1
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Jana ID, Kanjo K, Roy S, Bhasin M, Bhattacharya S, Banerjee I, Jana S, Chatterjee A, Chakrabarti AK, Chakraborty S, Mukherjee B, Varadarajan R, Mondal A. Early 2022 breakthrough infection sera from India target the conserved cryptic class 5 epitope to counteract immune escape by SARS-CoV-2 variants. J Virol 2025; 99:e0005125. [PMID: 40135898 PMCID: PMC11998512 DOI: 10.1128/jvi.00051-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2025] [Accepted: 02/24/2025] [Indexed: 03/27/2025] Open
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, the vast majority of epitope mapping studies have focused on sera from mRNA-vaccinated populations from high-income countries. In contrast, here, we report an analysis of 164 serum samples isolated from patients with breakthrough infection in India during early 2022 who received two doses of the ChAdOx viral vector vaccine. Sera were screened for neutralization breadth against wild-type (WT), Kappa, Delta, and Omicron BA.1 viruses. Three sera with the highest neutralization breadth and potency were selected for epitope mapping, using charged scanning mutagenesis coupled with yeast surface display and next-generation sequencing. The mapped sera primarily targeted the recently identified class 5 cryptic epitope and, to a lesser extent, the class 1 and class 4 epitopes. The class 5 epitope is completely conserved across all severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and for most sarbecoviruses. Based on these observations, an additional 26 sera were characterized, and all showed a broad neutralizing activity, including against XBB.1.5. This is in contrast with the results obtained with the sera from individuals receiving multiple doses of original and updated mRNA vaccines, where impaired neutralization of XBB and later variants of concern (VOCs) were observed. Our study demonstrates that two doses of the ChAdOx vaccine in a highly exposed population were sufficient to drive substantial neutralization breadth against emerging and upcoming variants of concern. These data highlight the important role of hybrid immunity in conferring broad protection and inform future vaccine strategies to protect against rapidly mutating viruses. IMPORTANCE Worldwide implementation of coronavirus disease 2019 (COVID-19) vaccines and the parallel emergence of newer severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have shaped the humoral immune response in a population-specific manner. While characterizing this immune response is important for monitoring disease progression at the population level, it is also imperative for developing effective countermeasures in the form of novel vaccines and therapeutics. India has implemented the world's second largest COVID-19 vaccination drive and encountered a large number of post-vaccination "breakthrough" infections. From a cohort of patients with breakthrough infection, we identified individuals whose sera showed broadly neutralizing immunity against different SARS-CoV-2 variants. Interestingly, these sera primarily target a novel cryptic epitope, which was not identified in previous population-level studies conducted in Western countries. This rare cryptic epitope remains conserved across all SARS-CoV-2 variants, including recently emerged ones and for the SARS-like coronaviruses that may cause future outbreaks, thus representing a potential target for future vaccines.
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Affiliation(s)
- Indrani Das Jana
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Kawkab Kanjo
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Subhanita Roy
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Munmun Bhasin
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Shatarupa Bhattacharya
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Indranath Banerjee
- B.C. Roy Technology Hospital, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | | | - Alok Kumar Chakrabarti
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Budhaditya Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | - Arindam Mondal
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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2
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Atarashi Y, Kim J, Irino Y, Amano M, Tsuchiya K, Maeda K, Terada M, Iwamoto N, Shimada S, Mitsuya H, Yanagida M, Takamatsu Y. A high-throughput, fully automated competition assay to evaluate SARS-CoV-2 neutralizing responses and epitope specificity in clinical samples. Sci Rep 2025; 15:11589. [PMID: 40185856 PMCID: PMC11971398 DOI: 10.1038/s41598-025-94317-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Accepted: 03/12/2025] [Indexed: 04/07/2025] Open
Abstract
Coronavirus disease-2019 (COVID-19) remains a critical global health concern. We developed a fully automated, high-throughput competition immunoassay to elucidate how epitope recognition on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike receptor-binding domain (RBD) correlates with neutralizing activity. Analysis of clinical samples from both SARS-CoV-2-infected and vaccinated individuals revealed that vaccination elicits significantly higher antibody titers across multiple S1 subunit epitopes compared to natural infection. Notably, median antibody levels against the receptor-binding motif (RBM) exceeded 50% in both cohorts, highlighting the RBM as a key target for antibody induction irrespective of immune origin. Furthermore, the strongest correlation with neutralizing activity was observed for antibodies directed against the broader S1 subunit, indicating that epitopes outside the RBM also contribute to neutralization. These findings underscore the importance of both RBM- and non-RBM-directed antibodies in effective immune defense against SARS-CoV-2. Our assay enables large-scale, reliable quantification of neutralizing antibodies and provides critical insights for developing improved diagnostic antigens and vaccine strategies aimed at eliciting robust, multi-epitope immune responses.
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Affiliation(s)
- Yusuke Atarashi
- Central Research Laboratories, Sysmex Corporation, Kobe, 651-2271, Japan
| | - Jeeeun Kim
- Central Research Laboratories, Sysmex Corporation, Kobe, 651-2271, Japan
| | - Yasuhiro Irino
- Central Research Laboratories, Sysmex Corporation, Kobe, 651-2271, Japan
| | - Masayuki Amano
- Department of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Kiyoto Tsuchiya
- AIDS Clinical Center, Center hospital of the National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Kenji Maeda
- Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
- Division of Antiviral Therapy, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan, 890-8544
| | - Mari Terada
- Department of Disease Control Center, Center Hospital of the National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Noriko Iwamoto
- Department of Disease Control Center, Center Hospital of the National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Shinya Shimada
- Japan Community Healthcare Organization, Kumamoto General Hospital, 866- 8660, Kumamoto, Japan
| | - Hiroaki Mitsuya
- Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, 20892-1868, Bethesda, MD, USA
- Division of Clinical Sciences, Kumamoto University Hospital, 860-8556, Kumamoto, Japan
| | - Masatoshi Yanagida
- Central Research Laboratories, Sysmex Corporation, Kobe, 651-2271, Japan
| | - Yuki Takamatsu
- Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
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3
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Liu J, Wu Y, Gao GF. A Structural Voyage Toward the Landscape of Humoral and Cellular Immune Escapes of SARS-CoV-2. Immunol Rev 2025; 330:e70000. [PMID: 39907512 DOI: 10.1111/imr.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Accepted: 01/08/2025] [Indexed: 02/06/2025]
Abstract
The genome-based surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the past nearly 5 years since its emergence has refreshed our understanding of virus evolution, especially on convergent co-evolution with the host. SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations that affect the functional properties of the virus by altering its infectivity, virulence, transmissibility, and interactions with host immunity. This poses a huge challenge to global prevention and control measures based on drug treatment and vaccine application. As one of the key evasion strategies in response to the immune profile of the human population, there are overwhelming amounts of evidence for the reduced antibody neutralization of SARS-CoV-2 variants. Additionally, data also suggest that the levels of CD4+ and CD8+ T-cell responses against variants or sub-variants decrease in the populations, although non-negligible cross-T-cell responses are maintained. Herein, from the perspectives of structural immunology, we outline the characteristics and mechanisms of the T cell and antibody responses to SARS-CoV and its variants/sub-variants. The molecular bases for the impact of the immune escaping variants on the interaction of the epitopes with the key receptors in adaptive immunity, that is, major histocompatibility complex (MHC), T-cell receptor (TCR), and antibody are summarized and discussed, the knowledge of which will widen our understanding of this pandemic-threatening virus and assist the preparedness for Pathogen X in the future.
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Affiliation(s)
- Jun Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yan Wu
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- The D. H. Chen School of Universal Health, Zhejiang University, Hangzhou, China
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4
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Mazigi O, Langley DB, Henry JY, Burnett DL, Sobti M, Walker GJ, Rouet R, Balachandran H, Lenthall H, Jackson J, Ubiparipovic S, Schofield P, Brown SHJ, Schulz SR, Hoffmann M, Pöhlmann S, Post J, Martinello M, Ahlenstiel G, Kelleher A, Rawlinson WD, Turville SG, Bull RA, Stewart AG, Jäck HM, Goodnow CC, Christ D. Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies. Proc Natl Acad Sci U S A 2025; 122:e2417544121. [PMID: 39746041 PMCID: PMC11725916 DOI: 10.1073/pnas.2417544121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 12/02/2024] [Indexed: 01/04/2025] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOCs) has greatly diminished the neutralizing activity of previously FDA-approved monoclonal antibodies (mAbs), including that of antibody cocktails and of first-generation broadly neutralizing antibodies such as S309 (Sotrovimab). In contrast, antibodies targeting cryptic conformational epitopes of the receptor binding domain (RBD) have demonstrated broad activity against emerging variants, but exert only moderate neutralizing activity, which has so far hindered clinical development. Here, we utilize in vitro display technology to identify and affinity-mature antibodies targeting the cryptic class 6 epitope, accessible only in the "up" conformation of the SARS-CoV-2 spike trimer. Increasing antibody affinity into the low picomolar range endowed potent neutralization of VOCs and protection of hACE2 mice from viral challenge. Cryoelectron microscopy and crystal structures of two affinity-matured antibodies (4C12-B12 and 4G1-C2) in complex with RBD highlighted binding modes and epitopes distal from mutational hotspots commonly overserved in VOCs, providing direct structural insights into the observed mutational resistance. Moreover, we further demonstrate that antibodies targeting the class 6 epitope, rather than being an artifact of in vitro selection, are common in the IgG1+ memory B cell repertoire of convalescent patients and can be induced in human antibody V-gene transgenic mice through immunization. Our results highlight the importance of very high (picomolar) affinity in the development of neutralizing antibodies and vaccines and suggest an affinity threshold in the provision of broad and long-lasting immunity against SARS-CoV-2.
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Affiliation(s)
- Ohan Mazigi
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
| | - David B. Langley
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
| | - Jake Y. Henry
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
| | - Deborah L. Burnett
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, School of Biomedical Sciences, Faculty of Medicine, Sydney, NSW2052, Australia
| | - Meghna Sobti
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
- Victor Chang Cardiac Research Institute, Sydney, NSW2010, Australia
| | - Gregory J. Walker
- University of New South Wales Sydney, School of Biomedical Sciences, Faculty of Medicine, Sydney, NSW2052, Australia
- Prince of Wales Hospital, Sydney, NSW2031, Australia
| | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
| | - Harikrishnan Balachandran
- University of New South Wales Sydney, School of Biomedical Sciences, Faculty of Medicine, Sydney, NSW2052, Australia
- Kirby Institute, University of New South Wales Sydney, Sydney, NSW2033, Australia
| | - Helen Lenthall
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
| | - Stephanie Ubiparipovic
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
| | - Simon H. J. Brown
- School of Chemistry and Molecular Bioscience, Molecular Horizons, and Australian Research Council Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW2522, Australia
| | - Sebastian R. Schulz
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen-Nürnberg91054, Germany
- University Hospital Erlangen, Erlangen-Nürnberg91054, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen37077, Germany
- Faculty of Biology and Psychology, Georg-August University Göttingen, Göttingen37073, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen37077, Germany
- Faculty of Biology and Psychology, Georg-August University Göttingen, Göttingen37073, Germany
| | - Jeffrey Post
- Prince of Wales Hospital, Sydney, NSW2031, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales Australia, Sydney, NSW2031, Australia
| | - Marianne Martinello
- Kirby Institute, University of New South Wales Sydney, Sydney, NSW2033, Australia
| | - Golo Ahlenstiel
- Blacktown Mt. Druitt Hospital, Blacktown, NSW2148, Australia
| | - Anthony Kelleher
- Kirby Institute, University of New South Wales Sydney, Sydney, NSW2033, Australia
| | - William D. Rawlinson
- University of New South Wales Sydney, School of Biomedical Sciences, Faculty of Medicine, Sydney, NSW2052, Australia
- Prince of Wales Hospital, Sydney, NSW2031, Australia
| | - Stuart G. Turville
- University of New South Wales Sydney, School of Biomedical Sciences, Faculty of Medicine, Sydney, NSW2052, Australia
- Kirby Institute, University of New South Wales Sydney, Sydney, NSW2033, Australia
| | - Rowena A. Bull
- University of New South Wales Sydney, School of Biomedical Sciences, Faculty of Medicine, Sydney, NSW2052, Australia
- Kirby Institute, University of New South Wales Sydney, Sydney, NSW2033, Australia
| | - Alastair G. Stewart
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
- Victor Chang Cardiac Research Institute, Sydney, NSW2010, Australia
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen-Nürnberg91054, Germany
- University Hospital Erlangen, Erlangen-Nürnberg91054, Germany
| | - Christopher C. Goodnow
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, School of Biomedical Sciences, Faculty of Medicine, Sydney, NSW2052, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW2010, Australia
- University of New South Wales Sydney, St. Vincent’s Clinical School, Faculty of Medicine, Sydney, NSW2010, Australia
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5
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Yuan M, Wilson IA. Structural Immunology of SARS-CoV-2. Immunol Rev 2025; 329:e13431. [PMID: 39731211 PMCID: PMC11727448 DOI: 10.1111/imr.13431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 12/10/2024] [Indexed: 12/29/2024]
Abstract
The SARS-CoV-2 spike (S) protein has undergone significant evolution, enhancing both receptor binding and immune evasion. In this review, we summarize ongoing efforts to develop antibodies targeting various epitopes of the S protein, focusing on their neutralization potency, breadth, and escape mechanisms. Antibodies targeting the receptor-binding site (RBS) typically exhibit high neutralizing potency but are frequently evaded by mutations in SARS-CoV-2 variants. In contrast, antibodies targeting conserved regions, such as the S2 stem helix and fusion peptide, exhibit broader reactivity but generally lower neutralization potency. However, several broadly neutralizing antibodies have demonstrated exceptional efficacy against emerging variants, including the latest omicron subvariants, underscoring the potential of targeting vulnerable sites such as RBS-A and RBS-D/CR3022. We also highlight public classes of antibodies targeting different sites on the S protein. The vulnerable sites targeted by public antibodies present opportunities for germline-targeting vaccine strategies. Overall, developing escape-resistant, potent antibodies and broadly effective vaccines remains crucial for combating future variants. This review emphasizes the importance of identifying key epitopes and utilizing antibody affinity maturation to inform future therapeutic and vaccine design.
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
- The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
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6
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Guerra D, Radić L, Brinkkemper M, Poniman M, van der Maas L, Torres JL, Ward AB, Sliepen K, Schinkel J, Sanders RW, van Gils MJ, Beaumont T. Broadening sarbecovirus neutralization with bispecific antibodies combining distinct conserved targets on the receptor binding domain. Hum Vaccin Immunother 2024; 20:2388344. [PMID: 39165108 PMCID: PMC11340772 DOI: 10.1080/21645515.2024.2388344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/05/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024] Open
Abstract
Monoclonal neutralizing antibodies (mAbs) are considered an important prophylactic against SARS-CoV-2 infection in at-risk populations and a strategy to counteract future sarbecovirus-induced disease. However, most mAbs isolated so far neutralize only a few sarbecovirus strains. Therefore, there is a growing interest in bispecific antibodies (bsAbs) which can simultaneously target different spike epitopes and thereby increase neutralizing breadth and prevent viral escape. Here, we generate and characterize a panel of 30 novel broadly reactive bsAbs using an efficient controlled Fab-arm exchange protocol. We specifically combine some of the broadest mAbs described so far, which target conserved epitopes on the receptor binding domain (RBD). Several bsAbs show superior cross-binding and neutralization compared to the parental mAbs and cocktails against sarbecoviruses from diverse clades, including recent SARS-CoV-2 variants. BsAbs which include mAb COVA2-02 are among the most potent and broad combinations. As a result, we study the unknown epitope of COVA2-02 and show that this mAb targets a distinct conserved region at the base of the RBD, which could be of interest when designing next-generation bsAb constructs to contribute to a better pandemic preparedness.
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Affiliation(s)
- Denise Guerra
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Laura Radić
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Mitch Brinkkemper
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Lara van der Maas
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, USA
| | - Jonathan L. Torres
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, USA
| | - Andrew B. Ward
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, USA
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Tim Beaumont
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
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7
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Michalewicz K, Barahona M, Bravi B. ANTIPASTI: Interpretable prediction of antibody binding affinity exploiting normal modes and deep learning. Structure 2024; 32:2422-2434.e5. [PMID: 39461331 DOI: 10.1016/j.str.2024.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/30/2024] [Accepted: 10/01/2024] [Indexed: 10/29/2024]
Abstract
The high binding affinity of antibodies toward their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as research and therapeutic tools. Here, we propose ANTIPASTI, a convolutional neural network model that achieves state-of-the-art performance in the prediction of antibody binding affinity using as input a representation of antibody-antigen structures in terms of normal mode correlation maps derived from elastic network models. This representation captures not only structural features but energetic patterns of local and global residue fluctuations. The learnt representations are interpretable: they reveal similarities of binding patterns among antibodies targeting the same antigen type, and can be used to quantify the importance of antibody regions contributing to binding affinity. Our results show the importance of the antigen imprint in the normal mode landscape, and the dominance of cooperative effects and long-range correlations between antibody regions to determine binding affinity.
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Affiliation(s)
- Kevin Michalewicz
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK.
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK
| | - Barbara Bravi
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK.
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8
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Zhang H, Wang Z, Nguyen HTT, Cornejo Pontelli M, Qi W, Rao L, Liu Z, Whelan SPJ, Zhu J. Facilitating and restraining virus infection using cell-attachable soluble viral receptors. Proc Natl Acad Sci U S A 2024; 121:e2414583121. [PMID: 39480852 PMCID: PMC11551432 DOI: 10.1073/pnas.2414583121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 10/02/2024] [Indexed: 11/02/2024] Open
Abstract
SARS-CoV-2 uses the receptor binding domain (RBD) of its spike protein to recognize and infect host cells by binding to the cell surface receptor angiotensin converting enzyme 2 (ACE2). The ACE2 receptor is composed of peptidase domain (PD), collectrin-like domain, transmembrane domain, and short cytoplasmic domain, and may exist as a dimer on cell surface. The RBD binding site is located atop of the ACE2 PD, but the involvement of other domains in virus infection is uncertain. We found that the ACE2 PD alone, whether anchored to cell membrane via a glycosylphosphatidylinositol anchor or attached to another surface protein, is fully functional as a receptor for spike-mediated cell fusion and virus infection. However, for ACE2 to function as the viral receptor, the RBD binding site must be positioned in close proximity to the cell membrane. Elevating the surface height of ACE2 using long and rigid protein spacers reduces or eliminates cell fusion and virus infection. Moreover, we found that the RBD-targeting neutralizing antibodies, nanobodies, and de novo designed miniprotein binders, when present on cell surface, also act as viral receptors, facilitating cell fusion and virus infection. Our data demonstrate that RBD binding and close membrane proximity are essential properties for a receptor to effectively mediate SARS-CoV-2 infection. Importantly, we show that soluble RBD-binders can be engineered to make cells either susceptible or resistant to virus infection, which has significant implications for antiviral therapy and various virus-mediated applications.
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Affiliation(s)
- Heng Zhang
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Zhengli Wang
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Huong T. T. Nguyen
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | | | - Wanrong Qi
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Liem Rao
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO63110
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO63110
| | - Jieqing Zhu
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
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9
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Wang WJ, Tang HT, Ou SC, Shen WJ, Chen CY, Li YC, Chang SY, Chang WC, Hsueh PR, Huang ST, Hung MC. Novel SARS-CoV-2 inhibition properties of the anti-cancer Kang Guan Recipe herbal formula. Cancer Lett 2024; 604:217198. [PMID: 39197583 DOI: 10.1016/j.canlet.2024.217198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/07/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024]
Abstract
The ongoing COVID-19 pandemic is a persistent challenge, with continued breakthrough infections despite vaccination efforts. This has spurred interest in alternative preventive measures, including dietary and herbal interventions. Previous research has demonstrated that herbal medicines can not only inhibit cancer progression but also combat viral infections, including COVID-19 by targeting SARS-CoV-2, indicating a multifaceted potential to address both viruses and cancer. Here, we found that the Kang Guan Recipe (KGR), a novel herbal medicine formula, associates with potent inhibition activity against the SARS-CoV-2 viral infection. We demonstrate that KGR exhibits inhibitory activity against several SARS-CoV-2 variants of concern (VOCs). Mechanistically, we found that KGR can block the interaction of the viral spike and human angiotensin-converting enzyme 2 (ACE2). Furthermore, we assessed the inhibitory effect of KGR on SARS-CoV-2 viral entry in vivo, observing that serum samples from healthy human subjects having taken KGR exhibited suppressive activity against SARS-CoV-2 variants. Our investigation provides valuable insights into the potential of KGR as a novel herbal-based preventive and therapeutic strategy against COVID-19.
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Affiliation(s)
- Wei-Jan Wang
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan; Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Hsuan-Ting Tang
- Department of Chinese Medicine, China Medical University Hospital, Taichung, 40402, Taiwan
| | - Shi-Chen Ou
- Department of Chinese Medicine, China Medical University Hospital, Taichung, 40402, Taiwan; School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Wan-Jou Shen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Chung-Yu Chen
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Yi-Chuan Li
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan
| | - Sui-Yuan Chang
- Dept of Clinical Laboratory Sciences and Medical Biotchnology, National Taiwan University College of Medicine, Taipei, Taiwan; Dept of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Chao Chang
- Center for Molecular Medicine, China Medical University Hospital, Taichung, 40402, Taiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, Taichung, Taiwan; PhD Program for Aging, School of Medicine, China Medical University, Taichung, Taiwan; Department of Laboratory Medicine, School of Medicine, China Medical University, Taichung, Taiwan
| | - Sheng-Teng Huang
- Department of Chinese Medicine, China Medical University Hospital, Taichung, 40402, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan; Research Cancer Center for Traditional Chinese Medicine, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; An-Nan Hospital, China Medical University, Tainan, Taiwan.
| | - Mien-Chie Hung
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung, 40402, Taiwan; Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan.
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10
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Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF. Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure 2024; 32:1055-1067.e6. [PMID: 39013463 DOI: 10.1016/j.str.2024.06.012] [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: 02/05/2024] [Revised: 05/16/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024]
Abstract
The recently emerged BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 variants have a growth advantage. In this study, we explore the structural bases of receptor binding and immune evasion for the Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Our findings reveal that BA.2.86 exhibits strong receptor binding, whereas its JN.1 sub-lineage displays a decreased binding affinity to human ACE2 (hACE2). Through complex structure analyses, we observed that the reversion of R493Q in BA.2.86 receptor binding domain (RBD) plays a facilitating role in receptor binding, while the L455S substitution in JN.1 RBD restores optimal affinity. Furthermore, the structure of monoclonal antibody (mAb) S309 complexed with BA.2.86 RBD highlights the importance of the K356T mutation, which brings a new N-glycosylation motif, altering the binding pattern of mAbs belonging to RBD-5 represented by S309. These findings emphasize the importance of closely monitoring BA.2.86 and its sub-lineages to prevent another wave of SARS-CoV-2 infections.
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MESH Headings
- Humans
- SARS-CoV-2/immunology
- SARS-CoV-2/metabolism
- SARS-CoV-2/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Immune Evasion
- Protein Binding
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- COVID-19/immunology
- COVID-19/virology
- COVID-19/metabolism
- Binding Sites
- Models, Molecular
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Mutation
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Affiliation(s)
- Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Beijing Life Science Academy, Beijing, China
| | - Kaiyuan Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Yuhang Gu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Junqing Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | | | - Xiaomei Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Guanghui Yu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hui Tan
- Shenzhen Children's Hospital, Shenzhen, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiaopeng Ma
- Shenzhen Children's Hospital, Shenzhen, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Beijing Life Science Academy, Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Beijing Life Science Academy, Beijing, China; College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China.
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11
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Chen J, Sun J, Xu Z, Li L, Kang X, Luo C, Wang Q, Guo X, Li Y, Liu K, Wu Y. The binding and structural basis of fox ACE2 to RBDs from different sarbecoviruses. Virol Sin 2024; 39:609-618. [PMID: 38866203 PMCID: PMC11401476 DOI: 10.1016/j.virs.2024.06.004] [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: 03/19/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Foxes are susceptible to SARS-CoV-2 in laboratory settings, and there have also been reports of natural infections of both SARS-CoV and SARS-CoV-2 in foxes. In this study, we assessed the binding capacities of fox ACE2 to important sarbecoviruses, including SARS-CoV, SARS-CoV-2, and animal-origin SARS-CoV-2 related viruses. Our findings demonstrated that fox ACE2 exhibits broad binding capabilities to receptor-binding domains (RBDs) of sarbecoviruses. We further determined the cryo-EM structures of fox ACE2 complexed with RBDs of SARS-CoV, SARS-CoV-2 prototype (PT), and Omicron BF.7. Through structural analysis, we identified that the K417 mutation can weaken the ability of SARS-CoV-2 sub-variants to bind to fox ACE2, thereby reducing the susceptibility of foxes to SARS-CoV-2 sub-variants. In addition, the Y498 residue in the SARS-CoV RBD plays a crucial role in forming a vital cation-π interaction with K353 in the fox ACE2 receptor. This interaction is the primary determinant for the higher affinity of the SARS-CoV RBD compared to that of the SARS-CoV-2 PT RBD. These results indicate that foxes serve as potential hosts for numerous sarbecoviruses, highlighting the critical importance of surveillance efforts.
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Affiliation(s)
- Junsen Chen
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Junqing Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Beijing Life Science Academy, Beijing, 102209, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Faculty of Health Sciences, University of Macau, Macau, SAR, 999078, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinrui Kang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunliang Luo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Xueyang Guo
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Yan Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kefang Liu
- Beijing Life Science Academy, Beijing, 102209, China.
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China.
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12
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Tong Z, Tong J, Lei W, Xie Y, Cui Y, Jia G, Li S, Zhang Z, Cheng Z, Xing X, Ma H, Deng L, Zhang R, Zhao X, Liu K, Wang Q, Qi J, Huang H, Song R, Su Z, Wu G, Lou J, Gao GF. Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1. Cell Rep 2024; 43:114338. [PMID: 38850530 DOI: 10.1016/j.celrep.2024.114338] [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: 01/25/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 06/10/2024] Open
Abstract
The game between therapeutic monoclonal antibodies (mAbs) and continuously emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has favored the virus, as most therapeutic mAbs have been evaded. Addressing this challenge, we systematically explored a reproducible bispecific antibody (bsAb)-dependent synergistic effect in this study. It could effectively restore the neutralizing activity of the bsAb when any of its single mAbs is escaped by variants. This synergy is primarily attributed to the binding angle of receptor-binding domain (RBD)-5, facilitating inter-spike cross-linking and promoting cryptic epitope exposure that classical antibody cocktails cannot achieve. Furthermore, RBD-5 with RBD-2, RBD-6, and RBD-7, alongside RBD-8, also exhibit significantly enhanced effects. This study not only shifts the paradigm in understanding antibody interactions but paves the way for developing more effective therapeutic antibodies against rapidly mutating SARS-CoV-2, with Dia-19 already showing promise against emerging variants like BA.2.86, EG.5.1, and JN.1.
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Affiliation(s)
- Zhou Tong
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Shanxi Academy of Advanced Research and Innovation, Xinhua Road, Taiyuan, Shanxi 030032, China
| | - Jianyu Tong
- Shanxi Academy of Advanced Research and Innovation, Xinhua Road, Taiyuan, Shanxi 030032, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingzi Cui
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610044, China
| | - Shihua Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zezhong Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhimin Cheng
- Shanxi Academy of Advanced Research and Innovation, Xinhua Road, Taiyuan, Shanxi 030032, China
| | - Xiao Xing
- Shanxi Academy of Advanced Research and Innovation, Xinhua Road, Taiyuan, Shanxi 030032, China
| | - Haiyun Ma
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610044, China
| | - Lan Deng
- Sunshine Guojian Pharmaceutical (Shanghai) Co., Ltd., a 3SBio, Inc., company, 399 Libing Road, Shanghai 201203, China
| | - Rong Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haomin Huang
- Sunshine Guojian Pharmaceutical (Shanghai) Co., Ltd., a 3SBio, Inc., company, 399 Libing Road, Shanghai 201203, China
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610044, China
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jing Lou
- Sunshine Guojian Pharmaceutical (Shanghai) Co., Ltd., a 3SBio, Inc., company, 399 Libing Road, Shanghai 201203, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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13
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Liu C, Xu S, Zheng Y, Xie Y, Xu K, Chai Y, Luo T, Dai L, Gao GF. Mosaic RBD nanoparticle elicits immunodominant antibody responses across sarbecoviruses. Cell Rep 2024; 43:114235. [PMID: 38748880 DOI: 10.1016/j.celrep.2024.114235] [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: 09/06/2023] [Revised: 03/09/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Nanoparticle vaccines displaying mosaic receptor-binding domains (RBDs) or spike (S) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or other sarbecoviruses are used in preparedness against potential zoonotic outbreaks. Here, we describe a self-assembling nanoparticle using lumazine synthase (LuS) as the scaffold to display RBDs from different sarbecoviruses. Mosaic nanoparticles induce sarbecovirus cross-neutralizing antibodies comparable to a nanoparticle cocktail. We find mosaic nanoparticles elicit a B cell receptor repertoire using an immunodominant germline gene pair of IGHV14-3:IGKV14-111. Most of the tested IGHV14-3:IGKV14-111 monoclonal antibodies (mAbs) are broadly cross-reactive to clade 1a, 1b, and 3 sarbecoviruses. Using mAb competition and cryo-electron microscopy, we determine that a representative IGHV14-3:IGKV14-111 mAb, M2-7, binds to a conserved epitope on the RBD, largely overlapping with the pan-sarbecovirus mAb S2H97. This suggests mosaic nanoparticles expand B cell recognition of the common epitopes shared by different clades of sarbecoviruses. These results provide immunological insights into the cross-reactive responses elicited by mosaic nanoparticles against sarbecoviruses.
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Affiliation(s)
- Chuanyu Liu
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Senyu Xu
- Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yuxuan Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kun Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingrong Luo
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Medical School, University of Chinese Academy of Sciences, Beijing 101408, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
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14
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Chen Y, Liu C, Fang Y, Chen W, Qiu J, Zhu M, Wei W, Tu J. Developing CAR-immune cell therapy against SARS-CoV-2: Current status, challenges and prospects. Biochem Pharmacol 2024; 222:116066. [PMID: 38373592 DOI: 10.1016/j.bcp.2024.116066] [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: 01/12/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Chimeric antigen receptor (CAR)-immune cell therapy has revolutionized the anti-tumor field, achieving efficient and precise tumor clearance by directly guiding immune cell activity to target tumors. In addition, the use of CAR-immune cells to influence the composition and function of the immune system and ultimately achieve virus clearance and immune system homeostasis has attracted the interest of researchers. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggered a global pandemic of coronavirus disease 2019 (COVID-19). To date, the rapidly mutating SARS-CoV-2 continues to challenge existing therapies and has raised public concerns regarding reinfection. In patients with COVID-19, the interaction of SARS-CoV-2 with the immune system influences the course of the disease, and the coexistence of over-activated immune system components, such as macrophages, and severely compromised immune system components, such as natural killer cells, reveals a dysregulated immune system. Dysregulated immune-induced inflammation may impair viral clearance and T-cell responses, causing cytokine storms and ultimately leading to patient death. Here, we summarize the research progress on the use of CAR-immune cells against SARS-CoV-2 infection. Furthermore, we discuss the feasibility, challenges and prospect of CAR-immune cells as a new immune candidate therapy against SARS-CoV-2.
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Affiliation(s)
- Yizhao Chen
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Chong Liu
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Yilong Fang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Weile Chen
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Jiaqi Qiu
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Mengjuan Zhu
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Wei Wei
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China.
| | - Jiajie Tu
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China.
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