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Wu H, Hu Z, Li J, Liu L, Wang J, Zhang J, Ou-Yang W. 60Co-γ Irradiation-Induced Shift and Polarity Reversal in the Triboelectric Series of Poly(ether sulfone)s. NANO LETTERS 2024; 24:5662-5668. [PMID: 38682870 DOI: 10.1021/acs.nanolett.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The sensitivity of triboelectric nanogenerators (TENGs) to the surface charge density highlights the significance of triboelectric materials and their modifications. Efforts have been directed toward developing effective strategies for increasing the surface charge density, expanding the potential applications of TENGs. This study proposes the use of irradiation technology for grafting to modify the electron-donating capability of poly(ether sulfone) (PES), thereby affording a dual benefit of enhancing the surface charge density and inducing a shift in the position of PES from negative to positive within the triboelectric series. The TENG based on grafted PES has resulted in a significant 3-fold increase in surface charge density compared to that of pristine PES, reaching 263 μC m-2. The surface charge density can be further increased to 502 μC m-2 through charge pumping. Notably, irradiation technology presents advantages over chemical grafting methods, particularly in terms of sustainability and environmental friendliness. This innovative approach shows great potential in advancing the domain of TENGs.
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Affiliation(s)
- Han Wu
- Department of Electronic Science and Technology, College of Electronic and Information Engineering, Tongji University, Shanghai 201804, China
| | - Zhen Hu
- Radiation Chemistry Department, Sichuan Institute of Atomic Energy, Chengdu 610101, China
| | - Jun Li
- Department of Electronic Science and Technology, College of Electronic and Information Engineering, Tongji University, Shanghai 201804, China
| | - Liqiang Liu
- Department of Electronic Science and Technology, College of Electronic and Information Engineering, Tongji University, Shanghai 201804, China
| | - Jingxia Wang
- Radiation Chemistry Department, Sichuan Institute of Atomic Energy, Chengdu 610101, China
| | - Jing Zhang
- Radiation Chemistry Department, Sichuan Institute of Atomic Energy, Chengdu 610101, China
| | - Wei Ou-Yang
- Engineering Research Center for Nanophotonics & Advanced Instrument, Ministry of Education, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
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Rubio AA, Baharani VA, Dadonaite B, Parada M, Abernathy ME, Wang Z, Lee YE, Eso MR, Phung J, Ramos I, Chen T, Nesr GE, Bloom JD, Bieniasz PD, Nussenzweig MC, Barnes CO. Bispecific antibodies with broad neutralization potency against SARS-CoV-2 variants of concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592584. [PMID: 38766244 PMCID: PMC11100608 DOI: 10.1101/2024.05.05.592584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The ongoing emergence of SARS-CoV-2 variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized N-terminal domain (NTD) and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from COVID-19 convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-EM structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite. Given C1596's favorable binding profile, we designed a series of bispecific antibodies (bsAbs) termed CoV2-biRNs, that featured both NTD and RBD specificities. Notably, two of the C1596-inclusive bsAbs, CoV2-biRN5 and CoV2-biRN7, retained potent in vitro neutralization activity against all Omicron variants tested, including XBB.1.5, EG.5.1, and BA.2.86, contrasting the diminished potency of parental antibodies delivered as monotherapies or as a cocktail. Furthermore, prophylactic delivery of CoV2-biRN5 significantly reduced the viral load within the lungs of K18-hACE2 mice following challenge with SARS-CoV-2 XBB.1.5. In conclusion, our NTD-RBD bsAbs offer promising potential for the design of resilient, next-generation antibody therapeutics against SARS-CoV-2 VOCs. One Sentence Summary Bispecific antibodies with a highly cross-reactive NTD antibody demonstrate resilience to SARS-CoV-2 variants of concern.
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Ng JCF, Montamat Garcia G, Stewart AT, Blair P, Mauri C, Dunn-Walters DK, Fraternali F. sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data. Nat Methods 2024; 21:823-834. [PMID: 37932398 PMCID: PMC11093741 DOI: 10.1038/s41592-023-02060-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023]
Abstract
Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline 'sterile' transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built to infer the dynamics and direction of CSR. Applying sciCSR on severe acute respiratory syndrome coronavirus 2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier time point in the collected time-course, the isotype distribution of B cell receptor repertoires of subsequent time points with high accuracy (cosine similarity ~0.9). Using processes specific to B cells, sciCSR identifies transitions that are often missed by conventional RNA velocity analyses and can reveal insights into the dynamics of B cell CSR during immune response.
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Affiliation(s)
- Joseph C F Ng
- Department of Structural and Molecular Biology, Division of Biosciences and Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Guillem Montamat Garcia
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | | | - Paul Blair
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | - Claudia Mauri
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | | | - Franca Fraternali
- Department of Structural and Molecular Biology, Division of Biosciences and Institute of Structural and Molecular Biology, University College London, London, UK.
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Bruhn M, Obara M, Salam A, Costa B, Ziegler A, Waltl I, Pavlou A, Hoffmann M, Graalmann T, Pöhlmann S, Schambach A, Kalinke U. Diversification of the VH3-53 immunoglobulin gene segment by somatic hypermutation results in neutralization of SARS-CoV-2 virus variants. Eur J Immunol 2024:e2451056. [PMID: 38593351 DOI: 10.1002/eji.202451056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
COVID-19 induces re-circulating long-lived memory B cells (MBC) that, upon re-encounter with the pathogen, are induced to mount immunoglobulin responses. During convalescence, antibodies are subjected to affinity maturation, which enhances the antibody binding strength and generates new specificities that neutralize virus variants. Here, we performed a single-cell RNA sequencing analysis of spike-specific B cells from a SARS-CoV-2 convalescent subject. After COVID-19 vaccination, matured infection-induced MBC underwent recall and differentiated into plasmablasts. Furthermore, the transcriptomic profiles of newly activated B cells transiently shifted toward the ones of atypical and CXCR3+ B cells and several B-cell clonotypes massively expanded. We expressed monoclonal antibodies (mAbs) from all B-cell clones from the largest clonotype that used the VH3-53 gene segment. The in vitro analysis revealed that some somatic hypermutations enhanced the neutralization breadth of mAbs in a putatively stochastic manner. Thus, somatic hypermutation of B-cell clonotypes generates an anticipatory memory that can neutralize new virus variants.
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Affiliation(s)
- Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Maureen Obara
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Abdus Salam
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Annett Ziegler
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Inken Waltl
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Theresa Graalmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- Junior Research Group for Translational Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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5
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Li Z, Zhang Z, Rosen ST, Feng M. Function and mechanism of bispecific antibodies targeting SARS-CoV-2. CELL INSIGHT 2024; 3:100150. [PMID: 38374826 PMCID: PMC10875118 DOI: 10.1016/j.cellin.2024.100150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/21/2024]
Abstract
As the dynamic evolution of SARS-CoV-2 led to reduced efficacy in monoclonal neutralizing antibodies and emergence of immune escape, the role of bispecific antibodies becomes crucial in bolstering antiviral activity and suppressing immune evasion. This review extensively assesses a spectrum of representative bispecific antibodies targeting SARS-CoV-2, delving into their characteristics, design formats, mechanisms of action, and associated advantages and limitations. The analysis encompasses factors influencing the selection of parental antibodies and strategies for incorporating added benefits in bispecific antibody design. Furthermore, how different classes of parental antibodies contribute to augmenting the broad-spectrum neutralization capability within bispecific antibodies is discussed. In summary, this review presents analyses and discussions aimed at offering valuable insights for shaping future strategies in bispecific antibody design to effectively confront the challenges posed by SARS-CoV-2 and propel advancements in antiviral therapeutic development.
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Affiliation(s)
- Zhaohui Li
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Zengyuan Zhang
- Department of Molecular Microbiology & Immunology, University of Southern California, CA, USA
| | - Steven T. Rosen
- Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Mingye Feng
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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6
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Chiyyeadu A, Asgedom G, Bruhn M, Rocha C, Schlegel TU, Neumann T, Galla M, Vollmer Barbosa P, Hoffmann M, Ehrhardt K, Ha TC, Morgan M, Schoeder CT, Pöhlmann S, Kalinke U, Schambach A. A tetravalent bispecific antibody outperforms the combination of its parental antibodies and neutralizes diverse SARS-CoV-2 variants. Clin Immunol 2024; 260:109902. [PMID: 38218210 DOI: 10.1016/j.clim.2024.109902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The devastating impact of COVID-19 on global health shows the need to increase our pandemic preparedness. Recombinant therapeutic antibodies were successfully used to treat and protect at-risk patients from COVID-19. However, the currently circulating Omicron subvariants of SARS-CoV-2 are largely resistant to therapeutic antibodies, and novel approaches to generate broadly neutralizing antibodies are urgently needed. Here, we describe a tetravalent bispecific antibody, A7A9 TVB, which actively neutralized many SARS-CoV-2 variants of concern, including early Omicron subvariants. Interestingly, A7A9 TVB neutralized more variants at lower concentration as compared to the combination of its parental monoclonal antibodies, A7K and A9L. A7A9 also reduced the viral load of authentic Omicron BA.1 virus in infected pseudostratified primary human nasal epithelial cells. Overall, A7A9 displayed the characteristics of a potent broadly neutralizing antibody, which may be suitable for prophylactic and therapeutic applications in the clinics, thus highlighting the usefulness of an effective antibody-designing approach.
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Affiliation(s)
- Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Girmay Asgedom
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany
| | - Cheila Rocha
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Tom U Schlegel
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Thomas Neumann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Katrin Ehrhardt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Teng-Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Clara T Schoeder
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Stefan Pöhlmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States of America.
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7
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Teng S, Hu Y, Wang Y, Tang Y, Wu Q, Zheng X, Lu R, Pan D, Liu F, Xie T, Wu C, Li YP, Liu W, Qu X. SARS-CoV-2 spike-reactive naïve B cells and pre-existing memory B cells contribute to antibody responses in unexposed individuals after vaccination. Front Immunol 2024; 15:1355949. [PMID: 38420128 PMCID: PMC10899457 DOI: 10.3389/fimmu.2024.1355949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction Since December 2019, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) has presented considerable public health challenges. Multiple vaccines have been used to induce neutralizing antibodies (nAbs) and memory B-cell responses against the viral spike (S) glycoprotein, and many essential epitopes have been defined. Previous reports have identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike-reactive naïve B cells and preexisting memory B cells in unexposed individuals. However, the role of these spike-reactive B cells in vaccine-induced immunity remains unknown. Methods To elucidate the characteristics of preexisting SARS-CoV-2 S-reactive B cells as well as their maturation after antigen encounter, we assessed the relationship of spike-reactive B cells before and after vaccination in unexposed human individuals. We further characterized the sequence identity, targeting domain, broad-spectrum binding activity and neutralizing activity of these SARS-CoV-2 S-reactive B cells by isolating monoclonal antibodies (mAbs) from these B cells. Results The frequencies of both spike-reactive naïve B cells and preexisting memory B cells before vaccination correlated with the frequencies of spike-reactive memory B cells after vaccination. Isolated mAbs from spike-reactive naïve B cells before vaccination had fewer somatic hypermutations (SHMs) than mAbs isolated from spike-reactive memory B cells before and after vaccination, but bound SARS-CoV-2 spike in vitro. Intriguingly, these germline-like mAbs possessed broad binding profiles for SARS-CoV-2 and its variants, although with low or no neutralizing capacity. According to tracking of the evolution of IGHV4-4/IGKV3-20 lineage antibodies from a single donor, the lineage underwent SHMs and developed increased binding activity after vaccination. Discussion Our findings suggest that spike-reactive naïve B cells can be expanded and matured by vaccination and cocontribute to vaccine-elicited antibody responses with preexisting memory B cells. Selectively and precisely targeting spike-reactive B cells by rational antigen design may provide a novel strategy for next-generation SARS-CoV-2 vaccine development.
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Affiliation(s)
- Shishan Teng
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Yabin Hu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - You Wang
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Yinggen Tang
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Qian Wu
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Xingyu Zheng
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Rui Lu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Dong Pan
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Fen Liu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Tianyi Xie
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Chanfeng Wu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Yi-Ping Li
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Wenpei Liu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
| | - Xiaowang Qu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
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8
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de Campos-Mata L, Trinité B, Modrego A, Tejedor Vaquero S, Pradenas E, Pons-Grífols A, Rodrigo Melero N, Carlero D, Marfil S, Santiago C, Raïch-Regué D, Bueno-Carrasco MT, Tarrés-Freixas F, Abancó F, Urrea V, Izquierdo-Useros N, Riveira-Muñoz E, Ballana E, Pérez M, Vergara-Alert J, Segalés J, Carolis C, Arranz R, Blanco J, Magri G. A monoclonal antibody targeting a large surface of the receptor binding motif shows pan-neutralizing SARS-CoV-2 activity. Nat Commun 2024; 15:1051. [PMID: 38316751 PMCID: PMC10844294 DOI: 10.1038/s41467-024-45171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024] Open
Abstract
Here we report the characterization of 17T2, a SARS-CoV-2 pan-neutralizing human monoclonal antibody isolated from a COVID-19 convalescent individual infected during the first pandemic wave. 17T2 is a class 1 VH1-58/κ3-20 antibody, derived from a receptor binding domain (RBD)-specific IgA+ memory B cell, with a broad neutralizing activity against former and new SARS-CoV-2 variants, including XBB.1.16 and BA.2.86 Omicron subvariants. Consistently, 17T2 demonstrates in vivo prophylactic and therapeutic activity against Omicron BA.1.1 infection in K18-hACE2 mice. Cryo-electron microscopy reconstruction shows that 17T2 binds the BA.1 spike with the RBD in "up" position and blocks the receptor binding motif, as other structurally similar antibodies do, including S2E12. Yet, unlike S2E12, 17T2 retains its neutralizing activity against all variants tested, probably due to a larger RBD contact area. These results highlight the impact of small structural antibody changes on neutralizing performance and identify 17T2 as a potential candidate for future clinical interventions.
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Affiliation(s)
- Leire de Campos-Mata
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Benjamin Trinité
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Andrea Modrego
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Sonia Tejedor Vaquero
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Edwards Pradenas
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Anna Pons-Grífols
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Natalia Rodrigo Melero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diego Carlero
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Silvia Marfil
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - César Santiago
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Dàlia Raïch-Regué
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | | | - Ferran Tarrés-Freixas
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Ferran Abancó
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Victor Urrea
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
| | - Eva Riveira-Muñoz
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Ester Ballana
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Mónica Pérez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Júlia Vergara-Alert
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joaquim Segalés
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Carlo Carolis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Rocío Arranz
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain.
- CIBERINFEC, ISCIII, Madrid, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain.
- Infectious Diseases and Immunity, Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain.
| | - Giuliana Magri
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
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9
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Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
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Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
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10
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Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L. Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted. EBioMedicine 2024; 100:104960. [PMID: 38232633 PMCID: PMC10803917 DOI: 10.1016/j.ebiom.2023.104960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes. METHODS Undertaking a nAB discovery program, we employed a classical workflow, while integrating artificial intelligence (AI)-based prediction to select non-competing nABs very early in the pipeline. We identified and in vivo validated (in female Syrian hamsters) two highly potent nABs. FINDINGS Despite the promising results, in depth cryo-EM structural analysis demonstrated that the AI-based prediction employed with the intention to ensure non-overlapping epitopes was inaccurate. The two nABs in fact bound to the same receptor-binding epitope in a remarkably similar manner. INTERPRETATION Our findings indicate that, even in the Alphafold era, AI-based predictions of paratope-epitope interactions are rough and experimental validation of epitopes remains an essential cornerstone of a successful nAB lead selection. FUNDING Full list of funders is provided at the end of the manuscript.
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Affiliation(s)
- Delphine Diana Acar
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Wojciech Witkowski
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Magdalena Wejda
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Ruifang Wei
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Tim Desmet
- Department of Basic and Applied Medical Sciences, Ghent University, Ghent 9000, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sieglinde De Cae
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Hannah Eeckhaut
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sandrine Vanmarcke
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | | | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xin Zhang
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Rana Abdelnabi
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Caroline S Foo
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven 3000, Belgium
| | - Dirk Reiter
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Han Remaut
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sarah Gerlo
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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11
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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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12
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Bruhn M, Obara M, Chiyyeadu A, Costa B, Salam A, Ziegler A, Waltl I, Pavlou A, Bonifacius A, Hoffmann M, Graalmann T, Pöhlmann S, Eiz-Vesper B, Schambach A, Kalinke U. Memory B cells anticipate SARS-CoV-2 variants through somatic hypermutation. J Infect 2024; 88:57-60. [PMID: 37913848 DOI: 10.1016/j.jinf.2023.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Affiliation(s)
- Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Maureen Obara
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Abdus Salam
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Annett Ziegler
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Inken Waltl
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany; Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Theresa Graalmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; Junior Research Group for Translational Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany; Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany; Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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13
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Korenkov M, Zehner M, Cohen-Dvashi H, Borenstein-Katz A, Kottege L, Janicki H, Vanshylla K, Weber T, Gruell H, Koch M, Diskin R, Kreer C, Klein F. Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants. Immunity 2023; 56:2803-2815.e6. [PMID: 38035879 DOI: 10.1016/j.immuni.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/19/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Somatic hypermutation (SHM) drives affinity maturation and continues over months in SARS-CoV-2-neutralizing antibodies (nAbs). However, several potent SARS-CoV-2 antibodies carry no or only a few mutations, leaving the question of how ongoing SHM affects neutralization unclear. Here, we reverted variable region mutations of 92 antibodies and tested their impact on SARS-CoV-2 binding and neutralization. Reverting higher numbers of mutations correlated with decreasing antibody functionality. However, for some antibodies, including antibodies of the public clonotype VH1-58, neutralization of Wu01 remained unaffected. Although mutations were dispensable for Wu01-induced VH1-58 antibodies to neutralize Alpha, Beta, and Delta variants, they were critical for Omicron BA.1/BA.2 neutralization. We exploited this knowledge to convert the clinical antibody tixagevimab into a BA.1/BA.2 neutralizer. These findings broaden our understanding of SHM as a mechanism that not only improves antibody responses during affinity maturation but also contributes to antibody diversification, thus increasing the chances of neutralizing viral escape variants.
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Affiliation(s)
- Michael Korenkov
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Matthias Zehner
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hadas Cohen-Dvashi
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Aliza Borenstein-Katz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lisa Kottege
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, University of Cologne, 50931 Cologne, Germany
| | - Ron Diskin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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14
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Schramm CA, Moon D, Peyton L, Lima NS, Wake C, Boswell KL, Henry AR, Laboune F, Ambrozak D, Darko SW, Teng IT, Foulds KE, Carfi A, Edwards DK, Kwong PD, Koup RA, Seder RA, Douek DC. Interaction dynamics between innate and adaptive immune cells responding to SARS-CoV-2 vaccination in non-human primates. Nat Commun 2023; 14:7961. [PMID: 38042809 PMCID: PMC10693617 DOI: 10.1038/s41467-023-43420-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/08/2023] [Indexed: 12/04/2023] Open
Abstract
As SARS-CoV-2 variants continue evolving, testing updated vaccines in non-human primates remains important for guiding human clinical practice. To date, such studies have focused on antibody titers and antigen-specific B and T cell frequencies. Here, we extend our understanding by integrating innate and adaptive immune responses to mRNA-1273 vaccination in rhesus macaques. We sorted innate immune cells from a pre-vaccine time point, as well as innate immune cells and antigen-specific peripheral B and T cells two weeks after each of two vaccine doses and used single-cell sequencing to assess the transcriptomes and adaptive immune receptors of each cell. We show that a subset of S-specific T cells expresses cytokines critical for activating innate responses, with a concomitant increase in CCR5-expressing intermediate monocytes and a shift of natural killer cells to a more cytotoxic phenotype. The second vaccine dose, administered 4 weeks after the first, elicits an increase in circulating germinal center-like B cells 2 weeks later, which are more clonally expanded and enriched for epitopes in the receptor binding domain. Both doses stimulate inflammatory response genes associated with elevated antibody production. Overall, we provide a comprehensive picture of bidirectional signaling between innate and adaptive components of the immune system and suggest potential mechanisms for the enhanced response to secondary exposure.
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Affiliation(s)
- Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Damee Moon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lowrey Peyton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Noemia S Lima
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christian Wake
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kristin L Boswell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Farida Laboune
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel W Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | | | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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15
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Wang R, Han Y, Zhang R, Zhu J, Nan X, Liu Y, Yang Z, Zhou B, Yu J, Lin Z, Li J, Chen P, Wang Y, Li Y, Liu D, Shi X, Wang X, Zhang Q, Yang YR, Li T, Zhang L. Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection. Immunity 2023; 56:2635-2649.e6. [PMID: 37924813 DOI: 10.1016/j.immuni.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to SARS-CoV-1 infection remains incomplete. Herein, we studied the antibody responses in 25 SARS-CoV-1 convalescent patients. Plasma neutralization was higher and lasted longer in SARS-CoV-1 patients than in severe SARS-CoV-2 patients. Among 77 monoclonal antibodies (mAbs) isolated, 60 targeted the receptor-binding domain (RBD) and formed 7 groups (RBD-1 to RBD-7) based on their distinct binding and structural profiles. Notably, RBD-7 antibodies bound to a unique RBD region interfaced with the N-terminal domain of the neighboring protomer (NTD proximal) and were more prevalent in SARS-CoV-1 patients. Broadly neutralizing antibodies for SARS-CoV-1, SARS-CoV-2, and bat and pangolin coronaviruses were also identified. These results provide further insights into the antibody response to SARS-CoV-1 and inform the design of more effective strategies against diverse human and animal coronaviruses.
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Affiliation(s)
- Ruoke Wang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Yang Han
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China
| | - Rui Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jiayi Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Xuanyu Nan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yaping Liu
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ziqing Yang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zichun Lin
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinqian Li
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yangjunqi Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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16
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Arons E, Henry K, Haas C, Gould M, Tsintolas J, Mauter J, Zhou H, Burbelo PD, Cohen JI, Kreitman RJ. Characterization of B-cell receptor clonality and immunoglobulin gene usage at multiple time points during active SARS-CoV-2 infection. J Med Virol 2023; 95:e29179. [PMID: 37877800 DOI: 10.1002/jmv.29179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Although monoclonal antibodies to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are known, B-cell receptor repertoire and its change in patients during coronavirus disease-2019 (COVID-19) progression is underreported. We aimed to study this molecularly. We used immunoglobulin heavy chain (IGH) variable region (IGHV) spectratyping and next-generation sequencing of peripheral blood B-cell genomic DNA collected at multiple time points during disease evolution to study B-cell response to SARS-CoV-2 infection in 14 individuals with acute COVID-19. We found a broad distribution of responding B-cell clones. The IGH gene usage was not significantly skewed but frequencies of individual IGH genes changed repeatedly. We found predominant usage of unmutated and low mutation-loaded IGHV rearrangements characterizing naïve and extrafollicular B cells among the majority of expanded peripheral B-cell clonal lineages at most tested time points in most patients. IGH rearrangement usage showed no apparent relation to anti-SARS-CoV-2 antibody titers. Some patients demonstrated mono/oligoclonal populations carrying highly mutated IGHV rearrangements indicating antigen experience at some of the time points tested, including even before anti-SARS-CoV-2 antibodies were detected. We present evidence demonstrating that the B-cell response to SARS-CoV-2 is individual and includes different lineages of B cells at various time points during COVID-19 progression.
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Affiliation(s)
- Evgeny Arons
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | | | - Christopher Haas
- Medstar Franklin Square Medical Center, Baltimore, Maryland, USA
| | - Mory Gould
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jack Tsintolas
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jack Mauter
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Hong Zhou
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Robert J Kreitman
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
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17
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Gonçalves J, Melro M, Alenquer M, Araújo C, Castro-Neves J, Amaral-Silva D, Ferreira F, Ramalho JS, Charepe N, Serrano F, Pontinha C, Amorim MJ, Soares H. Balance between maternal antiviral response and placental transfer of protection in gestational SARS-CoV-2 infection. JCI Insight 2023; 8:e167140. [PMID: 37490342 PMCID: PMC10544212 DOI: 10.1172/jci.insight.167140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
The intricate interplay between maternal immune response to SARS-CoV-2 and the transfer of protective factors to the fetus remains unclear. By analyzing mother-neonate dyads from second and third trimester SARS-CoV-2 infections, our study shows that neutralizing antibodies (NAbs) are infrequently detected in cord blood. We uncovered that this is due to impaired IgG-NAb placental transfer in symptomatic infection and to the predominance of maternal SARS-CoV-2 NAbs of the IgA and IgM isotypes, which are prevented from crossing the placenta. Crucially, the balance between maternal antiviral response and transplacental transfer of IgG-NAbs appears to hinge on IL-6 and IL-10 produced in response to SARS-CoV-2 infection. In addition, asymptomatic maternal infection was associated with expansion of anti-SARS-CoV-2 IgM and NK cell frequency. Our findings identify a protective role for IgA/IgM-NAbs in gestational SARS-CoV-2 infection and open the possibility that the maternal immune response to SARS-CoV-2 infection might benefit the neonate in 2 ways, first by skewing maternal immune response toward immediate viral clearance, and second by endowing the neonate with protective mechanisms to curtail horizontal viral transmission in the critical postnatal period, via the priming of IgA/IgM-NAbs to be transferred by the breast milk and via NK cell expansion in the neonate.
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Affiliation(s)
- Juliana Gonçalves
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Magda Melro
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Marta Alenquer
- Cell Biology of Viral Infection Lab, Gulbenkian Institute of Science, Oeiras, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Portuguese Catholic University, Lisbon, Portugal
| | - Catarina Araújo
- Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
| | - Júlia Castro-Neves
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Daniela Amaral-Silva
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Filipe Ferreira
- Cell Biology of Viral Infection Lab, Gulbenkian Institute of Science, Oeiras, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Portuguese Catholic University, Lisbon, Portugal
| | | | - Nádia Charepe
- Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
- CHRC, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Fátima Serrano
- Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
- CHRC, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Carlos Pontinha
- Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Gulbenkian Institute of Science, Oeiras, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Portuguese Catholic University, Lisbon, Portugal
| | - Helena Soares
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
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18
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Chiang HL, Liang KH, Lu RM, Kuo TW, Lin YL, Wu HC. Broadly neutralizing human antibodies against Omicron subvariants of SARS-CoV-2. J Biomed Sci 2023; 30:59. [PMID: 37525188 PMCID: PMC10388472 DOI: 10.1186/s12929-023-00955-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic continues to pose a significant worldwide threat to human health, as emerging SARS-CoV-2 Omicron variants exhibit resistance to therapeutic antibodies and the ability to evade vaccination-induced antibodies. Here, we aimed to identify human antibodies (hAbs) from convalescent patients that are potent and broadly neutralizing toward Omicron sublineages. METHODS Using a single B-cell cloning approach, we isolated BA.5 specific human antibodies. We further examined the neutralizing activities of the most promising neutralizing hAbs toward different variants of concern (VOCs) with pseudotyped virus. RESULTS Sixteen hAbs showed strong neutralizing activities against Omicron BA.5 with low IC50 values (IC50 < 20 ng/mL). Among four of the most promising neutralizing hAbs (RBD-hAb-B22, -B23, -B25 and -B34), RBD-hAb-B22 exhibited the most potent and broad neutralization profiles across Omicron subvariant pseudoviruses, with low IC50 values (7.7-41.6 ng/mL) and a low PRNT50 value (3.8 ng/mL) in plaque assays with authentic BA.5. It also showed potent therapeutic effects in BA.5-infected K18-hACE2 mice. CONCLUSIONS Thus, our efficient screening of BA.5-specific neutralizing hAbs from breakthrough infectious convalescent donors successfully yielded hAbs with potent therapeutic potential against multiple SARS-CoV-2 variants.
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Affiliation(s)
- Hsiao-Ling Chiang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan
| | - Kang-Hao Liang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan
| | - Ruei-Min Lu
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan
| | - Ting-Wen Kuo
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Sciences (IBMS), Academia Sinica, Taipei, Taiwan
| | - Han-Chung Wu
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan.
- Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
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19
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Lopes de Assis F, Hoehn KB, Zhang X, Kardava L, Smith CD, El Merhebi O, Buckner CM, Trihemasava K, Wang W, Seamon CA, Chen V, Schaughency P, Cheung F, Martins AJ, Chiang CI, Li Y, Tsang JS, Chun TW, Kleinstein SH, Moir S. Tracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine. Cell Rep 2023; 42:112780. [PMID: 37440409 PMCID: PMC10529190 DOI: 10.1016/j.celrep.2023.112780] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Protective immunity following vaccination is sustained by long-lived antibody-secreting cells and resting memory B cells (MBCs). Responses to two-dose SARS-CoV-2 mRNA-1273 vaccination are evaluated longitudinally by multimodal single-cell analysis in three infection-naïve individuals. Integrated surface protein, transcriptomics, and B cell receptor (BCR) repertoire analysis of sorted plasmablasts and spike+ (S-2P+) and S-2P- B cells reveal clonal expansion and accumulating mutations among S-2P+ cells. These cells are enriched in a cluster of immunoglobulin G-expressing MBCs and evolve along a bifurcated trajectory rooted in CXCR3+ MBCs. One branch leads to CD11c+ atypical MBCs while the other develops from CD71+ activated precursors to resting MBCs, the dominant population at month 6. Among 12 evolving S-2P+ clones, several are populated with plasmablasts at early timepoints as well as CD71+ activated and resting MBCs at later timepoints, and display intra- and/or inter-cohort BCR convergence. These relationships suggest a coordinated and predictable evolution of SARS-CoV-2 vaccine-generated MBCs.
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Affiliation(s)
- Felipe Lopes de Assis
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xiaozhen Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lela Kardava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connor D Smith
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Omar El Merhebi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clarisa M Buckner
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Krittin Trihemasava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Wang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Catherine A Seamon
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vicky Chen
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Schaughency
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Microbiology and Immunology and Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - John S Tsang
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA; Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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20
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Kalodimou G, Jany S, Freudenstein A, Schwarz JH, Limpinsel L, Rohde C, Kupke A, Becker S, Volz A, Tscherne A, Sutter G. Short- and Long-Interval Prime-Boost Vaccination with the Candidate Vaccines MVA-SARS-2-ST and MVA-SARS-2-S Induces Comparable Humoral and Cell-Mediated Immunity in Mice. Viruses 2023; 15:v15051180. [PMID: 37243266 DOI: 10.3390/v15051180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic caused significant human health and economic consequences. Due to the ability of SARS-CoV-2 to spread rapidly and to cause severe disease and mortality in certain population groups, vaccines are essential for controlling the pandemic in the future. Several licensed vaccines have shown improved protection against SARS-CoV-2 after extended-interval prime-boost immunizations in humans. Therefore, in this study, we aimed to compare the immunogenicity of our two Modified Vaccinia virus Ankara (MVA) based COVID-19 candidate vaccines MVA-SARS-2-S and MVA-SARS-2-ST after short- and long-interval prime-boost immunization schedules in mice. We immunized BALB/c mice using 21-day (short-interval) or 56-day (long-interval) prime-boost vaccination protocols and analyzed spike (S)-specific CD8 T cell immunity and humoral immunity. The two schedules induced robust CD8 T cell responses with no significant differences in their magnitude. Furthermore, both candidate vaccines induced comparable levels of total S, and S2-specific IgG binding antibodies. However, MVA-SARS-2-ST consistently elicited higher amounts of S1-, S receptor binding domain (RBD), and SARS-CoV-2 neutralizing antibodies in both vaccination protocols. Overall, we found very comparable immune responses following short- or long-interval immunization. Thus, our results suggest that the chosen time intervals may not be suitable to observe potential differences in antigen-specific immunity when testing different prime-boost intervals with our candidate vaccines in the mouse model. Despite this, our data clearly showed that MVA-SARS-2-ST induced superior humoral immune responses relative to MVA-SARS-2-S after both immunization schedules.
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Affiliation(s)
- Georgia Kalodimou
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 85764 Oberschleißheim, Germany
| | - Sylvia Jany
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
| | - Astrid Freudenstein
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
| | - Jan Hendrik Schwarz
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
| | - Leonard Limpinsel
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
| | - Cornelius Rohde
- Institute of Virology, Philipps University of Marburg, 35043 Marburg, Germany
- German Center for Infection Research (DZIF), Partner Site Gießen-Marburg-Langen, 35043 Marburg, Germany
| | - Alexandra Kupke
- Institute of Virology, Philipps University of Marburg, 35043 Marburg, Germany
- German Center for Infection Research (DZIF), Partner Site Gießen-Marburg-Langen, 35043 Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps University of Marburg, 35043 Marburg, Germany
- German Center for Infection Research (DZIF), Partner Site Gießen-Marburg-Langen, 35043 Marburg, Germany
| | - Asisa Volz
- Institute of Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30559 Hannover, Germany
| | - Alina Tscherne
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 85764 Oberschleißheim, Germany
| | - Gerd Sutter
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 85764 Oberschleißheim, Germany
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21
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Wang Q, Wang S, Liu Y, Wang S, Peng H, Hao Y, Hong K, Li D, Shao Y. Sequential Administration of SARS-CoV-2 Strains-Based Vaccines Effectively Induces Potent Immune Responses against Previously Unexposed Omicron Strain. Pathogens 2023; 12:pathogens12050655. [PMID: 37242325 DOI: 10.3390/pathogens12050655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
In the past few years, the continuous pandemic of COVID-19 caused by SARS-CoV-2 has placed a huge burden on public health. In order to effectively deal with the emergence of new SARS-CoV-2 variants, it becomes meaningful to further enhance the immune responses of individuals who have completed the first-generation vaccination. To understand whether sequential administration using different variant sequence-based inactivated vaccines could induce better immunity against the forthcoming variants, we tried five inactivated vaccine combinations in a mouse model and compared their immune responses. Our results showed that the sequential strategies have a significant advantage over homologous immunization by inducing robust antigen-specific T cell immune responses in the early stages of immunization. Furthermore, the three-dose vaccination strategies in our research elicited better neutralizing antibody responses against the BA.2 Omicron strain. These data provide scientific clues for finding the optimal strategy within the existing vaccine platform in generating cross-immunity against multiple variants including previously unexposed strains.
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Affiliation(s)
- Qianying Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuhui Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ying Liu
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuo Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hong Peng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanling Hao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Kunxue Hong
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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22
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Yang L, Van Beek M, Wang Z, Muecksch F, Canis M, Hatziioannou T, Bieniasz PD, Nussenzweig MC, Chakraborty AK. Antigen presentation dynamics shape the antibody response to variants like SARS-CoV-2 Omicron after multiple vaccinations with the original strain. Cell Rep 2023; 42:112256. [PMID: 36952347 PMCID: PMC9986127 DOI: 10.1016/j.celrep.2023.112256] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/07/2022] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
The Omicron variant of SARS-CoV-2 is not effectively neutralized by most antibodies elicited by two doses of mRNA vaccines, but a third dose increases anti-Omicron neutralizing antibodies. We reveal mechanisms underlying this observation by combining computational modeling with data from vaccinated humans. After the first dose, limited antigen availability in germinal centers (GCs) results in a response dominated by B cells that target immunodominant epitopes that are mutated in an Omicron-like variant. After the second dose, these memory cells expand and differentiate into plasma cells that secrete antibodies that are thus ineffective for such variants. However, these pre-existing antigen-specific antibodies transport antigen efficiently to secondary GCs. They also partially mask immunodominant epitopes. Enhanced antigen availability and epitope masking in secondary GCs together result in generation of memory B cells that target subdominant epitopes that are less mutated in Omicron. The third dose expands these cells and boosts anti-variant neutralizing antibodies.
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Affiliation(s)
- Leerang Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew Van Beek
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marie Canis
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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23
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Liu Y, Wang Z, Zhuang X, Zhang S, Chen Z, Zou Y, Sheng J, Li T, Tai W, Yu J, Wang Y, Zhang Z, Chen Y, Tong L, Yu X, Wu L, Chen D, Zhang R, Jin N, Shen W, Zhao J, Tian M, Wang X, Cheng G. Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants. Nat Commun 2023; 14:2179. [PMID: 37069158 PMCID: PMC10107573 DOI: 10.1038/s41467-023-37926-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
A full understanding of the inactivated COVID-19 vaccine-mediated antibody responses to SARS-CoV-2 circulating variants will inform vaccine effectiveness and vaccination development strategies. Here, we offer insights into the inactivated vaccine-induced antibody responses after prime-boost vaccination at both the polyclonal and monoclonal levels. We characterized the VDJ sequence of 118 monoclonal antibodies (mAbs) and found that 20 neutralizing mAbs showed varied potency and breadth against a range of variants including XBB.1.5, BQ.1.1, and BN.1. Bispecific antibodies (bsAbs) based on nonoverlapping mAbs exhibited enhanced neutralizing potency and breadth against the most antibody-evasive strains, such as XBB.1.5, BQ.1.1, and BN.1. The passive transfer of mAbs or their bsAb effectively protected female hACE2 transgenic mice from challenge with an infectious Delta or Omicron BA.2 variant. The neutralization mechanisms of these antibodies were determined by structural characterization. Overall, a broad spectrum of potent and distinct neutralizing antibodies can be induced in individuals immunized with the SARS-CoV-2 inactivated vaccine BBIBP-CorV, suggesting the application potential of inactivated vaccines and these antibodies for preventing infection by SARS-CoV-2 circulating variants.
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Affiliation(s)
- Yubin Liu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Ziyi Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinyu Zhuang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Zhicheng Chen
- Center for Translational Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Yan Zou
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Jie Sheng
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Tianpeng Li
- Center for Translational Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Wanbo Tai
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Yunfeng Chen
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Liangqin Tong
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xi Yu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Linjuan Wu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Dong Chen
- Wenzhou Central Hospital, Wenzhou, 325000, China
| | - Renli Zhang
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, China
| | - Ningyi Jin
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Weijun Shen
- Center for Translational Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China.
| | - Mingyao Tian
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Gong Cheng
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China.
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24
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Shrock EL, Timms RT, Kula T, Mena EL, West AP, Guo R, Lee IH, Cohen AA, McKay LGA, Bi C, Keerti, Leng Y, Fujimura E, Horns F, Li M, Wesemann DR, Griffiths A, Gewurz BE, Bjorkman PJ, Elledge SJ. Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses. Science 2023; 380:eadc9498. [PMID: 37023193 PMCID: PMC10273302 DOI: 10.1126/science.adc9498] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023]
Abstract
Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant "public epitopes" at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition. Systematic analysis of antibody-antigen structures uncovered 18 human and 21 partially overlapping mouse germline-encoded amino acid-binding (GRAB) motifs within heavy and light V gene segments that in case studies proved critical for public epitope recognition. GRAB motifs represent a fundamental component of the immune system's architecture that promotes recognition of pathogens and leads to species-specific public antibody responses that can exert selective pressure on pathogens.
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Affiliation(s)
- Ellen L. Shrock
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
| | - Richard T. Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
- Present address: Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Elijah L. Mena
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rui Guo
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - I-Hsiu Lee
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lindsay G. A. McKay
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Caihong Bi
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Keerti
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric Fujimura
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Felix Horns
- Department of Bioengineering, Department of Applied Physics, Chan Zuckerberg Biohub and Stanford University, Stanford, CA 94305, USA
| | - Mamie Li
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Duane R. Wesemann
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139 USA
| | - Anthony Griffiths
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Benjamin E. Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
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25
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Baldari CT, Onnis A, Andreano E, Del Giudice G, Rappuoli R. Emerging roles of SARS-CoV-2 Spike-ACE2 in immune evasion and pathogenesis. Trends Immunol 2023; 44:424-434. [PMID: 37137805 PMCID: PMC10076505 DOI: 10.1016/j.it.2023.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/23/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has caused an estimated 5 billion infections and 20 million deaths by respiratory failure. In addition to the respiratory disease, SARS-CoV-2 infection has been associated with many extrapulmonary complications not easily explainable by the respiratory infection. A recent study showed that the SARS-CoV-2 spike protein, which mediates cell entry by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, signals through ACE2 to change host cell behavior. In CD8+ T cells, spike-dependent ACE2-mediated signaling suppresses immunological synapse (IS) formation and impairs their killing ability, leading to immune escape of virus-infected cells. In this opinion article, we discuss the consequences of ACE2 signaling on the immune response and propose that it contributes to the extrapulmonary manifestations of COVID-19.
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Affiliation(s)
| | - Anna Onnis
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | | | - Rino Rappuoli
- Fondazione Biotecnopolo di Siena, Siena, Italy; Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
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26
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Diskin R. A structural perspective on the evolution of viral/cellular macromolecular complexes within the arenaviridae family of viruses. Curr Opin Struct Biol 2023; 79:102561. [PMID: 36857816 DOI: 10.1016/j.sbi.2023.102561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 03/02/2023]
Abstract
Viruses are obligatory parasites that can replicate only inside host cells. Therefore, the evolutionary drive to enter cells is immense, leading to diversification in the cell-entry strategies of viruses. One of the most critical steps for cell entry is the recognition of the target cell, a process driven by the formation of viral/host macromolecular complexes. The accumulation of recent structural data for viruses within the arenaviridae family allows us to examine how different viral species from the same viral family utilize evolutionarily-related viral glycoproteins to engage with a variety of different cellular receptors. These structural data, compared to other viruses from the coronaviridae family, hint about possible routes that such viruses use for evolving new receptor-binding capabilities, allowing them to switch from one receptor to another.
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Affiliation(s)
- Ron Diskin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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27
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Chang MR, Ke H, Losada Miguéns L, Coherd C, Nguyen K, Kamkaew M, Johnson R, Storm N, Honko A, Zhu Q, Griffiths A, Marasco WA. The variable conversion of neutralizing anti-SARS-CoV-2 single-chain antibodies to IgG provides insight into RBD epitope accessibility. Protein Eng Des Sel 2023; 36:gzad008. [PMID: 37561410 PMCID: PMC10505556 DOI: 10.1093/protein/gzad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 08/11/2023] Open
Abstract
Monoclonal antibody (mAb) therapies have rapidly become a powerful class of therapeutics with applications covering a diverse range of clinical indications. Though most widely used for the treatment of cancer, mAbs are also playing an increasing role in the defense of viral infections, most recently with palivizumab for prevention and treatment of severe RSV infections in neonatal and pediatric populations. In addition, during the COVID-19 pandemic, mAbs provided a bridge to the rollout of vaccines; however, their continued role as a therapeutic option for those at greatest risk of severe disease has become limited due to the emergence of neutralization resistant Omicron variants. Although there are many techniques for the identification of mAbs, including single B cell cloning and immunization of genetically engineered mice, the low cost, rapid throughput and technological simplicity of antibody phage display has led to its widespread adoption in mAb discovery efforts. Here we used our 27-billion-member naïve single-chain antibody (scFv) phage library to identify a panel of neutralizing anti-SARS-CoV-2 scFvs targeting diverse epitopes on the receptor binding domain (RBD). Although typically a routine process, we found that upon conversion to IgG, a number of our most potent clones failed to maintain their neutralization potency. Kinetic measurements confirmed similar affinity to the RBD; however, mechanistic studies provide evidence that the loss of neutralization is a result of structural limitations likely arising from initial choice of panning antigen. Thus this work highlights a risk of scFv-phage panning to mAb conversion and the importance of initial antigen selection.
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Affiliation(s)
- Matthew R Chang
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hanzhong Ke
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Losada Miguéns
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Christian Coherd
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Katrina Nguyen
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Maliwan Kamkaew
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rebecca Johnson
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nadia Storm
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anna Honko
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Quan Zhu
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Griffiths
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Wayne A Marasco
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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28
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Kumar N, Kaushik R, Zhang KYJ, Uversky VN, Sahu U, Sood R, Bhatia S. A novel consensus-based computational pipeline for screening of antibody therapeutics for efficacy against SARS-CoV-2 variants of concern including Omicron variant. Proteins 2023; 91:798-806. [PMID: 36629264 DOI: 10.1002/prot.26467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/11/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to evolve carrying flexible amino acid substitutions in the spike protein's receptor binding domain (RBD). These substitutions modify the binding of the SARS-CoV-2 to human angiotensin-converting enzyme 2 (hACE2) receptor and have been implicated in altered host fitness, transmissibility, and efficacy against antibody therapeutics and vaccines. Reliably predicting the binding strength of SARS-CoV-2 variants RBD to hACE2 receptor and neutralizing antibodies (NAbs) can help assessing their fitness, and rapid deployment of effective antibody therapeutics, respectively. Here, we introduced a two-step computational framework with 3-fold validation that first identified dissociation constant as a reliable predictor of binding affinity in hetero- dimeric and trimeric protein complexes. The second step implements dissociation constant as descriptor of the binding strengths of SARS-CoV-2 variants RBD to hACE2 and NAbs. Then, we examined several variants of concerns (VOCs) such as Alpha, Beta, Gamma, Delta, and Omicron and demonstrated that these VOCs RBD bind to the hACE2 with enhanced affinity. Furthermore, the binding affinity of Omicron variant's RBD was reduced with majority of the RBD-directed NAbs, which is highly consistent with the experimental neutralization data. By studying the atomic contacts between RBD and NAbs, we revealed the molecular footprints of four NAbs (GH-12, P2B-1A1, Asarnow_3D11, and C118)-that may likely neutralize the recently emerged Omicron variant-facilitating enhanced binding affinity. Finally, our findings suggest a computational pathway that could aid researchers identify a range of current NAbs that may be effective against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Naveen Kumar
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Rahul Kaushik
- Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi, UAE.,Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Russia
| | - Upasana Sahu
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Richa Sood
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
| | - Sandeep Bhatia
- Zoonotic Diseases Group, ICAR-National Institute of High Security Animal Diseases, Bhopal, India
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29
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Radic MZ, Zouali M. Editorial: SARS-CoV-2 variants, B lymphocytes, and autoreactivity. Front Immunol 2023; 13:1125732. [PMID: 36703988 PMCID: PMC9872959 DOI: 10.3389/fimmu.2022.1125732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Affiliation(s)
- Marko Z. Radic
- University of Tennessee, College of Medicine, Memphis, TN, United States,*Correspondence: Moncef Zouali, ; Marko Z. Radic,
| | - Moncef Zouali
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan,*Correspondence: Moncef Zouali, ; Marko Z. Radic,
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30
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Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies. Immunity 2023; 56:193-206.e7. [PMID: 36574772 PMCID: PMC9742198 DOI: 10.1016/j.immuni.2022.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence responses to infection and vaccination. For an improved understanding of inter-individual differences in antibody responses, we isolated SARS-CoV-2 spike-specific monoclonal antibodies from convalescent health care workers, focusing on the IGHV1-69 gene, which has the highest level of allelic variation of all IGHV genes. The IGHV1-69∗20-using CAB-I47 antibody and two similar antibodies isolated from an independent donor were critically dependent on allele usage. Neutralization was retained when reverting the V region to the germline IGHV1-69∗20 allele but lost when reverting to other IGHV1-69 alleles. Structural data confirmed that two germline-encoded polymorphisms, R50 and F55, in the IGHV1-69 gene were required for high-affinity receptor-binding domain interaction. These results demonstrate that polymorphisms in IGH genes can influence the function of SARS-CoV-2 neutralizing antibodies.
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31
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Safra M, Tamari Z, Polak P, Shiber S, Matan M, Karameh H, Helviz Y, Levy-Barda A, Yahalom V, Peretz A, Ben-Chetrit E, Brenner B, Tuller T, Gal-Tanamy M, Yaari G. Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity. Front Immunol 2023; 14:1031914. [PMID: 37153628 PMCID: PMC10154551 DOI: 10.3389/fimmu.2023.1031914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/22/2023] [Indexed: 05/10/2023] Open
Abstract
Introduction The success of the human body in fighting SARS-CoV2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance. Methods We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls. Results In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients. Discussion These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.
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Affiliation(s)
- Modi Safra
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Zvi Tamari
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Pazit Polak
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Shachaf Shiber
- Emergency Department, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Matan
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poriya, Israel
| | - Hani Karameh
- Jesselson Integrated Heart Center, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Yigal Helviz
- Intensive Care Unit, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Adva Levy-Barda
- Biobank, Department of Pathology, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
| | - Vered Yahalom
- Blood Services and Apheresis Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poriya, Israel
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Eli Ben-Chetrit
- Infectious Diseases Unit, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Baruch Brenner
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Oncology, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering and The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | | | - Gur Yaari
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
- *Correspondence: Gur Yaari,
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32
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Characterization of Systemic and Mucosal Humoral Immune Responses to an Adjuvanted Intranasal SARS-CoV-2 Protein Subunit Vaccine Candidate in Mice. Vaccines (Basel) 2022; 11:vaccines11010030. [PMID: 36679875 PMCID: PMC9865305 DOI: 10.3390/vaccines11010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Continuous viral evolution of SARS-CoV-2 has resulted in variants capable of immune evasion, vaccine breakthrough infections and increased transmissibility. New vaccines that invoke mucosal immunity may provide a solution to reducing virus transmission. Here, we evaluated the immunogenicity of intranasally administered subunit protein vaccines composed of a stabilized SARS-CoV-2 spike trimer or the receptor binding domain (RBD) adjuvanted with either cholera toxin (CT) or an archaeal lipid mucosal adjuvant (AMVAD). We show robust induction of immunoglobulin (Ig) G and IgA responses in plasma, nasal wash and bronchoalveolar lavage in mice only when adjuvant is used in the vaccine formulation. While the AMVAD adjuvant was more effective at inducing systemic antibodies against the RBD antigen than CT, CT was generally more effective at inducing overall higher IgA and IgG titers against the spike antigen in both systemic and mucosal compartments. Furthermore, vaccination with adjuvanted spike led to superior mucosal IgA responses than with the RBD antigen and produced broadly targeting neutralizing plasma antibodies against ancestral, Delta and Omicron variants in vitro; whereas adjuvanted RBD elicited a narrower antibody response with neutralizing activity only against ancestral and Delta variants. Our study demonstrates that intranasal administration of an adjuvanted protein subunit vaccine in immunologically naïve mice induced both systemic and mucosal neutralizing antibody responses that were most effective at neutralizing SARS-CoV-2 variants when the trimeric spike was used as an antigen compared to RBD.
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Meyer zu Natrup C, Tscherne A, Dahlke C, Ciurkiewicz M, Shin DL, Fathi A, Rohde C, Kalodimou G, Halwe S, Limpinsel L, Schwarz JH, Klug M, Esen M, Schneiderhan-Marra N, Dulovic A, Kupke A, Brosinski K, Clever S, Schünemann LM, Beythien G, Armando F, Mayer L, Weskamm ML, Jany S, Freudenstein A, Tuchel T, Baumgärtner W, Kremsner P, Fendel R, Addo MM, Becker S, Sutter G, Volz A. Stabilized recombinant SARS-CoV-2 spike antigen enhances vaccine immunogenicity and protective capacity. J Clin Invest 2022; 132:159895. [PMID: 36301637 PMCID: PMC9754005 DOI: 10.1172/jci159895] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022] Open
Abstract
The SARS-CoV-2 spike (S) glycoprotein is synthesized as a large precursor protein and must be activated by proteolytic cleavage into S1 and S2. A recombinant modified vaccinia virus Ankara (MVA) expressing native, full-length S protein (MVA-SARS-2-S) is currently under investigation as a candidate vaccine in phase I clinical studies. Initial results from immunogenicity monitoring revealed induction of S-specific antibodies binding to S2, but low-level antibody responses to the S1 domain. Follow-up investigations of native S antigen synthesis in MVA-SARS-2-S-infected cells revealed limited levels of S1 protein on the cell surface. In contrast, we found superior S1 cell surface presentation upon infection with a recombinant MVA expressing a stabilized version of SARS-CoV-2 S protein with an inactivated S1/S2 cleavage site and K986P and V987P mutations (MVA-SARS-2-ST). When comparing immunogenicity of MVA vector vaccines, mice vaccinated with MVA-SARS-2-ST mounted substantial levels of broadly reactive anti-S antibodies that effectively neutralized different SARS-CoV-2 variants. Importantly, intramuscular MVA-SARS-2-ST immunization of hamsters and mice resulted in potent immune responses upon challenge infection and protected from disease and severe lung pathology. Our results suggest that MVA-SARS-2-ST represents an improved clinical candidate vaccine and that the presence of plasma membrane-bound S1 is highly beneficial to induce protective antibody levels.
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Affiliation(s)
| | - Alina Tscherne
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany.,German Center for Infection Research, partner site Munich, and
| | - Christine Dahlke
- partner site Hamburg-Lübeck-Borstel-Riems.,University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany
| | - Malgorzata Ciurkiewicz
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Dai-Lun Shin
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Anahita Fathi
- partner site Hamburg-Lübeck-Borstel-Riems.,University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, Hamburg, Germany
| | - Cornelius Rohde
- German Center for Infection Research, partner site Gießen-Marburg-Langen.,Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Georgia Kalodimou
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany.,German Center for Infection Research, partner site Munich, and
| | - Sandro Halwe
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Leonard Limpinsel
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Jan H. Schwarz
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Martha Klug
- German Center for Infection Research, partner site Tübingen.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Meral Esen
- German Center for Infection Research, partner site Tübingen.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Alexandra Kupke
- German Center for Infection Research, partner site Gießen-Marburg-Langen.,Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Katrin Brosinski
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Sabrina Clever
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Lisa-Marie Schünemann
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Georg Beythien
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Leonie Mayer
- partner site Hamburg-Lübeck-Borstel-Riems.,University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, Hamburg, Germany
| | - Marie L. Weskamm
- partner site Hamburg-Lübeck-Borstel-Riems.,University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, Hamburg, Germany
| | - Sylvia Jany
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Astrid Freudenstein
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Tamara Tuchel
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Peter Kremsner
- German Center for Infection Research, partner site Tübingen.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambarene, Gabon
| | - Rolf Fendel
- German Center for Infection Research, partner site Tübingen.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Marylyn M. Addo
- University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany.,German Center for Infection Research, partner site Tübingen
| | - Stephan Becker
- German Center for Infection Research, partner site Gießen-Marburg-Langen.,Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Gerd Sutter
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany.,German Center for Infection Research, partner site Munich, and
| | - Asisa Volz
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany.,German Center for Infection Research, partner site Hanover-Braunschweig
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CXCL12 and CXCL13 Cytokine Serum Levels Are Associated with the Magnitude and the Quality of SARS-CoV-2 Humoral Responses. Viruses 2022; 14:v14122665. [PMID: 36560669 PMCID: PMC9785906 DOI: 10.3390/v14122665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
A better understanding of the immunological markers associated with long-lasting immune responses to SARS-CoV-2 infection is of paramount importance. In the present study, we characterized SARS-CoV-2-specific humoral responses in hospitalized (ICU and non-ICU) and non-hospitalized individuals at six months post-onset of symptoms (POS) (N = 95). We showed that the proportion of individuals with detectable anti-SARS-CoV-2 IgG or neutralizing (NAb) responses and the titers of antibodies were significantly reduced in non-hospitalized individuals, compared to ICU- or non-ICU-hospitalized individuals at 6 months POS. Interestingly, SARS-CoV-2-specific memory B cells persist at 6 months POS in both ICU and non-ICU patients and were enriched in cells harboring an activated and/or exhausted phenotype. The frequency/phenotype of SARS-CoV-2-specific memory B cells and the magnitude of IgG or NAb responses at 6 months POS correlated with the serum immune signature detected at patient admission. In particular, the serum levels of CXCL13, IL-1RA, and G-CSF directly correlated with the frequency of Spike-specific B cells and the magnitude of Spike-specific IgG or NAb, while the serum levels of CXCL12 showed an antagonizing effect. Our results indicate that the balance between CXCL12 and CXCL13 is an early marker associated with the magnitude and the quality of the SARS-CoV-2 humoral memory.
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Pons S, Uhel F, Frapy E, Sérémé Y, Zafrani L, Aschard H, Skurnik D. How Protective are Antibodies to SARS-CoV-2, the Main Weapon of the B-Cell Response? Stem Cell Rev Rep 2022; 19:585-600. [PMID: 36422774 PMCID: PMC9685122 DOI: 10.1007/s12015-022-10477-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2022] [Indexed: 11/25/2022]
Abstract
Since the beginning of the Coronavirus disease (COVID)-19 pandemic in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for more than 600 million infections and 6.5 million deaths worldwide. Given the persistence of SARS-CoV-2 and its ability to develop new variants, the implementation of an effective and long-term herd immunity appears to be crucial to overcome the pandemic. While a vast field of research has focused on the role of humoral immunity against SARS-CoV-2, a growing body of evidence suggest that antibodies alone only confer a partial protection against infection of reinfection which could be of high importance regarding the strategic development goals (SDG) of the United Nations (UN) and in particular UN SDG3 that aims towards the realization of good health and well being on a global scale in the context of the COVID-19 pandemic.In this review, we highlight the role of humoral immunity in the host defense against SARS-CoV-2, with a focus on highly neutralizing antibodies. We summarize the results of the main clinical trials leading to an overall disappointing efficacy of convalescent plasma therapy, variable results of monoclonal neutralizing antibodies in patients with COVID-19 but outstanding results for the mRNA based vaccines against SARS-CoV-2. Finally, we advocate that beyond antibody responses, the development of a robust cellular immunity against SARS-CoV-2 after infection or vaccination is of utmost importance for promoting immune memory and limiting disease severity, especially in case of (re)-infection by variant viruses.
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Affiliation(s)
- Stéphanie Pons
- DMU DREAM, Department of Anesthesiology and Critical Care, Sorbonne University, GRC 29, AP-HP, Pitié-Salpêtrière, Paris, France
- Université de Paris Cité, INSERM U976- Human Immunology, Pathophysiology, Immunotherapy (HIPI), Paris, France
| | - Fabrice Uhel
- INSERM, CNRS, Institut Necker Enfants Malades, Université de Paris Cité, Paris, France
- DMU ESPRIT, Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, 92700, Colombes, France
| | - Eric Frapy
- INSERM, CNRS, Institut Necker Enfants Malades, Université de Paris Cité, Paris, France
| | - Youssouf Sérémé
- INSERM, CNRS, Institut Necker Enfants Malades, Université de Paris Cité, Paris, France
| | - Lara Zafrani
- Université de Paris Cité, INSERM U976- Human Immunology, Pathophysiology, Immunotherapy (HIPI), Paris, France
- Medical Intensive Care Unit, Saint Louis Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | - Hugues Aschard
- Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris, France
| | - David Skurnik
- INSERM, CNRS, Institut Necker Enfants Malades, Université de Paris Cité, Paris, France.
- Department of Clinical Microbiology, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Université de Paris Cité, Paris, France.
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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36
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Abstract
The COVID-19 pandemic has posed a significant health threat globally. Timely and appropriate vaccination is a key step to reduce the morbidity and mortality from COVID-19. The clinical course of COVID-19 infection and the effects of COVID-19 vaccination are influenced by patients' health situations and involve a systemic physiological reaction. Just like an "endocrine phenotype" of COVID-19 infection, endocrine dysfunction after COVID-19 vaccination also acquired clinical concerns. In the present review, we briefly introduce the commonly available vaccines against SARS-CoV-2, summarize the influence of COVID-19 vaccines on the endocrine system, and explore the underlying pathogenic mechanisms.
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Affiliation(s)
- Ying Zhao
- Geriatric Medicine Center, Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Department of Endocrinology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xiaohong Wu
- Geriatric Medicine Center, Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Department of Endocrinology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
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Lunderberg JM, Dutta S, Collier ARY, Lee JS, Hsu YM, Wang Q, Zheng W, Hao S, Zhang H, Feng L, Robson SC, Gao W, Riedel S. Pan-neutralizing, germline-encoded antibodies against SARS-CoV-2: Addressing the long-term problem of escape variants. Front Immunol 2022; 13:1032574. [DOI: 10.3389/fimmu.2022.1032574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the initially reported high efficacy of vaccines directed against ancestral SARS-CoV-2, repeated infections in both unvaccinated and vaccinated populations remain a major global health challenge. Because of mutation-mediated immune escape by variants-of-concern (VOC), approved neutralizing antibodies (neutAbs) effective against the original strains have been rendered non-protective. Identification and characterization of mutation-independent pan-neutralizing antibody responses are therefore essential for controlling the pandemic. Here, we characterize and discuss the origins of SARS-CoV-2 neutAbs, arising from either natural infection or following vaccination. In our study, neutAbs in COVID-19 patients were detected using the combination of two lateral flow immunoassay (LFIA) tests, corroborated by plaque reduction neutralization testing (PRNT). A point-of-care neutAb LFIA, NeutraXpress™, was validated using serum samples from historical pre-COVID-19 negative controls, patients infected with other respiratory pathogens, and PCR-confirmed COVID-19 patients. Surprisingly, potent neutAb activity was mainly noted in patients generating both IgM and IgG against the Spike receptor-binding domain (RBD), in contrast to samples possessing anti-RBD IgG alone. We propose that low-affinity, high-avidity, germline-encoded natural IgM and subsequent generation of class-switched IgG may have an underappreciated role in cross-protection, potentially offsetting immune escape by SARS-CoV-2 variants. We suggest Reverse Vaccinology 3.0 to further exploit this innate-like defense mechanism. Our proposition has potential implications for immunogen design, and provides strategies to elicit pan-neutAbs from natural B1-like cells. Refinements in future immunization protocols might further boost long-term cross-protection, even at the mucosal level, against clinical manifestations of COVID-19.
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38
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Sherwani S, Raafat M, Rajendrasozhan S, Khan M, Saleem M, Husain Q, Khan S, Alam N, Khan MWA. Increased Levels of Autoantibodies against ROS-Modified Proteins in Depressed Individuals with Decrease in Antibodies against SARS-CoV-2 Antigen (S1-RBD). Curr Issues Mol Biol 2022; 44:5260-5276. [PMID: 36354670 PMCID: PMC9689329 DOI: 10.3390/cimb44110358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus 2019 (COVID-19) disease management is highly dependent on the immune status of the infected individual. An increase in the incidence of depression has been observed during the ongoing COVID-19 pandemic. Autoantibodies against in vitro reactive oxygen species (ROS) modified BSA and Lys as well as antibodies against receptor binding domain subunit S1 (S1-RBD) (S1-RBD-Abs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were estimated using direct binding and competition ELISA. Serum samples were also tested for fasting blood glucose (FBG), malondialdehyde (MDA), carbonyl content (CC), interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α). Significant structural changes were observed in ROS modified BSA and Lys. Female depressed subjects who were also smokers (F-D-S) showed the highest levels of oxidative stress (MDA and CC levels). Similarly, increased levels of autoantibodies against ROS modified proteins were detected in F-D-S subjects, in males who were depressed and in smokers (M-D-S) compared to the other subjects from the rest of the groups. However, contrary to this observation, levels of S1-RBD-Abs were found to be lowest in the F-D-S and M-D-S groups. During the pandemic, large numbers of individuals have experienced depression, which may induce excessive oxidative stress, causing modifications in circulatory proteins. Thus, the formation of neo-antigens is induced, which lead to the generation of autoantibodies. The concomitant effect of increased autoantibodies with elevated levels of IFN-γ and TNF-α possibly tilt the immune balance toward autoantibody generation rather than the formation of S1-RBD-Abs. Thus, it is important to identify individuals who are at risk of depression to determine immune status and facilitate the better management of COVID-19.
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Affiliation(s)
- Subuhi Sherwani
- Department of Biology, College of Sciences, University of Ha’il, Ha’il 2440, Saudi Arabia
- Correspondence: or
| | - Mohamed Raafat
- Department of Physiotherapy, College of Applied Medical Sciences, University of Ha’il, Ha’il 2440, Saudi Arabia
| | | | - Mahvish Khan
- Department of Biology, College of Sciences, University of Ha’il, Ha’il 2440, Saudi Arabia
| | - Mohd Saleem
- Department of Pathology, Sub-Division of Medical Microbiology, College of Medicine, University of Ha’il, Ha’il 2440, Saudi Arabia
| | - Qayyum Husain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Saif Khan
- Department of Basic Dental and Medical Sciences, University of Ha’il, Ha’il 2440, Saudi Arabia
| | - Noor Alam
- Department of Mathematics, College of Sciences, University of Ha’il, Ha’il 2440, Saudi Arabia
| | - Mohd Wajid Ali Khan
- Department of Chemistry, College of Sciences, University of Ha’il, Ha’il 2440, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 2440, Saudi Arabia
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Guerra D, Beaumont T, RadiÄ L, Kerster G, van der Straten K, Yuan M, Torres JL, Lee WH, Liu H, Poniman M, Bontjer I, Burger JA, Claireaux M, Caniels TG, Snitselaar JL, Bijl TPL, Kruijer S, Ozorowski G, Gideonse D, Sliepen K, Ward AB, Eggink D, de Bree GJ, Wilson IA, Sanders RW, van Gils MJ. Broad SARS-CoV-2 Neutralization by Monoclonal and Bispecific Antibodies Derived from a Gamma-infected Individual. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.14.512216. [PMID: 36263063 PMCID: PMC9580383 DOI: 10.1101/2022.10.14.512216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The worldwide pandemic caused by SARS-CoV-2 has remained a human medical threat due to the continued evolution of multiple variants that acquire resistance to vaccines and prior infection. Therefore, it is imperative to discover monoclonal antibodies (mAbs) that neutralize a broad range of SARS-CoV-2 variants for therapeutic and prophylactic use. A stabilized autologous SARS-CoV-2 spike glycoprotein was used to enrich antigen-specific B cells from an individual with a primary Gamma variant infection. Five mAbs selected from those B cells showed considerable neutralizing potency against multiple variants of concern, with COVA309-35 being the most potent against the autologous virus, as well as against Omicron BA.1 and BA.2. When combining the COVA309 mAbs as cocktails or bispecific antibody formats, the breadth and potency was significantly improved against all tested variants. In addition, the mechanism of cross-neutralization of the COVA309 mAbs was elucidated by structural analysis. Altogether these data indicate that a Gamma-infected individual can develop broadly neutralizing antibodies.
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40
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Maier I. Engineering recombinantly expressed lectin-based antiviral agents. Front Cell Infect Microbiol 2022; 12:990875. [PMID: 36211961 PMCID: PMC9539805 DOI: 10.3389/fcimb.2022.990875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/25/2022] [Indexed: 11/30/2022] Open
Abstract
Cyanovirin-N (CV-N), a lectin from Nostoc ellipsosporum was found an infusion inhibitory protein for human immunodeficiency virus (HIV)-1. A tandem-repeat of the engineered domain-swapped dimer bound specific sites at hemagglutinin (HA), Ebola and HIV spike glycoproteins as well as dimannosylated HA peptide, N-acetyl-D-glucosamine and high-mannose containing oligosaccharides. Among these, CV-N bound the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein at a dissociation constant (KD) of 18.6 µM (and KD=260 µM to RBD), which was low-affinity carbohydrate-binding as compared with the recognition of the other viral spikes. Binding of dimannosylated peptide to homo-dimeric CVN2 and variants of CVN2 that were pairing Glu-Arg residues sterically located close to its high-affinity carbohydrate binding sites, was measured using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). Binding affinity increased with polar interactions, when the mutated residues were used to substitute a single, or two disulfide bonds, in CVN2. Site-specific N-linked glycans on spikes were mediating the infection with influenza virus by broadly neutralizing antibodies to HA and lectin binding to HA was further investigated via modes of saturation transfer difference (STD)-NMR. Our findings showed that stoichiometry and the lectin’s binding affinity were revealed by an interaction of CVN2 with dimannose units and either the high- or low-affinity binding site. To understand how these binding mechanisms add to viral membrane fusion we compare our tested HA-derived peptides in affinity with SARS-CoV-2 glycoprotein and review lectins and their mechanisms of binding to enveloped viruses for a potential use to simulate neutralization ability.
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41
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Waltari E, Nafees S, McCutcheon KM, Wong J, Pak JE. AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses. PLoS Comput Biol 2022; 18:e1010052. [PMID: 36126074 PMCID: PMC9524643 DOI: 10.1371/journal.pcbi.1010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/30/2022] [Accepted: 09/04/2022] [Indexed: 11/18/2022] Open
Abstract
The sequencing of antibody repertoires of B-cells at increasing coverage and depth has led to the identification of vast numbers of immunoglobulin heavy and light chains. However, the size and complexity of these Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) datasets makes it difficult to perform exploratory analyses. To aid in data exploration, we have developed AIRRscape, an R Shiny-based interactive web browser application that enables B-cell receptor (BCR) and antibody feature discovery through comparisons among multiple repertoires. Using AIRR-seq data as input, AIRRscape starts by aggregating and sorting repertoires into interactive and explorable bins of germline V-gene, germline J-gene, and CDR3 length, providing a high-level view of the entire repertoire. Interesting subsets of repertoires can be quickly identified and selected, and then network topologies of CDR3 motifs can be generated for further exploration. Here we demonstrate AIRRscape using patient BCR repertoires and sequences of published monoclonal antibodies to investigate patterns of humoral immunity to three viral pathogens: SARS-CoV-2, HIV-1, and DENV (dengue virus). AIRRscape reveals convergent antibody sequences among datasets for all three pathogens, although HIV-1 antibody datasets display limited convergence and idiosyncratic responses. We have made AIRRscape available as a web-based Shiny application, along with code on GitHub to encourage its open development and use by immuno-informaticians, virologists, immunologists, vaccine developers, and other scientists that are interested in exploring and comparing multiple immune receptor repertoires.
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Affiliation(s)
- Eric Waltari
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (EW); (JEP)
| | - Saba Nafees
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (EW); (JEP)
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42
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Abstract
The COVID-19 pandemic has caused an unprecedented health crisis and economic burden worldwide. Its etiological agent SARS-CoV-2, a new virus in the coronavirus family, has infected hundreds of millions of people worldwide. SARS-CoV-2 has evolved over the past 2 years to increase its transmissibility as well as to evade the immunity established by previous infection and vaccination. Nevertheless, strong immune responses can be elicited by viral infection and vaccination, which have proved to be protective against the emergence of variants, particularly with respect to hospitalization or severe disease. Here, we review our current understanding of how the virus enters the host cell and how our immune system is able to defend against cell entry and infection. Neutralizing antibodies are a major component of our immune defense and have been extensively studied for SARS-CoV-2 and its variants. Structures of these neutralizing antibodies have provided valuable insights into epitopes that are protective against the original ancestral virus and the variants that have emerged. The molecular characterization of neutralizing epitopes as well as epitope conservation and resistance are important for design of next-generation vaccines and antibody therapeutics.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
- The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
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43
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Goldblatt D, Alter G, Crotty S, Plotkin SA. Correlates of protection against SARS-CoV-2 infection and COVID-19 disease. Immunol Rev 2022; 310:6-26. [PMID: 35661178 PMCID: PMC9348242 DOI: 10.1111/imr.13091] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Antibodies against epitopes in S1 give the most accurate CoP against infection by the SARS-CoV-2 coronavirus. Measurement of those antibodies by neutralization or binding assays both have predictive value, with binding antibody titers giving the highest statistical correlation. However, the protective functions of antibodies are multiple. Antibodies with multiple functions other than neutralization influence efficacy. The role of cellular responses can be discerned with respect to CD4+ T cells and their augmentation of antibodies, and with respect to CD8+ cells with regard to control of viral replication, particularly in the presence of insufficient antibody. More information is needed on mucosal responses.
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Affiliation(s)
- David Goldblatt
- Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Galit Alter
- Massachusetts General HospitalRagon Institute of MGH, MIT and HarvardCambridgeMassachusettsUSA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine ResearchLa Jolla Institute for Immunology (LJI)La JollaCaliforniaUSA
- Department of Medicine, Division of Infectious Diseases and Global Public HealthUniversity of California San Diego (UCSD)La JollaCaliforniaUSA
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44
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Yang L, Van Beek M, Wang Z, Muecksch F, Canis M, Hatziioannou T, Bieniasz PD, Nussenzweig MC, Chakraborty AK. Antigen presentation dynamics shape the response to emergent variants like SARS-CoV-2 Omicron strain after multiple vaccinations with wild type strain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.24.505127. [PMID: 36052368 PMCID: PMC9435403 DOI: 10.1101/2022.08.24.505127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Omicron variant of SARS-CoV-2 evades neutralization by most serum antibodies elicited by two doses of mRNA vaccines, but a third dose of the same vaccine increases anti-Omicron neutralizing antibodies. By combining computational modeling with data from vaccinated humans we reveal mechanisms underlying this observation. After the first dose, limited antigen availability in germinal centers results in a response dominated by B cells with high germline affinities for immunodominant epitopes that are significantly mutated in an Omicron-like variant. After the second dose, expansion of these memory cells and differentiation into plasma cells shape antibody responses that are thus ineffective for such variants. However, in secondary germinal centers, pre-existing higher affinity antibodies mediate enhanced antigen presentation and they can also partially mask dominant epitopes. These effects generate memory B cells that target subdominant epitopes that are less mutated in Omicron. The third dose expands these cells and boosts anti-variant neutralizing antibodies.
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Affiliation(s)
- Leerang Yang
- Departments of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Matthew Van Beek
- Departments of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marie Canis
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Arup K Chakraborty
- Departments of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139
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45
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Hale M, Netland J, Chen Y, Thouvenel CD, Smith KN, Rich LM, Vanderwall ER, Miranda MC, Eggenberger J, Hao L, Watson MJ, Mundorff CC, Rodda LB, King NP, Guttman M, Gale M, Abraham J, Debley JS, Pepper M, Rawlings DJ. IgM antibodies derived from memory B cells are potent cross-variant neutralizers of SARS-CoV-2. J Exp Med 2022; 219:213384. [PMID: 35938988 PMCID: PMC9365875 DOI: 10.1084/jem.20220849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/22/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
Humoral immunity to SARS-CoV-2 can be supplemented with polyclonal sera from convalescent donors or an engineered monoclonal antibody (mAb) product. While pentameric IgM antibodies are responsible for much of convalescent sera's neutralizing capacity, all available mAbs are based on the monomeric IgG antibody subtype. We now show that IgM mAbs derived from immune memory B cell receptors are potent neutralizers of SARS-CoV-2. IgM mAbs outperformed clonally identical IgG antibodies across a range of affinities and SARS-CoV-2 receptor-binding domain epitopes. Strikingly, efficacy against SARS-CoV-2 viral variants was retained for IgM but not for clonally identical IgG. To investigate the biological role for IgM memory in SARS-CoV-2, we also generated IgM mAbs from antigen-experienced IgM+ memory B cells in convalescent donors, identifying a potent neutralizing antibody. Our results highlight the therapeutic potential of IgM mAbs and inform our understanding of the role for IgM memory against a rapidly mutating pathogen.
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Affiliation(s)
- Malika Hale
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Jason Netland
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Yu Chen
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | - Marcos C. Miranda
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Linhui Hao
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Michael J. Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | | | - Lauren B. Rodda
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA,Department of Immunology, University of Washington School of Medicine, Seattle, WA,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA,Correspondence to David J. Rawlings:
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46
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Cohen AA, van Doremalen N, Greaney AJ, Andersen H, Sharma A, Starr TN, Keeffe JR, Fan C, Schulz JE, Gnanapragasam PNP, Kakutani LM, West AP, Saturday G, Lee YE, Gao H, Jette CA, Lewis MG, Tan TK, Townsend AR, Bloom JD, Munster VJ, Bjorkman PJ. Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models. Science 2022; 377:eabq0839. [PMID: 35857620 PMCID: PMC9273039 DOI: 10.1126/science.abq0839] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/29/2022] [Indexed: 12/12/2022]
Abstract
To combat future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants, including Omicrons, and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.
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Affiliation(s)
- Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences and 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
- Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jonathan E. Schulz
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | | | - Leesa M. Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Greg Saturday
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Tiong K. Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Alain R. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, Oxford OX3 9DS, UK
| | - 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
| | - Vincent J. Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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47
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Li R, Mor M, Ma B, Clark AE, Alter J, Werbner M, Lee JC, Leibel SL, Carlin AF, Dessau M, Gal-Tanamy M, Croker BA, Xiang Y, Freund NT. Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies. Commun Biol 2022; 5:789. [PMID: 35931732 PMCID: PMC9355996 DOI: 10.1038/s42003-022-03739-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
As new variants of SARS-CoV-2 continue to emerge, it is important to assess the cross-neutralizing capabilities of antibodies naturally elicited during wild type SARS-CoV-2 infection. In the present study, we evaluate the activity of nine anti-SARS-CoV-2 monoclonal antibodies (mAbs), previously isolated from convalescent donors infected with the Wuhan-Hu-1 strain, against the SARS-CoV-2 variants of concern (VOC) Alpha, Beta, Gamma, Delta and Omicron. By testing an array of mutated spike receptor binding domain (RBD) proteins, cell-expressed spike proteins from VOCs, and neutralization of SARS-CoV-2 VOCs as pseudoviruses, or as the authentic viruses in culture, we show that mAbs directed against the ACE2 binding site (ACE2bs) are more sensitive to viral evolution compared to anti-RBD non-ACE2bs mAbs, two of which retain their potency against all VOCs tested. At the second part of our study, we reveal the neutralization mechanisms at high molecular resolution of two anti-SARS-CoV-2 neutralizing mAbs by structural characterization. We solve the structures of the Delta-neutralizing ACE2bs mAb TAU-2303 with the SARS-CoV-2 spike trimer and RBD at 4.5 Å and 2.42 Å resolutions, respectively, revealing a similar mode of binding to that between the RBD and ACE2. Furthermore, we provide five additional structures (at resolutions of 4.7 Å, 7.3 Å, 6.4 Å, 3.3 Å, and 6.1 Å) of a second antibody, TAU-2212, complexed with the SARS-CoV-2 spike trimer. TAU-2212 binds an exclusively quaternary epitope, and exhibits a unique, flexible mode of neutralization that involves transitioning between five different conformations, with both arms of the antibody recruited for cross linking intra- and inter-spike RBD subunits. Our study provides additional mechanistic understanding about how antibodies neutralize SARS-CoV-2 and its emerging variants and provides insights on the likelihood of reinfections. The neutralization of SARS-CoV-2 and variants of concern by nine monoclonal antibodies (mAb) isolated from convalescent donors infected with the Wuhan-Hu-1 strain alongside structural characterization of two of the mAbs in complex with the RBD and spike are presented.
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Affiliation(s)
- Ruofan Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Michael Mor
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bingting Ma
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Alex E Clark
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joel Alter
- The Laboratory of Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Michal Werbner
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Jamie Casey Lee
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA
| | - Sandra L Leibel
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aaron F Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Moshe Dessau
- The Laboratory of Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Ben A Croker
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA.
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
| | - Natalia T Freund
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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48
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Claireaux M, Caniels TG, de Gast M, Han J, Guerra D, Kerster G, van Schaik BDC, Jongejan A, Schriek AI, Grobben M, Brouwer PJM, van der Straten K, Aldon Y, Capella-Pujol J, Snitselaar JL, Olijhoek W, Aartse A, Brinkkemper M, Bontjer I, Burger JA, Poniman M, Bijl TPL, Torres JL, Copps J, Martin IC, de Taeye SW, de Bree GJ, Ward AB, Sliepen K, van Kampen AHC, Moerland PD, Sanders RW, van Gils MJ. A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike. Nat Commun 2022; 13:4539. [PMID: 35927266 PMCID: PMC9352689 DOI: 10.1038/s41467-022-32232-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 07/22/2022] [Indexed: 12/21/2022] Open
Abstract
Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigate the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We show that ∼82% of SARS-CoV-2 S-reactive B cells harbor a naive phenotype, which represents an unusually high fraction of total human naive B cells (∼0.1%). Approximately 10% of these naive S-reactive B cells share an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.
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Affiliation(s)
- Mathieu Claireaux
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Tom G Caniels
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Marlon de Gast
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Denise Guerra
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Gius Kerster
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Barbera D C van Schaik
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Angela I Schriek
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Marloes Grobben
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Philip J M Brouwer
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Karlijn van der Straten
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Yoann Aldon
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Joan Capella-Pujol
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Jonne L Snitselaar
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Wouter Olijhoek
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Aafke Aartse
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Mitch Brinkkemper
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Judith A Burger
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Meliawati Poniman
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Tom P L Bijl
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Isabel Cuella Martin
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kwinten Sliepen
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Rogier W Sanders
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands.
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
| | - Marit J van Gils
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands.
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands.
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49
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Nguyen DC, Lamothe PA, Woodruff MC, Saini AS, Faliti CE, Sanz I, Lee FE. COVID-19 and plasma cells: Is there long-lived protection? Immunol Rev 2022; 309:40-63. [PMID: 35801537 PMCID: PMC9350162 DOI: 10.1111/imr.13115] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Infection with SARS-CoV-2, the etiology of the ongoing COVID-19 pandemic, has resulted in over 450 million cases with more than 6 million deaths worldwide, causing global disruptions since early 2020. Memory B cells and durable antibody protection from long-lived plasma cells (LLPC) are the mainstay of most effective vaccines. However, ending the pandemic has been hampered by the lack of long-lived immunity after infection or vaccination. Although immunizations offer protection from severe disease and hospitalization, breakthrough infections still occur, most likely due to new mutant viruses and the overall decline of neutralizing antibodies after 6 months. Here, we review the current knowledge of B cells, from extrafollicular to memory populations, with a focus on distinct plasma cell subsets, such as early-minted blood antibody-secreting cells and the bone marrow LLPC, and how these humoral compartments contribute to protection after SARS-CoV-2 infection and immunization.
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Affiliation(s)
- Doan C. Nguyen
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
| | - Pedro A. Lamothe
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
| | - Matthew C. Woodruff
- Division of Rheumatology, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Emory Autoimmunity Center of ExcellenceEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
| | - Ankur S. Saini
- Division of Rheumatology, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Emory Autoimmunity Center of ExcellenceEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
| | - Caterina E. Faliti
- Division of Rheumatology, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
| | - Ignacio Sanz
- Division of Rheumatology, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Emory Autoimmunity Center of ExcellenceEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
| | - Frances Eun‐Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
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Liu H, Kaku CI, Song G, Yuan M, Andrabi R, Burton DR, Walker LM, Wilson IA. Human antibodies to SARS-CoV-2 with a recurring YYDRxG motif retain binding and neutralization to variants of concern including Omicron. Commun Biol 2022; 5:766. [PMID: 35906394 PMCID: PMC9336126 DOI: 10.1038/s42003-022-03700-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 07/11/2022] [Indexed: 01/02/2023] Open
Abstract
Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally identified a YYDRxG motif encoded by IGHD3-22 in CDR H3 that facilitates antibody targeting to a functionally conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences uncovered 100 such antibodies, many of which can neutralize SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to target sarbecoviruses including the Omicron variant. These findings suggest an epitope-targeting strategy to identify potent and broadly neutralizing antibodies for design of pan-sarbecovirus vaccines and antibody therapeutics.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Laura M Walker
- Adimab, LLC, Lebanon, NH, USA. .,Adagio Therapeutics, Inc, Waltham, MA, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. .,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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