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SARS-Cov-2 RBD Antibodies That Maximize Breadth and Resistance to Escape W ­ 1,15 2,15 3,15 4 Tyler N

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SARS-Cov-2 RBD Antibodies That Maximize Breadth and Resistance to Escape W ­ 1,15 2,15 3,15 4 Tyler N https://doi.org/10.1038/s41586-021-03807-6 Accelerated Article Preview SARS-CoV-2 RBD antibodies that maximize W breadth and resistance to escape E VI Received: 29 March 2021 Tyler N. Starr, N ad in e Czudnochowski, Zhuoming Liu, Fabrizia Zatta, Young-Jun Park, Amin Addetia, Dora Pinto, Martina Beltramello, Patrick Hernandez, AllisonE J. Greaney, Accepted: 6 July 2021 Roberta Marzi, William G. Glass, Ivy Zhang, Adam S. Dingens, John E. B ow en­­, Accelerated Article Preview Published M . Alejandra Tortorici, Alexandra C. W al ls , J as on A. Wojcechowskyj,R Anna De Marco, online 14 July 2021 Laura E. Rosen, Jiayi Zhou, Martin Montiel-Ruiz, Hannah Kaiser, Josh Dillen, Heather Tucker, Jessica Bassi, Chiara Silacci-Fregni, Michael P. Housley,P Julia di Iulio, Gloria Lombardo, Cite this article as: Starr, T. N. et al. Maria Agostini, Nicole Sprugasci, Katja Culap, Stefano Jaconi, Marcel Meury, SARS-CoV-2 RBD antibodies that maximize Exequiel Dellota, Rana Abdelnabi, Shi-Yan Caroline Foo, Elisabetta Cameroni, breadth and resistance to escape. Nature Spencer Stumpf, Tristan I. Croll, Jay C. Nix, ColinE Havenar-Daughton, Luca Piccoli, https://doi.org/10.1038/s41586-021-03807-6 Fabio Benigni, Johan Neyts, Amalio Telenti, Florian A. Lempp, Matteo S. Pizzuto, (2021). John D. Chodera, Christy M. Hebner, HerbertL W. Virgin, Sean P. J. Whelan, David Veesler, Davide Corti, Jesse D. Bloom & Gyorgy Snell I C This is a PDF fle of a peer-reviewed paper that has been accepted for publication. Although unedited, the Tcontent has been subjected to preliminary formatting. Nature is providing this earlyR version of the typeset paper as a service to our authors and readers. The text and fgures will undergo copyediting and a proof review before the paper is publishedA in its fnal form. Please note that during the production process errors may be discovered which could afect the content, and all legal disclaimers apply.D E T A R E L E C C A Nature | www.nature.com Article SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape W 1,15 2,15 3,15 4 https://doi.org/10.1038/s41586-021-03807-6 Tyler N. Starr , Nadine Czudnochowski , Zhuoming Liu , Fabrizia Zatta , 5 1 4 4 E2 Young-Jun Park , Amin Addetia , Dora Pinto , Martina Beltramello , Patrick Hernandez , Received: 29 March 2021 Allison J. Greaney1,6, Roberta Marzi4, William G. Glass7, Ivy Zhang7,8, Adam S. DingensI 1, Accepted: 6 July 2021 John E. Bowen5, M. Alejandra Tortorici5, Alexandra C. Walls5, Jason A. Wojcechowskyj2, 4 2 2 2 V 2 Anna De Marco , Laura E. Rosen , Jiayi Zhou , Martin Montiel-Ruiz , Hannah Kaiser , Published online: 14 July 2021 Josh Dillen2, Heather Tucker2, Jessica Bassi4, Chiara Silacci-Fregni4, Michael P. Housley2, Julia di Iulio2, Gloria Lombardo4, Maria Agostini2, Nicole Sprugasci4,E Katja Culap4, Stefano Jaconi4, Marcel Meury2, Exequiel Dellota2, Rana Abdelnabi9, Shi-Yan Caroline Foo9, Elisabetta Cameroni4, Spencer Stumpf3, Tristan I. Croll10, Jay RC. Nix11, Colin Havenar-Daughton2, Luca Piccoli4, Fabio Benigni4, Johan Neyts9, Amalio Telenti2, Florian A. Lempp2, Matteo S. Pizzuto4, John D. ChoderaP7, Christy M. Hebner2, Herbert W. Virgin2,12,13, Sean P. J. Whelan3, David Veesler5, Davide Corti4 ✉, Jesse D. Bloom1,6,14 ✉ & Gyorgy Snell2 ✉ E An ideal anti-SARS-CoV-2 antibody wouldL resist viral escape 1–3, have activity against diverse SARS-related coronaviruses (sarbecoviruses)4–7, and be highly protective 8–11 C 12,13 through viral neutralization and efector functions . Understanding how these properties relate to each otherI and vary across epitopes would aid development of antibody therapeutics andT guide vaccine design. Here, we comprehensively characterize escape, breadth, and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-bindingR domain (RBD). Despite a tradeof between in vitro neutralization potency and breadth of sarbecovirus binding, we identify neutralizing antibodies withA exceptional sarbecovirus breadth and a corresponding resistance to SARS-CoV-2 escape. One of these antibodies, S2H97, binds with high afnity across all sarbecovirusD clades to a previously undescribed cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies targeting the ACE2 receptor Ebinding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we characterize one T potent RBM antibody (S2E128) with breadth across sarbecoviruses related to A SARS-CoV-2 and a high barrier to viral escape. These data highlight principles underlying variation in escape, breadth, and potency among antibodies targeting the R RBD, and identify epitopes and features to prioritize for therapeutic development E against the current and potential future pandemics. The most potentlyL neutralizing antibodies to SARS-CoV-2—including variants22,23 and the divergent sarbecovirus SARS-CoV-1. S309 forms the those in clinical use14 and dominant in polyclonal sera15,16—target the basis for an antibody therapy (VIR-7831, recently renamed sotrovimab) spike receptor-bindingE domain (RBD). Mutations in the RBD that reduce that has received Emergency Use Authorization from the FDA for treat- binding by antibodies have emerged among SARS-CoV-2 variants17–21, ment of COVID-1924. Longer term, antibodies with broad activity across highlightingC the need for antibodies and vaccines that are robust to viral SARS-related coronaviruses (sarbecoviruses) would be useful to com- escape. We have previously described an antibody, S3094, that exhib- bat potential future spillovers6. These efforts would be aided by a sys- Cits potent effector functions and neutralizes all current SARS-CoV-2 tematic understanding of the relationships among antibody epitope, 1Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. 2Vir Biotechnology, San Francisco, CA, 94158, USA. 3Department of Molecular Microbiology, A 4 5 Washington University School of Medicine, St. Louis, MO, 63110, USA. Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500, Bellinzona, Switzerland. Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA. 6Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. 7Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. 8Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA. 9Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium. 10Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK. 11Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. 12Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA. 13Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA. 14Howard Hughes Medical Institute, Seattle, WA, 98109, USA. 15These authors contributed equally: Tyler N. Starr, Nadine Czudnochowski, Zhuoming Liu. ✉e-mail: [email protected]; [email protected]; [email protected] Nature | www.nature.com | 1 Article resistance to viral escape, and breadth of sarbecovirus cross-reactivity. polar contacts with all three heavy chain CDRs and the light chain CDR2 Here we address this question by comprehensively characterizing a (Extended Data Fig. 5f). Molecular dynamics simulation of the S2H97 diverse panel of antibodies, including S309, using deep mutational Fab:RBD complex highlights the durability of many of these interactions scanning, pan-sarbecovirus binding assays, in vitro selection of viral (Fig. 2b). The surface bound by S2H97 is constrained by the deleteri- escape, and biochemical and structural analyses. ous effects of mutations on folded RBD expression (Fig. 2b)26, and this constraint is likely enhanced by quaternary packing with the NTD in the closed spike trimer (Extended Data Fig. 6a). Consistent with the conser- Potency, escapability, and breadth in a panel of RBD vation of the S2H97 epitope, S2H97 neutralizes diverse sarbecovirusesW W antibodies (Fig. 2c and Extended Data Fig. 4g) and SARS-CoV-2 variants (Fig. 2d). We identified a panel of anti-SARS-CoV-2 antibodies with distinct prop- To understand the evolution of S2H97 breadth, we measuredE breadth E erties (Fig. 1a, Extended Data Table 1), including six antibodies newly of binding by its germline form, S2H97GL, in which we reverted the described in this study. These antibodies bind different epitopes within 13 somatic mutations (Extended Data Fig. 4h,i). S2H97I GL bound all I the receptor-binding motif (RBM) and the non-RBM “core” of the RBD. tested sarbecovirus RBDs and exhibited particularlyV high affinity for V The antibody panel spans a range of neutralization potencies and bind- SARS-CoV-2-related RBDs. Somatic mutations enhanced affinity across ing affinities (Fig. 1a, Extended Data Fig. 1a-c). all sarbecoviruses by two orders of magnitude. This general increase We used deep mutational scanning to map how all amino-acid muta- in affinity together with the absence of non-conservativeE amino acid E tions in the SARS-CoV-2 RBD affect binding by each antibody3 (Fig. 1b,c replacements among paratope residues suggests that framework and Extended Data Fig. 2). Some antibodies have narrowly focused mutations may contribute to a generalR
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