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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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Chen Y, Zha J, Xu S, Shao J, Liu X, Li D, Zhang X. Structure-Based Optimization of One Neutralizing Antibody against SARS-CoV-2 Variants Bearing the L452R Mutation. Viruses 2024; 16:566. [PMID: 38675908 PMCID: PMC11053997 DOI: 10.3390/v16040566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Neutralizing antibodies (nAbs) play an important role against SARS-CoV-2 infections. Previously, we have reported one potent receptor binding domain (RBD)-binding nAb Ab08 against the SARS-CoV-2 prototype and a panel of variants, but Ab08 showed much less efficacy against the variants harboring the L452R mutation. To overcome the antibody escape caused by the L452R mutation, we generated several structure-based Ab08 derivatives. One derivative, Ab08-K99E, displayed the mostly enhanced neutralizing potency against the Delta pseudovirus bearing the L452R mutation compared to the Ab08 and other derivatives. Ab08-K99E also showed improved neutralizing effects against the prototype, Omicron BA.1, and Omicron BA.4/5 pseudoviruses. In addition, compared to the original Ab08, Ab08-K99E exhibited high binding properties and affinities to the RBDs of the prototype, Delta, and Omicron BA.4/5 variants. Altogether, our findings report an optimized nAb, Ab08-K99E, against SARS-CoV-2 variants and demonstrate structure-based optimization as an effective way for antibody development against pathogens.
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Affiliation(s)
- Yamin Chen
- Suzhou Medical College, Soochow University, Suzhou 215123, China; (Y.C.); (X.L.)
- Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; (S.X.); (J.S.)
| | - Jialu Zha
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China;
| | - Shiqi Xu
- Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; (S.X.); (J.S.)
- The CAS Key Laboratory of Receptor Research and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jiang Shao
- Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; (S.X.); (J.S.)
| | - Xiaoshan Liu
- Suzhou Medical College, Soochow University, Suzhou 215123, China; (Y.C.); (X.L.)
- Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; (S.X.); (J.S.)
| | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China;
| | - Xiaoming Zhang
- Suzhou Medical College, Soochow University, Suzhou 215123, China; (Y.C.); (X.L.)
- Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; (S.X.); (J.S.)
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai 200052, China
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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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Hillenbrand M, Esslinger C, Seidenberg J, Weber M, Zingg A, Townsend C, Eicher B, Rutkauskaite J, Riese P, Guzman CA, Fischer K, Schmitt S. Fast-Track Discovery of SARS-CoV-2-Neutralizing Antibodies from Human B Cells by Direct Functional Screening. Viruses 2024; 16:339. [PMID: 38543705 PMCID: PMC10975424 DOI: 10.3390/v16030339] [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: 01/30/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 05/23/2024] Open
Abstract
As the COVID-19 pandemic revealed, rapid development of vaccines and therapeutic antibodies are crucial to guarantee a quick return to the status quo of society. In early 2020, we deployed our droplet microfluidic single-cell-based platform DROPZYLLA® for the generation of cognate antibody repertoires of convalescent COVID-19 donors. Discovery of SARS-CoV-2-specific antibodies was performed upon display of antibodies on the surface of HEK293T cells by antigen-specific sorting using binding to the SARS-CoV-2 spike and absence of binding to huACE2 as the sort criteria. This efficiently yielded antibodies within 3-6 weeks, of which up to 100% were neutralizing. One of these, MTX-COVAB, displaying low picomolar neutralization IC50 of SARS-CoV-2 and with a neutralization potency on par with the Regeneron antibodies, was selected for GMP manufacturing and clinical development in June 2020. MTX-COVAB showed strong efficacy in vivo and neutralized all identified clinically relevant variants of SARS-CoV-2 at the time of its selection. MTX-COVAB completed GMP manufacturing by the end of 2020, but clinical development was stopped when the Omicron variant emerged, a variant that proved to be detrimental to all monoclonal antibodies already approved. The present study describes the capabilities of the DROPZYLLA® platform to identify antibodies of high virus-neutralizing capacity rapidly and directly.
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Affiliation(s)
- Matthias Hillenbrand
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Christoph Esslinger
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Jemima Seidenberg
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Marcel Weber
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Andreas Zingg
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Catherine Townsend
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Barbara Eicher
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Justina Rutkauskaite
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Peggy Riese
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (P.R.); (C.A.G.)
| | - Carlos A. Guzman
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (P.R.); (C.A.G.)
| | - Karsten Fischer
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
| | - Simone Schmitt
- Memo Therapeutics AG, 8952 Schlieren, Switzerland; (M.H.); (M.W.); (A.Z.); (B.E.); (J.R.); (K.F.); (S.S.)
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