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Greaney AJ, Loes AN, Gentles LE, Crawford KHD, Starr TN, Malone KD, Chu HY, Bloom JD. Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection. Sci Transl Med 2021; 13:eabi9915. [PMID: 34103407 PMCID: PMC8369496 DOI: 10.1126/scitranslmed.abi9915] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/02/2021] [Indexed: 12/18/2022]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with mutations in key antibody epitopes has raised concerns that antigenic evolution could erode adaptive immunity elicited by prior infection or vaccination. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted by antibodies elicited by vaccination or natural infection. To investigate how human antibody responses to vaccines are influenced by viral mutations, we used deep mutational scanning to compare the specificity of polyclonal antibodies elicited by either two doses of the mRNA-1273 COVID-19 vaccine or natural infection with SARS-CoV-2. The neutralizing activity of vaccine-elicited antibodies was more targeted to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein compared to antibodies elicited by natural infection. However, within the RBD, binding of vaccine-elicited antibodies was more broadly distributed across epitopes compared to infection-elicited antibodies. This greater binding breadth means that single RBD mutations have less impact on neutralization by vaccine sera compared to convalescent sera. Therefore, antibody immunity acquired by natural infection or different modes of vaccination may have a differing susceptibility to erosion by SARS-CoV-2 evolution.
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Affiliation(s)
- Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Lauren E Gentles
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Keara D Malone
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Ellis D, Brunette N, Crawford KHD, Walls AC, Pham MN, Chen C, Herpoldt KL, Fiala B, Murphy M, Pettie D, Kraft JC, Malone KD, Navarro MJ, Ogohara C, Kepl E, Ravichandran R, Sydeman C, Ahlrichs M, Johnson M, Blackstone A, Carter L, Starr TN, Greaney AJ, Lee KK, Veesler D, Bloom JD, King NP. Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design. Front Immunol 2021; 12:710263. [PMID: 34267764 PMCID: PMC8276696 DOI: 10.3389/fimmu.2021.710263] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
The unprecedented global demand for SARS-CoV-2 vaccines has demonstrated the need for highly effective vaccine candidates that are thermostable and amenable to large-scale manufacturing. Nanoparticle immunogens presenting the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein (S) in repetitive arrays are being advanced as second-generation vaccine candidates, as they feature robust manufacturing characteristics and have shown promising immunogenicity in preclinical models. Here, we used previously reported deep mutational scanning (DMS) data to guide the design of stabilized variants of the RBD. The selected mutations fill a cavity in the RBD that has been identified as a linoleic acid binding pocket. Screening of several designs led to the selection of two lead candidates that expressed at higher yields than the wild-type RBD. These stabilized RBDs possess enhanced thermal stability and resistance to aggregation, particularly when incorporated into an icosahedral nanoparticle immunogen that maintained its integrity and antigenicity for 28 days at 35-40°C, while corresponding immunogens displaying the wild-type RBD experienced aggregation and loss of antigenicity. The stabilized immunogens preserved the potent immunogenicity of the original nanoparticle immunogen, which is currently being evaluated in a Phase I/II clinical trial. Our findings may improve the scalability and stability of RBD-based coronavirus vaccines in any format and more generally highlight the utility of comprehensive DMS data in guiding vaccine design.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, United States
| | - Natalie Brunette
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Katharine H. D. Crawford
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Medical Scientist Training Program, University of Washington, Seattle, WA, United States
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Minh N. Pham
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Chengbo Chen
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
| | - Karla-Luise Herpoldt
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Brooke Fiala
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - John C. Kraft
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Keara D. Malone
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Cassandra Ogohara
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Elizabeth Kepl
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Claire Sydeman
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Max Johnson
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Alyssa Blackstone
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Tyler N. Starr
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Allison J. Greaney
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Medical Scientist Training Program, University of Washington, Seattle, WA, United States
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Jesse D. Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Howard Hughes Medical Institute, Seattle, WA, United States
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
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Greaney AJ, Loes AN, Gentles LE, Crawford KH, Starr TN, Malone KD, Chu HY, Bloom JD. The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD. bioRxiv 2021:2021.04.14.439844. [PMID: 33880474 PMCID: PMC8057239 DOI: 10.1101/2021.04.14.439844] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The emergence of SARS-CoV-2 variants with mutations in key antibody epitopes has raised concerns that antigenic evolution will erode immunity. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted. Here we compare the specificity of antibodies elicited by the mRNA-1273 vaccine versus natural infection. The neutralizing activity of vaccine-elicited antibodies is even more focused on the spike receptor-binding domain (RBD) than for infection-elicited antibodies. However, within the RBD, binding of vaccine-elicited antibodies is more broadly distributed across epitopes than for infection-elicited antibodies. This greater binding breadth means single RBD mutations have less impact on neutralization by vaccine sera than convalescent sera. Therefore, antibody immunity acquired by different means may have differing susceptibility to erosion by viral evolution. ONE SENTENCE SUMMARY Deep mutational scanning shows the mRNA-1273 RBD-binding antibody response is less affected by single viral mutations than the infection response.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Lauren E. Gentles
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Microbiology, University of Washington; Seattle, WA 98195, USA
| | - Katharine H.D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Keara D. Malone
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, Washington, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
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Greaney AJ, Loes AN, Crawford KHD, Starr TN, Malone KD, Chu HY, Bloom JD. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 2021; 29:463-476.e6. [PMID: 33592168 PMCID: PMC7869748 DOI: 10.1016/j.chom.2021.02.003] [Citation(s) in RCA: 788] [Impact Index Per Article: 262.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023]
Abstract
The evolution of SARS-CoV-2 could impair recognition of the virus by human antibody-mediated immunity. To facilitate prospective surveillance for such evolution, we map how convalescent plasma antibodies are impacted by all mutations to the spike's receptor-binding domain (RBD), the main target of plasma neutralizing activity. Binding by polyclonal plasma antibodies is affected by mutations in three main epitopes in the RBD, but longitudinal samples reveal that the impact of these mutations on antibody binding varies substantially both among individuals and within the same individual over time. Despite this inter- and intra-person heterogeneity, the mutations that most reduce antibody binding usually occur at just a few sites in the RBD's receptor-binding motif. The most important site is E484, where neutralization by some plasma is reduced >10-fold by several mutations, including one in the emerging 20H/501Y.V2 and 20J/501Y.V3 SARS-CoV-2 lineages. Going forward, these plasma escape maps can inform surveillance of SARS-CoV-2 evolution.
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MESH Headings
- Adult
- Aged
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Binding Sites
- COVID-19/virology
- Cell Line
- Female
- Humans
- Male
- Middle Aged
- Mutation
- Prospective Studies
- Protein Binding
- Protein Domains
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Young Adult
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Affiliation(s)
- Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Keara D Malone
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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Crawford KHD, Eguia R, Dingens AS, Loes AN, Malone KD, Wolf CR, Chu HY, Tortorici MA, Veesler D, Murphy M, Pettie D, King NP, Balazs AB, Bloom JD. Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays. Viruses 2020; 12:E513. [PMID: 32384820 PMCID: PMC7291041 DOI: 10.3390/v12050513] [Citation(s) in RCA: 526] [Impact Index Per Article: 131.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 12/17/2022] Open
Abstract
SARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral, and vesicular stomatitis virus (VSV) particles, but the reagents and protocols are not widely available. Here, we detailed how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also made all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrated how these pseudotyped lentiviral particles could be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization.
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Affiliation(s)
- Katharine H. D. Crawford
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.H.D.C.); (R.E.); (A.S.D.); (A.N.L.); (K.D.M.)
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Rachel Eguia
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.H.D.C.); (R.E.); (A.S.D.); (A.N.L.); (K.D.M.)
| | - Adam S. Dingens
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.H.D.C.); (R.E.); (A.S.D.); (A.N.L.); (K.D.M.)
| | - Andrea N. Loes
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.H.D.C.); (R.E.); (A.S.D.); (A.N.L.); (K.D.M.)
| | - Keara D. Malone
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.H.D.C.); (R.E.); (A.S.D.); (A.N.L.); (K.D.M.)
| | - Caitlin R. Wolf
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA; (C.R.W.); (H.Y.C.)
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA; (C.R.W.); (H.Y.C.)
| | - M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98109, USA; (M.A.T.); (D.V.); (N.P.K.)
- Institute Pasteur & CNRS UMR 3569, Unité de Virologie Structurale, Paris 75015, France
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98109, USA; (M.A.T.); (D.V.); (N.P.K.)
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; (M.M.); (D.P.)
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; (M.M.); (D.P.)
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98109, USA; (M.A.T.); (D.V.); (N.P.K.)
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; (M.M.); (D.P.)
| | - Alejandro B. Balazs
- The Ragon Institute of Massachusetts General Hospital, the Massachusetts Institute Technology, and Harvard University, Cambridge, MA 02139, USA;
| | - Jesse D. Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.H.D.C.); (R.E.); (A.S.D.); (A.N.L.); (K.D.M.)
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98103, USA
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