1
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Yan Q, Gao X, Liu B, Hou R, He P, Ma Y, Zhang Y, Zhang Y, Li Z, Chen Q, Wang J, Huang X, Liang H, Zheng H, Yao Y, Chen X, Niu X, He J, Chen L, Zhao J, Xiong X. Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants. Nat Commun 2024; 15:7585. [PMID: 39217172 PMCID: PMC11366018 DOI: 10.1038/s41467-024-51770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 08/17/2024] [Indexed: 09/04/2024] Open
Abstract
Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruitian Hou
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Guangzhou National Laboratory, Guangzhou, China
| | - Yong Ma
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Jingjing Wang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huiran Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yichen Yao
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xianying Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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2
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Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X. An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep 2024; 43:114265. [PMID: 38805396 DOI: 10.1016/j.celrep.2024.114265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/29/2023] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein continues to evolve antigenically, impacting antibody immunity. D1F6, an affinity-matured non-stereotypic VH1-2 antibody isolated from a patient infected with the SARS-CoV-2 ancestral strain, effectively neutralizes most Omicron variants tested, including XBB.1.5. We identify that D1F6 in the immunoglobulin G (IgG) form is able to overcome the effect of most Omicron mutations through its avidity-enhanced multivalent S-trimer binding. Cryo-electron microscopy (cryo-EM) and biochemical analyses show that three simultaneous epitope mutations are generally needed to substantially disrupt the multivalent S-trimer binding by D1F6 IgG. Antigenic mutations at spike positions 346, 444, and 445, which appeared in the latest variants, have little effect on D1F6 binding individually. However, these mutations are able to act synergistically with earlier Omicron mutations to impair neutralization by affecting the interaction between D1F6 IgG and the S-trimer. These results provide insight into the mechanism by which accumulated antigenic mutations facilitate evasion of affinity-matured antibodies.
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Affiliation(s)
- Banghui Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yijun Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qian Wang
- Guangzhou Laboratory & Bioland Laboratory, Guangzhou, China
| | - Yuanyi Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Shuangshuang Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingxian Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mengzhen Su
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Science and Technology of China, Hefei, China
| | - Xiancheng Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Science and Technology of China, Hefei, China
| | - Yinglin Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenyi Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Ling Chen
- Guangzhou Laboratory & Bioland Laboratory, Guangzhou, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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3
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Sharma D, Rawat P, Greiff V, Janakiraman V, Gromiha MM. Predicting the immune escape of SARS-CoV-2 neutralizing antibodies upon mutation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166959. [PMID: 37967796 DOI: 10.1016/j.bbadis.2023.166959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
COVID-19 has resulted in millions of deaths and severe impact on economies worldwide. Moreover, the emergence of SARS-CoV-2 variants presented significant challenges in controlling the pandemic, particularly their potential to avoid the immune system and evade vaccine immunity. This has led to a growing need for research to predict how mutations in SARS-CoV-2 reduces the ability of antibodies to neutralize the virus. In this study, we assembled a set of 1813 mutations from the interface of SARS-CoV-2 spike protein's receptor binding domain (RBD) and neutralizing antibody complexes and developed a machine learning model to classify high or low escape mutations using interaction energy, inter-residue contacts and predicted binding free energy change. Our approach achieved an Area under the Receiver Operating Characteristics (ROC) Curve (AUC) of 0.91 using the Random Forest classifier on the test dataset with 217 mutations. The model was further utilized to predict the escape mutations on a dataset of 29,165 mutations located at the interface of 83 RBD-neutralizing antibody complexes. A small subset of this dataset was also validated based on available experimental data. We found that top 10 % high escape mutations were dominated by charged to nonpolar mutations whereas low escape mutations were dominated by polar to nonpolar mutations. We believe that the present method will allow prioritization of high/low escape mutations in the context of neutralizing antibodies targeting SARS-CoV-2 RBD region and assist antibody design for current and emerging variants.
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Affiliation(s)
- Divya Sharma
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Puneet Rawat
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vani Janakiraman
- Infection Biology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Department of Computer Science, National University of Singapore, Singapore.
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4
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Korenkov M, Zehner M, Cohen-Dvashi H, Borenstein-Katz A, Kottege L, Janicki H, Vanshylla K, Weber T, Gruell H, Koch M, Diskin R, Kreer C, Klein F. Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants. Immunity 2023; 56:2803-2815.e6. [PMID: 38035879 DOI: 10.1016/j.immuni.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/19/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Somatic hypermutation (SHM) drives affinity maturation and continues over months in SARS-CoV-2-neutralizing antibodies (nAbs). However, several potent SARS-CoV-2 antibodies carry no or only a few mutations, leaving the question of how ongoing SHM affects neutralization unclear. Here, we reverted variable region mutations of 92 antibodies and tested their impact on SARS-CoV-2 binding and neutralization. Reverting higher numbers of mutations correlated with decreasing antibody functionality. However, for some antibodies, including antibodies of the public clonotype VH1-58, neutralization of Wu01 remained unaffected. Although mutations were dispensable for Wu01-induced VH1-58 antibodies to neutralize Alpha, Beta, and Delta variants, they were critical for Omicron BA.1/BA.2 neutralization. We exploited this knowledge to convert the clinical antibody tixagevimab into a BA.1/BA.2 neutralizer. These findings broaden our understanding of SHM as a mechanism that not only improves antibody responses during affinity maturation but also contributes to antibody diversification, thus increasing the chances of neutralizing viral escape variants.
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Affiliation(s)
- Michael Korenkov
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Matthias Zehner
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hadas Cohen-Dvashi
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Aliza Borenstein-Katz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lisa Kottege
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, University of Cologne, 50931 Cologne, Germany
| | - Ron Diskin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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5
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Thakur S, Planeta Kepp K, Mehra R. Predicting virus Fitness: Towards a structure-based computational model. J Struct Biol 2023; 215:108042. [PMID: 37931730 DOI: 10.1016/j.jsb.2023.108042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogens. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼380,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India
| | - Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kongens Lyngby, Denmark
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India; Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India.
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6
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Le K, Kannappan S, Kim T, Lee JH, Lee HR, Kim KK. Structural understanding of SARS-CoV-2 virus entry to host cells. Front Mol Biosci 2023; 10:1288686. [PMID: 38033388 PMCID: PMC10683510 DOI: 10.3389/fmolb.2023.1288686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health concern associated with millions of fatalities worldwide. Mutant variants of the virus have further exacerbated COVID-19 mortality and infection rates, emphasizing the urgent need for effective preventive strategies. Understanding the viral infection mechanism is crucial for developing therapeutics and vaccines. The entry of SARS-CoV-2 into host cells is a key step in the infection pathway and has been targeted for drug development. Despite numerous reviews of COVID-19 and the virus, there is a lack of comprehensive reviews focusing on the structural aspects of viral entry. In this review, we analyze structural changes in Spike proteins during the entry process, dividing the entry process into prebinding, receptor binding, proteolytic cleavage, and membrane fusion steps. By understanding the atomic-scale details of viral entry, we can better target the entry step for intervention strategies. We also examine the impacts of mutations in Spike proteins, including the Omicron variant, on viral entry. Structural information provides insights into the effects of mutations and can guide the development of therapeutics and vaccines. Finally, we discuss available structure-based approaches for the development of therapeutics and vaccines. Overall, this review provides a detailed analysis of the structural aspects of SARS-CoV-2 viral entry, highlighting its significance in the development of therapeutics and vaccines against COVID-19. Therefore, our review emphasizes the importance of structural information in combating SARS-CoV-2 infection.
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Affiliation(s)
- Kim Le
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Shrute Kannappan
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
| | - Truc Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
- School of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
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7
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Lima NS, Musayev M, Johnston TS, Wagner DA, Henry AR, Wang L, Yang ES, Zhang Y, Birungi K, Black WP, O'Dell S, Schmidt SD, Moon D, Lorang CG, Zhao B, Chen M, Boswell KL, Roberts-Torres J, Davis RL, Peyton L, Narpala SR, O'Connell S, Serebryannyy L, Wang J, Schrager A, Talana CA, Shimberg G, Leung K, Shi W, Khashab R, Biber A, Zilberman T, Rhein J, Vetter S, Ahmed A, Novik L, Widge A, Gordon I, Guech M, Teng IT, Phung E, Ruckwardt TJ, Pegu A, Misasi J, Doria-Rose NA, Gaudinski M, Koup RA, Kwong PD, McDermott AB, Amit S, Schacker TW, Levy I, Mascola JR, Sullivan NJ, Schramm CA, Douek DC. Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones. Nat Commun 2022; 13:7733. [PMID: 36517467 PMCID: PMC9748393 DOI: 10.1038/s41467-022-35456-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. However, the basis for such cross-protection at the molecular level is incompletely understood. Here, we characterized the repertoire and epitope specificity of antibodies elicited by infection with the Beta, Gamma and WA1 ancestral variants and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a method to obtain immunoglobulin sequences with concurrent rapid production and functional assessment of monoclonal antibodies from hundreds of single B cells sorted by flow cytometry. Infection with any variant elicited similar cross-binding antibody responses exhibiting a conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may account for the continued efficacy of vaccines based on a single ancestral variant.
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Affiliation(s)
- Noemia S Lima
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maryam Musayev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Timothy S Johnston
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Danielle A Wagner
- 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
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kevina Birungi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Walker P Black
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Damee Moon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cynthia G Lorang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bingchun Zhao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kristin L Boswell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jesmine Roberts-Torres
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rachel L Davis
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lowrey Peyton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sandeep R Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sarah O'Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Leonid Serebryannyy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jennifer Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexander Schrager
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Geoffrey Shimberg
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rawan Khashab
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan, 5262112, Israel
| | - Asaf Biber
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan, 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Tal Zilberman
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan, 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Joshua Rhein
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Sara Vetter
- Minnesota Department of Health, St Paul, MN, 55164, USA
| | - Afeefa Ahmed
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Laura Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alicia Widge
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ingelise Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mercy Guech
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tracy J Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Martin Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sharon Amit
- Clinical Microbiology, Sheba Medical Center, Ramat-Gan, 5262112, Israel
| | - Timothy W Schacker
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan, 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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8
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Fan C, Cohen AA, Park M, Hung AFH, Keeffe JR, Gnanapragasam PNP, Lee YE, Gao H, Kakutani LM, Wu Z, Kleanthous H, Malecek KE, Williams JC, Bjorkman PJ. Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes. Immunity 2022; 55:2419-2435.e10. [PMID: 36370711 PMCID: PMC9606073 DOI: 10.1016/j.immuni.2022.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/07/2022] [Accepted: 10/24/2022] [Indexed: 01/21/2023]
Abstract
Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.
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Affiliation(s)
- Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Miso Park
- Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | | | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ziyan Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Kathryn E Malecek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John C Williams
- Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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9
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Wang P, Casner RG, Nair MS, Yu J, Guo Y, Wang M, Chan JFW, Cerutti G, Iketani S, Liu L, Sheng Z, Chen Z, Yuen KY, Kwong PD, Huang Y, Shapiro L, Ho DD. A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerg Microbes Infect 2022; 11:147-157. [PMID: 34836485 PMCID: PMC8725896 DOI: 10.1080/22221751.2021.2011623] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/23/2021] [Indexed: 01/16/2023]
Abstract
The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses in vitro and confirmed that K378 T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.
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Affiliation(s)
- Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ryan G Casner
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jasper F-W Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zhiwei Chen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Peter D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Vaccine Research Center, National Institutes of Health, Bethesda, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lawrence Shapiro
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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10
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Gopal R, Fitzpatrick E, Pentakota N, Jayaraman A, Tharakaraman K, Capila I. Optimizing Antibody Affinity and Developability Using a Framework-CDR Shuffling Approach-Application to an Anti-SARS-CoV-2 Antibody. Viruses 2022; 14:2694. [PMID: 36560698 PMCID: PMC9784564 DOI: 10.3390/v14122694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
The computational methods used for engineering antibodies for clinical development have undergone a transformation from three-dimensional structure-guided approaches to artificial-intelligence- and machine-learning-based approaches that leverage the large sequence data space of hundreds of millions of antibodies generated by next-generation sequencing (NGS) studies. Building on the wealth of available sequence data, we implemented a computational shuffling approach to antibody components, using the complementarity-determining region (CDR) and the framework region (FWR) to optimize an antibody for improved affinity and developability. This approach uses a set of rules to suitably combine the CDRs and FWRs derived from naturally occurring antibody sequences to engineer an antibody with high affinity and specificity. To illustrate this approach, we selected a representative SARS-CoV-2-neutralizing antibody, H4, which was identified and isolated previously based on the predominant germlines that were employed in a human host to target the SARS-CoV-2-human ACE2 receptor interaction. Compared to screening vast CDR libraries for affinity enhancements, our approach identified fewer than 100 antibody framework-CDR combinations, from which we screened and selected an antibody (CB79) that showed a reduced dissociation rate and improved affinity against the SARS-CoV-2 spike protein (7-fold) when compared to H4. The improved affinity also translated into improved neutralization (>75-fold improvement) of SARS-CoV-2. Our rapid and robust approach for optimizing antibodies from parts without the need for tedious structure-guided CDR optimization will have broad utility for biotechnological applications.
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Affiliation(s)
- Ranjani Gopal
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Emmett Fitzpatrick
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Niharika Pentakota
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Akila Jayaraman
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Kannan Tharakaraman
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Ishan Capila
- Celltas Biosciences, 900 Middlesex Turnpike, Billerica, MA 01821, USA
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11
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Luo S, Zhang J, Kreutzberger AJ, Eaton A, Edwards RJ, Jing C, Dai HQ, Sempowski GD, Cronin K, Parks R, Ye AY, Mansouri K, Barr M, Pishesha N, Williams AC, Vieira Francisco L, Saminathan A, Peng H, Batra H, Bellusci L, Khurana S, Alam SM, Montefiori DC, Saunders KO, Tian M, Ploegh H, Kirchhausen T, Chen B, Haynes BF, Alt FW. An antibody from single human V H-rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion. Sci Immunol 2022; 7:eadd5446. [PMID: 35951767 PMCID: PMC9407951 DOI: 10.1126/sciimmunol.add5446] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
SARS-CoV-2 Omicron subvariants have generated a worldwide health crisis due to resistance to most approved SARS-CoV-2 neutralizing antibodies and evasion of vaccination-induced antibodies. To manage Omicron subvariants and prepare for new ones, additional means of isolating broad and potent humanized SARS-CoV-2 neutralizing antibodies are desirable. Here, we describe a mouse model in which the primary B cell receptor (BCR) repertoire is generated solely through V(D)J recombination of a human VH1-2 heavy chain (HC) and, substantially, a human Vκ1-33 light chain (LC). Thus, primary humanized BCR repertoire diversity in these mice derives from immensely diverse HC and LC antigen-contact CDR3 sequences generated by nontemplated junctional modifications during V(D)J recombination. Immunizing this mouse model with SARS-CoV-2 (Wuhan-Hu-1) spike protein immunogens elicited several VH1-2/Vκ1-33-based neutralizing antibodies that bound RBD in a different mode from each other and from those of many prior patient-derived VH1-2-based neutralizing antibodies. Of these, SP1-77 potently and broadly neutralized all SARS-CoV-2 variants through BA.5. Cryo-EM studies revealed that SP1-77 bound RBD away from the receptor-binding motif via a CDR3-dominated recognition mode. Lattice light-sheet microscopy-based studies showed that SP1-77 did not block ACE2-mediated viral attachment or endocytosis but rather blocked viral-host membrane fusion. The broad and potent SP1-77 neutralization activity and nontraditional mechanism of action suggest that it might have therapeutic potential. Likewise, the SP1-77 binding epitope may inform vaccine strategies. Last, the type of humanized mouse models that we have described may contribute to identifying therapeutic antibodies against future SARS-CoV-2 variants and other pathogens.
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Affiliation(s)
- Sai Luo
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Alex J.B. Kreutzberger
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Changbin Jing
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hai-Qiang Dai
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Adam Yongxin Ye
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Aimee Chapdelaine Williams
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lucas Vieira Francisco
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anand Saminathan
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Himanshu Batra
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hidde Ploegh
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Frederick W. Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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12
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Valério M, Borges-Araújo L, Melo MN, Lousa D, Soares CM. SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:1009451. [PMID: 36277437 PMCID: PMC9581196 DOI: 10.3389/fmedt.2022.1009451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is having a devastating social and economic impact around the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, as well as increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes. The spike glycoprotein binds to angiotensin-converting enzyme 2 (ACE2) via its receptor binding domain (RBD) initiating the infection process. Attempting to understand the effect of RBD mutations in VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect the RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (Alpha, Beta, Delta, and Omicron). Our results show that the wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The Alpha and Beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the Delta and Omicron variants showed extreme results, with the closed conformation being rarely observed. The Delta variant also differed substantially from the other variants, alternating between the open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge. This alternate conformation could provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the Omicron and Delta variants, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of Delta, may assist antibody escape.
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Affiliation(s)
- Mariana Valério
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
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13
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Abstract
Despite effective spike-based vaccines and monoclonal antibodies, the SARS-CoV-2 pandemic continues more than two and a half years post-onset. Relentless investigation has outlined a causative dynamic between host-derived antibodies and reciprocal viral subversion. Integration of this paradigm into the architecture of next generation antiviral strategies, predicated on a foundational understanding of the virology and immunology of SARS-CoV-2, will be critical for success. This review aims to serve as a primer on the immunity endowed by antibodies targeting SARS-CoV-2 spike protein through a structural perspective. We begin by introducing the structure and function of spike, polyclonal immunity to SARS-CoV-2 spike, and the emergence of major SARS-CoV-2 variants that evade immunity. The remainder of the article comprises an in-depth dissection of all major epitopes on SARS-CoV-2 spike in molecular detail, with emphasis on the origins, neutralizing potency, mechanisms of action, cross-reactivity, and variant resistance of representative monoclonal antibodies to each epitope.
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Affiliation(s)
- John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Lucas J Adams
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States; Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, United States; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, United States.
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14
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Windsor IW, Tong P, Lavidor O, Sanjari Moghaddam A, McKay LG, Gautam A, Chen Y, MacDonald EA, Yoo DK, Griffiths A, Wesemann DR, Harrison SC. Antibodies induced by an ancestral SARS-CoV-2 strain that cross-neutralize variants from Alpha to Omicron BA.1. Sci Immunol 2022; 7:eabo3425. [PMID: 35536154 PMCID: PMC9097876 DOI: 10.1126/sciimmunol.abo3425] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022]
Abstract
Neutralizing antibodies that recognize the SARS-CoV-2 spike glycoprotein are the principal host defense against viral invasion. Variants of SARS-CoV-2 bear mutations that allow escape from neutralization by many human antibodies, especially those in widely distributed ("public") classes. Identifying antibodies that neutralize these variants of concern and determining their prevalence are important goals for understanding immune protection. To determine the Delta and Omicron BA.1 variant specificity of B cell repertoires established by an initial Wuhan strain infection, we measured neutralization potencies of 73 antibodies from an unbiased survey of the early memory B cell response. Antibodies recognizing each of three previously defined epitopic regions on the spike receptor binding domain (RBD) varied in neutralization potency and variant-escape resistance. The ACE2 binding surface ("RBD-2") harbored the binding sites of neutralizing antibodies with the highest potency but with the greatest sensitivity to viral escape; two other epitopic regions on the RBD ("RBD-1" and "RBD-3") bound antibodies of more modest potency but greater breadth. The structures of several Fab:spike complexes that neutralized all five variants of concern tested, including one Fab each from the RBD-1, -2, and -3 clusters, illustrated the determinants of broad neutralization and showed that B cell repertoires can have specificities that avoid immune escape driven by public antibodies. The structure of the RBD-2 binding, broad neutralizer shows why it retains neutralizing activity for Omicron BA.1, unlike most others in the same public class. Our results correlate with real-world data on vaccine efficacy, which indicate mitigation of disease caused by Omicron BA.1.
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Affiliation(s)
- Ian W. Windsor
- Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Pei Tong
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Lavidor
- Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ali Sanjari Moghaddam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G.A. McKay
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115
| | - Avneesh Gautam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yuezhou Chen
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth A. MacDonald
- Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Duck Kyun Yoo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Griffiths
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Duane R. Wesemann
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Stephen C. Harrison
- Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
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15
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Lima NS, Musayev M, Johnston TS, Wagner DA, Henry AR, Wang L, Yang ES, Zhang Y, Birungi K, Black WP, O’Dell S, Schmidt SD, Moon D, Lorang CG, Zhao B, Chen M, Boswell KL, Roberts-Torres J, Davis RL, Peyton L, Narpala SR, O’Connell S, Wang J, Schrager A, Talana CA, Leung K, Shi W, Khashab R, Biber A, Zilberman T, Rhein J, Vetter S, Ahmed A, Novik L, Widge A, Gordon I, Guech M, Teng IT, Phung E, Ruckwardt TJ, Pegu A, Misasi J, Doria-Rose NA, Gaudinski M, Koup RA, Kwong PD, McDermott AB, Amit S, Schacker TW, Levy I, Mascola JR, Sullivan NJ, Schramm CA, Douek DC. Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.28.486152. [PMID: 35378757 PMCID: PMC8978934 DOI: 10.1101/2022.03.28.486152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. The basis for such cross-protection at the molecular level is incompletely understood. Here we characterized the repertoire and epitope specificity of antibodies elicited by Beta, Gamma and ancestral variant infection and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a high-throughput approach to obtain immunoglobulin sequences and produce monoclonal antibodies for functional assessment from single B cells. Infection with any variant elicited similar cross-binding antibody responses exhibiting a remarkably conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may represent a general immunological principle that accounts for the continued efficacy of vaccines based on a single ancestral variant.
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Affiliation(s)
- Noemia S. Lima
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Maryam Musayev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Timothy S. Johnston
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Danielle A. Wagner
- 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
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Kevina Birungi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Walker P. Black
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Stephen D. Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Damee Moon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Cynthia G. Lorang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Bingchun Zhao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Kristin L. Boswell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Jesmine Roberts-Torres
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Rachel L. Davis
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Lowrey Peyton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Sandeep R. Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Sarah O’Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Jennifer Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Alexander Schrager
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Rawan Khashab
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan 5262112, Israel
| | - Asaf Biber
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tal Zilberman
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Joshua Rhein
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Sara Vetter
- Minnesota Department of Health, St Paul, MN 55164, USA
| | - Afeefa Ahmed
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Laura Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Alicia Widge
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Ingelise Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Mercy Guech
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Tracy J. Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Martin Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Sharon Amit
- Clinical Microbiology, Sheba Medical Center, Ramat-Gan 5262112, Israel
| | - Timothy W. Schacker
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Ramat Gan 5262112, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv 6997801, Israel
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Chaim A. Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Bethesda, MD 20892, USA
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16
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Liu L, Iketani S, Guo Y, Casner RG, Reddem ER, Nair MS, Yu J, Chan JFW, Wang M, Cerutti G, Li Z, Morano NC, Castagna CD, Corredor L, Chu H, Yuan S, Poon VKM, Chan CCS, Chen Z, Luo Y, Cunningham M, Chavez A, Yin MT, Perlin DS, Tsuji M, Yuen KY, Kwong PD, Sheng Z, Huang Y, Shapiro L, Ho DD. An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses. Sci Transl Med 2022; 14:eabn6859. [PMID: 35438546 PMCID: PMC9017343 DOI: 10.1126/scitranslmed.abn6859] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/07/2022] [Indexed: 12/12/2022]
Abstract
The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.
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Affiliation(s)
- Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Ryan G. Casner
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Eswar R. Reddem
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Manoj S. Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jasper F-W. Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zhiteng Li
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Nicholas C. Morano
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Candace D. Castagna
- Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Laura Corredor
- Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Vincent Kwok-Man Poon
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Chris Chun-Sing Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Zhiwei Chen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Marcus Cunningham
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Michael T. Yin
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David S. Perlin
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Moriya Tsuji
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Kwok-Yung Yuen
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
- Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter D. Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lawrence Shapiro
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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17
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Isolation of human monoclonal antibodies with neutralizing activity to a broad spectrum of SARS-CoV-2 viruses including the Omicron variants. Antiviral Res 2022; 201:105297. [PMID: 35341809 PMCID: PMC8944172 DOI: 10.1016/j.antiviral.2022.105297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 11/25/2022]
Abstract
Monoclonal antibody therapy is a promising option for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and a cocktail of antibodies (REGN-COV) has been administered to infected patients with a favorable outcome. However, it is necessary to continue generating novel sets of monoclonal antibodies with neutralizing activity because viral variants can emerge that show resistance to the currently utilized antibodies. Here, we isolated a new cocktail of antibodies, EV053273 and EV053286, from peripheral blood mononuclear cells derived from convalescent patients infected with wild-type SARS-CoV-2. EV053273 exerted potent antiviral activity against the Wuhan wild-type virus as well as the Alpha and Delta variants in vitro, whereas the antiviral activity of EV053286 was moderate, but it had a wide-range of suppressive activity on the wild-type virus as well as the Alpha, Beta, Delta, Kappa, Omicron BA.1, and BA.2 variants. With the combined use of EV053273 and EV053286, we observed similar inhibitory effects on viral replication as with REGN-COV in vitro. We further assessed their activity in vivo by using a mouse model infected with a recently established viral strain with adopted infectious activity in mice. Independent experiments revealed that the combined use of EV053273 and EV053286 or the single use of each monoclonal antibody efficiently blocked infection in vivo. Together with data showing that these two monoclonal antibodies could neutralize REGN-COV escape variants and the Omicron variant, our findings suggest that the EV053273 and EV053286 monoclonal antibody cocktail is a novel clinically applicable therapeutic candidate for SARS-CoV-2 infection.
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18
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Fung KM, Lai SJ, Lin TL, Tseng TS. Antigen–Antibody Complex-Guided Exploration of the Hotspots Conferring the Immune-Escaping Ability of the SARS-CoV-2 RBD. Front Mol Biosci 2022; 9:797132. [PMID: 35392535 PMCID: PMC8981523 DOI: 10.3389/fmolb.2022.797132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
The COVID-19 pandemic resulting from the spread of SARS-CoV-2 spurred devastating health and economic crises around the world. Neutralizing antibodies and licensed vaccines were developed to combat COVID-19, but progress was slow. In addition, variants of the receptor-binding domain (RBD) of the spike protein confer resistance of SARS-CoV-2 to neutralizing antibodies, nullifying the possibility of human immunity. Therefore, investigations into the RBD mutations that disrupt neutralization through convalescent antibodies are urgently required. In this study, we comprehensively and systematically investigated the binding stability of RBD variants targeting convalescent antibodies and revealed that the RBD residues F456, F490, L452, L455, and K417 are immune-escaping hotspots, and E484, F486, and N501 are destabilizing residues. Our study also explored the possible modes of actions of emerging SARS-CoV-2 variants. All results are consistent with experimental observations of attenuated antibody neutralization and clinically emerging SARS-CoV-2 variants. We identified possible immune-escaping hotspots that could further promote resistance to convalescent antibodies. The results provide valuable information for developing and designing novel monoclonal antibody drugs to combat emerging SARS-CoV-2 variants.
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Affiliation(s)
- Kit-Man Fung
- Academia Sinica, Institute of Biological Chemistry, Taipei, Taiwan
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Tzu-Lu Lin
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Tien-Sheng Tseng,
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19
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Cerutti G, Guo Y, Liu L, Liu L, Zhang Z, Luo Y, Huang Y, Wang HH, Ho DD, Sheng Z, Shapiro L. Cryo-EM structure of the SARS-CoV-2 Omicron spike. Cell Rep 2022; 38:110428. [PMID: 35172173 PMCID: PMC8818377 DOI: 10.1016/j.celrep.2022.110428] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 02/02/2022] [Indexed: 11/23/2022] Open
Abstract
The recently reported B.1.1.529 Omicron variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) includes 34 mutations in the spike protein relative to the Wuhan strain, including 15 mutations in the receptor-binding domain (RBD). Functional studies have shown Omicron to substantially escape the activity of many SARS-CoV-2-neutralizing antibodies. Here, we report a 3.1 Å-resolution cryoelectron microscopy (cryo-EM) structure of the Omicron spike protein ectodomain. The structure depicts a spike that is exclusively in the 1-RBD-up conformation with high mobility of RBD. Many mutations cause steric clashes and/or altered interactions at antibody-binding surfaces, whereas others mediate changes of the spike structure in local regions to interfere with antibody recognition. Overall, the structure of the Omicron spike reveals how mutations alter its conformation and explains its extraordinary ability to evade neutralizing antibodies.
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Affiliation(s)
- Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Liyuan Liu
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zhening Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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20
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Reincke SM, Yuan M, Kornau HC, Corman VM, van Hoof S, Sánchez-Sendin E, Ramberger M, Yu W, Hua Y, Tien H, Schmidt ML, Schwarz T, Jeworowski LM, Brandl SE, Rasmussen HF, Homeyer MA, Stöffler L, Barner M, Kunkel D, Huo S, Horler J, von Wardenburg N, Kroidl I, Eser TM, Wieser A, Geldmacher C, Hoelscher M, Gänzer H, Weiss G, Schmitz D, Drosten C, Prüss H, Wilson IA, Kreye J. SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies. Science 2022; 375:782-787. [PMID: 35076281 PMCID: PMC8939768 DOI: 10.1126/science.abm5835] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Beta variant of concern (VOC) resists neutralization by major classes of antibodies from COVID-19 patients and vaccinated individuals. In this study, serum of Beta-infected patients revealed reduced cross-neutralization of wild-type virus. From these patients, we isolated Beta-specific and cross-reactive receptor-binding domain (RBD) antibodies. The Beta-specificity results from recruitment of VOC-specific clonotypes and accommodation of mutations present in Beta and Omicron into a major antibody class that is normally sensitive to these mutations. The Beta-elicited cross-reactive antibodies share genetic and structural features with wild type-elicited antibodies, including a public VH1-58 clonotype that targets the RBD ridge. These findings advance our understanding of the antibody response to SARS-CoV-2 shaped by antigenic drift, with implications for design of next-generation vaccines and therapeutics.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antigenic Drift and Shift
- COVID-19/immunology
- COVID-19/virology
- Cross Reactions
- Female
- Humans
- Male
- Middle Aged
- Neutralization Tests
- Protein Binding
- Protein Domains
- Protein Interaction Domains and Motifs
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- S. Momsen Reincke
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Neuroscience Research Center (NWFZ), Cluster NeuroCure, Berlin, Germany
| | - Victor M. Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
- Labor Berlin–Charité Vivantes GmbH, Berlin
| | - Scott van Hoof
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Elisa Sánchez-Sendin
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Melanie Ramberger
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yuanzi Hua
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry Tien
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marie Luisa Schmidt
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Tatjana Schwarz
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Lara Maria Jeworowski
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Sarah E. Brandl
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Helle Foverskov Rasmussen
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Marie A. Homeyer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Laura Stöffler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Martin Barner
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Désirée Kunkel
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Flow and Mass Cytometry Core Facility, Berlin, Germany
| | - Shufan Huo
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
| | - Johannes Horler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Niels von Wardenburg
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Tabea M. Eser
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Hannes Gänzer
- Department of Internal Medicine, BKH Schwaz, Schwaz, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Schmitz
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Neuroscience Research Center (NWFZ), Cluster NeuroCure, Berlin, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Harald Prüss
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jakob Kreye
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Pediatric Neurology, Berlin, Germany
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21
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Zhang S, Go EP, Ding H, Anang S, Kappes JC, Desaire H, Sodroski JG. Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. J Virol 2022; 96:e0162621. [PMID: 34817202 PMCID: PMC8827021 DOI: 10.1128/jvi.01626-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/12/2021] [Indexed: 12/17/2022] Open
Abstract
The SARS-CoV-2 coronavirus, the etiologic agent of COVID-19, uses its spike (S) glycoprotein anchored in the viral membrane to enter host cells. The S glycoprotein is the major target for neutralizing antibodies elicited by natural infection and by vaccines. Approximately 35% of the SARS-CoV-2 S glycoprotein consists of carbohydrate, which can influence virus infectivity and susceptibility to antibody inhibition. We found that virus-like particles produced by coexpression of SARS-CoV-2 S, M, E, and N proteins contained spike glycoproteins that were extensively modified by complex carbohydrates. We used a fucose-selective lectin to purify the Golgi-modified fraction of a wild-type SARS-CoV-2 S glycoprotein trimer and determined its glycosylation and disulfide bond profile. Compared with soluble or solubilized S glycoproteins modified to prevent proteolytic cleavage and to retain a prefusion conformation, more of the wild-type S glycoprotein N-linked glycans are processed to complex forms. Even Asn 234, a significant percentage of which is decorated by high-mannose glycans on other characterized S trimer preparations, is predominantly modified in the Golgi compartment by processed glycans. Three incompletely occupied sites of O-linked glycosylation were detected. Viruses pseudotyped with natural variants of the serine/threonine residues implicated in O-linked glycosylation were generally infectious and exhibited sensitivity to neutralization by soluble ACE2 and convalescent antisera comparable to that of the wild-type virus. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. These findings enhance our understanding of the Golgi processing of the native SARS-CoV-2 S glycoprotein carbohydrates and could assist the design of interventions. IMPORTANCE The SARS-CoV-2 coronavirus, which causes COVID-19, uses its spike glycoprotein to enter host cells. The viral spike glycoprotein is the main target of host neutralizing antibodies that help to control SARS-CoV-2 infection and are important for the protection provided by vaccines. The SARS-CoV-2 spike glycoprotein consists of a trimer of two subunits covered with a coat of carbohydrates (sugars). Here, we describe the disulfide bonds that assist the SARS-CoV-2 spike glycoprotein to assume the correct shape and the composition of the sugar moieties on the glycoprotein surface. We also evaluate the consequences of natural virus variation in O-linked sugar addition and in the cysteine residues involved in disulfide bond formation. This information can expedite the improvement of vaccines and therapies for COVID-19.
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Affiliation(s)
- Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, Alabama, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Joseph G. Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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22
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Parallel profiling of antigenicity alteration and immune escape of SARS-CoV-2 Omicron and other variants. Signal Transduct Target Ther 2022; 7:42. [PMID: 35136040 PMCID: PMC8826850 DOI: 10.1038/s41392-022-00910-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 variants have evolved a variety of critical mutations, leading to antigenicity changes and immune escape. The recent emerging SARS-CoV-2 Omicron variant attracted global attention due to its significant resistance to current antibody therapies and vaccines. Here, we profiled the mutations of Omicron and other various circulating SARS-CoV-2 variants in parallel by computational interface analysis and in vitro experimental assays. We identified critical mutations that lead to antigenicity changes and diminished neutralization efficiency of a panel of 14 antibodies due to diverse molecular mechanisms influencing the antigen-antibody interaction. Our study identified that Omicron exhibited extraordinary potency in immune escape compared to the other variants of concern, and explores the application of computational interface analysis in SARS-CoV-2 mutation surveillance and demonstrates its potential for the early identification of concerning variants, providing preliminary guidance for neutralizing antibody therapy.
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23
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Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. PLoS Pathog 2022; 18:e1010248. [PMID: 35134084 PMCID: PMC8856557 DOI: 10.1371/journal.ppat.1010248] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/18/2022] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the "class 3" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Rachel T. Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Sandile Cele
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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24
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Rapp M, Shapiro L, Frank J. Contributions of single-particle cryoelectron microscopy toward fighting COVID-19. Trends Biochem Sci 2022; 47:117-123. [PMID: 34799235 PMCID: PMC8556535 DOI: 10.1016/j.tibs.2021.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022]
Abstract
Single-particle cryoelectron microscopy (cryo-EM), whose full capabilities have been realized only within the past decade, has had a pivotal role in the fight against COVID-19. This is due to the technique's intrinsic power to depict both structural and dynamic features of molecules; in this case, of the spike protein of SARS-CoV-2. By now, numerous cryo-EM studies have furthered our understanding of spike protein-angiotensin-converting enzyme 2 (ACE2) receptor interactions, which has informed the design of effective vaccines, and have enabled the characterization of neutralizing antibody binding sites, which will lead to the design of novel therapeutics as the virus evolves.
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Affiliation(s)
- Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA.
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA; Department of Biological Sciences, Columbia University, New York, USA.
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25
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Zimanyi CM, Kopylov M, Potter CS, Carragher B, Eng ET. Broadening access to cryoEM through centralized facilities. Trends Biochem Sci 2022; 47:106-116. [PMID: 34823974 PMCID: PMC8760164 DOI: 10.1016/j.tibs.2021.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/03/2023]
Abstract
Cryogenic electron microscopy (cryoEM) uses images of frozen hydrated biological specimens to produce macromolecular structures, opening up previously inaccessible levels of biological organization to high-resolution structural analysis. CryoEM has the potential for broad impact in biomedical research, including basic cell, molecular, and structural biology, and increasingly in drug discovery and vaccine development. Recent advances have led to the expansion of molecular and cellular structure determination at an exponential rate. National and regional centers have emerged to support this growth by increasing the accessibility of cryoEM throughout the biomedical research community. Through cooperation and synergy, these centers form a network of resources that accelerate the adoption of best practices for access and training and establish sustainable workflows to build future research capacity.
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Affiliation(s)
- Christina M. Zimanyi
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S. Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Correspondence: (E.T. Eng)
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26
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Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
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Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
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27
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Hwang YC, Lu RM, Su SC, Chiang PY, Ko SH, Ke FY, Liang KH, Hsieh TY, Wu HC. Monoclonal antibodies for COVID-19 therapy and SARS-CoV-2 detection. J Biomed Sci 2022; 29:1. [PMID: 34983527 PMCID: PMC8724751 DOI: 10.1186/s12929-021-00784-w] [Citation(s) in RCA: 131] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an exceptional public health crisis that demands the timely creation of new therapeutics and viral detection. Owing to their high specificity and reliability, monoclonal antibodies (mAbs) have emerged as powerful tools to treat and detect numerous diseases. Hence, many researchers have begun to urgently develop Ab-based kits for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ab drugs for use as COVID-19 therapeutic agents. The detailed structure of the SARS-CoV-2 spike protein is known, and since this protein is key for viral infection, its receptor-binding domain (RBD) has become a major target for therapeutic Ab development. Because SARS-CoV-2 is an RNA virus with a high mutation rate, especially under the selective pressure of aggressively deployed prophylactic vaccines and neutralizing Abs, the use of Ab cocktails is expected to be an important strategy for effective COVID-19 treatment. Moreover, SARS-CoV-2 infection may stimulate an overactive immune response, resulting in a cytokine storm that drives severe disease progression. Abs to combat cytokine storms have also been under intense development as treatments for COVID-19. In addition to their use as drugs, Abs are currently being utilized in SARS-CoV-2 detection tests, including antigen and immunoglobulin tests. Such Ab-based detection tests are crucial surveillance tools that can be used to prevent the spread of COVID-19. Herein, we highlight some key points regarding mAb-based detection tests and treatments for the COVID-19 pandemic.
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Affiliation(s)
- Yu-Chyi Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Ruei-Min Lu
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Chieh Su
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Pao-Yin Chiang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Han Ko
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Feng-Yi Ke
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Kang-Hao Liang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Tzung-Yang Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan.
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28
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Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HM, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter T, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Clemens SAC, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Ditse Z, Da Silva K, Madhi S, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KYA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.03.471045. [PMID: 34981049 PMCID: PMC8722586 DOI: 10.1101/2021.12.03.471045] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
On the 24 th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.
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Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M.E. Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M. Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiste Dijokaite
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Suman Khan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mohammad Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Oxford, UK
| | | | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Thomas Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel Pan
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust
- Department of Respiratory Sciences, University of Leicester
| | - Sara Assadi
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust
| | - Adam Bellass
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust
| | - Nikki Omo-Dare
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust
| | | | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Jenkin
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios- IOC/FIOCRUZ, Rio de Janeiro, Brazil
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Ditse
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | | | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alain R Townsend
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Kuan-Ying A. Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Miles W. Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J. Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | | | - Neil G. Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A. Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R. Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E. Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - David I. Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
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29
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Robinson SA, Raybould MIJ, Schneider C, Wong WK, Marks C, Deane CM. Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies. PLoS Comput Biol 2021; 17:e1009675. [PMID: 34898603 PMCID: PMC8700021 DOI: 10.1371/journal.pcbi.1009675] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 12/23/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. Sequence-based clonal clustering can identify antibodies with similar epitope complementarity, however, antibodies from markedly different lineages but with similar structures can engage the same epitope. We describe a novel computational method for epitope profiling based on structural modelling and clustering. Using the method, we demonstrate that sequence dissimilar but functionally similar antibodies can be found across the Coronavirus Antibody Database, with high accuracy (92% of antibodies in multiple-occupancy structural clusters bind to consistent domains). Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than is suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis. Antibodies are a key component of the immune system that combat pathogens by binding to a defined region of their molecular surface (known as an ‘epitope’). The ability to map which antibodies target the same epitopes is crucial when designing non-competing antibody therapeutics or predicting the influence of pathogen mutation on population immunity. While one can use laboratory experiments to deduce when pairs of antibodies engage the same epitope, such experiments are very expensive and time consuming if used to compare on the order of thousands of antibodies. In this work, we report a new computational algorithm (SPACE) that clusters antibodies that target the same epitope based on their predicted 3D structure, as binding site structure is a property often conserved between binders complementary to the same epitope. Unlike existing antibody epitope profiling tools which assume two antibodies must share a high sequence identity/similar genetic basis to engage the same region, our orthogonal method can detect broader patterns of convergent evolution across binders to different pathogen strains, and between antibodies with different genetic and even species origins.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/metabolism
- Antibody Specificity
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/genetics
- Antigen-Antibody Reactions/genetics
- Antigen-Antibody Reactions/immunology
- Antigens, Viral/chemistry
- COVID-19/immunology
- COVID-19/virology
- Computational Biology
- Coronavirus/chemistry
- Coronavirus/genetics
- Coronavirus/immunology
- Databases, Chemical
- Epitope Mapping
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Humans
- Mice
- Models, Molecular
- Pandemics
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Single-Domain Antibodies/immunology
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Affiliation(s)
- Sarah A Robinson
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Constantin Schneider
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Wing Ki Wong
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Claire Marks
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
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30
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Feldman J, Bals J, Altomare CG, St. Denis K, Lam EC, Hauser BM, Ronsard L, Sangesland M, Moreno TB, Okonkwo V, Hartojo N, Balazs AB, Bajic G, Lingwood D, Schmidt AG. Naive human B cells engage the receptor binding domain of SARS-CoV-2, variants of concern, and related sarbecoviruses. Sci Immunol 2021; 6:eabl5842. [PMID: 34648356 PMCID: PMC8720485 DOI: 10.1126/sciimmunol.abl5842] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Initial exposure to a pathogen elicits an adaptive immune response to control and eradicate the threat. Interrogating the abundance and specificity of the naive B cell repertoire drives understanding of how to mount protective responses. Here, we isolated naive B cells from eight seronegative human donors targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD). Single-cell B cell receptor (BCR) sequencing identified diverse gene usage and no restriction on complementarity determining region length. A subset of recombinant antibodies produced by naive B cell precursors bound to SARS-CoV-2 RBD and engaged circulating variants including B.1.1.7, B.1.351, and B.1.617.2, as well as preemergent bat-derived coronaviruses RaTG13, SHC104, and WIV1. By structural characterization of a naive antibody in complex with SARS-CoV-2 spike, we identified a conserved mode of recognition shared with infection-induced antibodies. We found that representative naive antibodies could signal in a B cell activation assay, and by using directed evolution, we could select for a higher-affinity RBD interaction, conferred by a single amino acid change. The minimally mutated, affinity-matured antibodies also potently neutralized SARS-CoV-2. Understanding the SARS-CoV-2 RBD–specific naive repertoire may inform potential responses capable of recognizing future SARS-CoV-2 variants or emerging coronaviruses, enabling the development of pan-coronavirus vaccines aimed at engaging protective germline responses.
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Affiliation(s)
- Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Clara G. Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kerri St. Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Evan C. Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Vintus Okonkwo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Nathania Hartojo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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31
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Hardenbrook NJ, Zhang P. A structural view of the SARS-CoV-2 virus and its assembly. Curr Opin Virol 2021; 52:123-134. [PMID: 34915287 PMCID: PMC8642146 DOI: 10.1016/j.coviro.2021.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/11/2021] [Accepted: 11/22/2021] [Indexed: 12/15/2022]
Abstract
Structural biology plays a vital role in SARS-CoV-2 vaccine and treatment. High-resolution structures of SARS-CoV-2 proteins and complexes have been obtained. In situ structures of SARS-CoV-2 virus and its assembly are visualized by cryoET.
The SARS-CoV-2 pandemic that struck in 2019 has left the world crippled with hundreds of millions of cases and millions of people dead. During this time, we have seen unprecedented support and collaboration amongst scientists to respond to this deadly disease. Advances in the field of structural biology, in particular cryoEM and cryo-electron tomography, have allowed unprecedented structural analysis of SARS-CoV-2. Here, we review the structural work on the SARS-CoV-2 virus and viral components, as well as its cellular assembly process, highlighting some important structural findings that have made significant impact on the protection from and treatment of emerging viral infections.
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Affiliation(s)
- Nathan J Hardenbrook
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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32
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Khan MI, Baig MH, Mondal T, Alorabi M, Sharma T, Dong JJ, Cho JY. Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. Viruses 2021; 13:2295. [PMID: 34835101 PMCID: PMC8625741 DOI: 10.3390/v13112295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 01/08/2023] Open
Abstract
The recent emergence of novel SARS-CoV-2 variants has threatened the efforts to contain the COVID-19 pandemic. The emergence of these "variants of concern" has increased immune escape and has supplanted the ancestral strains. The novel variants harbored by the B.1.617 lineage (kappa and delta) carry mutations within the receptor-binding domain of spike (S) protein (L452R + E484Q and L452R + T478K), the region binding to the host receptor. The double mutations carried by these novel variants are primarily responsible for an upsurge number of COVID-19 cases in India. In this study, we thoroughly investigated the impact of these double mutations on the binding capability to the human host receptor. We performed several structural analyses and found that the studied double mutations increase the binding affinity of the spike protein to the human host receptor (ACE2). Furthermore, our study showed that these double mutants might be a dominant contributor enhancing the receptor-binding affinity of SARS-CoV-2 and consequently making it more stable. We also investigated the impact of these mutations on the binding affinity of two monoclonal antibodies (Abs) (2-15 and LY-CoV555) and found that the presence of the double mutations also hinders its binding with the studied Abs. The principal component analysis, free energy landscape, intermolecular interaction, and other investigations provided a deeper structural insight to better understand the molecular mechanism responsible for increased viral transmissibility of these variants.
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Affiliation(s)
- Mohd Imran Khan
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea;
| | - Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Tanmoy Mondal
- Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, 41345 Gothenburg, Sweden;
| | - Mohammed Alorabi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Tanuj Sharma
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Jae-June Dong
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Jae Yong Cho
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea;
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Yang L, Li J, Guo S, Hou C, Liao C, Shi L, Ma X, Jiang S, Zheng B, Fang Y, Ye L, He X. SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. Int J Mol Sci 2021; 22:12114. [PMID: 34829998 PMCID: PMC8619214 DOI: 10.3390/ijms222212114] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Since 2020, the receptor-binding domain (RBD) of the spike protein of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been constantly mutating, producing most of the notable missense mutations in the context of "variants of concern", probably in response to the vaccine-driven alteration of immune profiles of the human population. The Delta variant, in particular, has become the most prevalent variant of the epidemic, and it is spreading in countries with the highest vaccination rates, causing the world to face the risk of a new wave of the contagion. Understanding the physical mechanism responsible for the mutation-induced changes in the RBD's binding affinity, its transmissibility, and its capacity to escape vaccine-induced immunity is the "urgent challenge" in the development of preventive measures, vaccines, and therapeutic antibodies against the coronavirus disease 2019 (COVID-19) pandemic. In this study, entropy-enthalpy compensation and the Gibbs free energy change were used to analyze the impact of the RBD mutations on the binding affinity of SARS-CoV-2 variants with the receptor angiotensin converting enzyme 2 (ACE2) and existing antibodies. Through the analysis, we found that the existing mutations have already covered almost all possible detrimental mutations that could result in an increase of transmissibility, and that a possible mutation in amino-acid position 498 of the RBD can potentially enhance its binding affinity. A new calculation method for the binding energies of protein-protein complexes is proposed based on the entropy-enthalpy compensation rule. All known structures of RBD-antibody complexes and the RBD-ACE2 complex comply with the entropy-enthalpy compensation rule in providing the driving force behind the spontaneous protein-protein docking. The variant-induced risk of breakthrough infections in vaccinated people is attributed to the L452R mutation's reduction of the binding affinity of many antibodies. Mutations reversing the hydrophobic or hydrophilic performance of residues in the spike RBD potentially cause breakthrough infections of coronaviruses due to the changes in geometric complementarity in the entropy-enthalpy compensations between antibodies and the virus at the binding sites.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Chenchen Liao
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education) and School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Yi Fang
- Mathematical Science Institute, The Australian National University, Canberra, ACT 0200, Australia;
| | - Lin Ye
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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Cerutti G, Guo Y, Wang P, Nair MS, Wang M, Huang Y, Yu J, Liu L, Katsamba PS, Bahna F, Reddem ER, Kwong PD, Ho DD, Sheng Z, Shapiro L. Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain. Cell Rep 2021; 37:109928. [PMID: 34706271 PMCID: PMC8519878 DOI: 10.1016/j.celrep.2021.109928] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023] Open
Abstract
Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic supersite in NTD (site 1). Here, we report the cryo-EM structure of a potent NTD-directed neutralizing antibody 5-7, which recognizes a site distinct from other potently neutralizing antibodies, inserting a binding loop into an exposed hydrophobic pocket between the two sheets of the NTD β sandwich. Interestingly, this pocket was previously identified as the binding site for hydrophobic molecules, including heme metabolites, but we observe that their presence does not substantially impede 5-7 recognition. Mirroring its distinctive binding, antibody 5-7 retains neutralization potency with many variants of concern (VOCs). Overall, we reveal that a hydrophobic pocket in NTD proposed for immune evasion can be used by the immune system for recognition.
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Affiliation(s)
- Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Fabiana Bahna
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Eswar R Reddem
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Peter D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Wang P, Casner RG, Nair MS, Yu J, Guo Y, Wang M, Chan JFW, Cerutti G, Iketani S, Liu L, Sheng Z, Chen Z, Yuen KY, Kwong PD, Huang Y, Shapiro L, Ho DD. A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.10.13.464307. [PMID: 34671769 PMCID: PMC8528075 DOI: 10.1101/2021.10.13.464307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses in vitro and confirmed that K378T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.
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Affiliation(s)
- Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Ryan G. Casner
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Manoj S. Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jasper F.-W. Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zhiwei Chen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Peter D. Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lawrence Shapiro
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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36
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Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.10.12.464114. [PMID: 34671768 PMCID: PMC8528074 DOI: 10.1101/2021.10.12.464114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the "class 3" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Rachel T. Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Khadija Khan
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Sandile Cele
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, WA 98195, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, WA 98195, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
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Wheatley AK, Pymm P, Esterbauer R, Dietrich MH, Lee WS, Drew D, Kelly HG, Chan LJ, Mordant FL, Black KA, Adair A, Tan HX, Juno JA, Wragg KM, Amarasena T, Lopez E, Selva KJ, Haycroft ER, Cooney JP, Venugopal H, Tan LL, O Neill MT, Allison CC, Cromer D, Davenport MP, Bowen RA, Chung AW, Pellegrini M, Liddament MT, Glukhova A, Subbarao K, Kent SJ, Tham WH. Landscape of human antibody recognition of the SARS-CoV-2 receptor binding domain. Cell Rep 2021; 37:109822. [PMID: 34610292 PMCID: PMC8463300 DOI: 10.1016/j.celrep.2021.109822] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/22/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022] Open
Abstract
Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike protein can exhibit neutralization resistance, potentially affecting the effectiveness of some antibody-based therapeutics. Here, the generation of a diverse panel of 91 human, neutralizing monoclonal antibodies provides an in-depth structural and phenotypic definition of receptor binding domain (RBD) antigenic sites on the viral spike. These RBD antibodies ameliorate SARS-CoV-2 infection in mice and hamster models in a dose-dependent manner and in proportion to in vitro, neutralizing potency. Assessing the effect of mutations in the spike protein on antibody recognition and neutralization highlights both potent single antibodies and stereotypic classes of antibodies that are unaffected by currently circulating VOCs, such as B.1.351 and P.1. These neutralizing monoclonal antibodies and others that bind analogous epitopes represent potentially useful future anti-SARS-CoV-2 therapeutics.
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Affiliation(s)
- Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Phillip Pymm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Robyn Esterbauer
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Melanie H Dietrich
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Damien Drew
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hannah G Kelly
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Francesca L Mordant
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Katrina A Black
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amy Adair
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kathleen M Wragg
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thakshila Amarasena
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Ester Lopez
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kevin J Selva
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Ebene R Haycroft
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - James P Cooney
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hariprasad Venugopal
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Li Lynn Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Matthew T O Neill
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Cody C Allison
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Deborah Cromer
- Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
| | - Richard A Bowen
- Laboratory of Animal Reproduction and Biotechnology, Colorado State University, Fort Collins, CO 80523, USA
| | - Amy W Chung
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Alisa Glukhova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia; Drug Discovery Biology, Monash Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville VIC 3052, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC 3004, Australia.
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
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38
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Ferreira IATM, Kemp SA, Datir R, Saito A, Meng B, Rakshit P, Takaori-Kondo A, Kosugi Y, Uriu K, Kimura I, Shirakawa K, Abdullahi A, Agarwal A, Ozono S, Tokunaga K, Sato K, Gupta RK. SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. J Infect Dis 2021; 224:989-994. [PMID: 34260717 PMCID: PMC8420622 DOI: 10.1093/infdis/jiab368] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/14/2022] Open
Abstract
The SARS-CoV-2 B.1.617 variant emerged in the Indian state of Maharashtra in late 2020. There have been fears that 2 key mutations seen in the receptor-binding domain, L452R and E484Q, would have additive effects on evasion of neutralizing antibodies. We report that spike bearing L452R and E484Q confers modestly reduced sensitivity to BNT162b2 mRNA vaccine-elicited antibodies following either first or second dose. The effect is similar in magnitude to the loss of sensitivity conferred by L452R or E484Q alone. These data demonstrate reduced sensitivity to vaccine-elicited neutralizing antibodies by L452R and E484Q but lack of synergistic loss of sensitivity.
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Affiliation(s)
- Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Cambridge,United Kingdom
- Department of Medicine, University of Cambridge, Cambridge,United Kingdom
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Cambridge,United Kingdom
- Department of Medicine, University of Cambridge, Cambridge,United Kingdom
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Cambridge,United Kingdom
- Department of Medicine, University of Cambridge, Cambridge,United Kingdom
| | - Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki,Japan
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Cambridge,United Kingdom
- Department of Medicine, University of Cambridge, Cambridge,United Kingdom
| | | | | | - Yusuke Kosugi
- Divisionof Systems Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Divisionof Systems Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Izumi Kimura
- Divisionof Systems Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Kyoto University, Kyoto,Japan
| | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Cambridge,United Kingdom
- Department of Medicine, University of Cambridge, Cambridge,United Kingdom
| | - Anurag Agarwal
- CSIR Institute of Genomics and Integrative Biology, Delhi,India
| | - Seiya Ozono
- Department of Pathology, National Institute of Infectious Diseases, Tokyo,Japan
| | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo,Japan
| | - Kei Sato
- Divisionof Systems Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama,Japan
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Cambridge,United Kingdom
- Department of Medicine, University of Cambridge, Cambridge,United Kingdom
- Africa Health Research Institute, Durban,South Africa
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39
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Chen EC, Gilchuk P, Zost SJ, Suryadevara N, Winkler ES, Cabel CR, Binshtein E, Chen RE, Sutton RE, Rodriguez J, Day S, Myers L, Trivette A, Williams JK, Davidson E, Li S, Doranz BJ, Campos SK, Carnahan RH, Thorne CA, Diamond MS, Crowe JE. Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals. Cell Rep 2021; 36:109604. [PMID: 34411541 PMCID: PMC8352653 DOI: 10.1016/j.celrep.2021.109604] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/13/2021] [Accepted: 08/04/2021] [Indexed: 01/02/2023] Open
Abstract
Unrelated individuals can produce genetically similar clones of antibodies, known as public clonotypes, which have been seen in responses to different infectious diseases, as well as healthy individuals. Here we identify 37 public clonotypes in memory B cells from convalescent survivors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or in plasmablasts from an individual after vaccination with mRNA-encoded spike protein. We identify 29 public clonotypes, including clones recognizing the receptor-binding domain (RBD) in the spike protein S1 subunit (including a neutralizing, angiotensin-converting enzyme 2 [ACE2]-blocking clone that protects in vivo) and others recognizing non-RBD epitopes that bind the S2 domain. Germline-revertant forms of some public clonotypes bind efficiently to spike protein, suggesting these common germline-encoded antibodies are preconfigured for avid recognition. Identification of large numbers of public clonotypes provides insight into the molecular basis of efficacy of SARS-CoV-2 vaccines and sheds light on the immune pressures driving the selection of common viral escape mutants.
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Affiliation(s)
- Elaine C Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Emma S Winkler
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Carly R Cabel
- Department of Cellular & Molecular Medicine, University of Arizona College of Medicine, Tucson, AZ 85724, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85724, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Rachel E Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jessica Rodriguez
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Samuel Day
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Luke Myers
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew Trivette
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | | | - Shuaizhi Li
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | | | - Samuel K Campos
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85724, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Curtis A Thorne
- Department of Cellular & Molecular Medicine, University of Arizona College of Medicine, Tucson, AZ 85724, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85724, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - James E Crowe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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40
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Yuan M, Huang D, Lee CCD, Wu NC, Jackson AM, Zhu X, Liu H, Peng L, van Gils MJ, Sanders RW, Burton DR, Reincke SM, Prüss H, Kreye J, Nemazee D, Ward AB, Wilson IA. Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Science 2021; 373:818-823. [PMID: 34016740 PMCID: PMC8284396 DOI: 10.1126/science.abh1139] [Citation(s) in RCA: 255] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
Neutralizing antibodies (nAbs) elicited against the receptor binding site (RBS) of the spike protein of wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are generally less effective against recent variants of concern. RBS residues Glu484, Lys417, and Asn501 are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on angiotensin-converting enzyme 2 binding, as well as the effects of two of these mutations (K417N and E484K) on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternative binding modes, are abrogated by K417N, E484K, or both. These effects can be structurally explained by their extensive interactions with RBS nAbs. However, nAbs to the more conserved, cross-neutralizing CR3022 and S309 sites were largely unaffected. The results have implications for next-generation vaccines and antibody therapies.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antigenic Variation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Binding Sites
- Binding Sites, Antibody
- COVID-19/immunology
- COVID-19/virology
- Epitopes
- Humans
- Immune Evasion
- Mutation
- Protein Binding
- Protein Domains
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - S Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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41
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Feldman J, Bals J, Altomare CG, St Denis K, Lam EC, Hauser BM, Ronsard L, Sangesland M, Moreno TB, Okonkwo V, Hartojo N, Balazs AB, Bajic G, Lingwood D, Schmidt AG. Naive human B cells engage the receptor binding domain of SARS-CoV-2, variants of concern, and related sarbecoviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33594359 PMCID: PMC7885909 DOI: 10.1101/2021.02.02.429458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exposure to a pathogen elicits an adaptive immune response aimed to control and eradicate. Interrogating the abundance and specificity of the naive B cell repertoire contributes to understanding how to potentially elicit protective responses. Here, we isolated naive B cells from 8 seronegative human donors targeting the SARS-CoV-2 receptor-binding domain (RBD). Single B cell analysis showed diverse gene usage with no restricted complementarity determining region lengths. We show that recombinant antibodies engage SARS-CoV-2 RBD, circulating variants, and pre-emergent coronaviruses. Representative antibodies signal in a B cell activation assay and can be affinity matured through directed evolution. Structural analysis of a naive antibody in complex with spike shows a conserved mode of recognition shared with infection-induced antibodies. Lastly, both naive and affinity-matured antibodies can neutralize SARS-CoV-2. Understanding the naive repertoire may inform potential responses recognizing variants or emerging coronaviruses enabling the development of pan-coronavirus vaccines aimed at engaging germline responses. Isolation of antibody germline precursors targeting the receptor binding domain of coronaviruses.
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Affiliation(s)
- Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Clara G Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kerri St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Evan C Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Vintus Okonkwo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Nathania Hartojo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.,Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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42
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Cerutti G, Rapp M, Guo Y, Bahna F, Bimela J, Reddem ER, Yu J, Wang P, Liu L, Huang Y, Ho DD, Kwong PD, Sheng Z, Shapiro L. Structural basis for accommodation of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing antibodies. Structure 2021; 29:655-663.e4. [PMID: 34111408 PMCID: PMC8188728 DOI: 10.1016/j.str.2021.05.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/11/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022]
Abstract
Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively, show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical concern. However, the neutralization potency of two antibodies, 1-57 and 2-7, which target the receptor-binding domain (RBD) of the spike, was unaffected by these emerging strains. Here, we report cryo-EM structures of 1-57 and 2-7 in complex with spike, revealing each of these antibodies to utilize a distinct mechanism to bypass or accommodate RBD mutations. Notably, each antibody represented an immune response with recognition distinct from those of frequent antibody classes. Moreover, many epitope residues recognized by 1-57 and 2-7 were outside hotspots of evolutionary pressure for ACE2 binding and neutralizing antibody escape. We suggest the therapeutic use of antibodies, such as 1-57 and 2-7, which target less prevalent epitopes, could ameliorate issues of monoclonal antibody escape.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Binding Sites
- Cloning, Molecular
- Cryoelectron Microscopy
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Epitopes/metabolism
- Gene Expression
- HEK293 Cells
- Humans
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Receptors, Virus/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Recombinant Proteins/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Fabiana Bahna
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Jude Bimela
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Eswar R Reddem
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Peter D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Pymm P, Adair A, Chan LJ, Cooney JP, Mordant FL, Allison CC, Lopez E, Haycroft ER, O'Neill MT, Tan LL, Dietrich MH, Drew D, Doerflinger M, Dengler MA, Scott NE, Wheatley AK, Gherardin NA, Venugopal H, Cromer D, Davenport MP, Pickering R, Godfrey DI, Purcell DFJ, Kent SJ, Chung AW, Subbarao K, Pellegrini M, Glukhova A, Tham WH. Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Proc Natl Acad Sci U S A 2021; 118:e2101918118. [PMID: 33893175 PMCID: PMC8126837 DOI: 10.1073/pnas.2101918118] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensin-converting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody-Fc or as mixtures reduced viral loads by up to 104-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2.
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Affiliation(s)
- Phillip Pymm
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amy Adair
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Li-Jin Chan
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - James P Cooney
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Francesca L Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Cody C Allison
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Ester Lopez
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Ebene R Haycroft
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Matthew T O'Neill
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Li Lynn Tan
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Melanie H Dietrich
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Damien Drew
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Marcel Doerflinger
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael A Dengler
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hariprasad Venugopal
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Deborah Cromer
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raelene Pickering
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amy W Chung
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Marc Pellegrini
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alisa Glukhova
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Drug Discovery Biology, Monash Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Wai-Hong Tham
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
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Valdez-Cruz NA, García-Hernández E, Espitia C, Cobos-Marín L, Altamirano C, Bando-Campos CG, Cofas-Vargas LF, Coronado-Aceves EW, González-Hernández RA, Hernández-Peralta P, Juárez-López D, Ortega-Portilla PA, Restrepo-Pineda S, Zelada-Cordero P, Trujillo-Roldán MA. Integrative overview of antibodies against SARS-CoV-2 and their possible applications in COVID-19 prophylaxis and treatment. Microb Cell Fact 2021; 20:88. [PMID: 33888152 PMCID: PMC8061467 DOI: 10.1186/s12934-021-01576-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/03/2021] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2 is a novel β-coronavirus that caused the COVID-19 pandemic disease, which spread rapidly, infecting more than 134 million people, and killing almost 2.9 million thus far. Based on the urgent need for therapeutic and prophylactic strategies, the identification and characterization of antibodies has been accelerated, since they have been fundamental in treating other viral diseases. Here, we summarized in an integrative manner the present understanding of the immune response and physiopathology caused by SARS-CoV-2, including the activation of the humoral immune response in SARS-CoV-2 infection and therefore, the synthesis of antibodies. Furthermore, we also discussed about the antibodies that can be generated in COVID-19 convalescent sera and their associated clinical studies, including a detailed characterization of a variety of human antibodies and identification of antibodies from other sources, which have powerful neutralizing capacities. Accordingly, the development of effective treatments to mitigate COVID-19 is expected. Finally, we reviewed the challenges faced in producing potential therapeutic antibodies and nanobodies by cell factories at an industrial level while ensuring their quality, efficacy, and safety.
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Affiliation(s)
- Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México.
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Laura Cobos-Marín
- Facultad de Medicina Veterinaria Y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Claudia Altamirano
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil N° 2950, Valparaíso, Chile
| | - Carlos G Bando-Campos
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Luis F Cofas-Vargas
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Enrique W Coronado-Aceves
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Ricardo A González-Hernández
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Pablo Hernández-Peralta
- Facultad de Medicina Veterinaria Y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Daniel Juárez-López
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Paola A Ortega-Portilla
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Sara Restrepo-Pineda
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Patricio Zelada-Cordero
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México.
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