.M., Y.W., C.O.B., F.S., M.C.N., P.J.B., T.H., and P.D.B. conceived the study and analyzed the data. F.S. and J.D.S. generated the Spike plasmids. F.M., D.S.-B., J.C.C.L., and J.D.S. performed neutralization assays with natural SARS-CoV-2 variant and sarbecovirus HIV-1 pseudotypes. Y.W., F.S., and M.R. performed the selection and characterization of escape mutants using VSV/SARS-CoV-2 and HIV-1-pseudotypes. C.O.B. and K.E.H.-T. performed the protein purification and complex assembly. A.I.F. and C.O.B. performed the crystallographic studies and analyzed structures. C.O.B., A.T.D., and A.I.F. performed the cryo-EM studies and analyzed structures. S.H. and C.A.S. generated and performed the analyses of homology models. Z.W. performed the BLI experiments. Z.W., S.F., A.C., T.Y.O., M.C., K.G.M., V.R., and A.G. isolated and characterized monoclonal antibodies. C.G. and M.C. recruited the participants and executed the clinical protocols. F.M., Y.W., C.O.B., F.S., M.C.N., P.J.B., T.H., and P.D.B. wrote the paper, with contributions from the other authors. Declaration of interests: The Rockefeller University has filed provisional patent applications in connection with this work on which M.C.N. (US patent 63/021,387) is listed as inventor. P.D.B. has served on an advisory board to Pfizer relating to SARS-CoV-2 vaccines. Data and code availability: Coordinates and maps associated with data reported in this manuscript have been deposited in the Electron Microscopy Data Bank (EMDB: https://www.ebi.ac.uk/pdbe/emdb/) and Protein Data Bank (PDB: www.rcsb.org). The coordinates generated from X-ray crystallographic studies of the C032 Fab, C080 Fab, C098 Fab, C099 Fab, C098-RBD complex, and C099-CR3022-RBD complex have been deposited at the PDB with accession numbers 7N3E, 7N3F, 7N3G, 7N3H, 7N3I, and 7R8L, respectively. The coordinates and cryo-EM maps generated from cryo-EM studies of the C032-S 6P complex, C051-S 6P complex, and C548-S 6P complex have been deposited at the PDB and EMDB with accession numbers PDB: 7R8M, 7R8N, 7R8O and EMDB: 24318, 24319, 24320, respectively. This paper does not report original code. Any additional information required to reanalyze the data reported in this paper is available from the Lead Contact upon request.

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