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Johnson NV, Wall SC, Kramer KJ, Holt CM, Periasamy S, Richardson S, Suryadevara N, Andreano E, Paciello I, Pierleoni G, Piccini G, Huang Y, Ge P, Allen JD, Uno N, Shiakolas AR, Pilewski KA, Nargi RS, Sutton RE, Abu-Shmais AA, Parks R, Haynes BF, Carnahan RH, Crowe JE, Montomoli E, Rappuoli R, Bukreyev A, Ross TM, Sautto GA, McLellan JS, Georgiev IS. Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody. bioRxiv 2024:2024.01.15.575741. [PMID: 38293237 PMCID: PMC10827111 DOI: 10.1101/2024.01.15.575741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Three coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.
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Affiliation(s)
- Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Steven C. Wall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Kevin J. Kramer
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Clinton M. Holt
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Simone Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | - Giulio Pierleoni
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | | | - Ying Huang
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Pan Ge
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - James D. Allen
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Naoko Uno
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Andrea R. Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Kelsey A. Pilewski
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Rachel S. Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Rachel E. Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Alexandria A. Abu-Shmais
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Departments of Medicine and Immunology, Duke University, Durham, NC 27710, USA
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Emanuele Montomoli
- VisMederi Research S.r.l., Siena 53100, Italy
- VisMederi S.r.l, Siena 53100, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena 53100, Italy
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Ted M. Ross
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Giuseppe A. Sautto
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Computer Science, Vanderbilt University; Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University; Nashville, TN 37232, USA
- Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
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2
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Schaub JM, Chou CW, Kuo HC, Javanmardi K, Hsieh CL, Goldsmith J, DiVenere AM, Le KC, Wrapp D, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Wang N, Lavinder JJ, Ippolito GC, Maynard JA, McLellan JS, Finkelstein IJ. Expression and characterization of SARS-CoV-2 spike proteins. Nat Protoc 2021; 16:5339-5356. [PMID: 34611365 PMCID: PMC9665560 DOI: 10.1038/s41596-021-00623-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/06/2021] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 spike protein is a critical component of coronavirus disease 2019 vaccines and diagnostics and is also a therapeutic target. However, the spike protein is difficult to produce recombinantly because it is a large trimeric class I fusion membrane protein that is metastable and heavily glycosylated. We recently developed a prefusion-stabilized spike variant, termed HexaPro for six stabilizing proline substitutions, that can be expressed with a yield of >30 mg/L in ExpiCHO cells. This protocol describes an optimized workflow for expressing and biophysically characterizing rationally engineered spike proteins in Freestyle 293 and ExpiCHO cell lines. Although we focus on HexaPro, this protocol has been used to purify over a hundred different spike variants in our laboratories. We also provide guidance on expression quality control, long-term storage, and uses in enzyme-linked immunosorbent assays. The entire protocol, from transfection to biophysical characterization, can be completed in 7 d by researchers with basic tissue cell culture and protein purification expertise.
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Affiliation(s)
- Jeffrey M Schaub
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jory Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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3
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Kramer KJ, Johnson NV, Shiakolas AR, Suryadevara N, Periasamy S, Raju N, Williams JK, Wrapp D, Zost SJ, Walker LM, Wall SC, Holt CM, Hsieh CL, Sutton RE, Paulo A, Nargi RS, Davidson E, Doranz BJ, Crowe JE, Bukreyev A, Carnahan RH, McLellan JS, Georgiev IS. Potent neutralization of SARS-CoV-2 variants of concern by an antibody with an uncommon genetic signature and structural mode of spike recognition. Cell Rep 2021; 37:109784. [PMID: 34592170 PMCID: PMC8443366 DOI: 10.1016/j.celrep.2021.109784] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 05/26/2021] [Revised: 07/19/2021] [Accepted: 09/10/2021] [Indexed: 01/19/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that are more transmissible and resistant to currently approved antibody therapies poses a considerable challenge to the clinical treatment of coronavirus disease (COVID-19). Therefore, the need for ongoing discovery efforts to identify broadly reactive monoclonal antibodies to SARS-CoV-2 is of utmost importance. Here, we report a panel of SARS-CoV-2 antibodies isolated using the linking B cell receptor to antigen specificity through sequencing (LIBRA-seq) technology from an individual who recovered from COVID-19. Of these antibodies, 54042-4 shows potent neutralization against authentic SARS-CoV-2 viruses, including variants of concern (VOCs). A cryoelectron microscopy (cryo-EM) structure of 54042-4 in complex with the SARS-CoV-2 spike reveals an epitope composed of residues that are highly conserved in currently circulating SARS-CoV-2 lineages. Further, 54042-4 possesses uncommon genetic and structural characteristics that distinguish it from other potently neutralizing SARS-CoV-2 antibodies. Together, these findings provide motivation for the development of 54042-4 as a lead candidate to counteract current and future SARS-CoV-2 VOCs.
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Affiliation(s)
- Kevin J Kramer
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrea R Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Nagarajan Raju
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lauren M Walker
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Steven C Wall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Clinton M Holt
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rachel E Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ariana Paulo
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel S Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | | | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Electrical Engineering and Computer Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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4
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Voss WN, Hou YJ, Johnson NV, Delidakis G, Kim JE, Javanmardi K, Horton AP, Bartzoka F, Paresi CJ, Tanno Y, Chou CW, Abbasi SA, Pickens W, George K, Boutz DR, Towers DM, McDaniel JR, Billick D, Goike J, Rowe L, Batra D, Pohl J, Lee J, Gangappa S, Sambhara S, Gadush M, Wang N, Person MD, Iverson BL, Gollihar JD, Dye JM, Herbert AS, Finkelstein IJ, Baric RS, McLellan JS, Georgiou G, Lavinder JJ, Ippolito GC. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Science 2021; 372:1108-1112. [PMID: 33947773 PMCID: PMC8224265 DOI: 10.1126/science.abg5268] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [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: 01/12/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.
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MESH Headings
- Animals
- Antibodies, Monoclonal/blood
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity
- COVID-19/immunology
- COVID-19/prevention & control
- Epitopes/immunology
- Humans
- Immune Evasion
- Immunoglobulin G/blood
- Immunoglobulin G/chemistry
- Immunoglobulin G/immunology
- Immunoglobulin Heavy Chains/immunology
- Immunoglobulin Variable Region/immunology
- Mice
- Mice, Inbred BALB C
- Mutation
- Protein Domains
- Proteomics
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- William N Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - George Delidakis
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jin Eyun Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew P Horton
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Chelsea J Paresi
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Yuri Tanno
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Shawn A Abbasi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Whitney Pickens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Katia George
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, The University of Texas at Austin, Austin, TX, USA
| | - Dalton M Towers
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | | | - Daniel Billick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Lori Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Tulane National Primate Research Center Department of Microbiology 18703 Three Rivers Road Covington, LA, USA
| | - Dhwani Batra
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jan Pohl
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Justin Lee
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shivaprakash Gangappa
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suryaprakash Sambhara
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michelle Gadush
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Maria D Person
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA
| | - Brent L Iverson
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, The University of Texas at Austin, Austin, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - George Georgiou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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5
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Jones BE, Brown-Augsburger PL, Corbett KS, Westendorf K, Davies J, Cujec TP, Wiethoff CM, Blackbourne JL, Heinz BA, Foster D, Higgs RE, Balasubramaniam D, Wang L, Zhang Y, Yang ES, Bidshahri R, Kraft L, Hwang Y, Žentelis S, Jepson KR, Goya R, Smith MA, Collins DW, Hinshaw SJ, Tycho SA, Pellacani D, Xiang P, Muthuraman K, Sobhanifar S, Piper MH, Triana FJ, Hendle J, Pustilnik A, Adams AC, Berens SJ, Baric RS, Martinez DR, Cross RW, Geisbert TW, Borisevich V, Abiona O, Belli HM, de Vries M, Mohamed A, Dittmann M, Samanovic MI, Mulligan MJ, Goldsmith JA, Hsieh CL, Johnson NV, Wrapp D, McLellan JS, Barnhart BC, Graham BS, Mascola JR, Hansen CL, Falconer E. The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates. Sci Transl Med 2021; 13:eabf1906. [PMID: 33820835 PMCID: PMC8284311 DOI: 10.1126/scitranslmed.abf1906] [Citation(s) in RCA: 287] [Impact Index Per Article: 95.7] [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: 10/09/2020] [Revised: 01/19/2021] [Accepted: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses a public health threat for which preventive and therapeutic agents are urgently needed. Neutralizing antibodies are a key class of therapeutics that may bridge widespread vaccination campaigns and offer a treatment solution in populations less responsive to vaccination. Here, we report that high-throughput microfluidic screening of antigen-specific B cells led to the identification of LY-CoV555 (also known as bamlanivimab), a potent anti-spike neutralizing antibody from a hospitalized, convalescent patient with coronavirus disease 2019 (COVID-19). Biochemical, structural, and functional characterization of LY-CoV555 revealed high-affinity binding to the receptor-binding domain, angiotensin-converting enzyme 2 binding inhibition, and potent neutralizing activity. A pharmacokinetic study of LY-CoV555 conducted in cynomolgus monkeys demonstrated a mean half-life of 13 days and a clearance of 0.22 ml hour-1 kg-1, consistent with a typical human therapeutic antibody. In a rhesus macaque challenge model, prophylactic doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract in samples collected through study day 6 after viral inoculation. This antibody has entered clinical testing and is being evaluated across a spectrum of COVID-19 indications, including prevention and treatment.
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Affiliation(s)
- Bryan E Jones
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA.
| | | | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Julian Davies
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Thomas P Cujec
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | | | | | | | - Denisa Foster
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | | | | | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Lucas Kraft
- AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada
| | - Yuri Hwang
- AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada
| | | | | | - Rodrigo Goya
- AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada
| | - Maia A Smith
- AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada
| | | | | | - Sean A Tycho
- AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada
| | | | - Ping Xiang
- AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada
| | | | | | - Marissa H Piper
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Franz J Triana
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Jorg Hendle
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Anna Pustilnik
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | | | | | - Ralph S Baric
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R Martinez
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert W Cross
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thomas W Geisbert
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Viktoriya Borisevich
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Olubukola Abiona
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hayley M Belli
- Department of Population Health, Division of Biostatistics, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Maren de Vries
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Adil Mohamed
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Meike Dittmann
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marie I Samanovic
- NYU Langone Vaccine Center, Department of Medicine, Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Mark J Mulligan
- NYU Langone Vaccine Center, Department of Medicine, Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | | | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carl L Hansen
- AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada
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6
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Jones SK, Hawkins JA, Johnson NV, Jung C, Hu K, Rybarski JR, Chen JS, Doudna JA, Press WH, Finkelstein IJ. Massively Parallel Kinetic Profiling of Natural and Engineered CRISPR Nucleases. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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7
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Jones SK, Hawkins JA, Johnson NV, Jung C, Hu K, Rybarski JR, Chen JS, Doudna JA, Press WH, Finkelstein IJ. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases. Nat Biotechnol 2021; 39:84-93. [PMID: 32895548 PMCID: PMC9665413 DOI: 10.1038/s41587-020-0646-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/14/2020] [Indexed: 12/26/2022]
Abstract
Engineered SpCas9s and AsCas12a cleave fewer off-target genomic sites than wild-type (wt) Cas9. However, understanding their fidelity, mechanisms and cleavage outcomes requires systematic profiling across mispaired target DNAs. Here we describe NucleaSeq-nuclease digestion and deep sequencing-a massively parallel platform that measures the cleavage kinetics and time-resolved cleavage products for over 10,000 targets containing mismatches, insertions and deletions relative to the guide RNA. Combining cleavage rates and binding specificities on the same target libraries, we benchmarked five SpCas9 variants and AsCas12a. A biophysical model built from these data sets revealed mechanistic insights into off-target cleavage. Engineered Cas9s, especially Cas9-HF1, dramatically increased cleavage specificity but not binding specificity compared to wtCas9. Surprisingly, AsCas12a cleavage specificity differed little from that of wtCas9. Initial DNA cleavage sites and end trimming varied by nuclease, guide RNA and the positions of mispaired nucleotides. More broadly, NucleaSeq enables rapid, quantitative and systematic comparisons of specificity and cleavage outcomes across engineered and natural nucleases.
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Affiliation(s)
- Stephen K Jones
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
| | - John A Hawkins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
- Oden Institute for Computational Engineering and Science, University of Texas at Austin, Austin, TX, USA.
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - Cheulhee Jung
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kuang Hu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - James R Rybarski
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - Janice S Chen
- Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, CA, USA
| | - William H Press
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Oden Institute for Computational Engineering and Science, University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
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8
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Andreano E, Piccini G, Licastro D, Casalino L, Johnson NV, Paciello I, Dal Monego S, Pantano E, Manganaro N, Manenti A, Manna R, Casa E, Hyseni I, Benincasa L, Montomoli E, Amaro RE, McLellan JS, Rappuoli R. SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. bioRxiv 2020:2020.12.28.424451. [PMID: 33398278 PMCID: PMC7781313 DOI: 10.1101/2020.12.28.424451] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 11/11/2022]
Abstract
To investigate the evolution of SARS-CoV-2 in the immune population, we co-incubated authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for 7 passages, but after 45 days, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed at day 80 by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom and South Africa of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed. ONE SENTENCE SUMMARY Three mutations allowed SARS-CoV-2 to evade the polyclonal antibody response of a highly neutralizing COVID-19 convalescent plasma.
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Affiliation(s)
- Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | | | - Danilo Licastro
- ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Padriciano, 99, 34149, Trieste, Italy
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Simeone Dal Monego
- ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Padriciano, 99, 34149, Trieste, Italy
| | - Elisa Pantano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Noemi Manganaro
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | | | | | - Elisa Casa
- VisMederi S.r.l, Siena, Italy
- VisMederi Research S.r.l., Siena, Italy
| | - Inesa Hyseni
- VisMederi S.r.l, Siena, Italy
- VisMederi Research S.r.l., Siena, Italy
| | | | - Emanuele Montomoli
- VisMederi S.r.l, Siena, Italy
- VisMederi Research S.r.l., Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
- Faculty of Medicine, Imperial College, London, United Kingdom
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9
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Voss WN, Hou YJ, Johnson NV, Kim JE, Delidakis G, Horton AP, Bartzoka F, Paresi CJ, Tanno Y, Abbasi SA, Pickens W, George K, Boutz DR, Towers DM, McDaniel JR, Billick D, Goike J, Rowe L, Batra D, Pohl J, Lee J, Gangappa S, Sambhara S, Gadush M, Wang N, Person MD, Iverson BL, Gollihar JD, Dye J, Herbert A, Baric RS, McLellan JS, Georgiou G, Lavinder JJ, Ippolito GC. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma. bioRxiv 2020. [PMID: 33398269 DOI: 10.1101/2020.12.20.423708] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq 1 ) to the spike ectodomain (S-ECD 2 ) in four convalescent study subjects revealed that the plasma response is oligoclonal and directed predominantly (>80%) to S-ECD epitopes that lie outside the receptor binding domain (RBD). When comparing antibodies directed to either the RBD, the N-terminal domain (NTD) or the S2 subunit (S2) in one subject, just four IgG lineages (1 anti-S2, 2 anti-NTD and 1 anti-RBD) accounted for 93.5% of the repertoire. Although the anti-RBD and one of the anti-NTD antibodies were equally potently neutralizing in vitro , we nonetheless found that the anti-NTD antibody was sufficient for protection to lethal viral challenge, either alone or in combination as a cocktail where it dominated the effect of the other plasma antibodies. We identified in vivo protective plasma anti-NTD antibodies in 3/4 subjects analyzed and discovered a shared class of antibodies targeting the NTD that utilize unmutated or near-germline IGHV1-24, the most electronegative IGHV gene in the human genome. Structural analysis revealed that binding to NTD is dominated by interactions with the heavy chain, accounting for 89% of the entire interfacial area, with germline residues uniquely encoded by IGHV1-24 contributing 20% (149 Å 2 ). Together with recent reports of germline IGHV1-24 antibodies isolated by B-cell cloning 3,4 our data reveal a class of shared IgG antibodies that are readily observed in convalescent plasma and underscore the role of NTD-directed antibodies in protection against SARS-CoV-2 infection.
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10
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Jones BE, Brown-Augsburger PL, Corbett KS, Westendorf K, Davies J, Cujec TP, Wiethoff CM, Blackbourne JL, Heinz BA, Foster D, Higgs RE, Balasubramaniam D, Wang L, Bidshahri R, Kraft L, Hwang Y, Žentelis S, Jepson KR, Goya R, Smith MA, Collins DW, Hinshaw SJ, Tycho SA, Pellacani D, Xiang P, Muthuraman K, Sobhanifar S, Piper MH, Triana FJ, Hendle J, Pustilnik A, Adams AC, Berens SJ, Baric RS, Martinez DR, Cross RW, Geisbert TW, Borisevich V, Abiona O, Belli HM, de Vries M, Mohamed A, Dittmann M, Samanovic M, Mulligan MJ, Goldsmith JA, Hsieh CL, Johnson NV, Wrapp D, McLellan JS, Barnhart BC, Graham BS, Mascola JR, Hansen CL, Falconer E. LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection. bioRxiv 2020. [PMID: 33024963 DOI: 10.1101/2020.09.30.318972] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 poses a public health threat for which therapeutic agents are urgently needed. Herein, we report that high-throughput microfluidic screening of antigen-specific B-cells led to the identification of LY-CoV555, a potent anti-spike neutralizing antibody from a convalescent COVID-19 patient. Biochemical, structural, and functional characterization revealed high-affinity binding to the receptor-binding domain, ACE2 binding inhibition, and potent neutralizing activity. In a rhesus macaque challenge model, prophylaxis doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract. These data demonstrate that high-throughput screening can lead to the identification of a potent antiviral antibody that protects against SARS-CoV-2 infection. One Sentence Summary LY-CoV555, an anti-spike antibody derived from a convalescent COVID-19 patient, potently neutralizes SARS-CoV-2 and protects the upper and lower airways of non-human primates against SARS-CoV-2 infection.
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11
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito GC, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020. [PMID: 32703906 DOI: 10.1126/science:abd0826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Alison G Lee
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Juyeon Park
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Dzifa Amengor
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Oncology, Dell Medical School, University of Texas, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
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12
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito GC, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020; 369:1501-1505. [PMID: 32703906 PMCID: PMC7402631 DOI: 10.1126/science.abd0826] [Citation(s) in RCA: 792] [Impact Index Per Article: 198.0] [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: 05/30/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Alison G Lee
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Juyeon Park
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Dzifa Amengor
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Oncology, Dell Medical School, University of Texas, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
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13
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Wec AZ, Wrapp D, Herbert AS, Maurer DP, Haslwanter D, Sakharkar M, Jangra RK, Dieterle ME, Lilov A, Huang D, Tse LV, Johnson NV, Hsieh CL, Wang N, Nett JH, Champney E, Burnina I, Brown M, Lin S, Sinclair M, Johnson C, Pudi S, Bortz R, Wirchnianski AS, Laudermilch E, Florez C, Fels JM, O'Brien CM, Graham BS, Nemazee D, Burton DR, Baric RS, Voss JE, Chandran K, Dye JM, McLellan JS, Walker LM. Broad neutralization of SARS-related viruses by human monoclonal antibodies. Science 2020; 369:731-736. [PMID: 32540900 PMCID: PMC7299279 DOI: 10.1126/science.abc7424] [Citation(s) in RCA: 431] [Impact Index Per Article: 107.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/11/2020] [Indexed: 12/15/2022]
Abstract
As scientists develop therapeutic antibodies and vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the risk of emergent coronaviruses makes it important to also identify broadly protective antibodies. Wec et al. isolated and characterized hundreds of antibodies against the viral spike protein of SARS-CoV-2 from the memory B cells of a survivor of the 2003 outbreak caused by the related coronavirus, SARS-CoV. In both of these viruses, the spike protein facilitated viral entry by binding to the angiotensin-converting enzyme 2 (ACE2) receptor on human cells. The antibodies targeted multiple sites on the spike protein, but of nine antibodies that showed strong cross-neutralization, eight targeted the domain that binds to ACE2. These eight antibodies also neutralized a bat SARS-related virus. Illuminating the epitopes on the viral spike protein that bind cross-neutralizing antibodies could guide the design of broadly protective vaccines. Science, this issue p. 731 Broadly protective vaccines against known and preemergent human coronaviruses (HCoVs) are urgently needed. To gain a deeper understanding of cross-neutralizing antibody responses, we mined the memory B cell repertoire of a convalescent severe acute respiratory syndrome (SARS) donor and identified 200 SARS coronavirus 2 (SARS-CoV-2) binding antibodies that target multiple conserved sites on the spike (S) protein. A large proportion of the non-neutralizing antibodies display high levels of somatic hypermutation and cross-react with circulating HCoVs, suggesting recall of preexisting memory B cells elicited by prior HCoV infections. Several antibodies potently cross-neutralize SARS-CoV, SARS-CoV-2, and the bat SARS-like virus WIV1 by blocking receptor attachment and inducing S1 shedding. These antibodies represent promising candidates for therapeutic intervention and reveal a target for the rational design of pan-sarbecovirus vaccines.
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Affiliation(s)
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | | | - Denise Haslwanter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | | | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | - M Eugenia Dieterle
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | | | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Longping V Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | | | | - Shu Lin
- Adimab LLC, Lebanon, NH 03766, USA
| | | | | | | | - Robert Bortz
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | - Ariel S Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | - Ethan Laudermilch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | - Catalina Florez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | - J Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | - Cecilia M O'Brien
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, USA
| | - Ralph S Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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14
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AGW, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes. bioRxiv 2020:2020.05.30.125484. [PMID: 32577660 PMCID: PMC7302215 DOI: 10.1101/2020.05.30.125484] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to ~10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jory A. Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jeffrey M. Schaub
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andrea M. DiVenere
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kevin C. Le
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Alison Gene-Wei Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Patrick O. Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Christy K. Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - John Ludes-Meyers
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Annalee W. Nguyen
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Juyeon Park
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Dzifa Amengor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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15
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Wec AZ, Wrapp D, Herbert AS, Maurer D, Haslwanter D, Sakharkar M, Jangra RK, Dieterle ME, Lilov A, Huang D, Tse LV, Johnson NV, Hsieh CL, Wang N, Nett JH, Champney E, Burnina I, Brown M, Lin S, Sinclair M, Johnson C, Pudi S, Bortz R, Wirchnianski AS, Laudermilch E, Florez C, Fels JM, O’Brien CM, Graham BS, Nemazee D, Burton DR, Baric RS, Voss JE, Chandran K, Dye JM, McLellan JS, Walker LM. Broad sarbecovirus neutralizing antibodies define a key site of vulnerability on the SARS-CoV-2 spike protein. bioRxiv 2020:2020.05.15.096511. [PMID: 32511337 PMCID: PMC7241100 DOI: 10.1101/2020.05.15.096511] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 01/06/2023]
Abstract
Broadly protective vaccines against known and pre-emergent coronaviruses are urgently needed. Critical to their development is a deeper understanding of cross-neutralizing antibody responses induced by natural human coronavirus (HCoV) infections. Here, we mined the memory B cell repertoire of a convalescent SARS donor and identified 200 SARS-CoV-2 binding antibodies that target multiple conserved sites on the spike (S) protein. A large proportion of the antibodies display high levels of somatic hypermutation and cross-react with circulating HCoVs, suggesting recall of pre-existing memory B cells (MBCs) elicited by prior HCoV infections. Several antibodies potently cross-neutralize SARS-CoV, SARS-CoV-2, and the bat SARS-like virus WIV1 by blocking receptor attachment and inducing S1 shedding. These antibodies represent promising candidates for therapeutic intervention and reveal a new target for the rational design of pan-sarbecovirus vaccines.
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Affiliation(s)
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew S. Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | | | - Denise Haslwanter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | | | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - M. Eugenia Dieterle
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | | | - Deli Huang
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Longping V. Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | | | | - Shu Lin
- Adimab LLC, Lebanon, NH 03766, USA
| | | | | | | | - Robert Bortz
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Ariel S. Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Ethan Laudermilch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Catalina Florez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - J. Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Cecilia M. O’Brien
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | | | - David Nemazee
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard
| | - Ralph S. Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James E. Voss
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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16
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Dillard KE, Brown MW, Johnson NV, Xiao Y, Dolan A, Hernandez E, Dahlhauser SD, Kim Y, Myler LR, Anslyn EV, Ke A, Finkelstein IJ. Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex. Cell 2018; 175:934-946.e15. [PMID: 30343903 DOI: 10.1016/j.cell.2018.09.039] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/20/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022]
Abstract
CRISPR-Cas systems confer an adaptive immunity against viruses. Following viral injection, Cas1-Cas2 integrates segments of the viral genome (spacers) into the CRISPR locus. In type I CRISPR-Cas systems, efficient "primed" spacer acquisition and viral degradation (interference) require both the Cascade complex and the Cas3 helicase/nuclease. Here, we present single-molecule characterization of the Thermobifida fusca (Tfu) primed acquisition complex (PAC). We show that TfuCascade rapidly samples non-specific DNA via facilitated one-dimensional diffusion. Cas3 loads at target-bound Cascade and the Cascade/Cas3 complex translocates via a looped DNA intermediate. Cascade/Cas3 complexes stall at diverse protein roadblocks, resulting in a double strand break at the stall site. In contrast, Cas1-Cas2 samples DNA transiently via 3D collisions. Moreover, Cas1-Cas2 associates with Cascade and translocates with Cascade/Cas3, forming the PAC. PACs can displace different protein roadblocks, suggesting a mechanism for long-range spacer acquisition. This work provides a molecular basis for the coordinated steps in CRISPR-based adaptive immunity.
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Affiliation(s)
- Kaylee E Dillard
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Maxwell W Brown
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Adam Dolan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Erik Hernandez
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Samuel D Dahlhauser
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R Myler
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA.
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17
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Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S, Chen F, Wang Z. A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci Rep 2014; 4:4519. [PMID: 24682209 PMCID: PMC3970191 DOI: 10.1038/srep04519] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 02/26/2014] [Indexed: 02/04/2023] Open
Abstract
RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.
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Affiliation(s)
- Jeffrey A Martin
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Nicole V Johnson
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Stephen M Gross
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - James Schnable
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Xiandong Meng
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Mei Wang
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Devin Coleman-Derr
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Erika Lindquist
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Shawn Kaeppler
- Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
| | - Feng Chen
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Zhong Wang
- 1] Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA [2] Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
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