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Dugan HL, Stamper CT, Li L, Changrob S, Asby NW, Halfmann PJ, Zheng NY, Huang M, Shaw DG, Cobb MS, Erickson SA, Guthmiller JJ, Stovicek O, Wang J, Winkler ES, Madariaga ML, Shanmugarajah K, Jansen MO, Amanat F, Stewart I, Utset HA, Huang J, Nelson CA, Dai YN, Hall PD, Jedrzejczak RP, Joachimiak A, Krammer F, Diamond MS, Fremont DH, Kawaoka Y, Wilson PC. Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets. Immunity 2021; 54:1290-1303.e7. [PMID: 34022127 PMCID: PMC8101792 DOI: 10.1016/j.immuni.2021.05.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [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: 02/17/2021] [Revised: 04/06/2021] [Accepted: 04/29/2021] [Indexed: 12/16/2022]
Abstract
Dissecting the evolution of memory B cells (MBCs) against SARS-CoV-2 is critical for understanding antibody recall upon secondary exposure. Here, we used single-cell sequencing to profile SARS-CoV-2-reactive B cells in 38 COVID-19 patients. Using oligo-tagged antigen baits, we isolated B cells specific to the SARS-CoV-2 spike, nucleoprotein (NP), open reading frame 8 (ORF8), and endemic human coronavirus (HCoV) spike proteins. SARS-CoV-2 spike-specific cells were enriched in the memory compartment of acutely infected and convalescent patients several months post symptom onset. With severe acute infection, substantial populations of endemic HCoV-reactive antibody-secreting cells were identified and possessed highly mutated variable genes, signifying preexisting immunity. Finally, MBCs exhibited pronounced maturation to NP and ORF8 over time, especially in older patients. Monoclonal antibodies against these targets were non-neutralizing and non-protective in vivo. These findings reveal antibody adaptation to non-neutralizing intracellular antigens during infection, emphasizing the importance of vaccination for inducing neutralizing spike-specific MBCs.
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Affiliation(s)
- Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | | | - Lei Li
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Siriruk Changrob
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Nicholas W Asby
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Nai-Ying Zheng
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Min Huang
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Dustin G Shaw
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Mari S Cobb
- Section of Genetic Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Steven A Erickson
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Jenna J Guthmiller
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Olivia Stovicek
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Jiaolong Wang
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Emma S Winkler
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63130, USA; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63130, USA
| | | | | | - Maud O Jansen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Isabelle Stewart
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Henry A Utset
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA
| | - Jun Huang
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Christopher A Nelson
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63130, USA
| | - Ya-Nan Dai
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63130, USA
| | - Paige D Hall
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63130, USA
| | - Robert P Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA; Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA; Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63130, USA; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63130, USA; Department of Molecular Immunology, Washington University School of Medicine, St Louis, MO 63130, USA
| | - Daved H Fremont
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63130, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Department of Medicine, Section of Rheumatology, Chicago, IL 60637, USA.
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