Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies

Creators: Muecksch, Frauke; Weisblum, Yiska; Barnes, Christopher O.; Schmidt, Fabian; Schaefer-Babajew, Dennis; Lorenzi, Julio C. C.; Flyak, Andrew I.; DeLaitsch, Andrew T.; Huey-Tubman, Kathryn E.; Hou, Shurong; Schiffer, Celia A.; Gaebler, Christian; Wang, Zijun; 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.

Abstract

Antibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on the properties of SARS-CoV-2 spike receptor-binding domain (RBD)-specific antibodies, we analyzed six independent antibody lineages. As well as increased neutralization potency, antibody evolution changed pathways for acquisition of resistance and, in some cases, restricted the range of neutralization escape options. For some antibodies, maturation apparently imposed a requirement for multiple spike mutations to enable escape. For certain antibody lineages, maturation enabled 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

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. This version posted March 8, 2021. We thank all study participants and clinical staff. We thank members of the Bjorkman, Nussenzweig, and Bieniasz laboratories for helpful discussions, 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 and Beckman Foundations 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 U.S. 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 (P.J.B. and M.C.N.), K99 AI153465 (to A.I.F.), 2U19AI111825 (to M.C.N.). This work was also supported by a George Mason University Fast Grant (P.J.B.), a grant from the NSF GRFP DGE-1745301 (to A.T.D.), and by the Caltech Merkin Institute for Translational Research (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 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 data. F.S. and J.D.S. generated spike plasmids. F.M., D.S.B., J.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.H.T. performed protein purification and complex assembly. A.I.F. and C.O.B. performed crystallographic studies and analyzed structures. C.O.B., A.T.D., and A.I.F. performed cryo-EM studies and analyzed structures. S.H. and C.A.S. generated and performed analyses of homology models. 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 participants and executed 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 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) and Y.W., F.S., T.H. and P.D.B. (US patent 63/036,124) are listed as inventors.

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