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He Q, An Y, Zhou X, Xie H, Tao L, Li D, Zheng A, Li L, Xu Z, Yu S, Wang R, Hu H, Liu K, Wang Q, Dai L, Xu K, Gao GF. Neutralization of EG.5, EG.5.1, BA.2.86, and JN.1 by antisera from dimeric receptor-binding domain subunit vaccines and 41 human monoclonal antibodies. Med 2024; 5:401-413.e4. [PMID: 38574739 DOI: 10.1016/j.medj.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/03/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND The recently circulating Omicron variants BA.2.86 and JN.1 were identified with more than 30 amino acid changes on the spike protein compared to BA.2 or XBB.1.5. This study aimed to comprehensively assess the immune escape potential of BA.2.86, JN.1, EG.5, and EG.5.1. METHODS We collected human and murine sera to evaluate serological neutralization activities. The participants received three doses of coronavirus disease 2019 (COVID-19) vaccines or a booster dose of the ZF2022-A vaccine (Delta-BA.5 receptor-binding domain [RBD]-heterodimer immunogen) or experienced a breakthrough infection (BTI). The ZF2202-A vaccine is under clinical trial study (ClinicalTrials.gov: NCT05850507). BALB/c mice were vaccinated with a panel of severe acute respiratory syndrome coronavirus 2 RBD-dimer proteins. The antibody evasion properties of these variants were analyzed with 41 representative human monoclonal antibodies targeting the eight RBD epitopes. FINDINGS We found that BA.2.86 had less neutralization evasion than EG.5 and EG.5.1 in humans. The ZF2202-A booster induced significantly higher neutralizing titers than BTI. Furthermore, BA.2.86 and JN.1 exhibited stronger antibody evasion than EG.5 and EG.5.1 on RBD-4 and RBD-5 epitopes. Compared to BA.2.86, JN.1 further lost the ability to bind to several RBD-1 monoclonal antibodies and displayed further immune escape. CONCLUSIONS Our data showed that the currently dominating sub-variant, JN.1, showed increased immune evasion compared to BA.2.86 and EG.5.1, which is highly concerning. This study provides a timely risk assessment of the interested sub-variants and the basis for updating COVID-19 vaccines. FUNDING This work was funded by the National Key R&D Program of China, the National Natural Science Foundation of China, the Beijing Life Science Academy, the Bill & Melinda Gates Foundation, and the Postdoctoral Fellowship Program of China Postdoctoral Science Foundation (CPSF).
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MESH Headings
- Humans
- Animals
- Antibodies, Monoclonal/immunology
- SARS-CoV-2/immunology
- Mice
- Mice, Inbred BALB C
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- COVID-19/prevention & control
- COVID-19/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Vaccines, Subunit/immunology
- Vaccines, Subunit/administration & dosage
- Female
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Betacoronavirus/immunology
- Male
- Immune Sera/immunology
- Adult
- Immune Evasion
- Neutralization Tests
- Epitopes/immunology
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Affiliation(s)
- Qingwen He
- Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yaling An
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xuemei Zhou
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; School of Life Sciences, Hebei University, Baoding, Hebei Province, China
| | - Haitang Xie
- Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Lifeng Tao
- Anhui Zhifei Longcom Biopharmaceutical Co., Ltd., Hefei, Anhui Province, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Shufan Yu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ruyue Wang
- Anhui Zhifei Longcom Biopharmaceutical Co., Ltd., Hefei, Anhui Province, China
| | - Hua Hu
- Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Kun Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences (CAS), Beijing, China.
| | - George F Gao
- Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences (CAS), Beijing, China; D. H. Chen School of Universal Health and School of Public Health, Zhejiang University, Hangzhou, Zhejiang Province, China.
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2
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Li Z, Zhang Z, Rosen ST, Feng M. Function and mechanism of bispecific antibodies targeting SARS-CoV-2. Cell Insight 2024; 3:100150. [PMID: 38374826 PMCID: PMC10875118 DOI: 10.1016/j.cellin.2024.100150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/21/2024]
Abstract
As the dynamic evolution of SARS-CoV-2 led to reduced efficacy in monoclonal neutralizing antibodies and emergence of immune escape, the role of bispecific antibodies becomes crucial in bolstering antiviral activity and suppressing immune evasion. This review extensively assesses a spectrum of representative bispecific antibodies targeting SARS-CoV-2, delving into their characteristics, design formats, mechanisms of action, and associated advantages and limitations. The analysis encompasses factors influencing the selection of parental antibodies and strategies for incorporating added benefits in bispecific antibody design. Furthermore, how different classes of parental antibodies contribute to augmenting the broad-spectrum neutralization capability within bispecific antibodies is discussed. In summary, this review presents analyses and discussions aimed at offering valuable insights for shaping future strategies in bispecific antibody design to effectively confront the challenges posed by SARS-CoV-2 and propel advancements in antiviral therapeutic development.
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Affiliation(s)
- Zhaohui Li
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Zengyuan Zhang
- Department of Molecular Microbiology & Immunology, University of Southern California, CA, USA
| | - Steven T. Rosen
- Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Mingye Feng
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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3
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Li W, Xu Z, Niu T, Xie Y, Zhao Z, Li D, He Q, Sun W, Shi K, Guo W, Chang Z, Liu K, Fan Z, Qi J, Gao GF. Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins. EMBO J 2024; 43:1484-1498. [PMID: 38467833 PMCID: PMC11021471 DOI: 10.1038/s44318-024-00062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding and immune evasion are recognized as two major drivers for evolution of the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, the underlying mechanism of interplay between two factors remains incompletely understood. Herein, we determined the structures of human ACE2 complexed with BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5 RBDs. Based on the ACE2/RBD structures of these sub-variants and a comparison with the known complex structures, we found that R346T substitution in the RBD enhanced ACE2 binding upon an interaction with the residue R493, but not Q493, via a mechanism involving long-range conformation changes. Furthermore, we found that R493Q and F486V exert a balanced impact, through which immune evasion capability was somewhat compromised to achieve an optimal receptor binding. We propose a "two-steps-forward and one-step-backward" model to describe such a compromise between receptor binding affinity and immune evasion during RBD evolution of Omicron sub-variants.
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Affiliation(s)
- Weiwei Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Tianhui Niu
- Air Force Medical University, Air Force Medical center, PLA, Beijing, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Zhennan Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Qingwen He
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wenqiao Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Kaiyuan Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wenjing Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Chang
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zheng Fan
- Institutional Core Facility, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
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4
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Yang J, Wang X, Zhang Y, He R, Fu Z, Wang R, Ma Y, Fu D, Meng S, Cai W, Zhou Y, Chen C, Chen G, Gong X. Intra-Articular Injection of Interleukin-8 Neutralizing Monoclonal Antibody Effectively Attenuates Osteoarthritis Progression in Rabbits. Cartilage 2024:19476035241240361. [PMID: 38525935 DOI: 10.1177/19476035241240361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
OBJECTIVE Cytokines are implicated in the pathogenesis of osteoarthritis (OA), and this study aims to assess the therapeutic potential of an IL-8 neutralizing monoclonal antibody (mAb) for OA intervention. DESIGN The study employed a rabbit model of OA induced by anterior cruciate ligament transection (ACLT) surgery to investigate the effects of an interleukin (IL)-8 neutralizing mAb, with hyaluronic acid (HA) used as a positive control. Primary outcomes assessed in the rabbits included cartilage repair, synovitis, joint effusion, changes in footprints, and lower limb loading conditions. RESULTS Compared to HA, intra-articular injection of the IL-8 neutralizing mAb demonstrated a more pronounced attenuation of OA progression and enhancement of cartilage repair. We observed a reduction in synovitis and joint effusion, indications of bone marrow edema, as well as improvements in lower limb function. In knees treated with the neutralizing IL-8 mAb, there was a significant decrease in IL-8 levels within the synovial tissues. CONCLUSIONS The IL-8 neutralizing mAb exhibits promising therapeutic potential in the management of OA by attenuating inflammation and facilitating cartilage repair. However, further investigations are warranted to comprehensively elucidate the underlying mechanisms, optimize treatment protocols, and ensure the long-term safety and efficacy of this innovative therapeutic approach.
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Affiliation(s)
- Junjun Yang
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
- Key Laboratory of Biorheological Science and Technology, College of Bioengineering, Chongqing University, Ministry of Education, Chongqing, China
| | - Xin Wang
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | | | - Rui He
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zhenlan Fu
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Rong Wang
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yanming Ma
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Dejie Fu
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Shuo Meng
- College of Medical Informatics, Chongqing Medical University, Chongqing, China
| | - Wang Cai
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yizhao Zhou
- Department of Orthopedics, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Cheng Chen
- College of Medical Informatics, Chongqing Medical University, Chongqing, China
| | - Guangxing Chen
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Xiaoyuan Gong
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
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5
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Hu Y, Hu C, Wang S, Ren L, Hao Y, Wang Z, Liu Y, Su J, Zhu B, Li D, Shao Y, Liang H. Identification of an IGHV3-53-Encoded RBD-Targeting Cross-Neutralizing Antibody from an Early COVID-19 Convalescent. Pathogens 2024; 13:272. [PMID: 38668227 PMCID: PMC11054858 DOI: 10.3390/pathogens13040272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/10/2024] [Accepted: 03/20/2024] [Indexed: 04/29/2024] Open
Abstract
Since November 2021, Omicron has emerged as the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, and its sublineages continue to appear one after another, significantly reducing the effectiveness of existing therapeutic neutralizing antibodies (NAbs). It is urgent to develop effective NAbs against circulating Omicron variants. Here, we isolated receptor binding domain (RBD)-specific single memory B cells via flow cytometry from a COVID-19 convalescent. The antibody variable region genes of the heavy chain (VHs) and light chain (VLs) were amplified and cloned into expression vectors. After antibody expression, ELISA screening and neutralizing activity detection, we obtained an IGHV3-53-encoded RBD-targeting cross-neutralizing antibody D6, whose VL originated from the IGKV1-9*01 germlines. D6 could potently neutralize circulating Omicron variants (BA.1, BA.2, BA.4/5 and BF.7), with IC50 values of less than 0.04 μg/mL, and the neutralizing ability against XBB was reduced but still effective. The KD values of D6 binding with RBD of the prototype and BA.1 were both less than 1.0 × 10-12 M. The protein structure of the D6-RBD model indicates that D6 interacts with the RBD external subdomain and belongs to the RBD-1 community. The sufficient contact and deep interaction of D6 HCDR3 and LCDR3 with RBD may be the crucial reason for its cross-neutralizing activity. The sorting and analysis of mAb D6 will provide important information for the development of anti-COVID-19 reagents.
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Affiliation(s)
- Yuanyuan Hu
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Biosafety III Laboratory, Guangxi Medical University, Nanning 530021, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Caiqin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Shuo Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Li Ren
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanling Hao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zheng Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ying Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Junwei Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Dan Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yiming Shao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Biosafety III Laboratory, Guangxi Medical University, Nanning 530021, China
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6
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Ye F, Li C, Liu FL, Liu X, Xu P, Luo RH, Song W, Zheng YT, Ying T, Yu B, Wang P. Semisynthesis of homogeneous spike RBD glycoforms from SARS-CoV-2 for profiling the correlations between glycan composition and function. Natl Sci Rev 2024; 11:nwae030. [PMID: 38333067 PMCID: PMC10852988 DOI: 10.1093/nsr/nwae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/28/2023] [Accepted: 10/15/2023] [Indexed: 02/10/2024] Open
Abstract
Vaccines have been the primary remedy in the global fight against coronavirus disease 2019 (COVID-19). The receptor-binding domain (RBD) of the spike protein, a critical viral immunogen, is affected by the heterogeneity of its glycan structures and relatively low immunogenicity. Here, we describe a scalable synthetic platform that enables the precise synthesis of homogeneously glycosylated RBD, facilitating the elucidation of carbohydrate structure-function relationships. Five homogeneously glycosylated RBDs bearing biantennary glycans were prepared, three of which were conjugated to T-helper epitope (Tpep) from tetanus toxoid to improve their weak immune response. Relative to natural HEK293-derived RBD, synthetic RBDs with biantennary N-glycan elicited a higher level of neutralising antibodies against SARS-CoV-2 in mice. Furthermore, RBDs containing Tpep elicited significant immune responses in transgenic mice expressing human angiotensin-converting enzyme 2. Our collective data suggest that trimming the N-glycans and Tpep conjugation of RBD could potentially serve as an effective strategy for developing subunit vaccines providing efficient protection.
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Affiliation(s)
- Farong Ye
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng Li
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Engineering Research Center for Synthetic Immunology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Feng-Liang Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xinliang Liu
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wenping Song
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Engineering Research Center for Synthetic Immunology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Engineering Research Center for Synthetic Immunology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Biao Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ping Wang
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Shenzhen Research Institute of Shanghai Jiao Tong University, Shenzhen 518057, China
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7
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Rao X, Zhao R, Tong Z, Guo S, Peng W, Liu K, Li S, Wu L, Tong J, Chai Y, Han P, Wang F, Jia P, Li Z, Zhao X, Li D, Zhang R, Zhang X, Zou W, Li W, Wang Q, Gao GF, Wu Y, Dai L, Gao F. Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2314193120. [PMID: 38109549 PMCID: PMC10756187 DOI: 10.1073/pnas.2314193120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/20/2023] Open
Abstract
Currently, monoclonal antibodies (MAbs) targeting the SARS-CoV-2 receptor binding domain (RBD) of spike (S) protein are classified into seven classes based on their binding epitopes. However, most of these antibodies are seriously impaired by SARS-CoV-2 Omicron and its subvariants, especially the recent BQ.1.1, XBB and its derivatives. Identification of broadly neutralizing MAbs against currently circulating variants is imperative. In this study, we identified a "breathing" cryptic epitope in the S protein, named as RBD-8. Two human MAbs, BIOLS56 and IMCAS74, were isolated recognizing this epitope with broad neutralization abilities against tested sarbecoviruses, including SARS-CoV, pangolin-origin coronaviruses, and all the SARS-CoV-2 variants tested (Omicron BA.4/BA.5, BQ.1.1, and XBB subvariants). Searching through the literature, some more RBD-8 MAbs were defined. More importantly, BIOLS56 rescues the immune-evaded antibody, RBD-5 MAb IMCAS-L4.65, by making a bispecific MAb, to neutralize BQ.1 and BQ.1.1, thereby producing an MAb to cover all the currently circulating Omicron subvariants. Structural analysis reveals that the neutralization effect of RBD-8 antibodies depends on the extent of epitope exposure, which is affected by the angle of antibody binding and the number of up-RBDs induced by angiotensin-converting enzyme 2 binding. This cryptic epitope which recognizes non- receptor binding motif (non-RBM) provides guidance for the development of universal therapeutic antibodies and vaccines against COVID-19.
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Affiliation(s)
- Xia Rao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin300308, China
- Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Runchu Zhao
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
- Institute of Physical Science and Information, Anhui University, Hefei230039, China
| | - Zhou Tong
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
- Shanxi Academy of Advanced Research and Innovation, Taiyuan030032, China
| | - Shuxin Guo
- Faculty of Health Sciences, University of Macau, Macau Special Administrative Region999078, China
| | - Weiyu Peng
- Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen518038, China
| | - Kefang Liu
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Shihua Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Lili Wu
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Jianyu Tong
- Shanxi Academy of Advanced Research and Innovation, Taiyuan030032, China
| | - Yan Chai
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Pu Han
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Feiran Wang
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei230026, China
| | - Peng Jia
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Zhaohui Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Xin Zhao
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Dedong Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Rong Zhang
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
- Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning530004, China
| | - Xue Zhang
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing100069, China
| | - Weiwei Zou
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing100069, China
| | - Weiwei Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Qihui Wang
- University of Chinese Academy of Sciences, Beijing100049, China
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - George Fu Gao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin300308, China
- Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing100101, China
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Yan Wu
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing100069, China
| | - Lianpan Dai
- University of Chinese Academy of Sciences, Beijing100049, China
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Feng Gao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin300308, China
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8
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Hu S, Wu C, Wu X, Ma X, Shu C, Chen Q, Zheng A, Yang H, Lu J, Du P, Gao GF, Wang Q. Classification of five SARS-CoV-2 serotypes based on RBD antigenicities. Sci Bull (Beijing) 2023; 68:3003-3012. [PMID: 37919162 DOI: 10.1016/j.scib.2023.09.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/24/2023] [Accepted: 09/25/2023] [Indexed: 11/04/2023]
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a significant number of variants, particularly with the emergence of Omicron with many sub-variants. These variants have exhibited increased immune escape, leading to reduced efficacy of existing vaccines and therapeutic antibodies. Given the diminished cross-neutralization observed among these variants, it is plausible that SARS-CoV-2 has developed multiple serotypes. As the major antigenic site, the receptor-binding domain (RBD) of viral spike (S) protein was chosen for serotyping. We selected 23 representative variants, including pre-Omicron variants and Omicron sub-variants, and classified them into five serotypes based on systematic evaluation of the antigenicities of their RBDs. Each serotype includes several genetically distinct variants. Serotype-I encompasses all pre-Omicron variants (with two subtypes), while the remaining four serotypes are all comprised of Omicron sub-variants at different stages of evolution. We propose that these serotypes can serve as a foundation for rapid classification of newly emerging SARS-CoV-2 variants, and guide the development of future broad-spectrum vaccines and neutralizing antibodies against the coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Shixiong Hu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunli Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Xinkai Wu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuehui Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Chen
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiting Yang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Lu
- School of Life Sciences, Peking University, Beijing 100871, China.
| | - Pei Du
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qihui Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Yunnan University, Kunming 650091, China; Faculty of Health Sciences, University of Macau, Macau 999078, China.
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9
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Najafi N, Soleimanjahi H, Moghaddam-Banaem L, Raoufy MR, Shahali S, Kazemnejad A, Nasiri Z. Humoral immunogenicity assessment after receiving three types of SARS-CoV-2 vaccine. Sci Rep 2023; 13:20213. [PMID: 37980441 PMCID: PMC10657424 DOI: 10.1038/s41598-023-47611-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/16/2023] [Indexed: 11/20/2023] Open
Abstract
Several vaccines have been developed against SARS-CoV-2 and subsequently approved by national/international regulators. Detecting specific antibodies after vaccination enables us to evaluate the vaccine's effectiveness. We conducted a prospective longitudinal study among members of Tarbiat Modares University of Tehran, Iran, from 4 September 2021 until 29 December 2021. We aimed to compare the humoral immunogenicity of 3 vaccine types. Participants consisted of 462 adults. Anti-SARS-CoV-2 receptor-binding domain [RBD] IgG titer was compared in 3 groups, each vaccinated by available vaccines in Iran at the time: Oxford/AstraZeneca, COVIran Barekat, and Sinopharm. The median IgG titer was: 91.2, 105.6, 224.0 BAU/ml for Sinopharm, COVIran Barekat and Oxford/AstraZeneca respectively after the first dose; 195.2, 192.0, 337.6 BAU/ml after the second one. We also analyzed the frequency of antibody presence in each vaccine group, in the same order the results were 59.0%, 62.6% and 89.4% after the first dose and 92.1%,89.5% and 98.9% after the second. The comparison of results demonstrated that AstraZeneca vaccine is a superior candidate vaccine for COVID-19 vaccination out of the three. Our data also demonstrated statistically significant higher antibody titer among recipients with an infection history.
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Affiliation(s)
- Niloofar Najafi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-331, Tehran, Iran
| | - Hoorieh Soleimanjahi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-331, Tehran, Iran.
| | - Lida Moghaddam-Banaem
- Department of Reproductive Health and Midwifery, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Reza Raoufy
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shadab Shahali
- Department of Reproductive Health and Midwifery, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Anoshirvan Kazemnejad
- Department of Biostatistics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zeynab Nasiri
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-331, Tehran, Iran
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10
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Zhao R, Niu S, Han P, Gao Y, Liu D, Luo C, Liu H, Liu B, Xu Y, Qi J, Chen Z, Shi W, Wu L, Gao GF, Wang Q. Cross-species recognition of bat coronavirus RsYN04 and cross-reaction of SARS-CoV-2 antibodies against the virus. Zool Res 2023; 44:1015-1025. [PMID: 37804113 PMCID: PMC10802104 DOI: 10.24272/j.issn.2095-8137.2023.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023] Open
Abstract
Following the outbreak of coronavirus disease 2019 (COVID-19), several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related coronaviruses have been discovered. Previous research has identified a novel lineage of SARS-CoV-2-related CoVs in bats, including RsYN04, which recognizes human angiotensin-converting enzyme 2 (ACE2) and thus poses a potential threat to humans. Here, we screened the binding of the RsYN04 receptor-binding domain (RBD) to ACE2 orthologs from 52 animal species and found that the virus showed a narrower ACE2-binding spectrum than SARS-CoV-2. However, the presence of the T484W mutation in the RsYN04 RBD broadened its range. We also evaluated 44 SARS-CoV-2 antibodies targeting seven epitope communities in the SARS-CoV-2 RBD, together with serum obtained from COVID-19 convalescents and vaccinees, to determine their cross-reaction against RsYN04. Results showed that no antibodies, except for the RBD-6 and RBD-7 classes, bound to the RsYN04 RBD, indicating substantial immune differences from SARS-CoV-2. Furthermore, the structure of the RsYN04 RBD in complex with cross-reactive antibody S43 in RBD-7 revealed a potently broad epitope for the development of therapeutics and vaccines. Our findings suggest RsYN04 and other viruses belonging to the same clade have the potential to infect several species, including humans, highlighting the necessity for viral surveillance and development of broad anti-coronavirus countermeasures.
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Affiliation(s)
- Runchu Zhao
- Institute of Physical Science and Information, Anhui University, Hefei, Anhui 230039, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng Niu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi 030801, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Dezhi Liu
- Institute of Physical Science and Information, Anhui University, Hefei, Anhui 230039, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunliang Luo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi 030801, China
| | - Honghui Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi 030801, China
| | - Yanli Xu
- Center of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihai Chen
- Center of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China
| | - Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China. E-mail:
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qihui Wang
- Institute of Physical Science and Information, Anhui University, Hefei, Anhui 230039, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China. E-mail:
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11
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Shi H, Sun J, Zeng Y, Wang X, Liu S, Zhang L, Shao E. Immune escape of SARS-CoV-2 variants to therapeutic monoclonal antibodies: a system review and meta-analysis. Virol J 2023; 20:266. [PMID: 37968649 PMCID: PMC10652597 DOI: 10.1186/s12985-023-01977-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/25/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Omicron's high transmissibility and variability present new difficulties for COVID-19 vaccination prevention and therapy. In this article, we analyzed the sensitivity of vaccine-induced antibodies as well as the effect of booster vaccinations against Omicron sublineages. METHODS We looked for Randomized Controlled Trials and cohort studies that reported the COVID-19 vaccines against Omicron sublineages up to 28 July 2022 through PubMed, the Cochrane Library, EMBASE, and Web of Science. Quantitative synthesis was carried out using Stata 16.0 and RevMa5.3, then the serum NT50 and antibody sensitivity to neutralize Omicron sublineages were assessed before and after booster vaccination. This study was registered with PROSPERO number CRD42022350477. RESULTS This meta-analysis included 2138 patients from 20 studies, and the booster vaccination against Omicron sublineages showed a significant difference compared to 2 dosage: BA.1/BA.1.1 (SMD = 0.80, 95% CI: 0.75-0.85, P = 0.00), BA.2/BA.2.12.1 (SMD = 0.77, 95% CI: 0.69-0.85, P = 0.00), BA.3 (SMD = 0.91, 95% CI: 0.83-1.0, P = 0.00), and BA.4/5 (SMD = 0.77, 95% CI: 0.60-0.94, P = 0.00). The sensitivity of vaccines-induced antibodies decreased by at least 5-folds after booster vaccination, particularly in the case of BA.4/5 which had the most notable decline in vaccine effectiveness. CONCLUSION After the booster vaccination, the NT50 and the neutralization ability of vaccine-induced antibodies increased, but the susceptibility of antibodies decreased compared with the control virus, which may be a clue for future Omicron sublineages prevention.
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Affiliation(s)
- Huichun Shi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jiajia Sun
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450099, China
| | - Yigang Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Xiaomeng Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Shanshan Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Enming Shao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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12
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Wu L, Gao Y, Yu D, Liu S, Zhao R, Liu D, Xu L, Liu H, Wang X, Qi J, Chai Y, Wei L, Yao YG, Gao GF, Wang Q. VH-CH1 switch region-inserting multispecific antibody designs and their efficacy against SARS-CoV-2 in vitro and in vivo. Cell Discov 2023; 9:113. [PMID: 37952031 PMCID: PMC10640590 DOI: 10.1038/s41421-023-00616-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Affiliation(s)
- Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yue Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, Hebei University, Baoding, Hebei, China
| | - Dandan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Sheng Liu
- Cryo-EM Center, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Runchu Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dezhi Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Institute of Physical Science and Information, Anhui University, Hefei, Anhui, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Honghui Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyun Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liya Wei
- College of Life Science, Hebei University, Baoding, Hebei, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- College of Life Science, Hebei University, Baoding, Hebei, China.
- Institute of Physical Science and Information, Anhui University, Hefei, Anhui, China.
- University of the Chinese Academy of Sciences, Beijing, China.
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13
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Tulsian NK, Palur RV, Qian X, Gu Y, D/O Shunmuganathan B, Samsudin F, Wong YH, Lin J, Purushotorman K, Kozma MM, Wang B, Lescar J, Wang CI, Gupta RK, Bond PJ, MacAry PA. Defining neutralization and allostery by antibodies against COVID-19 variants. Nat Commun 2023; 14:6967. [PMID: 37907459 PMCID: PMC10618280 DOI: 10.1038/s41467-023-42408-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
The changing landscape of SARS-CoV-2 Spike protein is linked to the emergence of variants, immune-escape and reduced efficacy of the existing repertoire of anti-viral antibodies. The functional activity of neutralizing antibodies is linked to their quaternary changes occurring as a result of antibody-Spike trimer interactions. Here, we reveal the conformational dynamics and allosteric perturbations linked to binding of novel human antibodies and the viral Spike protein. We identified epitope hotspots, and associated changes in Spike dynamics that distinguish weak, moderate and strong neutralizing antibodies. We show the impact of mutations in Wuhan-Hu-1, Delta, and Omicron variants on differences in the antibody-induced conformational changes in Spike and illustrate how these render certain antibodies ineffective. Antibodies with similar binding affinities may induce destabilizing or stabilizing allosteric effects on Spike, with implications for neutralization efficacy. Our results provide mechanistic insights into the functional modes and synergistic behavior of human antibodies against COVID-19 and may assist in designing effective antiviral strategies.
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Affiliation(s)
- Nikhil Kumar Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Department of Biochemistry, National University of Singapore, Singapore, 117546, Singapore.
| | - Raghuvamsi Venkata Palur
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore
| | - Xinlei Qian
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
| | - Yue Gu
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Bhuvaneshwari D/O Shunmuganathan
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Kiren Purushotorman
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Mary McQueen Kozma
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
| | - Bei Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Ravindra Kumar Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Peter John Bond
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore.
| | - Paul Anthony MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore.
- Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore.
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14
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Yang J, Lin S, Chen Z, Yang F, Guo L, Wang L, Duan Y, Zhang X, Dai Y, Yin K, Yu C, Yuan X, Sun H, He B, Cao Y, Ye H, Dong H, Liu X, Chen B, Li J, Zhao Q, Lu G. Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization. PLoS Pathog 2023; 19:e1011804. [PMID: 38033141 PMCID: PMC10688893 DOI: 10.1371/journal.ppat.1011804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023] Open
Abstract
The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility and profound immune-escape capacity makes it an urgent need to develop broad-spectrum therapeutics. Nanobodies have recently attracted extensive attentions due to their excellent biochemical and binding properties. Here, we report two high-affinity nanobodies (Nb-015 and Nb-021) that target non-overlapping epitopes in SARS-CoV-2 S-RBD. Both nanobodies could efficiently neutralize diverse viruses of SARS-CoV-2. The neutralizing mechanisms for the two nanobodies are further delineated by high-resolution nanobody/S-RBD complex structures. In addition, an Fc-based tetravalent nanobody format is constructed by combining Nb-015 and Nb-021. The resultant nanobody conjugate, designated as Nb-X2-Fc, exhibits significantly enhanced breadth and potency against all-tested SARS-CoV-2 variants, including Omicron sub-lineages. These data demonstrate that Nb-X2-Fc could serve as an effective drug candidate for the treatment of SARS-CoV-2 infection, deserving further in-vivo evaluations in the future.
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Affiliation(s)
- Jing Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fanli Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Wang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Duan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xindan Zhang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yushan Dai
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Keqing Yin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chongzhang Yu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xin Yuan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Honglu Sun
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haoyu Ye
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianbo Liu
- CHENGDU NB BIOLAB CO., LTD, Chengdu, Sichuan, China
| | - Bo Chen
- CHENGDU NB BIOLAB CO., LTD, Chengdu, Sichuan, China
| | - Jian Li
- School of Basic Medical Sciences, Chengdu University, Chengdu, Sichuan, China
| | - Qi Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Wu L, Zheng A, Tang Y, Chai Y, Chen J, Cheng L, Hu Y, Qu J, Lei W, Liu WJ, Wu G, Zeng S, Yang H, Wang Q, Gao GF. A pan-coronavirus peptide inhibitor prevents SARS-CoV-2 infection in mice by intranasal delivery. Sci China Life Sci 2023; 66:2201-2213. [PMID: 37574525 DOI: 10.1007/s11427-023-2410-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023]
Abstract
Coronaviruses (CoVs) have brought serious threats to humans, particularly severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), which continually evolves into multiple variants. These variants, especially Omicron, reportedly escape therapeutic antibodies and vaccines, indicating an urgent need for new antivirals with pan-SARS-CoV-2 inhibitory activity. We previously reported that a peptide fusion inhibitor, P3, targeting heptad repeated-1 (HR1) of SARS-CoV-2 spike (S) protein, could inhibit viral infections. Here, we further designed multiple derivatives of the P3 based on structural analysis and found that one derivative, the P315V3, showed the most efficient antiviral activity against SARS-CoV-2 variants and several other sarbecoviruses, as well as other human-CoVs (HCoVs). P315V3 also exhibited effective prophylactic efficacy against the SARS-CoV-2 Delta and Omicron variants in mice via intranasal administration. These results suggest that P315V3, which is in Phase II clinical trial, is promising for further development as a nasal pan-SARS-CoV-2 or pan-CoVs inhibitor to prevent or treat CoV diseases.
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Affiliation(s)
- Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangming Tang
- Hybio Pharmaceutical Co., Ltd., Shenzhen, 518109, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiantao Chen
- Hybio Pharmaceutical Co., Ltd., Shenzhen, 518109, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Yu Hu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Jing Qu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - William Jun Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Shaogui Zeng
- Hybio Pharmaceutical Co., Ltd., Shenzhen, 518109, China
| | - Hang Yang
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Hubei Jiangxia Laboratory, Wuhan, 430299, China.
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
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16
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Vardhan S, Sahoo SK. Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols. Phytochem Anal 2023; 34:800-815. [PMID: 36606391 DOI: 10.1002/pca.3204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The SARS-CoV-2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes caused by mutations, we conducted a comparative analysis of BA.2 with variants BA.1 and BA.3. OBJECTIVE In the present study, we aimed to investigate the interactions of the spike glycoprotein receptor-binding domain (SGp RBD) of Omicron variants BA.1, BA.2, and BA.3 with the human receptor hACE2. Further, a library of 233 polyphenols was screened by molecular docking with the SGp RBDs of Omicron variants BA.1, BA.2, and BA.3. METHODS Protein-protein and protein-ligand molecular docking simulations were performed with AutoDock Vina and the ClusPro 2.0 server, respectively. The protein-ligand interactions were evaluated by BIOVIA Discovery Studio and ChimeraX 1.4. The molecular dynamics simulations for 100 ns were performed using GROMACS 2021. RESULTS Compared to other variants of concern, the structural changes in Omicron caused by mutations at key positions improved its ability to cause infection. Despite multiple mutations, many important polyphenols bind effectively at the RBDs of Omicron variants, with the required pharmacokinetic and ADME features and obeying the Lipinski rule. CONCLUSION Even though Omicron variants have multiple mutations and their transmission rate is relatively high, the computed binding affinities of lead polyphenols like epigallocatechin-3-O-gallate (EGCG) and luteolin-7-O-glucuronide (L7G) indicate that traditional medicines and proper immunity booster diets may be useful in the long-term fight against SARS-CoV-2.
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Affiliation(s)
- Seshu Vardhan
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, Gujarat, India
| | - Suban K Sahoo
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, Gujarat, India
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Pondé RADA. Physicochemical effects of emerging exchanges on the spike protein's RBM of the SARS-CoV-2 Omicron subvariants BA.1-BA.5 and its influence on the biological properties and attributes developed by these subvariants. Virology 2023; 587:109850. [PMID: 37562286 DOI: 10.1016/j.virol.2023.109850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Emerging in South Africa, SARS-CoV-2 Omicron variant was marked by the expression of an exaggerated number of mutations throughout its genome and by the emergence of subvariants, whose attributes developed by them have been associated with amino acid exchanges that occur mainly in the RBM region of the spike protein. The RBM comprises a region within the RBD and is directly involved in the SARS-CoV-2 spike protein interaction with the host cell ACE2 receptor, during the infection mechanism and viral transmission. Defined as the region from aa 437 to aa 508, there are several residues in certain positions that interact directly with the human ACE-2 receptor during these processes. The occurrence of amino acid exchanges in these positions causes physicochemical alterations in the SARS-CoV-2 spike protein, which confer additional advantages and attributes to the agent. In addition, these exchanges serve as a basis for the characterization of new variants and subvariants of SARS-CoV-2. In this review, the amino acid exchanges that have occurred in the RBM of the subvariants BA.1 to BA.5 of SARS-CoV-2 that emerged from the Omicron are described. The physicochemical effects caused by them on spike protein are also described, as well as their influence on the biological properties and attributes developed by the subvariants BA.1, BA.2, BA.3, BA.4 and BA.5.
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Affiliation(s)
- Robério Amorim de Almeida Pondé
- Secretaria de Estado da Saúde -SES/Superintendência de Vigilância em Saúde-SUVISA/GO, Gerência de Vigilância Epidemiológica de Doenças Transmissíveis-GVEDT/Coordenação de Análises e Pesquisas-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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Verkhivker G, Alshahrani M, Gupta G. Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites. Viruses 2023; 15:2009. [PMID: 37896786 PMCID: PMC10610873 DOI: 10.3390/v15102009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants and the identification of cryptic dynamic binding pockets in the S protein is of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study, we explore conformational landscapes and characterize the universe of binding pockets in multiple open and closed functional spike states of the BA.1 and BA.2 Omicron variants. By using a combination of atomistic simulations, a dynamics network analysis, and an allostery-guided network screening of binding pockets in the conformational ensembles of the BA.1 and BA.2 spike conformations, we identified all experimentally known allosteric sites and discovered significant variant-specific differences in the distribution of binding sites in the BA.1 and BA.2 trimers. This study provided a structural characterization of the predicted cryptic pockets and captured the experimentally known allosteric sites, revealing the critical role of conformational plasticity in modulating the distribution and cross-talk between functional binding sites. We found that mutational and dynamic changes in the BA.1 variant can induce the remodeling and stabilization of a known druggable pocket in the N-terminal domain, while this pocket is drastically altered and may no longer be available for ligand binding in the BA.2 variant. Our results predicted the experimentally known allosteric site in the receptor-binding domain that remains stable and ranks as the most favorable site in the conformational ensembles of the BA.2 variant but could become fragmented and less probable in BA.1 conformations. We also uncovered several cryptic pockets formed at the inter-domain and inter-protomer interface, including functional regions of the S2 subunit and stem helix region, which are consistent with the known role of pocket residues in modulating conformational transitions and antibody recognition. The results of this study are particularly significant for understanding the dynamic and network features of the universe of available binding pockets in spike proteins, as well as the effects of the Omicron-variant-specific modulation of preferential druggable pockets. The exploration of predicted druggable sites can present a new and previously underappreciated opportunity for therapeutic interventions for Omicron variants through the conformation-selective and variant-specific targeting of functional sites involved in allosteric changes.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
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Zhang Y, Kang X, Liu S, Han P, Lei W, Xu K, Xu Z, Gao Z, Zhou X, An Y, Han Y, Liu K, Zhao X, Dai L, Wang P, Wu G, Qi J, Xu K, Gao GF. Broad protective RBD heterotrimer vaccines neutralize SARS-CoV-2 including Omicron sub-variants XBB/BQ.1.1/BF.7. PLoS Pathog 2023; 19:e1011659. [PMID: 37721934 PMCID: PMC10538664 DOI: 10.1371/journal.ppat.1011659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/28/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023] Open
Abstract
SARS-CoV-2 variants with severe immune evasion are a major challenge for COVID-19 prevention, especially the circulating Omicron XBB/BQ.1.1/BF.7 strains. Thus, the next-generation of broad-spectrum vaccines are urgently needed. Previously, we developed a COVID-19 protein subunit vaccine, ZF2001, based on the RBD-homodimer as the immunogen. To adapt SARS-CoV-2 variants, we developed chimeric RBD-heterodimers to induce broad immune responses. In this study, we further explored the concept of tandem RBD homotrimer and heterotrimer. Prototype SARS-CoV-2 RBD-homotrimer, prototype-Delta-BA.1 (PDO) RBD-heterotrimer and Delta-BA.2-BA.5 (DBA2BA5) RBD-heterotrimer were designed. Biochemical and cryo-EM structural characterization demonstrated total epitope exposure of the RBD-trimers. In mouse experiments, PDO and DBA2BA5 elicited broad SARS-CoV-2 neutralization. Potent protection against SARS-CoV-2 variants was observed in challenge assays and was correlated with neutralizing antibody titer. This study validated the design strategy of tandem RBD-heterotrimers as multivalent immunogens and presented a promising vaccine candidate, DBA2BA5, eliciting broad-spectrum immune responses, including against the circulating XBB/BF.7/BQ.1.1.
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Affiliation(s)
- Yanfang Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinrui Kang
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Sheng Liu
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ke Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Zhengrong Gao
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Children’s Hospital, Shenzhen, China
| | - Xuemei Zhou
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Hebei University, Baoding, China
| | - Yaling An
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxuan Han
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Peiyi Wang
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen, China
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kun Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
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20
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Wen K, Cai JP, Fan X, Zhang X, Luo C, Tang KM, Shuai H, Chen LL, Zhang RR, Situ J, Tsoi HW, Wang K, Chan JFW, Yuan S, Yuen KY, Zhou H, To KKW. Broad-spectrum humanized monoclonal neutralizing antibody against SARS-CoV-2 variants, including the Omicron variant. Front Cell Infect Microbiol 2023; 13:1213806. [PMID: 37645378 PMCID: PMC10461085 DOI: 10.3389/fcimb.2023.1213806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/20/2023] [Indexed: 08/31/2023] Open
Abstract
Introduction Therapeutic monoclonal antibodies (mAbs) against the SARS-CoV-2 spike protein have been shown to improve the outcome of severe COVID-19 patients in clinical trials. However, novel variants with spike protein mutations can render many currently available mAbs ineffective. Methods We produced mAbs by using hybridoma cells that generated from mice immunized with spike protein trimer and receptor binding domain (RBD). The panel of mAbs were screened for binding and neutralizing activity against different SARS-CoV-2 variants. The in vivo effectiveness of WKS13 was evaluated in a hamster model. Results Out of 960 clones, we identified 18 mAbs that could bind spike protein. Ten of the mAbs could attach to RBD, among which five had neutralizing activity against the ancestral strain and could block the binding between the spike protein and human ACE2. One of these mAbs, WKS13, had broad neutralizing activity against all Variants of Concern (VOCs), including the Omicron variant. Both murine or humanized versions of WKS13 could reduce the lung viral load in hamsters infected with the Delta variant. Conclusions Our data showed that broad-spectrum high potency mAbs can be produced from immunized mice, which can be used in humans after humanization of the Fc region. Our method represents a versatile and rapid strategy for generating therapeutic mAbs for upcoming novel variants.
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Affiliation(s)
- Kun Wen
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian-Piao Cai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Xiaodi Fan
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Xiaojuan Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Cuiting Luo
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Kai-Ming Tang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Huiping Shuai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Lin-Lei Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ricky Ruiqi Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jianwen Situ
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hoi-Wah Tsoi
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Kun Wang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Center for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Shuofeng Yuan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Center for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Center for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Center for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Center for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
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21
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Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has led to hundreds of millions of infections and millions of deaths, however, human monoclonal antibodies (mAbs) can be an effective treatment. Since SARS-CoV-2 emerged, a variety of strains have acquired increasing numbers of mutations to gain increased transmissibility and escape from the immune response. Most reported neutralizing human mAbs, including all approved therapeutic ones, have been knocked down or out by these mutations. Broadly neutralizing mAbs are therefore of great value, to treat current and possible future variants. Here, we review four types of neutralizing mAbs against the spike protein with broad potency against previously and currently circulating variants. These mAbs target the receptor-binding domain, the subdomain 1, the stem helix, or the fusion peptide. Understanding how these mAbs retain potency in the face of mutational change could guide future development of therapeutic antibodies and vaccines.
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Affiliation(s)
- Daming Zhou
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7FZ, UK.
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7FZ, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK; Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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22
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Guo S, Zheng Y, Gao Z, Duan M, Liu S, Du P, Xu X, Xu K, Zhao X, Chai Y, Wang P, Zhao Q, Gao GF, Dai L. Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine. Cell Discov 2023; 9:79. [PMID: 37507370 PMCID: PMC10382582 DOI: 10.1038/s41421-023-00585-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Vaccination with different vaccines has been implemented globally to counter the continuous COVID-19 pandemic. However, the vaccine-elicited antibodies have reduced efficiency against the highly mutated Omicron sub-variants. Previously, we developed a protein subunit COVID-19 vaccine called ZF2001, based on the dimeric receptor-binding domain (RBD). This vaccine has been administered using different dosing intervals in real-world setting. Some individuals received three doses of ZF2001, with a one-month interval between each dose, due to urgent clinical requirements. Others had an extended dosing interval of up to five months between the second and third dose, a standard vaccination regimen for the protein subunit vaccine against hepatitis B. In this study, we profile B cell responses in individuals who received three doses of ZF2001, and compared those with long or short dosing intervals. We observed that the long-interval group exhibited higher and broader serologic antibody responses. These responses were associated with the increased size and evolution of vaccine-elicited B-cell receptor repertoires, characterized by the elevation of expanded clonotypes and somatic hypermutations. Both groups of individuals generated substantial amounts of broadly neutralizing antibodies (bnAbs) against various SARS-CoV-2 variants, including Omicron sub-variants such as XBB. These bnAbs target four antigenic sites within the RBD. To determine the vulnerable site of SARS-CoV-2, we employed cryo-electron microscopy to identify the epitopes of highly potent bnAbs that targeted two major sites. Our findings provide immunological insights into the B cell responses elicited by RBD-based vaccine, and suggest that a vaccination regimen of prolonging time interval should be used in practice.
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Affiliation(s)
- Shuxin Guo
- Faculty of Health Sciences, University of Macau, Macau SAR, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxuan Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhengrong Gao
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
- Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Minrun Duan
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Sheng Liu
- Department of Biology, Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Pan Du
- Vazyme Biotech, Nanjing, Jiangsu, China
| | - XiaoYu Xu
- Vazyme Biotech, Nanjing, Jiangsu, China
| | - Kun Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Peiyi Wang
- Department of Biology, Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Qi Zhao
- MoE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - George F Gao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Lianpan Dai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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23
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Govindaraj S, Cheedarla N, Cheedarla S, Irby LS, Neish AS, Roback JD, Smith AK, Velu V. COVID-19 vaccine induced poor neutralization titers for SARS-CoV-2 omicron variants in maternal and cord blood. Front Immunol 2023; 14:1211558. [PMID: 37465682 PMCID: PMC10350671 DOI: 10.3389/fimmu.2023.1211558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction Maternally derived antibodies are crucial for neonatal immunity. Understanding the binding and cross-neutralization capacity of maternal and cord antibody responses to SARS-CoV-2 variants following COVID-19 vaccination in pregnancy can inform neonatal immunity. Methods Here we characterized the binding and neutralizing antibody profile at delivery in 24 pregnant individuals following two doses of Moderna mRNA-1273 or Pfizer BNT162b2 vaccination. We analyzed for SARS-CoV-2 multivariant cross-neutralizing antibody levels for wildtype Wuhan, Delta, Omicron BA1, BA2, and BA4/BA5 variants. In addition, we evaluated the transplacental antibody transfer by profiling maternal and umbilical cord blood. Results Our results reveal that the current COVID-19 vaccination induced significantly higher RBD-specific binding IgG titers in cord blood compared to maternal blood for both the Wuhan and Omicron BA1 strain. Interestingly, the binding IgG antibody levels for the Omicron BA1 strain were significantly lower when compared to the Wuhan strain in both maternal and cord blood. In contrast to the binding, the Omicron BA1, BA2, and BA4/5 specific neutralizing antibody levels were significantly lower compared to the Wuhan and Delta variants. It is interesting to note that the BA4/5 neutralizing capacity was not detected in either maternal or cord blood. Discussion Our data suggest that the initial series of COVID-19 mRNA vaccines were immunogenic in pregnant women, and vaccine-elicited binding antibodies were detectable in cord blood at significantly higher levels for the Wuhan and Delta variants but not for the Omicron variants. Interestingly, the vaccination did not induce neutralizing antibodies for Omicron variants. These results provide novel insight into the impact of vaccination on maternal humoral immune response and transplacental antibody transfer for SARS-CoV-2 variants and support the need for bivalent boosters as new variants emerge.
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Affiliation(s)
- Sakthivel Govindaraj
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - LesShon S. Irby
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Alicia K. Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Vijayakumar Velu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory University, Atlanta, GA, United States
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24
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Ju B, Fan Q, Liu C, Shen S, Wang M, Guo H, Zhou B, Ge X, Zhang Z. Omicron BQ.1.1 and XBB.1 unprecedentedly escape broadly neutralizing antibodies elicited by prototype vaccination. Cell Rep 2023; 42:112532. [PMID: 37219999 PMCID: PMC10201307 DOI: 10.1016/j.celrep.2023.112532] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/02/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants have seriously attacked the antibody barrier established by natural infection and/or vaccination, especially the recently emerged BQ.1.1 and XBB.1. However, crucial mechanisms underlying the virus escape and the broad neutralization remain elusive. Here, we present a panoramic analysis of broadly neutralizing activity and binding epitopes of 75 monoclonal antibodies isolated from prototype inactivated vaccinees. Nearly all neutralizing antibodies (nAbs) partly or totally lose their neutralization against BQ.1.1 and XBB.1. We report a broad nAb, VacBB-551, that effectively neutralizes all tested subvariants including BA.2.75, BQ.1.1, and XBB.1. We determine the cryoelectron microscopy (cryo-EM) structure of VacBB-551 complexed with the BA.2 spike and perform detailed functional verification to reveal the molecular basis of N460K and F486V/S mutations mediating the partial escape of BA.2.75, BQ.1.1, and XBB.1 from the neutralization of VacBB-551. Overall, BQ.1.1 and XBB.1 raised the alarm over SARS-CoV-2 evolution with unprecedented antibody evasion from broad nAbs elicited by prototype vaccination.
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Affiliation(s)
- Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China; Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen 518112, Guangdong Province, China; Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong Province, China.
| | - Qing Fan
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Congcong Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Senlin Shen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Miao Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Huimin Guo
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Bing Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China; Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong Province, China
| | - Xiangyang Ge
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China; Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen 518112, Guangdong Province, China; Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong Province, China; Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen 518112, Guangdong Province, China.
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25
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Guo Y, Zhang G, Yang Q, Xie X, Lu Y, Cheng X, Wang H, Liang J, Tang J, Gao Y, Shang H, Dai J, Shi Y, Zhou J, Zhou J, Guo H, Yang H, Qi J, Liu L, Ma S, Zhang B, Huo Q, Xie Y, Wu J, Dong F, Zhang S, Lou Z, Gao Y, Song Z, Wang W, Sun Z, Yang X, Xiong D, Liu F, Chen X, Zhu P, Wang X, Cheng T, Rao Z. Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun 2023; 14:3537. [PMID: 37322000 PMCID: PMC10267556 DOI: 10.1038/s41467-023-39267-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/30/2023] [Indexed: 06/17/2023] Open
Abstract
The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT50 values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection.
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Grants
- National Natural Science Foundation of China (National Science Foundation of China)
- Chinese Academy of Medical Sciences (CAMS)
- This work was supported by the National Program on Key Research Project of China (2018YFE0200400, 2021YFE0201900, 2021YFA1100900 and 2018YFA0507200),The Key Program of Natural Science Foundation of Tianjin (20JCYBJC01340), Haihe Laboratory of Cell Ecosystem Innovation Fund (22HHXBSS00001),Science and Technology Project of Tianjin (22ZYJDSS00080),the Non-CAMS Fundamental Research Funds for Central Research Institutes (3332021093), Application for Basic and Applied Basic Research Projects of Guangzhou Basic Research Program (SL2023A04J00076), Emergency Key Program of Guangzhou Laboratory (EKPGL2021008), R&D Program of Guangzhou Laboratory (SRPG22-003, SRPG22-002).
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Affiliation(s)
- Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China.
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
- Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China.
| | - Guangshun Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Qi Yang
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
| | - Xiaowei Xie
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yang Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xuelian Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Hui Wang
- Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Jielin Tang
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
| | - Yuxin Gao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Hang Shang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jun Dai
- Guangzhou Customs District Technology Center, Guangzhou, 510700, China
| | - Yongxia Shi
- Guangzhou Customs District Technology Center, Guangzhou, 510700, China
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jun Zhou
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Hangtian Guo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Jianwei Qi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Lijun Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Shihui Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Biao Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Qianyu Huo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yi Xie
- Tianjin Haihe Hospital, Jingu Road, Tianjin, 300071, China
| | - Junping Wu
- Tianjin Haihe Hospital, Jingu Road, Tianjin, 300071, China
| | - Fang Dong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Song Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Zhiyong Lou
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Zidan Song
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Wenming Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Zixian Sun
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
| | - Xiaoming Yang
- Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China.
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
| | - Dongsheng Xiong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Fengjiang Liu
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
| | - Xinwen Chen
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Ximo Wang
- Tianjin Haihe Hospital, Jingu Road, Tianjin, 300071, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China.
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China.
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26
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Ren Z, Shen C, Peng J. Status and Developing Strategies for Neutralizing Monoclonal Antibody Therapy in the Omicron Era of COVID-19. Viruses 2023; 15:1297. [PMID: 37376597 DOI: 10.3390/v15061297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The monoclonal antibody (mAb)-based treatment is a highly valued therapy against COVID-19, especially for individuals who may not have strong immune responses to the vaccine. However, with the arrival of the Omicron variant and its evolving subvariants, along with the occurrence of remarkable resistance of these SARS-CoV-2 variants to the neutralizing antibodies, mAbs are facing tough challenges. Future strategies for developing mAbs with improved resistance to viral evasion will involve optimizing the targeting epitopes on SARS-CoV-2, enhancing the affinity and potency of mAbs, exploring the use of non-neutralizing antibodies that bind to conserved epitopes on the S protein, as well as optimizing immunization regimens. These approaches can improve the viability of mAb therapy in the fight against the evolving threat of the coronavirus.
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Affiliation(s)
- Zuning Ren
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jie Peng
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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27
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Yi Y, Li W, Liu K, Xue H, Yu R, Zhang M, Bao YO, Lai X, Fan J, Huang Y, Wang J, Shi X, Li J, Wei H, Xiang K, Li L, Zhang R, Zhao X, Qiao X, Yang H, Ye M. Licorice-saponin A3 is a broad-spectrum inhibitor for COVID-19 by targeting viral spike and anti-inflammation. J Pharm Anal 2023:S2095-1779(23)00099-0. [PMID: 37363744 PMCID: PMC10201890 DOI: 10.1016/j.jpha.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
Currently, human health due to corona virus disease 2019 (COVID-19) pandemic has been seriously threatened. The coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein plays a crucial role in virus transmission and several S-based therapeutic approaches have been approved for the treatment of COVID-19. However, the efficacy is compromised by the SARS-CoV-2 evolvement and mutation. Here we report the SARS-CoV-2 S protein receptor-binding domain (RBD) inhibitor licorice-saponin A3 (A3) could widely inhibit RBD of SARS-CoV-2 variants, including Beta, Delta, and Omicron BA.1, XBB and BQ1.1. Furthermore, A3 could potently inhibit SARS-CoV-2 Omicron virus in Vero E6 cells, with EC50 of 1.016 μM. The mechanism was related with binding with Y453 of RBD determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis combined with quantum mechanics/molecular mechanics (QM/MM) simulations. Interestingly, phosphoproteomics analysis and multi fluorescent immunohistochemistry (mIHC) respectively indicated that A3 also inhibits host inflammation by directly modulating the JNK and p38 MAPK pathways and rebalancing the corresponding immune dysregulation. This work supports A3 as a promising broad-spectrum small molecule drug candidate for COVID-19.
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Affiliation(s)
- Yang Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Wenzhe Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shenzhen Children's Hospital, 7019 Yitian Road, Shenzhen 518036, China
| | - Heng Xue
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yang-Oujie Bao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Xinyuan Lai
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Jingjing Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yuxi Huang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Xiaomeng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Junhua Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuanhui Xiang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Hubei Jiangxia Laboratory, Wuhan 430000, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
- Yunnan Baiyao International Medical Research Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
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Guo L, Lin S, Chen Z, Cao Y, He B, Lu G. Targetable elements in SARS-CoV-2 S2 subunit for the design of pan-coronavirus fusion inhibitors and vaccines. Signal Transduct Target Ther 2023; 8:197. [PMID: 37164987 PMCID: PMC10170451 DOI: 10.1038/s41392-023-01472-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/04/2023] [Accepted: 04/23/2023] [Indexed: 05/12/2023] Open
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused devastating impacts on the public health and the global economy. Rapid viral antigenic evolution has led to the continual generation of new variants. Of special note is the recently expanding Omicron subvariants that are capable of immune evasion from most of the existing neutralizing antibodies (nAbs). This has posed new challenges for the prevention and treatment of COVID-19. Therefore, exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In sharp contrast to the massive accumulation of mutations within the SARS-CoV-2 receptor-binding domain (RBD), the S2 fusion subunit has remained highly conserved among variants. Hence, S2-based therapeutics may provide effective cross-protection against new SARS-CoV-2 variants. Here, we summarize the most recently developed broad-spectrum fusion inhibitors (e.g., nAbs, peptides, proteins, and small-molecule compounds) and candidate vaccines targeting the conserved elements in SARS-CoV-2 S2 subunit. The main focus includes all the targetable S2 elements, namely, the fusion peptide, stem helix, and heptad repeats 1 and 2 (HR1-HR2) bundle. Moreover, we provide a detailed summary of the characteristics and action-mechanisms for each class of cross-reactive fusion inhibitors, which should guide and promote future design of S2-based inhibitors and vaccines against new coronaviruses.
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Affiliation(s)
- Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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29
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Chi X, Xia L, Zhang G, Chi X, Huang B, Zhang Y, Chen Z, Han J, Wu L, Li Z, Sun H, Huang P, Yu C, Chen W, Zhou Q. Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants. Cell Discov 2023; 9:37. [PMID: 37015915 PMCID: PMC10071473 DOI: 10.1038/s41421-023-00535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/02/2023] [Indexed: 04/06/2023] Open
Abstract
The pandemic of COVID-19 caused by SARS-CoV-2 continues to spread around the world. Mutant strains of SARS-CoV-2 are constantly emerging. At present, Omicron variants have become mainstream. In this work, we carried out a systematic and comprehensive analysis of the reported spike protein antibodies, counting the epitopes and genotypes of these antibodies. We further comprehensively analyzed the impact of Omicron mutations on antibody epitopes and classified these antibodies according to their binding patterns. We found that the epitopes of the H-RBD class antibodies were significantly less affected by Omicron mutations than other classes. Binding and virus neutralization experiments showed that such antibodies could effectively inhibit the immune escape of Omicron. Cryo-EM results showed that this class of antibodies utilized a conserved mechanism to neutralize SARS-CoV-2. Our results greatly help us deeply understand the impact of Omicron mutations. Meanwhile, it also provides guidance and insights for developing Omicron antibodies and vaccines.
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Affiliation(s)
- Xiangyang Chi
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Lingyun Xia
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Guanying Zhang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Ximin Chi
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Bangdong Huang
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Yuanyuan Zhang
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Zhengshan Chen
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Jin Han
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Liushu Wu
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Zeya Li
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Hancong Sun
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Ping Huang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Changming Yu
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China.
| | - Wei Chen
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China.
| | - Qiang Zhou
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
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30
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Gupta A, Konnova A, Smet M, Berkell M, Savoldi A, Morra M, Van Averbeke V, De Winter FH, Peserico D, Danese E, Hotterbeekx A, Righi E, De Nardo P, Tacconelli E, Malhotra-Kumar S, Kumar-Singh S. Host immunological responses facilitate development of SARS-CoV-2 mutations in patients receiving monoclonal antibody treatments. J Clin Invest 2023; 133:166032. [PMID: 36727404 PMCID: PMC10014108 DOI: 10.1172/jci166032] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/05/2023] [Indexed: 02/03/2023] Open
Abstract
BackgroundThe role of host immunity in emergence of evasive SARS-CoV-2 Spike mutations under therapeutic monoclonal antibody (mAb) pressure remains to be explored.MethodsIn a prospective, observational, monocentric ORCHESTRA cohort study, conducted between March 2021 and November 2022, mild-to-moderately ill COVID-19 patients (n = 204) receiving bamlanivimab, bamlanivimab/etesevimab, casirivimab/imdevimab, or sotrovimab were longitudinally studied over 28 days for viral loads, de novo Spike mutations, mAb kinetics, seroneutralization against infecting variants of concern, and T cell immunity. Additionally, a machine learning-based circulating immune-related biomarker (CIB) profile predictive of evasive Spike mutations was constructed and confirmed in an independent data set (n = 19) that included patients receiving sotrovimab or tixagevimab/cilgavimab.ResultsPatients treated with various mAbs developed evasive Spike mutations with remarkable speed and high specificity to the targeted mAb-binding sites. Immunocompromised patients receiving mAb therapy not only continued to display significantly higher viral loads, but also showed higher likelihood of developing de novo Spike mutations. Development of escape mutants also strongly correlated with neutralizing capacity of the therapeutic mAbs and T cell immunity, suggesting immune pressure as an important driver of escape mutations. Lastly, we showed that an antiinflammatory and healing-promoting host milieu facilitates Spike mutations, where 4 CIBs identified patients at high risk of developing escape mutations against therapeutic mAbs with high accuracy.ConclusionsOur data demonstrate that host-driven immune and nonimmune responses are essential for development of mutant SARS-CoV-2. These data also support point-of-care decision making in reducing the risk of mAb treatment failure and improving mitigation strategies for possible dissemination of escape SARS-CoV-2 mutants.FundingThe ORCHESTRA project/European Union's Horizon 2020 research and innovation program.
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Affiliation(s)
- Akshita Gupta
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Angelina Konnova
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mathias Smet
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Matilda Berkell
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Alessia Savoldi
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Matteo Morra
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Vincent Van Averbeke
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Fien Hr De Winter
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Denise Peserico
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - An Hotterbeekx
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Elda Righi
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | | | - Pasquale De Nardo
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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31
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Liu H, Wu L, Liu B, Xu K, Lei W, Deng J, Rong X, Du P, Wang L, Wang D, Zhang X, Su C, Bi Y, Chen H, Liu WJ, Qi J, Cui Q, Qi S, Fan R, Jiang J, Wu G, Gao GF, Wang Q. Two pan-SARS-CoV-2 nanobodies and their multivalent derivatives effectively prevent Omicron infections in mice. Cell Rep Med 2023; 4:100918. [PMID: 36702124 PMCID: PMC9834170 DOI: 10.1016/j.xcrm.2023.100918] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 12/11/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023]
Abstract
With the widespread vaccinations against coronavirus disease 2019 (COVID-19), we are witnessing gradually waning neutralizing antibodies and increasing cases of breakthrough infections, necessitating the development of drugs aside from vaccines, particularly ones that can be administered outside of hospitals. Here, we present two cross-reactive nanobodies (R14 and S43) and their multivalent derivatives, including decameric ones (fused to the immunoglobulin M [IgM] Fc) that maintain potent neutralizing activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after aerosolization and display not only pan-SARS-CoV-2 but also varied pan-sarbecovirus activities. Through respiratory administration to mice, monovalent and decameric R14 significantly reduce the lung viral RNAs at low dose and display potent pre- and post-exposure protection. Furthermore, structural studies reveal the neutralizing mechanisms of R14 and S43 and the multiple inhibition effects that the multivalent derivatives exert. Our work demonstrates promising convenient drug candidates via respiratory administration against SARS-CoV-2 infection, which can contribute to containing the COVID-19 pandemic.
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Affiliation(s)
- Honghui Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Bo Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, China
| | - Ke Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jianguo Deng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xiaoyu Rong
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Pei Du
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Lebing Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Dongbin Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xiaolong Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Centre for Bioinformation, Beijing, China
| | - Chao Su
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Hua Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Centre for Bioinformation, Beijing, China
| | - William J Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qingwei Cui
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, Shanxi Province, China
| | - Shuhui Qi
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, China
| | - Ruiwen Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, China.
| | - Jingkun Jiang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Research Units of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, China.
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
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32
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Hu Y, Liu K, Han P, Xu Z, Zheng A, Pan X, Jia Y, Su C, Tang L, Wu L, Bai B, Zhao X, Tian D, Chen Z, Qi J, Wang Q, Gao GF. Host range and structural analysis of bat-origin RshSTT182/200 coronavirus binding to human ACE2 and its animal orthologs. EMBO J 2023; 42:e111737. [PMID: 36519268 PMCID: PMC9877840 DOI: 10.15252/embj.2022111737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
Bat-origin RshSTT182 and RshSTT200 coronaviruses (CoV) from Rhinolophus shameli in Southeast Asia (Cambodia) share 92.6% whole-genome identity with SARS-CoV-2 and show identical receptor-binding domains (RBDs). In this study, we determined the structure of the RshSTT182/200 receptor binding domain (RBD) in complex with human angiotensin-converting enzyme 2 (hACE2) and identified the key residues that influence receptor binding. The binding of the RshSTT182/200 RBD to ACE2 orthologs from 39 animal species, including 18 bat species, was used to evaluate its host range. The RshSTT182/200 RBD broadly recognized 21 of 39 ACE2 orthologs, although its binding affinities for the orthologs were weaker than those of the RBD of SARS-CoV-2. Furthermore, RshSTT182 pseudovirus could utilize human, fox, and Rhinolophus affinis ACE2 receptors for cell entry. Moreover, we found that SARS-CoV-2 induces cross-neutralizing antibodies against RshSTT182 pseudovirus. Taken together, these findings indicate that RshSTT182/200 can potentially infect susceptible animals, but requires further evolution to obtain strong interspecies transmission abilities like SARS-CoV-2.
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Affiliation(s)
- Yu Hu
- School of Life Sciences, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Zepeng Xu
- Faculty of Health SciencesUniversity of MacauMacau SARChina
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoqian Pan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yunfei Jia
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
| | - Chao Su
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Department of Biomedical SciencesCity University of Hong KongHong Kong SARChina
| | - Lingfeng Tang
- Faculty of Health SciencesUniversity of MacauMacau SARChina
| | - Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Di Tian
- Center of Infectious Disease, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Zhihai Chen
- Center of Infectious Disease, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - George F Gao
- School of Life Sciences, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Witte L, Baharani VA, Schmidt F, Wang Z, Cho A, Raspe R, Guzman-Cardozo C, Muecksch F, Canis M, Park DJ, Gaebler C, Caskey M, Nussenzweig MC, Hatziioannou T, Bieniasz PD. Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape. Nat Commun 2023; 14:302. [PMID: 36653360 PMCID: PMC9849103 DOI: 10.1038/s41467-023-35927-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
Waves of SARS-CoV-2 infection have resulted from the emergence of viral variants with neutralizing antibody resistance mutations. Simultaneously, repeated antigen exposure has generated affinity matured B cells, producing broadly neutralizing receptor binding domain (RBD)-specific antibodies with activity against emergent variants. To determine how SARS-CoV-2 might escape these antibodies, we subjected chimeric viruses encoding spike proteins from ancestral, BA.1 or BA.2 variants to selection by 40 broadly neutralizing antibodies. We identify numerous examples of epistasis, whereby in vitro selected and naturally occurring substitutions in RBD epitopes that do not confer antibody resistance in the Wuhan-Hu-1 spike, do so in BA.1 or BA.2 spikes. As few as 2 or 3 of these substitutions in the BA.5 spike, confer resistance to nearly all of the 40 broadly neutralizing antibodies, and substantial resistance to plasma from most individuals. Thus, epistasis facilitates the acquisition of resistance to antibodies that remained effective against early omicron variants.
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Affiliation(s)
- Leander Witte
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Viren A Baharani
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Raphael Raspe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | | | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Marie Canis
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Debby J Park
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, 10065, USA.
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, 10065, USA.
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Okada Y, Kayano T, Anzai A, Zhang T, Nishiura H. Protection against SARS-CoV-2 BA.4 and BA.5 subvariants via vaccination and natural infection: A modeling study. Math Biosci Eng 2023; 20:2530-2543. [PMID: 36899545 DOI: 10.3934/mbe.2023118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
With continuing emergence of new SARS-CoV-2 variants, understanding the proportion of the population protected against infection is crucial for public health risk assessment and decision-making and so that the general public can take preventive measures. We aimed to estimate the protection against symptomatic illness caused by SARS-CoV-2 Omicron variants BA.4 and BA.5 elicited by vaccination against and natural infection with other SARS-CoV-2 Omicron subvariants. We used a logistic model to define the protection rate against symptomatic infection caused by BA.1 and BA.2 as a function of neutralizing antibody titer values. Applying the quantified relationships to BA.4 and BA.5 using two different methods, the estimated protection rate against BA.4 and BA.5 was 11.3% (95% confidence interval [CI]: 0.01-25.4) (method 1) and 12.9% (95% CI: 8.8-18.0) (method 2) at 6 months after a second dose of BNT162b2 vaccine, 44.3% (95% CI: 20.0-59.3) (method 1) and 47.3% (95% CI: 34.1-60.6) (method 2) at 2 weeks after a third BNT162b2 dose, and 52.3% (95% CI: 25.1-69.2) (method 1) and 54.9% (95% CI: 37.6-71.4) (method 2) during the convalescent phase after infection with BA.1 and BA.2, respectively. Our study indicates that the protection rate against BA.4 and BA.5 are significantly lower compared with those against previous variants and may lead to substantial morbidity, and overall estimates were consistent with empirical reports. Our simple yet practical models enable prompt assessment of public health impacts posed by new SARS-CoV-2 variants using small sample-size neutralization titer data to support public health decisions in urgent situations.
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Affiliation(s)
- Yuta Okada
- Kyoto University School of Public Health, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8601, Japan
| | - Taishi Kayano
- Kyoto University School of Public Health, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8601, Japan
| | - Asami Anzai
- Kyoto University School of Public Health, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8601, Japan
| | - Tong Zhang
- Kyoto University School of Public Health, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8601, Japan
| | - Hiroshi Nishiura
- Kyoto University School of Public Health, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8601, Japan
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35
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Jia Y, Niu S, Hu Y, Chai Y, Zheng A, Su C, Wu L, Han P, Han P, Lu D, Liu Z, Yan X, Tian D, Chen Z, Qi J, Tian WX, Wang Q, Gao GF. Cross-reaction of current available SARS-CoV-2 MAbs against the pangolin-origin coronavirus GX/P2V/2017. Cell Rep 2022; 41:111831. [PMID: 36493785 DOI: 10.1016/j.celrep.2022.111831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/27/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, multiple SARS-CoV-2-related viruses have been characterized, including pangolin-origin GD/1/2019 and GX/P2V/2017. Our previous study indicated that both viruses have the potential to infect humans. Here, we find that CB6 (commercial name etesevimab), a COVID-19 therapeutic monoclonal antibody (MAb) developed by our group, efficiently inhibits GD/1/2019 but not GX/P2V/2017. A total of 50 SARS-CoV-2 MAbs divided into seven groups based on their receptor-binding domain (RBD) epitopes, together with the COVID-19 convalescent sera, are systematically screened for their cross-binding and cross-neutralizing properties against GX/P2V/2017. We find that GX/P2V/2017 displays substantial immune difference from SARS-CoV-2. Furthermore, we solve two complex structures of the GX/P2V/2017 RBD with MAbs belonging to RBD-1 and RBD-5, providing a structural basis for their different antigenicity. These results highlight the necessity for broad anti-coronavirus countermeasures and shed light on potential therapeutic targets.
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36
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Xie L, Li J, Ai Y, He H, Chen X, Yin M, Li W, Huang W, Luo MY, He J. Current strategies for SARS-CoV-2 molecular detection. Anal Methods 2022; 14:4625-4642. [PMID: 36349688 DOI: 10.1039/d2ay01313d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.
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Affiliation(s)
- Lei Xie
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Junlin Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Ying Ai
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510080, China
| | - Haolan He
- Guangzhou Eighth People's Hospital, Guangzhou 510080, China
| | - Xiuyun Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Mingyu Yin
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wanxi Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wenguan Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Min-Yi Luo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Jinyang He
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
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37
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Han Y, An Y, Chen Q, Xu K, Liu X, Xu S, Duan H, Vogel AB, Şahin U, Wang Q, Dai L, Gao GF. mRNA vaccines expressing homo-prototype/Omicron and hetero-chimeric RBD-dimers against SARS-CoV-2. Cell Res 2022; 32:1022-1025. [PMID: 36104506 PMCID: PMC9472730 DOI: 10.1038/s41422-022-00720-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/24/2022] [Indexed: 01/31/2023] Open
Affiliation(s)
- Yuxuan Han
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yaling An
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qian Chen
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kun Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine and Laboratory Medicine, The First Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China
| | - Xueyuan Liu
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Senyu Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Huixin Duan
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Qihui Wang
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Lianpan Dai
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine and Laboratory Medicine, The First Affiliated Hospital, Hainan Medical University, Haikou, Hainan, China.
| | - George F Gao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
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38
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Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. SARS-CoV-2 carries a unique group of mutations, and the transmission of the virus has led to the emergence of other mutants such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.617.1), Delta (B.1.617.2) and Omicron (B.1.1.529). The advent of a vaccine has raised hopes of ending the pandemic. However, the mutation variants of SARS-CoV-2 have raised concerns about the effectiveness of vaccines because the data showed that the vaccine was less effective against mutation variants compared to the previous variants. Mutation variants could easily mutate the N-segment structure and receptor domain of its spike glycoprotein (S) protein to escape antibody recognition. Therefore, it is vital to understand the potential immune response and evasion mechanism of SARS-CoV-2 variants. In this review, immune response and evasion mechanisms of several SARS-CoV-2 variants are described, which could provide some helpful advice for future vaccines.
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Affiliation(s)
- Qiuli Chen
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang 310018, China
| | - Jiawei Zhang
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Peter Wang
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang 310018, China
| | - Zuyong Zhang
- The Affiliated Hangzhou Xixi Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310023, China
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39
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Rahman S, Hossain MJ, Nahar Z, Shahriar M, Bhuiyan MA, Islam MR. Emerging SARS-CoV-2 Variants and Subvariants: Challenges and Opportunities in the Context of COVID-19 Pandemic. Environ Health Insights 2022; 16:11786302221129396. [PMID: 36299441 PMCID: PMC9585367 DOI: 10.1177/11786302221129396] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/09/2022] [Indexed: 05/30/2023]
Abstract
The COVID-19 pandemic has become the most devastating pandemic of the 21st century since its appearance in December 2019. Like other RNA viruses, continuous mutation is common for coronavirus to create several variants and subvariants. The main reason behind this mutation and evolvement of SARS-CoV-2 was its structural spike (S) glycoprotein. Coronavirus has become a threat to global public health due to its high mutation capability and antibody neutralizing capacity. According to the World Health Organization (WHO), there are 5 major variants of concern (VOC) are Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529). Recently, different Omicron subvariants have gained worldwide dominance, such as BA.1, BA.2, BA.3, BA.4, and BA.5. However, there is a discernible drop in this symptomatic sickness globally due to the success of numerous monoclonal antibodies and vaccinations. Here we also discussed the currently dominant Omicron subvariants and the effectiveness of antiviral agents and vaccines. Based on the available data and our knowledge, we can suggest that the global healthcare organizations can decide on the declaration of the end of the pandemic phase of COVID-19 soon; however, the covid-19 will continue.
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Affiliation(s)
- Smaranika Rahman
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | - Md. Jamal Hossain
- Department of Pharmacy, State
University of Bangladesh, Dhanmondi, Dhaka, Bangladesh
| | - Zabun Nahar
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | - Mohammad Shahriar
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | | | - Md. Rabiul Islam
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
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40
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Coderc de Lacam EG, Blazhynska M, Chen H, Gumbart JC, Chipot C. When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy. J Chem Theory Comput 2022; 18:5890-5900. [PMID: 36108303 PMCID: PMC9518821 DOI: 10.1021/acs.jctc.2c00604] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Accurate determination of binding free energy is pivotal for the study of many biological processes and has been applied in a number of theoretical investigations to compare the affinity of severe acute respiratory syndrome coronavirus 2 variants toward the host cell. Diversity of these variants challenges the development of effective general therapies, their transmissibility relying either on an increased affinity toward their dedicated human receptor, the angiotensin-converting enzyme 2 (ACE2), or on escaping the immune response. Now that robust structural data are available, we have determined with utmost accuracy the standard binding free energy of the receptor-binding domain to the most widespread variants, namely, Alpha, Beta, Delta, and Omicron BA.2, as well as the wild type (WT) in complex either with ACE2 or with antibodies, namely, S2E12 and H11-D4, using a rigorous theoretical framework that combines molecular dynamics and potential-of-mean-force calculations. Our results show that an appropriate starting structure is crucial to ensure appropriate reproduction of the binding affinity, allowing the variants to be compared. They also emphasize the necessity to apply the relevant methodology, bereft of any shortcut, to account for all the contributions to the standard binding free energy. Our estimates of the binding affinities support the view that while the Alpha and Beta variants lean on an increased affinity toward the host cell, the Delta and Omicron BA.2 variants choose immune escape. Moreover, the S2E12 antibody, already known to be active against the WT (Starr et al., 2021; Mlcochova et al., 2021), proved to be equally effective against the Delta variant. In stark contrast, H11-D4 retains a low affinity toward the WT compared to that of ACE2 for the latter. Assuming robust structural information, the methodology employed herein successfully addresses the challenging protein-protein binding problem in the context of coronavirus disease 2019 while offering promising perspectives for predictive studies of ever-emerging variants.
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Affiliation(s)
- Emma Goulard Coderc de Lacam
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - Marharyta Blazhynska
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - Haochuan Chen
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - James C. Gumbart
- School of Physics, Georgia Institute of
Technology, Atlanta, Georgia30332, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
- Theoretical and Computational Biophysics Group, Beckman
Institute, and Department of Physics, University of Illinois at
Urbana-Champaign, UrbanaIllinois61802, United
States
- Department of Biochemistry and Molecular Biology,
The University of Chicago, 929 E. 57th Street W225, Chicago,
Illinois60637, United States
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Dong Y, Zhai W, Fang B, Liu C, Yuan S, Wang Y, Song Q, Li H, Chen B, Cui D, Wang J, Wu Q, Zhou C, Zhou M, Li S, Zhuang X, Xu Q, Zheng Y, Wu Y, Zheng J, Cao M. A retrospective study of Pupingqinghua prescription versus Lianhuaqingwen in Chinese participants infected with SARS-CoV-2 Omicron variants. Front Pharmacol 2022; 13:988524. [PMID: 36278166 PMCID: PMC9585249 DOI: 10.3389/fphar.2022.988524] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/05/2022] [Indexed: 08/27/2023] Open
Abstract
Background: Coronavirus disease (COVID-19) seriously endangers global public health. Pupingqinghua prescription (PPQH) is an herbal formula from traditional Chinese medicine used for treatment of SARS-CoV-2 infection. This study aims to evaluate the clinical efficacy and safety of PPQH in Chinese participants infected with the SARS-CoV-2 Omicron variant. Methods: A total of 873 SARS-CoV-2 (Omicron)-infected patients were included. Among them, the patients were divided into the PPQH group (653 cases) and LHQW group (220 cases) according to different medications. The effectiveness indicators (hematological indicators, Ct values of novel Coronavirus nucleic acid tests, and viral load-shedding time) and safety indicators (liver and kidney function and adverse events) were analyzed. Results: There was no significant difference in baseline characteristics between the PPQH group and the LHQW group, except the gender; After the treatment, the levels of IL-5, IL-6, IL-10, NK cells, and INF-α of the patients in the PPQH group showed a downward trend (p < 0.05); The viral load shedding time was 5.0 (5.0, 7.0) in the PPQH group and 5.0 (4.0, 7.0) in the LHQW group; both PPQH and LHQW can shorten the duration of symptoms of fever, cough, and sore throat. The re-positive rate of COVID-19 test was 1.5 % in the PPQH group and 2.3 % in the LHQW group. In terms of safety, the levels of γ-GTT decreased significantly (p < 0.01); gastrointestinal reaction was the primary adverse reaction, and the reaction rate was 4.7 % in the PPQH group and 9.5 % in the LHQW group. Conclusion: PPQH can shorten the length of hospital stay and improve clinical symptoms of patients with SARS-COV-2 (Omicron), and it also has a good safety profile.
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Affiliation(s)
- Yidan Dong
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Zhai
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Bangjiang Fang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chenyang Liu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Suyun Yuan
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Youhua Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qixiang Song
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Hai Li
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Bin Chen
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Dan Cui
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Jun Wang
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Qiong Wu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chang Zhou
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Maolin Zhou
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shuchun Li
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xu Zhuang
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Qingrong Xu
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zheng
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Yingen Wu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Junhua Zheng
- Renji Hospital, School of Medicine in Shanghai Jiao Tong University, Shanghai, China
| | - Min Cao
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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42
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Kumar S, Patel A, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Davis-Gardner ME, Edara VV, Linderman S, Nayak K, Dixit K, Sharma P, Bajpai P, Singh V, Frank F, Cheedarla N, Verkerke HP, Neish AS, Roback JD, Mantus G, Goel PK, Rahi M, Davis CW, Wrammert J, Godbole S, Henry AR, Douek DC, Suthar MS, Ahmed R, Ortlund E, Sharma A, Murali-Krishna K, Chandele A. Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody. Sci Adv 2022; 8:eadd2032. [PMID: 36197988 PMCID: PMC9534492 DOI: 10.1126/sciadv.add2032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In this study, by characterizing several human monoclonal antibodies (mAbs) isolated from single B cells of the COVID-19–recovered individuals in India who experienced ancestral Wuhan strain (WA.1) of SARS-CoV-2 during early stages of the pandemic, we found a receptor binding domain (RBD)–specific mAb 002-S21F2 that has rare gene usage and potently neutralized live viral isolates of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron sublineages (BA.1, BA.2, BA.2.12.1, BA.4, and BA.5) with IC
50
ranging from 0.02 to 0.13 μg/ml. Structural studies of 002-S21F2 in complex with spike trimers of Omicron and WA.1 showed that it targets a conformationally conserved epitope on the outer face of RBD (class 3 surface) outside the ACE2-binding motif, thereby providing a mechanistic insights for its broad neutralization activity. The discovery of 002-S21F2 and the broadly neutralizing epitope it targets have timely implications for developing a broad range of therapeutic and vaccine interventions against SARS-CoV-2 variants including Omicron sublineages.
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Affiliation(s)
- Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lilin Lai
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi-110 016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kaustuv Nayak
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Vanshika Singh
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P. Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grace Mantus
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Pawan Kumar Goel
- Shaheed Hasan Khan Mewat Government Medical College, Haryana, India
| | - Manju Rahi
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi-110 029, India
| | - Carl W. Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R. Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Eric Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Amit Sharma
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi-110 077, India
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
- Department of Pediatrics, Emory University School of Medicine, Emory University Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi-110 067, India
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Abstract
Since the SARS-CoV-2 Omicron variant (B.1.1.529) was declared a variant of concern (VOC) by the WHO on 24 November 2021, it has caused another global surge of cases. With extensive mutations in its spike glycoprotein, Omicron gained substantial capabilities to evade the antiviral immunity provided by vaccination, hybrid immunity, or monoclonal antibodies. The Omicron subvariants BA.1, BA.2, BA.2.12.1, BA.4 and BA.5 extended this immune evasion capability by having additional unique mutations in their respective spike proteins. The ongoing Omicron wave and emergence of new Omicron subvariants leads to additional concerns regarding the efficacy of the current antiviral measurements. To have a better understanding of the Omicron subvariants, this review summarizes reports of the immune evasion of subvariants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5 as well as the molecular basis of immune evasion.
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Affiliation(s)
- Hanzhong Ke
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew R. Chang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Wayne A. Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
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44
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He X, Su J, Ma Y, Zhang W, Tang S. A comprehensive analysis of the efficacy and effectiveness of COVID-19 vaccines. Front Immunol 2022; 13:945930. [PMID: 36090988 PMCID: PMC9459021 DOI: 10.3389/fimmu.2022.945930] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
It is urgently needed to update the comprehensive analysis about the efficacy or effectiveness of COVID-19 vaccines especially during the COVID-19 pandemic caused by SARS-CoV-2 Delta and Omicron variants. In general, the current COVID-19 vaccines showed a cumulative efficacy of 66.4%, 79.7%, and 93.6% to prevent SARS-CoV-2 infection, symptomatic COVID-19, and severe COVID-19, respectively, but could not prevent the asymptomatic infection of SARS-CoV-2. Furthermore, the current COVID-19 vaccines could effectively prevent COVID-19 caused by the Delta variant although the incidence of breakthrough infection of the SARS-CoV-2 Delta variant increased when the intervals post full vaccination extended, suggesting the waning effectiveness of COVID-19 vaccines. In addition, one-dose booster immunization showed an effectiveness of 74.5% to prevent COVID-19 caused by the Delta variant. However, current COVID-19 vaccines could not prevent the infection of Omicron sub-lineage BA.1.1.529 and had about 50% effectiveness to prevent COVID-19 caused by Omicron sub-lineage BA.1.1.529. Furthermore, the effectiveness was 87.6% and 90.1% to prevent severe COVID-19 and COVID-19-related death caused by Omicron sub-lineage BA.2, respectively, while one-dose booster immunization could enhance the effectiveness of COVID-19 vaccines to prevent the infection and COVID-19 caused by Omicron sub-lineage BA.1.1.529 and sub-lineage BA.2. Two-dose booster immunization showed an increased effectiveness of 81.8% against severe COVID-19 caused by the Omicron sub-lineage BA.1.1.529 variant compared with one-dose booster immunization. The effectiveness of the booster immunization with RNA-based vaccine BNT162b2 or mRNA-1273 was over 75% against severe COVID-19 more than 17 weeks after booster immunization whereas the heterogenous booster immunization showed better effectiveness than homologous booster immunization. In summary, the current COVID-19 vaccines could effectively protect COVID-19 caused by Delta and Omicron variants but was less effective against Omicron variant infection. One-dose booster immunization could enhance protection capability, and two-dose booster immunization could provide additional protection against severe COVID-19.
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Affiliation(s)
- Xiaofeng He
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- Institute of Evidence-Based Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
| | - Jiao Su
- Department of biochemistry, Changzhi Medical College, Changzhi, China
| | - Yu’nan Ma
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wenping Zhang
- Department of Cardiothoracic Surgery, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Shixing Tang,
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45
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Witte L, Baharani V, Schmidt F, Wang Z, Cho A, Raspe R, Guzman-Cardozo MC, Muecksch F, Gaebler C, Caskey M, Nussenzweig MC, Hatziioannou T, Bieniasz PD. Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape. bioRxiv 2022:2022.08.17.504313. [PMID: 36032981 PMCID: PMC9413706 DOI: 10.1101/2022.08.17.504313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Consecutive waves of SARS-CoV-2 infection have been driven in part by the repeated emergence of variants with mutations that confer resistance to neutralizing antibodies Nevertheless, prolonged or repeated antigen exposure generates diverse memory B-cells that can produce affinity matured receptor binding domain (RBD)-specific antibodies that likely contribute to ongoing protection against severe disease. To determine how SARS-CoV-2 omicron variants might escape these broadly neutralizing antibodies, we subjected chimeric viruses encoding spike proteins from ancestral, BA.1 or BA.2 variants to selection pressure by a collection of 40 broadly neutralizing antibodies from individuals with various SARS-CoV-2 antigen exposures. Notably, pre-existing substitutions in the BA.1 and BA.2 spikes facilitated acquisition of resistance to many broadly neutralizing antibodies. Specifically, selection experiments identified numerous RBD substitutions that did not confer resistance to broadly neutralizing antibodies in the context of the ancestral Wuhan-Hu-1 spike sequence, but did so in the context of BA.1 and BA.2. A subset of these substitutions corresponds to those that have appeared in several BA.2 daughter lineages that have recently emerged, such as BA.5. By including as few as 2 or 3 of these additional changes in the context of BA.5, we generated spike proteins that were resistant to nearly all of the 40 broadly neutralizing antibodies and were poorly neutralized by plasma from most individuals. The emergence of omicron variants has therefore not only allowed SARS-CoV-2 escape from previously elicited neutralizing antibodies but also lowered the genetic barrier to the acquisition of resistance to the subset of antibodies that remained effective against early omicron variants.
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Affiliation(s)
- Leander Witte
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Viren Baharani
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA.,Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Raphael Raspe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute The Rockefeller University, New York, NY 10065, USA
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