1
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Yan Q, Zhang Y, Hou R, Pan W, Liang H, Gao X, Deng W, Huang X, Qu L, Tang C, He P, Liu B, Wang Q, Zhao X, Lin Z, Chen Z, Li P, Han J, Xiong X, Zhao J, Li S, Niu X, Chen L. Deep immunoglobulin repertoire sequencing depicts a comprehensive atlas of spike-specific antibody lineages shared among COVID-19 convalescents. Emerg Microbes Infect 2024; 13:2290841. [PMID: 38044868 PMCID: PMC10810631 DOI: 10.1080/22221751.2023.2290841] [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: 09/07/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Neutralizing antibodies are a key component in protective humoral immunity against SARS-CoV-2. Currently, available technologies cannot track epitope-specific antibodies in global antibody repertoires. Thus, the comprehensive repertoire of spike-specific neutralizing antibodies elicited by SARS-CoV-2 infection is not fully understood. We therefore combined high-throughput immunoglobulin heavy chain (IgH) repertoire sequencing, and structural and bioinformatics analysis to establish an antibodyomics pipeline, which enables tracking spike-specific antibody lineages that target certain neutralizing epitopes. We mapped the neutralizing epitopes on the spike and determined the epitope-preferential antibody lineages. This analysis also revealed numerous overlaps between immunodominant neutralizing antibody-binding sites and mutation hotspots on spikes as observed so far in SARS-CoV-2 variants. By clustering 2677 spike-specific antibodies with 360 million IgH sequences that we sequenced, a total of 329 shared spike-specific antibody clonotypes were identified from 33 COVID-19 convalescents and 24 SARS-CoV-2-naïve individuals. Epitope mapping showed that the shared antibody responses target not only neutralizing epitopes on RBD and NTD but also non-neutralizing epitopes on S2. The immunodominance of neutralizing antibody response is determined by the occurrence of specific precursors in human naïve B-cell repertoires. We identified that only 28 out of the 329 shared spike-specific antibody clonotypes persisted for at least 12 months. Among them, long-lived IGHV3-53 antibodies are likely to evolve cross-reactivity to Omicron variants through accumulating somatic hypermutations. Altogether, we created a comprehensive atlas of spike-targeting antibody lineages in COVID-19 convalescents and antibody precursors in human naïve B cell repertoires, providing a valuable reference for future vaccine design and evaluation.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Ruitian Hou
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenjing Pan
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Weiqi Deng
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linbing Qu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qian Wang
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Zihan Lin
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Zhaoming Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jian Han
- iRepertoire Inc., Huntsville, AL, USA
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Song Li
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
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2
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Nel I, Ithayakumar A, Blumenthal N, Duneton C, Khourouj VGE, Viala J, Dollfus C, Baudouin V, Guilmin-Crepon S, Theodorou I, Carcelain G. Strategies to determine positive anti-SARS-CoV-2 memory T lymphocyte response during the evolution of an epidemic. J Immunol Methods 2024; 531:113712. [PMID: 38906414 DOI: 10.1016/j.jim.2024.113712] [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: 12/05/2023] [Revised: 05/22/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
During SARS-CoV-2 pandemic, the assessment of immune protection of people at risk of severe infection was an important goal. The appearance of VOCs (Variant of Concern) highlighted the limits of evaluating immune protection through the humoral response. While the humoral response partly loses its neutralizing activity, the anti-SARS-CoV-2 memory T cell response strongly cross protects against VOCs becoming an indispensable tool to assess immune protection. We compared two techniques available in laboratory to evaluate anti-SARS-CoV-2 memory T cell response in a cohort of infected or vaccinated patients with different levels of risk to develop a severe disease: the ELISpot assay and the T-Cell Lymphocyte Proliferation Assay respectively exploring IFNγ production and cell proliferation. We showed that the ELISpot assay detected more anti-Spike memory T cell response than the Lymphocyte Proliferation Assay. We next observed that the use of two different suppliers as antigenic source in the ELISpot assay did not affect the detection of anti-Spike memory T cell response. Finally, we explored a new approach for defining the positivity threshold, using unsupervised mixed Gaussian modeling, challenging the traditional ROC curve used by the supplier. That will be helpful in endemic situation where it could be difficult to recruit "negative" patients.
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Affiliation(s)
- Isabelle Nel
- Immunology Department, Robert-Debré Hospital, APHP, Paris, France; University Paris Cité, INSERM U976, France
| | | | | | - Charlotte Duneton
- Immunology Department, Robert-Debré Hospital, APHP, Paris, France; University Paris Cité, INSERM U976, France; Pediatric Nephrology Department, Robert-Debré Hospital, APHP, Paris, France
| | | | - Jérôme Viala
- Department of Pediatric Gastroenterology, Robert-Debré Hospital, APHP, Paris, France
| | - Catherine Dollfus
- Pediatric Hematology and Oncology Department, Trousseau Hospital, APHP, Paris, France
| | - Véronique Baudouin
- Pediatric Nephrology Department, Robert-Debré Hospital, APHP, Paris, France
| | - Sophie Guilmin-Crepon
- Clinical Epidemiology Unit, Inserm CIC-EC 1426, Robert-Debré Hospital, APHP, Paris, France
| | | | - Guislaine Carcelain
- Immunology Department, Robert-Debré Hospital, APHP, Paris, France; University Paris Cité, INSERM U976, France.
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3
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Florova M, Abreu-Mota T, Paesen GC, Beetschen AS, Cornille K, Marx AF, Narr K, Sahin M, Dimitrova M, Swarnalekha N, Beil-Wagner J, Savic N, Pelczar P, Buch T, King CG, Bowden TA, Pinschewer DD. Central tolerance shapes the neutralizing B cell repertoire against a persisting virus in its natural host. Proc Natl Acad Sci U S A 2024; 121:e2318657121. [PMID: 38446855 PMCID: PMC10945855 DOI: 10.1073/pnas.2318657121] [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: 10/25/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024] Open
Abstract
Viral mimicry of host cell structures has been postulated to curtail the B cell receptor (BCR) repertoire against persisting viruses through tolerance mechanisms. This concept awaits, however, experimental testing in a setting of natural virus-host relationship. We engineered mouse models expressing a monoclonal BCR specific for the envelope glycoprotein of lymphocytic choriomeningitis virus (LCMV), a naturally persisting mouse pathogen. When the heavy chain of the LCMV-neutralizing antibody KL25 was paired with its unmutated ancestor light chain, most B cells underwent receptor editing, a behavior reminiscent of autoreactive clones. In contrast, monoclonal B cells expressing the same heavy chain in conjunction with the hypermutated KL25 light chain did not undergo receptor editing but exhibited low levels of surface IgM, suggesting that light chain hypermutation had lessened KL25 autoreactivity. Upon viral challenge, these IgMlow cells were not anergic but up-regulated IgM, participated in germinal center reactions, produced antiviral antibodies, and underwent immunoglobulin class switch as well as further affinity maturation. These studies on a persisting virus in its natural host species suggest that central tolerance mechanisms prune the protective antiviral B cell repertoire.
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Affiliation(s)
- Marianna Florova
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
| | - Tiago Abreu-Mota
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
| | - Guido C. Paesen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Anna Sophia Beetschen
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
| | - Karen Cornille
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
| | - Anna-Friederike Marx
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
| | - Kerstin Narr
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
| | - Mehmet Sahin
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
| | - Mirela Dimitrova
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
| | - Nivedya Swarnalekha
- Department of Biomedicine, Immune Cell Biology Laboratory, University Hospital Basel, Basel4031, Switzerland
| | - Jane Beil-Wagner
- Institute of Laboratory Animal Science, University of Zurich, Zurich8093, Switzerland
| | - Natasa Savic
- ETH Phenomics Center, ETH Zürich, Zürich8093, Switzerland
| | - Pawel Pelczar
- Center for Transgenic Models, University of Basel, Basel4001, Switzerland
| | - Thorsten Buch
- Institute of Laboratory Animal Science, University of Zurich, Zurich8093, Switzerland
| | - Carolyn G. King
- Department of Biomedicine, Immune Cell Biology Laboratory, University Hospital Basel, Basel4031, Switzerland
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Daniel D. Pinschewer
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel4009, Switzerland
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4
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Xiao J, Luo Y, Li Y, Yao X. The characteristics of BCR-CDR3 repertoire in COVID-19 patients and SARS-CoV-2 vaccinated volunteers. J Med Virol 2024; 96:e29488. [PMID: 38415507 DOI: 10.1002/jmv.29488] [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: 11/04/2023] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
The global COVID-19 pandemic has caused more than 1 billion infections, and numerous SARS-CoV-2 vaccines developed rapidly have been administered over 10 billion doses. The world is continuously concerned about the cytokine storms induced by the interaction between SARS-CoV-2 and host, long COVID, breakthrough infections postvaccination, and the impact of SARS-CoV-2 variants. BCR-CDR3 repertoire serves as a molecular target for monitoring the antiviral response "trace" of B cells, evaluating the effects, mechanisms, and memory abilities of individual responses to B cells, and has been successfully applied in analyzing the infection mechanisms, vaccine improvement, and neutralizing antibodies preparation of influenza virus, HIV, MERS, and Ebola virus. Based on research on BCR-CDR3 repertoire of COVID-19 patients and volunteers who received different SARS-CoV-2 vaccines in multiple laboratories worldwide, we focus on analyzing the characteristics and changes of BCR-CDR3 repertoire, such as diversity, clonality, V&J genes usage and pairing, SHM, CSR, shared CDR3 clones, as well as the summary on BCR sequences targeting virus-specific epitopes in the preparation and application research of SARS-CoV-2 potential therapeutic monoclonal antibodies. This review provides comparative data and new research schemes for studying the possible mechanisms of differences in B cell response between SARS-CoV-2 infection or vaccination, and supplies a foundation for improving vaccines after SARS-CoV-2 mutations and potential antibody therapy for infected individuals.
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Affiliation(s)
- Jiaping Xiao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
- Fushun People's Hospital, Zigong, Sichuan, China
| | - Yan Luo
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Yangyang Li
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
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5
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Bohmwald K, Diethelm-Varela B, Rodríguez-Guilarte L, Rivera T, Riedel CA, González PA, Kalergis AM. Pathophysiological, immunological, and inflammatory features of long COVID. Front Immunol 2024; 15:1341600. [PMID: 38482000 PMCID: PMC10932978 DOI: 10.3389/fimmu.2024.1341600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/09/2024] [Indexed: 04/12/2024] Open
Abstract
The COVID-19 pandemic continues to cause severe global disruption, resulting in significant excess mortality, overwhelming healthcare systems, and imposing substantial social and economic burdens on nations. While most of the attention and therapeutic efforts have concentrated on the acute phase of the disease, a notable proportion of survivors experience persistent symptoms post-infection clearance. This diverse set of symptoms, loosely categorized as long COVID, presents a potential additional public health crisis. It is estimated that 1 in 5 COVID-19 survivors exhibit clinical manifestations consistent with long COVID. Despite this prevalence, the mechanisms and pathophysiology of long COVID remain poorly understood. Alarmingly, evidence suggests that a significant proportion of cases within this clinical condition develop debilitating or disabling symptoms. Hence, urgent priority should be given to further studies on this condition to equip global public health systems for its management. This review provides an overview of available information on this emerging clinical condition, focusing on the affected individuals' epidemiology, pathophysiological mechanisms, and immunological and inflammatory profiles.
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Affiliation(s)
- Karen Bohmwald
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Benjamín Diethelm-Varela
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Linmar Rodríguez-Guilarte
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Thomas Rivera
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia A. Riedel
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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6
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Beaudoin-Bussières G, Finzi A. Deciphering Fc-effector functions against SARS-CoV-2. Trends Microbiol 2024:S0966-842X(24)00005-2. [PMID: 38365562 DOI: 10.1016/j.tim.2024.01.005] [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: 12/08/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
Major efforts were deployed to study the antibody response against SARS-CoV-2. Antibodies neutralizing SARS-CoV-2 have been extensively studied in the context of infections, vaccinations, and breakthrough infections. Antibodies, however, are pleiotropic proteins that have many functions in addition to neutralization. These include Fc-effector functions such as antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). Although important to combat viral infections, these Fc-effector functions were less studied in the context of SARS-CoV-2 compared with binding and neutralization. This is partly due to the difficulty in developing reliable assays to measure Fc-effector functions compared to antibody binding and neutralization. Multiple assays have now been developed and can be used to measure different Fc-effector functions. Here, we review these assays and what is known regarding anti-SARS-CoV-2 Fc-effector functions. Overall, this review summarizes and updates our current state of knowledge regarding anti-SARS-CoV-2 Fc-effector functions.
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Affiliation(s)
- Guillaume Beaudoin-Bussières
- Centre de recherche du CHUM, Montréal, Québec H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec H2X 0A9, Canada
| | - Andrés Finzi
- Centre de recherche du CHUM, Montréal, Québec H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec H2X 0A9, Canada.
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7
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Adams LJ, VanBlargan LA, Liu Z, Gilchuk P, Zhao H, Chen RE, Raju S, Chong Z, Whitener BM, Shrihari S, Jethva PN, Gross ML, Crowe JE, Whelan SPJ, Diamond MS, Fremont DH. A broadly reactive antibody targeting the N-terminal domain of SARS-CoV-2 spike confers Fc-mediated protection. Cell Rep Med 2023; 4:101305. [PMID: 38039973 PMCID: PMC10772349 DOI: 10.1016/j.xcrm.2023.101305] [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: 11/24/2021] [Revised: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
Most neutralizing anti-SARS-CoV-2 monoclonal antibodies (mAbs) target the receptor binding domain (RBD) of the spike (S) protein. Here, we characterize a panel of mAbs targeting the N-terminal domain (NTD) or other non-RBD epitopes of S. A subset of NTD mAbs inhibits SARS-CoV-2 entry at a post-attachment step and avidly binds the surface of infected cells. One neutralizing NTD mAb, SARS2-57, protects K18-hACE2 mice against SARS-CoV-2 infection in an Fc-dependent manner. Structural analysis demonstrates that SARS2-57 engages an antigenic supersite that is remodeled by deletions common to emerging variants. In neutralization escape studies with SARS2-57, this NTD site accumulates mutations, including a similar deletion, but the addition of an anti-RBD mAb prevents such escape. Thus, our study highlights a common strategy of immune evasion by SARS-CoV-2 variants and how targeting spatially distinct epitopes, including those in the NTD, may limit such escape.
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Affiliation(s)
- Lucas J Adams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhenlu Chong
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Prashant N Jethva
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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8
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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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9
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Guerra D, Beaumont T, Radić 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 TP, 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. iScience 2023; 26:108009. [PMID: 37841584 PMCID: PMC10570122 DOI: 10.1016/j.isci.2023.108009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 07/10/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has remained a medical threat due to the 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. A stabilized 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, with COVA309-35 being the most potent against the autologous virus, as well as Omicron BA.1 and BA.2, and COVA309-22 having binding and neutralization activity against Omicron BA.4/5, BQ.1.1, and XBB.1. When combining the COVA309 mAbs as cocktails or bispecific antibodies, the breadth and potency were improved. 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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Affiliation(s)
- Denise Guerra
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tim Beaumont
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Laura Radić
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Gius Kerster
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Karlijn van der Straten
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Internal Medicine, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meliawati Poniman
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Judith A. Burger
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Mathieu Claireaux
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom G. Caniels
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jonne L. Snitselaar
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom P.L. Bijl
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Sabine Kruijer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Gideonse
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, the Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dirk Eggink
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, the Netherlands
| | - Godelieve J. de Bree
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Internal Medicine, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier W. Sanders
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, 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, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
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10
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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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11
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Bassanello M, Geppini R, Bonsembiante E, Coli U, Farencena A, D’Aquino M, Gambaro A, Buja A, Baldovin T. Risk of SARS-CoV-2 transmission in the close contacts in a small rural area in the Veneto Region (NE-Italy): past evidence for future scenarios. Front Public Health 2023; 11:1223109. [PMID: 37732097 PMCID: PMC10507707 DOI: 10.3389/fpubh.2023.1223109] [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: 05/15/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023] Open
Abstract
Background During the first pandemic phase of COVID-19, an epidemiological study, named First survey, was conducted on the population of a small rural area in northern Italy. In spring 2020, the results showed how a prolonged lockdown slowed down the spread of the virus. Methods After contacting positive First Survey subjects and their families, those who decided to join voluntarily underwent a blood test to assess the presence of qualitative lgG about 2 months after the previous one. This was to determine if IgG persisted in individuals who tested positive in the First Survey as well as to assess the antibody status of their close family members, to determine if they were unintentionally infected. Results Based on serological analysis, 35.1% of the samples contained blood IgG. In subjects who tested positive during the First Survey, 62.5% remained IgG positive more than 2 months later. Among family members who were exposed to a positive relative, 23.7% were infected. Linear regression analysis showed that the presence of an infected person within a household resulted in the infection spreading to the others, but not excessively. Induced isolation extinguished the infection regardless of the extent of the contagion (intra-family or extra-family). Micro-outbreaks of SARS-Cov-2 infection which arose in the same household from extra-familial infections played a decisive role on the statistical significance of IgG-positive subjects (p < 0.001). Discussion The study reveal 52.6% of the IgG-positive subjects in the Second Survey came from the First Survey and 47.4% were family members previously in contact with positive subjects. Data suggest that there have been undiagnosed patients feeding the spread of the virus since the beginning of the pandemic. In conclusion, for future pandemics, it will be necessary: i) to ensure the rapid isolation of symptomatic patients and the early identification of their close contacts, ii) to carry out the maximum number of tests in the shortest possible time, both on symptomatic and asymptomatic subjects, and iii) to implement information campaigns to make people aware of their risks, and implement clear, non-conflicting communication.
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Affiliation(s)
- Marco Bassanello
- Emergency and Health Department, Monastier di Treviso Hospital, Treviso, Italy
- Hygiene and Public Health Unit, Department of Cardiac, Thoracic and Vascular Sciences, School of Medicine and Surgery, University of Padua, Padua, Italy
| | - Ruggero Geppini
- Hygiene and Public Health Unit, Department of Cardiac, Thoracic and Vascular Sciences, School of Medicine and Surgery, University of Padua, Padua, Italy
| | | | - Ugo Coli
- Health Department, Monastier di Treviso Hospital, Treviso, Italy
| | - Aldo Farencena
- Laboratory and Microbiology Monastier di Treviso Hospital, Treviso, Italy
| | | | - Andrea Gambaro
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca’ Foscari University of Venice, Venice, Italy
| | - Alessandra Buja
- Hygiene and Public Health Unit, Department of Cardiac, Thoracic and Vascular Sciences, School of Medicine and Surgery, University of Padua, Padua, Italy
| | - Tatjana Baldovin
- Hygiene and Public Health Unit, Department of Cardiac, Thoracic and Vascular Sciences, School of Medicine and Surgery, University of Padua, Padua, Italy
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12
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Guo M, Xiong M, Peng J, Guan T, Su H, Huang Y, Yang CG, Li Y, Boraschi D, Pillaiyar T, Wang G, Yi C, Xu Y, Chen C. Multi-omics for COVID-19: driving development of therapeutics and vaccines. Natl Sci Rev 2023; 10:nwad161. [PMID: 37936830 PMCID: PMC10627145 DOI: 10.1093/nsr/nwad161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 11/09/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and economy. The development of therapeutics and vaccines to combat this virus is continuously progressing. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, epigenomics and metallomics, have helped understand the structural and molecular features of the virus, thereby assisting in the design of potential therapeutics and accelerating vaccine development for COVID-19. Here, we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19, in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.
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Affiliation(s)
- Mengyu Guo
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Tong Guan
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Diana Boraschi
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Institute of Biochemistry and Cell Biology, National Research Council, Napoli 80131, Italy
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Guanbo Wang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Chen
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
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13
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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: 5] [Impact Index Per Article: 5.0] [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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14
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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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15
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Moustafa RI, Faraag AHI, El-Shenawy R, Agwa MM, Elsayed H. Harnessing immunoinformatics for developing a multiple-epitope peptide-based vaccination approach against SARS-CoV-2 spike protein. Saudi J Biol Sci 2023; 30:103661. [PMID: 37163156 PMCID: PMC10141799 DOI: 10.1016/j.sjbs.2023.103661] [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: 02/27/2023] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 05/11/2023] Open
Abstract
COVID-19 has spread to over 200 countries with variable severity and mortality rates. Computational analysis is a valuable tool for developing B-cell and T-cell epitope-based vaccines. In this study, by harnessing immunoinformatics tools, we designed a multiple-epitope vaccine to protect against COVID-19. The candidate epitopes were designed from highly conserved regions of the SARS-CoV-2 spike (S) glycoprotein. The consensus amino acids sequence of ten SARS-CoV-2 variants including Gamma, Beta, Epsilon, Delta, Alpha, Kappa, Iota, Lambda, Mu, and Omicron was involved. Applying the multiple sequence alignment plugin and the antigenic prediction tools of Geneious prime 2021, ten predicted variants were identified and consensus S-protein sequences were used to predict the antigenic part. According to ElliPro analysis of S-protein B-cell prediction, we explored 22 continuous linear epitopes with high scores ranging from 0.879 to 0.522. First, we reported five promising epitopes: BE1 1115-1192, BE2 481-563, BE3 287-313, BE4 62-75, and BE5 112-131 with antigenicity scores of 0.879, 0.86, 0.813, 0.779, and 0.765, respectively, while only nine discontinuous epitopes scored between 0.971 and 0.511. Next, we identified 194 Major Histocompatibility Complex (MHC) - I and 156 MHC - II epitopes with antigenic characteristics. These spike-specific peptide-epitopes with characteristically high immunogenic and antigenic scores have the potential as a SARS-CoV-2 multiple-epitope peptide-based vaccination strategy. Nevertheless, further experimental investigations are needed to test for the vaccine efficacy and efficiency.
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Affiliation(s)
- Rehab I Moustafa
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, Egypt
| | - Ahmed H I Faraag
- Botany and Microbiology Department, Faculty of Science, Helwan University, Egypt
- School of Biotechnology, Badr University in Cairo, Egypt
| | | | - Mona M Agwa
- Department of Chemistry of Natural and Microbial Products, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Egypt
| | - Hassan Elsayed
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, Egypt
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16
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Fitzpatrick KS, Degefu HN, Poljakov K, Bibby MG, Remington AJ, Searles TG, Gray MD, Boonyaratanakornkit J, Rosato PC, Taylor JJ. Validation of Ligand Tetramers for the Detection of Antigen-Specific Lymphocytes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1156-1165. [PMID: 36883850 PMCID: PMC10073333 DOI: 10.4049/jimmunol.2200934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/07/2023] [Indexed: 03/09/2023]
Abstract
The study of Ag-specific lymphocytes has been a key advancement in immunology over the past few decades. The development of multimerized probes containing Ags, peptide:MHC complexes, or other ligands was one innovation allowing the direct study of Ag-specific lymphocytes by flow cytometry. Although these types of study are now common and performed by thousands of laboratories, quality control and assessment of probe quality are often minimal. In fact, many of these types of probe are made in-house, and protocols vary between laboratories. Although peptide:MHC multimers can often be obtained from commercial sources or core facilities, few such services exist for Ag multimers. To ensure high quality and consistency with ligand probes, we have developed an easy and robust multiplexed approach using commercially available beads able to bind Abs specific for the ligand of interest. Using this assay, we have sensitively assessed the performance of peptide:MHC and Ag tetramers and have found considerable batch-to-batch variability in performance and stability over time more easily than using murine or human cell-based assays. This bead-based assay can also reveal common production errors such as miscalculation of Ag concentration. This work could set the stage for the development of standardized assays for all commonly used ligand probes to limit laboratory-to-laboratory technical variation and experimental failure caused by probe underperformance.
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Affiliation(s)
- Kristin S Fitzpatrick
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Molecular Medicine and Mechanisms of Disease PhD Program, University of Washington, Seattle, WA
| | - Hanna N Degefu
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Katrina Poljakov
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Madeleine G Bibby
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Allison J Remington
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Tyler G Searles
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Matthew D Gray
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jim Boonyaratanakornkit
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Pamela C Rosato
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Justin J Taylor
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Immunology, University of Washington, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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17
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Shitaoka K, Higashiura A, Kawano Y, Yamamoto A, Mizoguchi Y, Hashiguchi T, Nishimichi N, Huang S, Ito A, Ohki S, Kanda M, Taniguchi T, Yoshizato R, Azuma H, Kitajima Y, Yokosaki Y, Okada S, Sakaguchi T, Yasuda T. Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants. Commun Biol 2023; 6:395. [PMID: 37041231 PMCID: PMC10088672 DOI: 10.1038/s42003-023-04782-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/30/2023] [Indexed: 04/13/2023] Open
Abstract
The decrease of antibody efficacy to mutated SARS-CoV-2 spike RBD explains the breakthrough infections and reinfections by Omicron variants. Here, we analyzed broadly neutralizing antibodies isolated from long-term hospitalized convalescent patients of early SARS-CoV-2 strains. One of the antibodies named NCV2SG48 is highly potent to broad SARS-CoV-2 variants including Omicron BA.1, BA.2, and BA.4/5. To reveal the mode of action, we determined the sequence and crystal structure of the Fab fragment of NCV2SG48 in a complex with spike RBD from the original, Delta, and Omicron BA.1. NCV2SG48 is from a minor VH but the multiple somatic hypermutations contribute to a markedly extended binding interface and hydrogen bonds to interact with conserved residues at the core receptor-binding motif of RBD, which efficiently neutralizes a broad spectrum of variants. Thus, eliciting the RBD-specific B cells to the longitudinal germinal center reaction confers potent immunity to broad SARS-CoV-2 variants emerging one after another.
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Affiliation(s)
- Kiyomi Shitaoka
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akifumi Higashiura
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yohei Kawano
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akima Yamamoto
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yoko Mizoguchi
- Department of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Norihisa Nishimichi
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Integrin-Matrix Biomedical Science, Translational Research Center, Hiroshima University, Hiroshima, Japan
| | - Shiyu Huang
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ayano Ito
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shun Ohki
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Miyuki Kanda
- Collaborative laboratory of Liquid Biopsy, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomohiro Taniguchi
- Division of General Internal Medicine and Infectious Diseases, Hiroshima Prefectural Hospital, Hiroshima, Japan
| | - Rin Yoshizato
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hitoshi Azuma
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuo Kitajima
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuyuki Yokosaki
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Integrin-Matrix Biomedical Science, Translational Research Center, Hiroshima University, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takemasa Sakaguchi
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoharu Yasuda
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
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18
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Arimura K, Tagaya E, Kikuchi K, Mitsuda T, Ebihara F, Maruyama T, Hamada Y, Unagami K, Kanzawa T, Sekiguchi H, Shimamoto K, Ishida H, Egawa H, Tanaka J, Kawana M. The efficacy of neutralizing monoclonal antibodies in transplant recipients with mild-to-moderate COVID-19. Transpl Immunol 2023; 77:101777. [PMID: 36584927 PMCID: PMC9796351 DOI: 10.1016/j.trim.2022.101777] [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: 10/21/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Transplant recipients (TRs) are at high risk for severe coronavirus disease 2019 (COVID-19). Neutralizing monoclonal antibodies (mAbs) are used for treating mild-to-moderate COVID-19. However, reports comparing the efficacy of COVID-19 treatment without/with mAbs in TRs are limited. We assessed the efficacy of casirivimab/imdevimab against mild-to-moderate COVID-19 in TRs. METHODS Forty-one patients were retrospectively evaluated. The duration until defervescence, oxygen (O2) requirement ≥5 L, and neutralizing antibody levels were compared in TRs with COVID-19 without/with casirivimab/imdevimab. RESULTS Casirivimab/imdevimab was correlated with shorter duration until defervescence and non-requirement of O2 ≥ 5 L in TRs with COVID-19 [mean: without/with: 6 vs. 2; P = 0.0002, hazard ratio (HR) = 0.3333, 95% confidence interval (CI) = 0.1763-0.6301; 15 vs. 8; P < 0.0001, HR = 0.5333, 95% CI = 0.2878-0.9883; P = 0.0377, HR = 0.1502, 95% CI = 0.02511-0.8980]. Casirivimab/imdevimab was associated with early defervescence after adjusting for sex and age (P = 0.013, HR = 0.412, 95% CI = 0.205-0.826). The antibody levels between patients without/with casirivimab/imdevimab on the day of hospitalization were not significantly different (P = 0.1055), including 13 TRs with vaccination. Antibody levels were higher in patients with casirivimab/imdevimab at 3-5 days after hospitalization than in those without, at 7-9 days after hospitalization (P < 0.0001, mean, without/with: 414.9/40000 AU/mL). CONCLUSION Casirivimab/imdevimab was effective and increased the neutralizing antibody in TRs with mild-to-moderate COVID-19, it may contribute toward preventing the progression.
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Affiliation(s)
- Ken Arimura
- Department of Respiratory Medicine, Tokyo Women's Medical University, Tokyo, Japan.
| | - Etsuko Tagaya
- Department of Respiratory Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Ken Kikuchi
- Department of Infectious Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshihiro Mitsuda
- Department of Infection Prevention and Control, Tokyo Women's Medical University, Tokyo, Japan
| | - Fumiya Ebihara
- Department of Pharmacy, Tokyo Women's Medical University, Tokyo, Japan
| | - Takumi Maruyama
- Department of Pharmacy, Tokyo Women's Medical University, Tokyo, Japan
| | - Yukihiro Hamada
- Department of Pharmacy, Tokyo Women's Medical University, Tokyo, Japan
| | - Kohei Unagami
- Department of Urology, Tokyo Women's Medical University, Tokyo, Japan
| | - Taichi Kanzawa
- Department of Urology, Tokyo Women's Medical University, Tokyo, Japan
| | - Haruki Sekiguchi
- Department of General Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Ken Shimamoto
- Department of General Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Hideki Ishida
- Department of Urology, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroto Egawa
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Junji Tanaka
- Department of Hematology, Tokyo Women's Medical University, Tokyo, Japan
| | - Masatoshi Kawana
- Department of General Medicine, Tokyo Women's Medical University, Tokyo, Japan
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19
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Li W, Wang F, Li Y, Yan L, Liu L, Zhu W, Ma P, Shi X, Yang G. Potent NTD-Targeting Neutralizing Antibodies against SARS-CoV-2 Selected from a Synthetic Immune System. Vaccines (Basel) 2023; 11:vaccines11040771. [PMID: 37112683 PMCID: PMC10143083 DOI: 10.3390/vaccines11040771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
The majority of neutralizing antibodies (NAbs) against SARS-CoV-2 recognize the receptor-binding domain (RBD) of the spike (S) protein. As an escaping strategy, the RBD of the virus is highly variable, evolving mutations to thwart a natural immune response or vaccination. Targeting non-RBD regions of the S protein thus provides a viable alternative to generating potential, robust NAbs. Using a pre-pandemic combinatorial antibody library of 1011, through an alternate negative and positive screening strategy, 11 non-RBD-targeting antibodies are identified. Amongst one NAb that binds specifically to the N-terminal domain of the S protein, SA3, shows mutually non-exclusive binding of the angiotensin-converting enzyme 2 receptor with the S protein. SA3 appears to be insensitive to the conformational change and to interact with both the “open” and “closed” configurations of the trimeric S protein. SA3 shows compatible neutralization as S-E6, an RBD-targeting NAb, against the wild type and variant of concern (VOC) B.1.351 (Beta) of the SARS-CoV-2 pseudo virus. More importantly, the combination of SA3 with S-E6 is synergistic and recovers from the 10-fold loss in neutralization efficacy against the VOC B.1.351 pseudo virus.
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Affiliation(s)
- Wenping Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Fulian Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yu Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lei Yan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Xiaojie Shi
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- Correspondence: (X.S.); (G.Y.); Tel.: +86-21-20685030 (G.Y.)
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (W.L.)
- Correspondence: (X.S.); (G.Y.); Tel.: +86-21-20685030 (G.Y.)
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20
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Serwanga J, Ankunda V, Sembera J, Kato L, Oluka GK, Baine C, Odoch G, Kayiwa J, Auma BO, Jjuuko M, Nsereko C, Cotten M, Onyachi N, Muwanga M, Lutalo T, Fox J, Musenero M, Kaleebu P. Rapid, early, and potent Spike-directed IgG, IgM, and IgA distinguish asymptomatic from mildly symptomatic COVID-19 in Uganda, with IgG persisting for 28 months. Front Immunol 2023; 14:1152522. [PMID: 37006272 PMCID: PMC10060567 DOI: 10.3389/fimmu.2023.1152522] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/28/2023] [Indexed: 04/04/2023] Open
Abstract
Introduction Understanding how spike (S)-, nucleoprotein (N)-, and RBD-directed antibody responses evolved in mild and asymptomatic COVID-19 in Africa and their interactions with SARS-CoV-2 might inform development of targeted treatments and vaccines. Methods Here, we used a validated indirect in-house ELISA to characterise development and persistence of S- and N-directed IgG, IgM, and IgA antibody responses for 2430 SARS-CoV-2 rt-PCR-diagnosed Ugandan specimens from 320 mild and asymptomatic COVID-19 cases, 50 uninfected contacts, and 54 uninfected non-contacts collected weekly for one month, then monthly for 28 months. Results During acute infection, asymptomatic patients mounted a faster and more robust spike-directed IgG, IgM, and IgA response than those with mild symptoms (Wilcoxon rank test, p-values 0.046, 0.053, and 0.057); this was more pronounced in males than females. Spike IgG antibodies peaked between 25 and 37 days (86.46; IQR 29.47-242.56 BAU/ml), were significantly higher and more durable than N- and RBD IgG antibodies and lasted for 28 months. Anti-spike seroconversion rates consistently exceeded RBD and nucleoprotein rates. Spike- and RBD-directed IgG antibodies were positively correlated until 14 months (Spearman's rank correlation test, p-values 0.0001 to 0.05), although RBD diminished faster. Significant anti-spike immunity persisted without RBD. 64% and 59% of PCR-negative, non-infected non-contacts and suspects, exhibited baseline SARS-CoV-2 N-IgM serological cross-reactivity, suggesting undetected exposure or abortive infection. N-IgG levels waned after 787 days, while N-IgM levels remained undetectable throughout. Discussion Lower N-IgG seroconversion rates and the absence of N-IgM indicate that these markers substantially underestimate the prior exposure rates. Our findings provide insights into the development of S-directed antibody responses in mild and asymptomatic infections, with varying degrees of symptoms eliciting distinct immune responses, suggesting distinct pathogenic pathways. These longer-lasting data inform vaccine design, boosting strategies, and surveillance efforts in this and comparable settings.
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Affiliation(s)
- Jennifer Serwanga
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Violet Ankunda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jackson Sembera
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Laban Kato
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Gerald Kevin Oluka
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Claire Baine
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Geoffrey Odoch
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - John Kayiwa
- Department of Virology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Betty Oliver Auma
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Mark Jjuuko
- Department of Internal Medicine, Masaka Regional Referral Hospital, Masaka, Uganda
| | - Christopher Nsereko
- Department of Internal Medicine, Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Matthew Cotten
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nathan Onyachi
- Department of Internal Medicine, Masaka Regional Referral Hospital, Masaka, Uganda
| | - Moses Muwanga
- Department of Internal Medicine, Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Tom Lutalo
- Department of Epidemiology and Data Management, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julie Fox
- Guy’s and St Thomas’ National Health Services Foundation Trust, King’s College London, London, United Kingdom
| | - Monica Musenero
- Science, Technology, and Innovation Secretariat, Office of the President, Government of Uganda, Kampala, Uganda
| | - Pontiano Kaleebu
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
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21
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Takano T, Sato T, Kotaki R, Moriyama S, Fukushi S, Shinoda M, Kabasawa K, Shimada N, Kousaka M, Adachi Y, Onodera T, Terahara K, Isogawa M, Matsumura T, Shinkai M, Takahashi Y. Heterologous SARS-CoV-2 spike protein booster elicits durable and broad antibody responses against the receptor-binding domain. Nat Commun 2023; 14:1451. [PMID: 36922492 PMCID: PMC10016167 DOI: 10.1038/s41467-023-37128-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The immunogenicity of mRNA vaccines has not been well studied when compared to different vaccine modalities in the context of additional boosters. Here we show that longitudinal analysis reveals more sustained SARS-CoV-2 spike receptor-binding domain (RBD)-binding IgG titers with the breadth to antigenically distinct variants by the S-268019-b spike protein booster compared to the BNT162b2 mRNA homologous booster. The durability and breadth of RBD-angiotensin-converting enzyme 2 (ACE2) binding inhibitory antibodies are pronounced in the group without systemic adverse events (AEs) after the S-268019-b booster, leading to the elevated neutralizing activities against Omicron BA.1 and BA.5 variants in the stratified group. In contrast, BNT162b2 homologous booster elicited antibodies to spike N-terminal domain in proportion to the AE scores. High-dimensional immune profiling identifies early CD16+ natural killer cell dynamics with CCR3 upregulation, as one of the correlates for the distinct anti-RBD antibody responses by the S-268019-b booster. Our results illustrate the combinational effects of heterologous booster on the immune dynamics and the durability and breadth of recalled anti-RBD antibody responses against emerging virus variants.
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Affiliation(s)
- Tomohiro Takano
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Takashi Sato
- Tokyo Shinagawa Hospital, Tokyo, 140-8522, Japan
| | - Ryutaro Kotaki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Shuetsu Fukushi
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | | | | | - Mio Kousaka
- Tokyo Shinagawa Hospital, Tokyo, 140-8522, Japan
| | - Yu Adachi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Kazutaka Terahara
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Masanori Isogawa
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Takayuki Matsumura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| | | | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
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22
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Pushparaj P, Nicoletto A, Castro Dopico X, Sheward DJ, Kim S, Ekström S, Murrell B, Corcoran M, Karlsson Hedestam GB. Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses. FRONTIERS IN VIROLOGY 2023; 3:1128253. [PMID: 37041983 PMCID: PMC7614418 DOI: 10.3389/fviro.2023.1128253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The antibody response to SARS-CoV-2 shows biased immunoglobulin heavy chain variable (IGHV) gene usage, allowing definition of genetic signatures for some classes of neutralizing antibodies. We investigated IGHV gene usage frequencies by sorting spike-specific single memory B cells from individuals infected with SARS-CoV-2 early in the pandemic. From two study participants and 703 spike-specific B cells, the most used genes were IGHV1-69, IGHV3-30-3, and IGHV3-30. Here, we focused on the IGHV3-30 group of genes and an IGHV3-30-3-using ultrapotent neutralizing monoclonal antibody, CAB-F52, which displayed broad neutralizing activity also in its germline-reverted form. IGHV3-30-3 is encoded by a region of the IGH locus that is highly variable at both the allelic and structural levels. Using personalized IG genotyping, we found that 4 of 14 study participants lacked the IGHV3-30-3 gene on both chromosomes, raising the question if other, highly similar IGHV genes could substitute for IGHV3-30-3 in persons lacking this gene. In the context of CAB-F52, we found that none of the tested IGHV3-33 alleles, but several IGHV3-30 alleles could substitute for IGHV3-30-3, suggesting functional redundancy between the highly homologous IGHV3-30 and IGHV3-30-3 genes for this antibody.
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Affiliation(s)
- Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Nicoletto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Simon Ekström
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla B. Karlsson Hedestam
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- CORRESPONDENCE Gunilla B. Karlsson Hedestam
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23
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Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. J Mol Biol 2023; 435:167928. [PMID: 36565991 PMCID: PMC9769069 DOI: 10.1016/j.jmb.2022.167928] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity, whether arisen naturally or through vaccination. Understanding the structure of the viral spike assists in determining the impact of mutations on the antigenic surface. One class of mutation impacts glycosylation attachment sites, which have the capacity to influence the antigenic structure beyond the immediate site of attachment. Here, we compare the site-specific glycosylation of recombinant viral spike mimetics of B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), B.1.1.529 (Omicron). The P.1 strain exhibits two additional N-linked glycan sites compared to the other variants analyzed and we investigate the impact of these glycans by molecular dynamics. The acquired N188 site is shown to exhibit very limited glycan maturation, consistent with limited enzyme accessibility. Structural modeling and molecular dynamics reveal that N188 is located within a cavity by the receptor binding domain, which influences the dynamics of these attachment domains. These observations suggest a mechanism whereby mutations affecting viral glycosylation sites have a structural impact across the protein surface.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/Maddy_Newby
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland. https://twitter.com/2016Carl
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/JoelDalllen
| | - John Butler
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK.
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24
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Xu Z, Wei D, Zhang H, Demongeot J. A Novel Mathematical Model That Predicts the Protection Time of SARS-CoV-2 Antibodies. Viruses 2023; 15:v15020586. [PMID: 36851801 PMCID: PMC9962246 DOI: 10.3390/v15020586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Infectious diseases such as SARS-CoV-2 pose a considerable threat to public health. Constructing a reliable mathematical model helps us quantitatively explain the kinetic characteristics of antibody-virus interactions. A novel and robust model is developed to integrate antibody dynamics with virus dynamics based on a comprehensive understanding of immunology principles. This model explicitly formulizes the pernicious effect of the antibody, together with a positive feedback stimulation of the virus-antibody complex on the antibody regeneration. Besides providing quantitative insights into antibody and virus dynamics, it demonstrates good adaptivity in recapturing the virus-antibody interaction. It is proposed that the environmental antigenic substances help maintain the memory cell level and the corresponding neutralizing antibodies secreted by those memory cells. A broader application is also visualized in predicting the antibody protection time caused by a natural infection. Suitable binding antibodies and the presence of massive environmental antigenic substances would prolong the protection time against breakthrough infection. The model also displays excellent fitness and provides good explanations for antibody selection, antibody interference, and self-reinfection. It helps elucidate how our immune system efficiently develops neutralizing antibodies with good binding kinetics. It provides a reasonable explanation for the lower SARS-CoV-2 mortality in the population that was vaccinated with other vaccines. It is inferred that the best strategy for prolonging the vaccine protection time is not repeated inoculation but a directed induction of fast-binding antibodies. Eventually, this model will inform the future construction of an optimal mathematical model and help us fight against those infectious diseases.
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Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou 253023, China
- Correspondence: (Z.X.); (J.D.)
| | - Dongqing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hongmei Zhang
- Department of Life Science, Dezhou University, Dezhou 253023, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France
- Correspondence: (Z.X.); (J.D.)
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25
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Aguilar R, Li X, Crowell CS, Burrell T, Vidal M, Rubio R, Jiménez A, Hernández-Luis P, Hofmann D, Mijočević H, Jeske S, Christa C, D'Ippolito E, Lingor P, Knolle PA, Roggendorf H, Priller A, Yazici S, Carolis C, Mayor A, Schreiner P, Poppert H, Beyer H, Schambeck SE, Izquierdo L, Tortajada M, Angulo A, Soutschek E, Engel P, Garcia-Basteiro A, Busch DH, Moncunill G, Protzer U, Dobaño C, Gerhard M. RBD-Based ELISA and Luminex Predict Anti-SARS-CoV-2 Surrogate-Neutralizing Activity in Two Longitudinal Cohorts of German and Spanish Health Care Workers. Microbiol Spectr 2023; 11:e0316522. [PMID: 36622140 PMCID: PMC9927417 DOI: 10.1128/spectrum.03165-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/04/2022] [Indexed: 01/10/2023] Open
Abstract
The ability of antibodies to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important correlate of protection. For routine evaluation of protection, however, a simple and cost-efficient anti-SARS-CoV-2 serological assay predictive of serum neutralizing activity is needed. We analyzed clinical epidemiological data and blood samples from two cohorts of health care workers in Barcelona and Munich to compare several immunological readouts for evaluating antibody levels that could be surrogates of neutralizing activity. We measured IgG levels against SARS-CoV-2 spike protein (S), its S2 subunit, the S1 receptor binding domain (RBD), and the full length and C terminus of nucleocapsid (N) protein by Luminex, and against RBD by enzyme-linked immunosorbent assay (ELISA), and assessed those as predictors of plasma surrogate-neutralizing activity measured by a flow cytometry assay. In addition, we determined the clinical and demographic factors affecting plasma surrogate-neutralizing capacity. Both cohorts showed a high positive correlation between IgG levels to S antigen, especially to RBD, and the levels of plasma surrogate-neutralizing activity, suggesting RBD IgG as a good correlate of plasma neutralizing activity. Symptomatic infection, with symptoms such as loss of taste, dyspnea, rigors, fever and fatigue, was positively associated with anti-RBD IgG positivity by ELISA and Luminex, and with plasma surrogate-neutralizing activity. Our serological assays allow for the prediction of serum neutralization activity without the cost, hazards, time, and expertise needed for surrogate or conventional neutralization assays. Once a cutoff is established, these relatively simple high-throughput antibody assays will provide a fast and cost-effective method of assessing levels of protection from SARS-CoV-2 infection. IMPORTANCE Neutralizing antibody titers are the best correlate of protection against SARS-CoV-2. However, current tests to measure plasma or serum neutralizing activity do not allow high-throughput screening at the population level. Serological tests could be an alternative if they are proved to be good predictors of plasma neutralizing activity. In this study, we analyzed the SARS-CoV-2 serological profiles of two cohorts of health care workers by applying Luminex and ELISA in-house serological assays. Correlations of both serological tests were assessed between them and with a flow cytometry assay to determine plasma surrogate-neutralizing activity. Both assays showed a high positive correlation between IgG levels to S antigens, especially RBD, and the levels of plasma surrogate-neutralizing activity. This result suggests IgG to RBD as a good correlate of plasma surrogate-neutralizing activity and indicates that serology of IgG to RBD could be used to assess levels of protection from SARS-CoV-2 infection.
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Affiliation(s)
- Ruth Aguilar
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Xue Li
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Claudia S. Crowell
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Teresa Burrell
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Marta Vidal
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Rocio Rubio
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alfons Jiménez
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Pablo Hernández-Luis
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Dieter Hofmann
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Hrvoje Mijočević
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Samuel Jeske
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Catharina Christa
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Elvira D'Ippolito
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Paul Lingor
- Klinikum rechts der Isar, Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Percy A. Knolle
- German Center for Infection Research (DZIF), Munich, Germany
- Klinikum rechts der Isar, Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Hedwig Roggendorf
- Klinikum rechts der Isar, Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Alina Priller
- Klinikum rechts der Isar, Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sarah Yazici
- Klinikum rechts der Isar, Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Carlo Carolis
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | | | | | | | - Sophia E. Schambeck
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Helios Klinikum München West, Munich, Germany
| | - Luis Izquierdo
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Marta Tortajada
- Occupational Health Department, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Ana Angulo
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | | | - Pablo Engel
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Alberto Garcia-Basteiro
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
- Department of Preventive Medicine and Epidemiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - Dirk H. Busch
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Gemma Moncunill
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Markus Gerhard
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
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26
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Ruiz Ortega M, Spisak N, Mora T, Walczak AM. Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals. PLoS Genet 2023; 19:e1010652. [PMID: 36827454 PMCID: PMC10075420 DOI: 10.1371/journal.pgen.1010652] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/05/2023] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
Adaptive immunity's success relies on the extraordinary diversity of protein receptors on B and T cell membranes. Despite this diversity, the existence of public receptors shared by many individuals gives hope for developing population-wide vaccines and therapeutics. Using probabilistic modeling, we show many of these public receptors are shared by chance in healthy individuals. This predictable overlap is driven not only by biases in the random generation process of receptors, as previously reported, but also by their common functional selection. However, the model underestimates sharing between repertoires of individuals infected with SARS-CoV-2, suggesting strong specific antigen-driven convergent selection. We exploit this discrepancy to identify COVID-associated receptors, which we validate against datasets of receptors with known viral specificity. We study their properties in terms of sequence features and network organization, and use them to design an accurate diagnostic tool for predicting SARS-CoV-2 status from repertoire data.
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Affiliation(s)
- María Ruiz Ortega
- Laboratoire de physique de l’École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Natanael Spisak
- Laboratoire de physique de l’École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Thierry Mora
- Laboratoire de physique de l’École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
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27
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Kante B, Vuyyuru SK, Gupta R, Dwivedi T, Kumar P, Mundhra S, Golla R, Virmani S, Verma M, Makharia G, Ahuja V, Kedia S. High seroprevalence against SARS-CoV-2 in non-vaccinated patients with inflammatory bowel disease from Northern India. Indian J Gastroenterol 2023; 42:70-78. [PMID: 36738383 PMCID: PMC9898695 DOI: 10.1007/s12664-022-01310-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 11/07/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND The information on seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among patients with inflammatory bowel disease (IBD) and its comparison to healthy controls is sparse. We compared the seroprevalence rates in patients with IBD and healthy controls (HCs). METHODS Patients with IBD and HCs (contact of patients) underwent SARS-CoV-2 antibody testing (chemiluminescent immunoassay: Siemens kit IgG against antigen-S1RBD) between July 2020 and April 2021. Information on demography, disease characteristics, drug history and past history of SARS-CoV-2 infection were noted. Patients on 5-aminosalicylic acid or no treatment were considered not on immunosuppressants and those who had received steroids, thiopurines or methotrexate within six months of inclusion were considered being on immunosuppressants. RESULTS A total of 235 patients (51.9%, males; mean age, 38.7 ± 12.4 years; median disease duration, 60 months [interquartile range, IQR: 36-120]) (ulcerative colitis [UC]: 69.4%, Crohn's disease [CD]: 28.9%, IBD unclassified [IBDU]: 1.7%) and 73 HCs (mean age, 39.6 ± 10.9 years, 80% males) were enrolled. Of the 235 patients, 128 (54.5%) patients were on immunosuppressants and 107 (45.5%) were not on immunosuppressants. Seventy-four (31.5%) patients were seropositive, of which two (0.9%) had previous history of SARS-CoV-2 infection and none received coronavirus disease-19 (COVID-19) vaccine. Seroprevalence between IBD patients and HCs (32% vs. 27%, p > 0.05) and between patients with and without immunosuppressants (28.1% vs. 36%, p > 0.05) was similar. Age, gender, disease type, duration and activity in the last six months; and medication use were similar between patients with positive and negative serology. There was a progressive increase in seroprevalence from July 2020 to April 2021. CONCLUSION Up to 1/3rd of patients with IBD were seropositive for immunoglobulin G (IgG) SARS-Cov-2 antibody indicating high seroprevalence in patients with IBD from Northern India.
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Affiliation(s)
- Bhaskar Kante
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Sudheer Kumar Vuyyuru
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Ritu Gupta
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Tanima Dwivedi
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Peeyush Kumar
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Sandeep Mundhra
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Rithvik Golla
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Shubi Virmani
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Mahak Verma
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Govind Makharia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India.
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28
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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: 14] [Impact Index Per Article: 14.0] [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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29
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Cheng ZJ, Li B, Zhan Z, Zhao Z, Xue M, Zheng P, Lyu J, Hu C, He J, Chen R, Sun B. Clinical Application of Antibody Immunity Against SARS-CoV-2: Comprehensive Review on Immunoassay and Immunotherapy. Clin Rev Allergy Immunol 2023; 64:17-32. [PMID: 35031959 PMCID: PMC8760112 DOI: 10.1007/s12016-021-08912-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 02/07/2023]
Abstract
The current COVID-19 global pandemic poses immense challenges to global health, largely due to the difficulty to detect infection in the early stages of the disease, as well as the current lack of effective antiviral therapy. Research and understanding of the human immune system can provide important theoretical and technical support for the clinical diagnosis and treatment of COVID-19, the clinical implementations of which include immunoassays and immunotherapy, which play a crucial role in the fight against the pandemic. This review consolidates the current scientific evidence for immunoassay, which includes multiple methods of detecting antigen and antibody against SARS-CoV-2. We compared the characteristics, advantages and disadvantages, and clinical applications of these three detection techniques. In addition to detecting viral infections, knowledge on the body's immunity against the virus is desirable; thus, the immunotherapy-based neutralizing antibody (nAb) detection methods were discussed. We also gave a brief introduction to the new immunoassay technology such as biosensing. This was followed by an in-depth and extensive review on a variety of immunotherapy methods. It includes convalescent plasma therapy, neutralizing antibody-based treatments targeting different regions of SARS-CoV-2, immunotherapy targeted on the host cell including inhibiting the host cell receptor and cytokine storm, as well as cocktail antibodies, cross-neutralizing antibodies, and immunotherapy based on cross-reactivity between viral epitopes and autoepitopes and autoantibody. Despite the development of various immunological testing methods and antibody therapies, the current global situation of COVID-19 is still tense. We need more efficient detection methods and more reliable antibody therapies. The up-to-date knowledge on therapeutic strategies will likely help clinicians worldwide to protect patients from life-threatening viral infections.
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Affiliation(s)
- Zhangkai J. Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Bizhou Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Zhiqing Zhan
- Guangzhou Medical University, Guangzhou, 511436 China
| | - Zifan Zhao
- Guangzhou Medical University, Guangzhou, 511436 China
| | - Mingshan Xue
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Peiyan Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Jiali Lyu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Chundi Hu
- Guangzhou Medical University, Guangzhou, 511436 China
| | - Jianxing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Ruchong Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
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30
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He L, Zhong J, Li G, Lin Z, Zhao P, Yang C, Wang H, Zhang Y, Yang X, Wang Z. Development of SARS-CoV-2 animal vaccines using a stable and efficient NDV expression system. J Med Virol 2023; 95:e28237. [PMID: 36258299 PMCID: PMC9874532 DOI: 10.1002/jmv.28237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/24/2022] [Accepted: 10/16/2022] [Indexed: 01/27/2023]
Abstract
With the continuation of the coronavirus disease 2019 pandemic and the emergence of new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants, the control of the spread of the virus remains urgent. Various animals, including cats, ferrets, hamsters, nonhuman primates, minks, tree shrews, fruit bats, and rabbits, are susceptible to SARS-CoV-2 infection naturally or experimentally. Therefore, to avoid animals from becoming mixing vessels of the virus, vaccination of animals should be considered. In the present study, we report the establishment of an efficient and stable system using Newcastle disease virus (NDV) as a vector to express SARS-CoV-2 spike protein/subunit for the rapid generation of vaccines against SARS-CoV-2 in animals. Our data showed that the S and S1 protein was sufficiently expressed in rNDV-S and rNDV-S1-infected cells, respectively. The S protein was incorporated into and displayed on the surface of rNDV-S viral particles. Intramuscular immunization with rNDV-S was found to induce the highest level of binding and neutralizing antibodies, as well as strong S-specific T-cell response in mice. Intranasal immunization with rNDV-S1 provoked a robust T-cell response but barely any detectable antibodies. Overall, the NDV-vectored vaccine candidates were able to induce profound humoral and cellular immunity, which will provide a good system for developing vaccines targeting both T-cell and antibody responses.
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Affiliation(s)
- Lei He
- College of Animal Science and Technology, Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and ControlHenan University of Science and TechnologyHenanLuoyangChina
| | - Jiaying Zhong
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Guichang Li
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Zhengfang Lin
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Peijing Zhao
- Division of MicrobiologyGuangdong Huawei Testing Co., Ltd.GuangzhouChina
| | - Chuhua Yang
- Division of MicrobiologyGuangdong Huawei Testing Co., Ltd.GuangzhouChina
| | - Hairong Wang
- College of Animal Science and Technology, Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and ControlHenan University of Science and TechnologyHenanLuoyangChina
| | - Yuhao Zhang
- College of Animal Science and Technology, Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and ControlHenan University of Science and TechnologyHenanLuoyangChina
| | - Xiaoyun Yang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina,Guangzhou LaboratoryGuangzhouChina
| | - Zhongfang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina,Guangzhou LaboratoryGuangzhouChina
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31
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Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones. Nat Commun 2022; 13:7733. [PMID: 36517467 PMCID: PMC9748393 DOI: 10.1038/s41467-022-35456-2] [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: 07/06/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. However, the basis for such cross-protection at the molecular level is incompletely understood. Here, we characterized the repertoire and epitope specificity of antibodies elicited by infection with the Beta, Gamma and WA1 ancestral variants and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a method to obtain immunoglobulin sequences with concurrent rapid production and functional assessment of monoclonal antibodies from hundreds of single B cells sorted by flow cytometry. Infection with any variant elicited similar cross-binding antibody responses exhibiting a conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may account for the continued efficacy of vaccines based on a single ancestral variant.
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32
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Akhtar M, Basher SR, Nizam NN, Kamruzzaman M, Khaton F, Banna HA, Kaisar MH, Karmakar PC, Hakim A, Akter A, Ahmed T, Tauheed I, Islam S, Ahmmed F, Mahamud S, Hasnat MA, Sumon MA, Rashed A, Ghosh S, Calderwood SB, Harris JB, Charles RC, LaRocque RC, Ryan ET, Banu S, Shirin T, Chowdhury F, Bhuiyan TR, Qadri F. Longevity of memory B cells and antibodies, as well as the polarization of effector memory helper T cells, are associated with disease severity in patients with COVID-19 in Bangladesh. Front Immunol 2022; 13:1052374. [PMID: 36578502 PMCID: PMC9791541 DOI: 10.3389/fimmu.2022.1052374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
The longevity of immune responses induced by different degrees of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection provides information important to understanding protection against coronavirus disease 2019 (COVID-19). Here, we report the persistence of SARS-CoV-2 spike receptor-binding domain (RBD) specific antibodies and memory B cells recognizing this antigen in sequential samples from patients in Bangladesh with asymptomatic, mild, moderate and severe COVID-19 out to six months following infection. Since the development of long-lived memory B cells, as well as antibody production, is likely to be dependent on T helper (Th) cells, we also investigated the phenotypic changes of Th cells in COVID-19 patients over time following infection. Our results show that patients with moderate to severe COVID-19 mounted significant levels of IgG antibodies out to six months following infection, while patients with asymptomatic or mild disease had significant levels of IgG antibodies out to 3 months following infection, but these then fell more rapidly at 6 months than in patients with higher disease severity. Patients from all severity groups developed circulating memory B cells (MBCs) specific to SARS-CoV-2 spike RBD by 3 months following infection, and these persisted until the last timepoint measured at 6 months. A T helper cell response with an effector memory phenotype was observed following infection in all symptomatic patients, while patients with asymptomatic infection had no significant increases in effector Th1, Th2 and Th17 effector memory cell responses. Our results suggest that the strength and magnitude of antibody and memory B cells induced following SARS-CoV-2 infection depend on the severity of the disease. Polarization of the Th cell response, with an increase in Th effector memory cells, occurs in symptomatic patients by day 7 following infection, with increases seen in Th1, Th2, Th17 and follicular helper T cell subsets.
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Affiliation(s)
- Marjahan Akhtar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Salima Raiyan Basher
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Nuder Nower Nizam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Mohammad Kamruzzaman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Fatema Khaton
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Hasan Al Banna
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - M Hasanul Kaisar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Polash Chandra Karmakar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Al Hakim
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Afroza Akter
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Tasnuva Ahmed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Imam Tauheed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Shaumik Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Faisal Ahmmed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Shakil Mahamud
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Mohammad Abul Hasnat
- Department of Cardiology, Department of Oncology, Kurmitola General Hospital, Dhaka, Bangladesh
| | - Mostafa Aziz Sumon
- Department of Cardiology, Department of Oncology, Kurmitola General Hospital, Dhaka, Bangladesh
| | - Asif Rashed
- Department of Microbiology, Department of Medicine, Mugda Medical College and Hospital, Dhaka, Bangladesh
| | - Shuvro Ghosh
- Department of Microbiology, Department of Medicine, Mugda Medical College and Hospital, Dhaka, Bangladesh
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Sayera Banu
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Fahima Chowdhury
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Taufiqur Rahman Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
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Schultz MD, Suschak JJ, Botta D, Silva-Sanchez A, King RG, Detchemendy TW, Meshram CD, Foote JB, Zhou F, Tipper JL, Zhang J, Harrod KS, Leal SM, Randall TD, Roberts MS, Georges B, Lund FE. A single intranasal administration of AdCOVID protects against SARS-CoV-2 infection in the upper and lower respiratory tracts. Hum Vaccin Immunother 2022; 18:2127292. [PMID: 36194255 PMCID: PMC9746417 DOI: 10.1080/21645515.2022.2127292] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/06/2022] [Accepted: 09/19/2022] [Indexed: 02/05/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has illustrated the critical need for effective prophylactic vaccination to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Intranasal vaccination is an attractive approach for preventing COVID-19 as the nasal mucosa is the site of initial SARS-CoV-2 entry and viral replication prior to aspiration into the lungs. We previously demonstrated that a single intranasal administration of a candidate adenovirus type 5-vectored vaccine encoding the receptor-binding domain of the SARS-CoV-2 spike protein (AdCOVID) induced robust immunity in both the airway mucosa and periphery, and completely protected K18-hACE2 mice from lethal SARS-CoV-2 challenge. Here we show that a single intranasal administration of AdCOVID limits viral replication in the nasal cavity of K18-hACE2 mice. AdCOVID also induces sterilizing immunity in the lungs of mice as reflected by the absence of infectious virus. Finally, AdCOVID prevents SARS-CoV-2 induced pathological damage in the lungs of mice. These data show that AdCOVID not only limits viral replication in the respiratory tract, but it also prevents virus-induced inflammation and immunopathology following SARS-CoV-2 infection.
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Affiliation(s)
- Michael D. Schultz
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Davide Botta
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aaron Silva-Sanchez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - R. Glenn King
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Thomas W. Detchemendy
- Department of Pathology, Division of Laboratory Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Chetan D. Meshram
- Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeremy B. Foote
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fen Zhou
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jennifer L. Tipper
- Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Kevin S. Harrod
- Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sixto M. Leal
- Department of Pathology, Division of Laboratory Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Troy D. Randall
- Department of Medicine, Division of Clinical Immunology and Rheumatology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Frances E. Lund
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
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34
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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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35
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Schuster DJ, Karuna S, Brackett C, Wesley M, Li SS, Eisel N, Tenney D, Hilliard S, Yates NL, Heptinstall JR, Williams LD, Shen X, Rolfe R, Cabello R, Zhang L, Sawant S, Hu J, Randhawa AK, Hyrien O, Hural JA, Corey L, Frank I, Tomaras GD, Seaton KE. Lower SARS-CoV-2-specific humoral immunity in people living with HIV-1 recovered from nonhospitalized COVID-19. JCI Insight 2022; 7:e158402. [PMID: 36136590 PMCID: PMC9675463 DOI: 10.1172/jci.insight.158402] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/14/2022] [Indexed: 12/15/2022] Open
Abstract
People living with HIV-1 (PLWH) exhibit more rapid antibody decline following routine immunization and elevated baseline chronic inflammation than people without HIV-1 (PWOH), indicating potential for diminished humoral immunity during SARS-CoV-2 infection. Conflicting reports have emerged on the ability of PLWH to maintain humoral protection against SARS-CoV-2 coinfection during convalescence. It is unknown whether peak COVID-19 severity, along with HIV-1 infection status, associates with the quality and quantity of humoral immunity following recovery. Using a cross-sectional observational cohort from the United States and Peru, adults were enrolled 1-10 weeks after SARS-CoV-2 infection diagnosis or symptom resolution. Serum antibodies were analyzed for SARS-CoV-2-specific response rates, binding magnitudes, ACE2 receptor blocking, and antibody-dependent cellular phagocytosis. Overall, (a) PLWH exhibited a trend toward decreased magnitude of SARS-CoV-2-specific antibodies, despite modestly increased overall response rates when compared with PWOH; (b) PLWH recovered from symptomatic outpatient COVID-19 had comparatively diminished immune responses; and (c) PLWH lacked a corresponding increase in SARS-CoV-2 antibodies with increased COVID-19 severity when asymptomatic versus symptomatic outpatient disease was compared.
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Affiliation(s)
- Daniel J. Schuster
- Center for Human Systems Immunology
- Department of Surgery, and
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Shelly Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Martina Wesley
- Center for Human Systems Immunology
- Department of Surgery, and
| | - Shuying S. Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nathan Eisel
- Center for Human Systems Immunology
- Department of Surgery, and
| | - DeAnna Tenney
- Center for Human Systems Immunology
- Department of Surgery, and
| | | | - Nicole L. Yates
- Center for Human Systems Immunology
- Department of Surgery, and
| | | | | | - Xiaoying Shen
- Center for Human Systems Immunology
- Department of Surgery, and
| | - Robert Rolfe
- Center for Human Systems Immunology
- Department of Surgery, and
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Lu Zhang
- Center for Human Systems Immunology
- Department of Surgery, and
| | - Sheetal Sawant
- Center for Human Systems Immunology
- Department of Surgery, and
| | - Jiani Hu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - April Kaur Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John A. Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Ian Frank
- Division of Infectious Disease, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Georgia D. Tomaras
- Center for Human Systems Immunology
- Department of Surgery, and
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Kelly E. Seaton
- Center for Human Systems Immunology
- Department of Surgery, and
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36
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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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37
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Xu Z, Ismanto HS, Zhou H, Saputri DS, Sugihara F, Standley DM. Advances in antibody discovery from human BCR repertoires. FRONTIERS IN BIOINFORMATICS 2022; 2:1044975. [PMID: 36338807 PMCID: PMC9631452 DOI: 10.3389/fbinf.2022.1044975] [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: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans.
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Affiliation(s)
- Zichang Xu
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hao Zhou
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Department Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
- *Correspondence: Daron M. Standley,
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38
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Hartley GE, Edwards ESJ, O’Hehir RE, van Zelm MC. New insights into human immune memory from SARS-CoV-2 infection and vaccination. Allergy 2022; 77:3553-3566. [PMID: 36048132 PMCID: PMC9538469 DOI: 10.1111/all.15502] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/13/2022] [Accepted: 08/29/2022] [Indexed: 01/28/2023]
Abstract
Since early 2020, the world has been embroiled in an ongoing viral pandemic with SARS-CoV-2 and emerging variants resulting in mass morbidity and an estimated 6 million deaths globally. The scientific community pivoted rapidly, providing unique and innovative means to identify infected individuals, technologies to evaluate immune responses to infection and vaccination, and new therapeutic strategies to treat infected individuals. Never before has immunology been so critically at the forefront of combatting a global pandemic. It has now become evident that not just antibody responses, but formation and durability of immune memory cells following vaccination are associated with protection against severe disease from SARS-CoV-2 infection. Furthermore, the emergence of variants of concern (VoC) highlight the need for immunological markers to quantify the protective capacity of Wuhan-based vaccines. Thus, harnessing and modulating the immune response is key to successful vaccination and treatment of disease. We here review the latest knowledge about immune memory generation and durability following natural infection and vaccination, and provide insights into the attributes of immune memory that may protect from emerging variants.
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Affiliation(s)
- Gemma E. Hartley
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Emily S. J. Edwards
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Robyn E. O’Hehir
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia,Allergy, Asthma and Clinical Immunology ServiceAlfred HospitalMelbourneVictoriaAustralia
| | - Menno C. van Zelm
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia,Allergy, Asthma and Clinical Immunology ServiceAlfred HospitalMelbourneVictoriaAustralia
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39
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Weidenbacher PAB, Waltari E, de Los Rios Kobara I, Bell BN, Morris MK, Cheng YC, Hanson C, Pak JE, Kim PS. Converting non-neutralizing SARS-CoV-2 antibodies into broad-spectrum inhibitors. Nat Chem Biol 2022; 18:1270-1276. [PMID: 36076082 PMCID: PMC9596371 DOI: 10.1038/s41589-022-01140-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/10/2022] [Indexed: 01/07/2023]
Abstract
Omicron and its subvariants have rendered most authorized monoclonal antibody-based treatments for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ineffective, highlighting the need for biologics capable of overcoming SARS-CoV-2 evolution. These mostly ineffective antibodies target variable epitopes. Here we describe broad-spectrum SARS-CoV-2 inhibitors developed by tethering the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), to known non-neutralizing antibodies that target highly conserved epitopes in the viral spike protein. These inhibitors, called receptor-blocking conserved non-neutralizing antibodies (ReconnAbs), potently neutralize all SARS-CoV-2 variants of concern (VOCs), including Omicron. Neutralization potency is lost when the linker joining the binding and inhibitory ReconnAb components is severed. In addition, a bi-functional ReconnAb, made by linking ACE2 to a bi-specific antibody targeting two non-overlapping conserved epitopes, defined here, shows sub-nanomolar neutralizing activity against all VOCs, including Omicron and BA.2. Given their conserved targets and modular nature, ReconnAbs have the potential to act as broad-spectrum therapeutics against SARS-CoV-2 and other emerging pandemic diseases. ![]()
SARS-CoV-2 spike-directed, non-neutralizing antibodies were converted into broad-spectrum inhibitors by conjugation to the SARS-CoV-2 receptor, ACE2, resulting in fusion proteins that target all SARS-CoV-2 variants of concern tested.
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Affiliation(s)
- Payton A-B Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | | | - Benjamin N Bell
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Ya-Chen Cheng
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.,Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter S Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA. .,Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA.
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Effects of Prior Infection with SARS-CoV-2 on B Cell Receptor Repertoire Response during Vaccination. Vaccines (Basel) 2022; 10:vaccines10091477. [PMID: 36146555 PMCID: PMC9506540 DOI: 10.3390/vaccines10091477] [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: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding the B cell response to SARS-CoV-2 vaccines is a high priority. High-throughput sequencing of the B cell receptor (BCR) repertoire allows for dynamic characterization of B cell response. Here, we sequenced the BCR repertoire of individuals vaccinated by the Pfizer SARS-CoV-2 mRNA vaccine. We compared BCR repertoires of individuals with previous COVID-19 infection (seropositive) to individuals without previous infection (seronegative). We discovered that vaccine-induced expanded IgG clonotypes had shorter heavy-chain complementarity determining region 3 (HCDR3), and for seropositive individuals, these expanded clonotypes had higher somatic hypermutation (SHM) than seronegative individuals. We uncovered shared clonotypes present in multiple individuals, including 28 clonotypes present across all individuals. These 28 shared clonotypes had higher SHM and shorter HCDR3 lengths compared to the rest of the BCR repertoire. Shared clonotypes were present across both serotypes, indicating convergent evolution due to SARS-CoV-2 vaccination independent of prior viral exposure.
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Shi W, Wang L, Zhou T, Sastry M, Yang ES, Zhang Y, Chen M, Chen X, Choe M, Creanga A, Leung K, Olia AS, Pegu A, Rawi R, Schön A, Shen CH, Stancofski ESD, Talana CA, Teng IT, Wang S, Corbett KS, Tsybovsky Y, Mascola JR, Kwong PD. Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability. Structure 2022; 30:1233-1244.e7. [PMID: 35841885 PMCID: PMC9284671 DOI: 10.1016/j.str.2022.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Immunization with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike elicits diverse antibodies, but it is unclear if any of the antibodies can neutralize broadly against other beta-coronaviruses. Here, we report antibody WS6 from a mouse immunized with mRNA encoding the SARS-CoV-2 spike. WS6 bound diverse beta-coronavirus spikes and neutralized SARS-CoV-2 variants, SARS-CoV, and related sarbecoviruses. Epitope mapping revealed WS6 to target a region in the S2 subunit, which was conserved among SARS-CoV-2, Middle East respiratory syndrome (MERS)-CoV, and hCoV-OC43. The crystal structure at 2 Å resolution of WS6 revealed recognition to center on a conserved S2 helix, which was occluded in both pre- and post-fusion spike conformations. Structural and neutralization analyses indicated WS6 to neutralize by inhibiting fusion and post-viral attachment. Comparison of WS6 with other recently identified antibodies that broadly neutralize beta-coronaviruses indicated a stem-helical supersite-centered on hydrophobic residues Phe1148, Leu1152, Tyr1155, and Phe1156-to be a promising target for vaccine design.
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Affiliation(s)
- Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwan Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erik-Stephane D Stancofski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chloe Adrienna Talana
- 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
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - John R Mascola
- 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.
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Ghotloo S, Maghsood F, Golsaz‐Shirazi F, Amiri MM, Moog C, Shokri F. Epitope mapping of neutralising anti-SARS-CoV-2 monoclonal antibodies: Implications for immunotherapy and vaccine design. Rev Med Virol 2022; 32:e2347. [PMID: 35394093 PMCID: PMC9111153 DOI: 10.1002/rmv.2347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. This disease has currently affected more than 346 million people and resulted in more than 5.5 million deaths in many countries. Neutralising monoclonal antibodies (MAbs) against the SARS-CoV-2 virus could serve as prophylactic/therapeutic agents in COVID-19 infection by providing passive protection against the virus in individuals. Until now, no Food and Drug Administration/European Medicines Agency-approved neutralising MAb against SARS-CoV-2 virus exists in the market, though a number of MAbs have been authorised for emergency use. Therefore, there is an urgent need for development of efficient anti-SARS-CoV-2 neutralising MAbs for use in the clinic. Moreover, neutralising anti-SARS-CoV-2 MAbs could be used as beneficial tools for designing epitope-based vaccines against the virus. Given that the target epitope of a MAb is a crucial feature influencing its neutralising potency, target epitopes of neutralising anti-SARS-CoV-2 MAbs already reported in the literature and reactivity of these MAbs with SARS-CoV-2 variants are reviewed herein.
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Affiliation(s)
- Somayeh Ghotloo
- Department of Medical Laboratory SciencesSchool of Allied Medical SciencesKashan University of Medical SciencesKashanIran
| | - Faezeh Maghsood
- Department of ImmunologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Forough Golsaz‐Shirazi
- Department of ImmunologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Mohammad Mehdi Amiri
- Department of ImmunologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Christiane Moog
- Laboratoire d’ImmunoRhumatologie MoléculaireInstitut national de la santé et de la recherche médicale (INSERM) UMR_S 1109Institut thématique interdisciplinaire (ITI) de Médecine de Précision de StrasbourgTransplantex NGFaculté de MédecineFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de Strasbourg (FMTS)Université de StrasbourgStrasbourgFrance
| | - Fazel Shokri
- Department of ImmunologySchool of Public HealthTehran University of Medical SciencesTehranIran
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Kumar S, Dutta D, Ravichandiran V, Sukla S. Monoclonal antibodies: a remedial approach to prevent SARS-CoV-2 infection. 3 Biotech 2022; 12:227. [PMID: 35982759 PMCID: PMC9383686 DOI: 10.1007/s13205-022-03281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/26/2022] [Indexed: 11/07/2022] Open
Abstract
SARS-CoV-2, the newly emerged virus of the Coronaviridae family is causing havoc worldwide. The novel coronavirus 2019 was first reported in Wuhan, China marked as the third highly infectious pathogenic virus of the twenty-first century. The typical manifestations of COVID-19 include cough, sore throat, fever, fatigue, loss of sense of taste and difficulties in breathing. Large numbers of SARS-CoV-2 infected patients have mild to moderate symptoms, however severe and life-threatening cases occur in about 5-10% of infections with an approximately 2% mortality rate. For the treatment of SARS-CoV-2, the use of neutralizing monoclonal antibodies (mAbs) could be one approach. The receptor binding domain (RBD) and N-terminal domain (NTD) situated on the peak of the spike protein (S-Protein) of SARS-CoV-2 are immunogenic in nature, therefore, can be targeted by neutralizing monoclonal antibodies. Several bioinformatics approaches highlight the identification of novel SARS-CoV-2 epitopes which can be targeted for the development of COVID-19 therapeutics. Here we present a summary of neutralizing mAbs isolated from COVID-19 infected patients which are anticipated to be a better therapeutic alternative against SARS-CoV-2. However, provided the vast escalation of the disease worldwide affecting people from all strata, affording expensive mAb therapy will not be feasible. Hence other strategies are also being employed to find suitable vaccine candidates and antivirals against SARS-CoV-2 that can be made easily available to the population.
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Affiliation(s)
- Sonu Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Debrupa Dutta
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Soumi Sukla
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
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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: 114] [Impact Index Per Article: 57.0] [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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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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Aiello A, Grossi A, Meschi S, Meledandri M, Vanini V, Petrone L, Casetti R, Cuzzi G, Salmi A, Altera AM, Pierelli L, Gualano G, Ascoli Bartoli T, Castilletti C, Agrati C, Girardi E, Palmieri F, Nicastri E, Di Rosa E, Goletti D. Coordinated innate and T-cell immune responses in mild COVID-19 patients from household contacts of COVID-19 cases during the first pandemic wave. Front Immunol 2022; 13:920227. [PMID: 35967321 PMCID: PMC9364317 DOI: 10.3389/fimmu.2022.920227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/30/2022] [Indexed: 01/08/2023] Open
Abstract
Objective To better define the immunopathogenesis of COVID-19, the present study aims to characterize the early immune responses to SARS-CoV-2 infection in household contacts of COVID-19 cases. In particular, innate, T- and B-cell specific responses were evaluated over time. Methods Household contacts of COVID-19 cases screened for SARS−CoV−2 infection by nasopharyngeal swab for surveillance purposes were enrolled (T0, n=42). Of these, 28 subjects returned for a follow-up test (T1). The innate response was assessed by detecting a panel of soluble factors by multiplex-technology in plasma samples. Cell-mediated response was evaluated by measuring interferon (IFN)-γ levels by ELISA in plasma harvested from whole-blood stimulated with SARS−CoV−2 peptide pools, including spike (S), nucleocapsid (N) and membrane (M) proteins. The serological response was assessed by quantifying anti-Receptor-Binding-Domain (RBD), anti-Nucleocapsid (N), whole virus indirect immunofluorescence, and neutralizing antibodies. Results At T0, higher levels of plasmatic IFN-α, IL-1ra, MCP-1 and IP-10, and lower levels of IL-1β, IL-9, MIP-1β and RANTES were observed in subjects with positive swab compared to individuals with a negative one (p<0.05). Plasmatic IFN-α was the only cytokine detectable in subjects with positive SARS-CoV-2 swabs with high accuracy for swab score positivity (0.93, p<0.0001). Among subjects with positive swabs, significant negative correlations were found among the RT-PCR cycle threshold values reported for genes S and N and IFN-α or IP-10 levels. At T0, the IFN-γ T-cell specific response was detected in 50% (5/10) of subjects with positive swab, while anti-RBD/anti-N antibodies showed a positivity rate of 10% (1/10). At T1, the IFN-γ T-cell specific response was detected in most of the confirmed-infection subjects (77.8%, 7/9), whereas the serological response was still observed in a minority of them (44.4%, 4/9). Overall, the swab test showed a moderate concordance with the T-cell response (78.6%, k=0.467), and a scarce concordance with the serological one (72.9%, k=0.194). Conclusions Plasmatic IFN-α and the IFN-γ T-cell specific response appear early even in the absence of seroconversion, and show a greater positivity rate than the serological response in household contacts with positive swab.
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Affiliation(s)
- Alessandra Aiello
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Adriano Grossi
- Local Public Health Office, Azienda Sanitaria Locale (ASL) Roma 1, Rome, Italy
| | - Silvia Meschi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Marcello Meledandri
- Unità Operativa Complessa (UOC) Microbiology and Virology, Azienda Sanitaria Locale (ASL) Roma 1-San Filippo Neri Hospital, Rome, Italy
| | - Valentina Vanini
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
- Unità Operativa Semplice (UOS) Professioni Sanitarie Tecniche, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Linda Petrone
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Rita Casetti
- Laboratory of Cellular Immunology, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Gilda Cuzzi
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Andrea Salmi
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Anna Maria Altera
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Luca Pierelli
- Unità Operativa Complessa (UOC) Transfusion Medicine and Stem Cell, San Camillo Forlanini Hospital, Rome, Italy
| | - Gina Gualano
- Respiratory Infectious Diseases Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Tommaso Ascoli Bartoli
- Clinical Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Concetta Castilletti
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Chiara Agrati
- Laboratory of Cellular Immunology, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Enrico Girardi
- Clinical Epidemiology, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Fabrizio Palmieri
- Respiratory Infectious Diseases Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Emanuele Nicastri
- Clinical Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Enrico Di Rosa
- Local Public Health Office, Azienda Sanitaria Locale (ASL) Roma 1, Rome, Italy
| | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
- *Correspondence: Delia Goletti,
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Yang L, Liang T, Pierson LM, Wang H, Fletcher JK, Wang S, Bao D, Zhang L, Huang Z, Zheng W, Zhang X, Park H, Li Y, Robinson JE, Feehan AK, Lyon CJ, Cao J, Morici LA, Li C, Roy CJ, Yu X, Hu T. SARS-CoV-2 Epitopes following Infection and Vaccination Overlap Known Neutralizing Antibody Sites. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9769803. [PMID: 35928300 PMCID: PMC9297724 DOI: 10.34133/2022/9769803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/27/2022] [Indexed: 11/06/2022]
Abstract
Identification of epitopes targeted following virus infection or vaccination can guide vaccine design and development of therapeutic interventions targeting functional sites, but can be laborious. Herein, we employed peptide microarrays to map linear peptide epitopes (LPEs) recognized following SARS-CoV-2 infection and vaccination. LPEs detected by nonhuman primate (NHP) and patient IgMs after SARS-CoV-2 infection extensively overlapped, localized to functionally important virus regions, and aligned with reported neutralizing antibody binding sites. Similar LPE overlap occurred after infection and vaccination, with LPE clusters specific to each stimulus, where strong and conserved LPEs mapping to sites known or likely to inhibit spike protein function. Vaccine-specific LPEs tended to map to sites known or likely to be affected by structural changes induced by the proline substitutions in the mRNA vaccine's S protein. Mapping LPEs to regions of known functional importance in this manner may accelerate vaccine evaluation and discovery of targets for site-specific therapeutic interventions.
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Affiliation(s)
- Li Yang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Te Liang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
| | - Lane M. Pierson
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jesse K. Fletcher
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Shu Wang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Duran Bao
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Lili Zhang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Zhen Huang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Wenshu Zheng
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Heewon Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Yuwen Li
- Hayward Genetics Center, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - James E. Robinson
- Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Amy K. Feehan
- Infectious Disease Department, Ochsner Clinic Foundation, New Orleans, LA 70121, USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Jing Cao
- University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Lisa A. Morici
- Department of Microbiology & Immunology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Chenzhong Li
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Chad J. Roy
- Department of Microbiology & Immunology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Division of Microbiology, Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA 70433, USA
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
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48
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VH3-53/66-Class RBD-Specific Human Monoclonal Antibody iB20 Displays Cross-Neutralizing Activity against Emerging SARS-CoV-2 Lineages. J Pers Med 2022; 12:jpm12060895. [PMID: 35743680 PMCID: PMC9224930 DOI: 10.3390/jpm12060895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Abstract
Immune evasion of SARS-CoV-2 undermines current strategies tocounteract the pandemic, with the efficacy of therapeutic virus-neutralizing monoclonal antibodies (nAbs) being affected the most. In this work, we asked whether two previously identified human cross-neutralizing nAbs, iB14 (class VH1-58) and iB20 (class VH3-53/66), are capable of neutralizing the recently emerged Omicron (BA.1) variant. Both nAbs were found to bind the Omicron RBD with a nanomolar affinity, yet they displayed contrasting functional features. When tested against Omicron, the neutralizing activity of iB14 was reduced 50-fold, whereas iB20 displayed a surprising increase in activity. Thus, iB20 is a unique representative of the VH3-53/66-class of nAbs in terms of breadth of neutralization, which establishes it as a candidate for COVID-19 therapy and prophylactics.
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49
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Paschold L, Klee B, Gottschick C, Willscher E, Diexer S, Schultheiß C, Simnica D, Sedding D, Girndt M, Gekle M, Mikolajczyk R, Binder M. Rapid Hypermutation B Cell Trajectory Recruits Previously Primed B Cells Upon Third SARS-Cov-2 mRNA Vaccination. Front Immunol 2022; 13:876306. [PMID: 35615365 PMCID: PMC9126551 DOI: 10.3389/fimmu.2022.876306] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic shows that vaccination strategies building on an ancestral viral strain need to be optimized for the control of potentially emerging viral variants. Therefore, aiming at strong B cell somatic hypermutation to increase antibody affinity to the ancestral strain - not only at high antibody titers - is a priority when utilizing vaccines that are not targeted at individual variants since high affinity may offer some flexibility to compensate for strain-individual mutations. Here, we developed a next-generation sequencing based SARS-CoV-2 B cell tracking protocol to rapidly determine the level of immunoglobulin somatic hypermutation at distinct points during the immunization period. The percentage of somatically hypermutated B cells in the SARS-CoV-2 specific repertoire was low after the primary vaccination series, evolved further over months and increased steeply after boosting. The third vaccination mobilized not only naïve, but also antigen-experienced B cell clones into further rapid somatic hypermutation trajectories indicating increased affinity. Together, the strongly mutated post-booster repertoires and antibodies deriving from this may explain why the third, but not the primary vaccination series, offers some protection against immune-escape variants such as Omicron B.1.1.529.
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Affiliation(s)
- Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Bianca Klee
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Cornelia Gottschick
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Edith Willscher
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Sophie Diexer
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Donjete Simnica
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Daniel Sedding
- Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Matthias Girndt
- Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Gekle
- Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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50
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Seow J, Graham C, Hallett SR, Lechmere T, Maguire TJA, Huettner I, Cox D, Khan H, Pickering S, Roberts R, Waters A, Ward CC, Mant C, Pitcher MJ, Spencer J, Fox J, Malim MH, Doores KJ. ChAdOx1 nCoV-19 vaccine elicits monoclonal antibodies with cross-neutralizing activity against SARS-CoV-2 viral variants. Cell Rep 2022; 39:110757. [PMID: 35477023 PMCID: PMC9010245 DOI: 10.1016/j.celrep.2022.110757] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 11/29/2022] Open
Abstract
Although the antibody response to COVID-19 vaccination has been studied extensively at the polyclonal level using immune sera, little has been reported on the antibody response at the monoclonal level. Here, we isolate a panel of 44 anti-SARS-CoV-2 monoclonal antibodies (mAbs) from an individual who received two doses of the ChAdOx1 nCoV-19 (AZD1222) vaccine at a 12-week interval. We show that, despite a relatively low serum neutralization titer, Spike-reactive IgG+ B cells are still detectable 9 months post-boost. Furthermore, mAbs with potent neutralizing activity against the current SARS-CoV-2 variants of concern (Alpha, Gamma, Beta, Delta, and Omicron) are present. The vaccine-elicited neutralizing mAbs form eight distinct competition groups and bind epitopes overlapping with neutralizing mAbs elicited following SARS-CoV-2 infection. AZD1222-elicited mAbs are more mutated than mAbs isolated from convalescent donors 1-2 months post-infection. These findings provide molecular insights into the AZD1222 vaccine-elicited antibody response.
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Affiliation(s)
- Jeffrey Seow
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Sadie R Hallett
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Daniel Cox
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Anele Waters
- Harrison Wing, Guy's and St Thomas' NHS Trust, London, UK
| | - Christopher C Ward
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Christine Mant
- Infectious Diseases Biobank, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Michael J Pitcher
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jo Spencer
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Julie Fox
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK; Harrison Wing, Guy's and St Thomas' NHS Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
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