1
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Xu J, Gong J, Bo X, Tong Y, Ren Z, Ni M. A benchmark for evaluation of structure-based online tools for antibody-antigen binding affinity. Biophys Chem 2024; 311:107253. [PMID: 38768531 DOI: 10.1016/j.bpc.2024.107253] [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] [Revised: 04/08/2024] [Accepted: 04/28/2024] [Indexed: 05/22/2024]
Abstract
The prediction of binding affinity changes caused by missense mutations can elucidate antigen-antibody interactions. A few accessible structure-based online computational tools have been proposed. However, selecting suitable software for particular research is challenging, especially research on the SARS-CoV-2 spike protein with antibodies. Therefore, benchmarking of the mutation-diverse SARS-CoV-2 datasets is critical. Here, we collected the datasets including 1216 variants about the changes in binding affinity of antigens from 22 complexes for SARS-CoV-2 S proteins and 22 monoclonal antibodies as well as applied them to evaluate the performance of seven binding affinity prediction tools. The tested tools' Pearson correlations between predicted and measured changes in binding affinity were between -0.158 and 0.657, while accuracy in classification tasks on predicting increasing or decreasing affinity ranged from 0.444 to 0.834. These tools performed relatively better on predicting single mutations, especially at epitope sites, whereas poor performance on extremely decreasing affinity. The tested tools were relatively insensitive to the experimental techniques used to obtain structures of complexes. In summary, we constructed a list of datasets and evaluated a range of structure-based online prediction tools that will explicate relevant processes of antigen-antibody interactions and enhance the computational design of therapeutic monoclonal antibodies.
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Affiliation(s)
- Jiayi Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jianting Gong
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zilin Ren
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China.
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2
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Lee J, Naoe Y, Bang U, Nakagama Y, Saito A, Kido Y, Hotta A. Neutralization sensitivity of SARS-CoV-2 Omicron variants FL.1 and GE.1 by therapeutic antibodies and XBB sera. Virology 2024; 595:110067. [PMID: 38653156 DOI: 10.1016/j.virol.2024.110067] [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: 05/18/2023] [Revised: 02/22/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Two SARS-CoV-2 XBB sub-variants, FL.1 and GE.1, have been increasing in prevalence worldwide, but limited information is available about their ability to evade the immune system. FL.1 and GE.1 are emerging Omicron XBB variants possessing additional mutations in the spike RBD raising concerns of increased neutralization escape. In this study, we assessed the neutralizing ability of eleven FDA-approved monoclonal antibody combinations against different Omicron variants, including BA.2.75, BA.2.76, BA.4/5, XBB.1.5, and CH.1.1. Among the eleven antibodies, Sotrovimab was the only antibody to show broad neutralization ability against XBB.1.5. However, Sotrovimab showed attenuated neutralization efficiency against recently emerging XBB sub-lineages EG.5, FL.1, and GE.1 compared to XBB.1.5. Additionally, XBB.1.5 seropositive convalescent sera displayed lower neutralization activity against EG.5, FL.1, and GE.1. Overall, our findings present enhanced immune evasion capacity of emerging XBB variants and emphasize the importance of continued monitoring of novel variants.
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Affiliation(s)
- Joseph Lee
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Youichi Naoe
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Uikyu Bang
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Yu Nakagama
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Yasutoshi Kido
- Department of Virology & Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan.
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3
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Wang Y, Hao A, Ji P, Ma Y, Zhang Z, Chen J, Mao Q, Xiong X, Rehati P, Wang Y, Wang Y, Wen Y, Lu L, Chen Z, Zhao J, Wu F, Huang J, Sun L. A bispecific antibody exhibits broad neutralization against SARS-CoV-2 Omicron variants XBB.1.16, BQ.1.1 and sarbecoviruses. Nat Commun 2024; 15:5127. [PMID: 38879565 PMCID: PMC11180174 DOI: 10.1038/s41467-024-49096-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 05/22/2024] [Indexed: 06/19/2024] Open
Abstract
The Omicron subvariants BQ.1.1, XBB.1.5, and XBB.1.16 of SARS-CoV-2 are known for their adeptness at evading immune responses. Here, we isolate a neutralizing antibody, 7F3, with the capacity to neutralize all tested SARS-CoV-2 variants, including BQ.1.1, XBB.1.5, and XBB.1.16. 7F3 targets the receptor-binding motif (RBM) region and exhibits broad binding to a panel of 37 RBD mutant proteins. We develop the IgG-like bispecific antibody G7-Fc using 7F3 and the cross-neutralizing antibody GW01. G7-Fc demonstrates robust neutralizing activity against all 28 tested SARS-CoV-2 variants and sarbecoviruses, providing potent prophylaxis and therapeutic efficacy against XBB.1 infection in both K18-ACE and BALB/c female mice. Cryo-EM structure analysis of the G7-Fc in complex with the Omicron XBB spike (S) trimer reveals a trimer-dimer conformation, with G7-Fc synergistically targeting two distinct RBD epitopes and blocking ACE2 binding. Comparative analysis of 7F3 and LY-CoV1404 epitopes highlights a distinct and highly conserved epitope in the RBM region bound by 7F3, facilitating neutralization of the immune-evasive Omicron variant XBB.1.16. G7-Fc holds promise as a potential prophylactic countermeasure against SARS-CoV-2, particularly against circulating and emerging variants.
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Affiliation(s)
- Yingdan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Aihua Hao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ping Ji
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yunping Ma
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, 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, Guangdong, China
| | - Jiali Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qiyu Mao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xinyi Xiong
- 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, Guangdong, China
| | - Palizhati Rehati
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yajie Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 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, Guangdong, China
| | - Yumei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhenguo Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 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, Guangdong, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Fan Wu
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, China.
| | - Jinghe Huang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China.
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Lei Sun
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China.
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4
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Adair A, Tan LL, Feng J, Girkin J, Bryant N, Wang M, Mordant F, Chan LJ, Bartlett NW, Subbarao K, Pymm P, Tham WH. Human coronavirus OC43 nanobody neutralizes virus and protects mice from infection. J Virol 2024; 98:e0053124. [PMID: 38709106 DOI: 10.1128/jvi.00531-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
Human coronavirus (hCoV) OC43 is endemic to global populations and usually causes asymptomatic or mild upper respiratory tract illness. Here, we demonstrate the neutralization efficacy of isolated nanobodies from alpacas immunized with the S1B and S1C domain of the hCoV-OC43 spike glycoprotein. A total of 40 nanobodies bound to recombinant OC43 protein with affinities ranging from 1 to 149 nM. Two nanobodies WNb 293 and WNb 294 neutralized virus at 0.21 and 1.79 nM, respectively. Intranasal and intraperitoneal delivery of WNb 293 fused to an Fc domain significantly reduced nasal viral load in a mouse model of hCoV-OC43 infection. Using X-ray crystallography, we observed that WNb 293 bound to an epitope on the OC43 S1B domain, distal from the sialoglycan-binding site involved in host cell entry. This result suggests that neutralization mechanism of this nanobody does not involve disruption of glycan binding. Our work provides characterization of nanobodies against hCoV-OC43 that blocks virus entry and reduces viral loads in vivo and may contribute to future nanobody-based therapies for hCoV-OC43 infections. IMPORTANCE The pandemic potential presented by coronaviruses has been demonstrated by the ongoing COVID-19 pandemic and previous epidemics caused by severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Outside of these major pathogenic coronaviruses, there are four endemic coronaviruses that infect humans: hCoV-OC43, hCoV-229E, hCoV-HKU1, and hCoV-NL63. We identified a collection of nanobodies against human coronavirus OC43 (hCoV-OC43) and found that two high-affinity nanobodies potently neutralized hCoV-OC43 at low nanomolar concentrations. Prophylactic administration of one neutralizing nanobody reduced viral loads in mice infected with hCoV-OC43, showing the potential for nanobody-based therapies for hCoV-OC43 infections.
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Affiliation(s)
- Amy Adair
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Li Lynn Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jackson Feng
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Girkin
- 3College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Nathan Bryant
- 3College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Mingyang Wang
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Francesca Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nathan W Bartlett
- 3College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Infection Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Phillip Pymm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
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5
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Ma MT, Jiang Q, Chen CH, Badeti S, Wang X, Zeng C, Evans D, Bodnar B, Marras SAE, Tyagi S, Bharaj P, Yehia G, Romanienko P, Hu W, Liu SL, Shi L, Liu D. S309-CAR-NK cells bind the Omicron variants in vitro and reduce SARS-CoV-2 viral loads in humanized ACE2-NSG mice. J Virol 2024; 98:e0003824. [PMID: 38767356 DOI: 10.1128/jvi.00038-24] [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: 01/29/2024] [Accepted: 04/11/2024] [Indexed: 05/22/2024] Open
Abstract
Recent progress on chimeric antigen receptor (CAR)-NK cells has shown promising results in treating CD19-positive lymphoid tumors with minimal toxicities [including graft versus host disease (GvHD) and cytokine release syndrome (CRS) in clinical trials. Nevertheless, the use of CAR-NK cells in combating viral infections has not yet been fully explored. Previous studies have shown that CAR-NK cells expressing S309 single-chain fragment variable (scFv), hereinafter S309-CAR-NK cells, can bind to SARS-CoV-2 wildtype pseudotyped virus (PV) and effectively kill cells expressing wild-type spike protein in vitro. In this study, we further demonstrate that the S309-CAR-NK cells can bind to different SARS-CoV-2 variants, including the B.1.617.2 (Delta), B.1.621 (Mu), and B.1.1.529 (Omicron) variants in vitro. We also show that S309-CAR-NK cells reduce virus loads in the NOD/SCID gamma (NSG) mice expressing the human angiotensin-converting enzyme 2 (hACE2) receptor challenged with SARS-CoV-2 wild-type (strain USA/WA1/2020). Our study demonstrates the potential use of S309-CAR-NK cells for inhibiting infection by SARS-CoV-2 and for the potential treatment of COVID-19 patients unresponsive to otherwise currently available therapeutics. IMPORTANCE Chimeric antigen receptor (CAR)-NK cells can be "off-the-shelf" products that treat various diseases, including cancer, infections, and autoimmune diseases. In this study, we engineered natural killer (NK) cells to express S309 single-chain fragment variable (scFv), to target the Spike protein of SARS-CoV-2, hereinafter S309-CAR-NK cells. Our study shows that S309-CAR-NK cells are effective against different SARS-CoV-2 variants, including the B.1.617.2 (Delta), B.1.621 (Mu), and B.1.1.529 (Omicron) variants. The S309-CAR-NK cells can (i) directly bind to SARS-CoV-2 pseudotyped virus (PV), (ii) competitively bind to SARS-CoV-2 PV with 293T cells expressing the human angiotensin-converting enzyme 2 (hACE2) receptor (293T-hACE2 cells), (iii) specifically target and lyse A549 cells expressing the spike protein, and (iv) significantly reduce the viral loads of SARS-CoV-2 wild-type (strain USA/WA1/2020) in the lungs of NOD/SCID gamma (NSG) mice expressing hACE2 (hACE2-NSG mice). Altogether, the current study demonstrates the potential use of S309-CAR-NK immunotherapy as an alternative treatment for COVID-19 patients.
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Affiliation(s)
- Minh Tuyet Ma
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
| | - Qingkui Jiang
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Chih-Hsiung Chen
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
| | - Saiaditya Badeti
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
| | - Xuening Wang
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
| | - Cong Zeng
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
| | - Deborah Evans
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Brittany Bodnar
- Center for Metabolic Disease Research, Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Salvatore A E Marras
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Preeti Bharaj
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Ghassan Yehia
- Genome Editing Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Peter Romanienko
- Genome Editing Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Wenhui Hu
- Center for Metabolic Disease Research, Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Lanbo Shi
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Dongfang Liu
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
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6
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Ives CM, Nguyen L, Fogarty CA, Harbison AM, Durocher Y, Klassen J, Fadda E. Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern. eLife 2024; 13:RP95708. [PMID: 38864493 PMCID: PMC11168744 DOI: 10.7554/elife.95708] [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] [Indexed: 06/13/2024] Open
Abstract
Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both viral evasion and fitness. Successful variations in the glycan shield are difficult to achieve though, as protein glycosylation is also critical to folding and structural stability. Within this framework, the identification of glycosylation sites that are structurally dispensable can provide insight into the evolutionary mechanisms of the shield and inform immune surveillance. In this work, we show through over 45 μs of cumulative sampling from conventional and enhanced molecular dynamics (MD) simulations, how the structure of the immunodominant S receptor binding domain (RBD) is regulated by N-glycosylation at N343 and how this glycan's structural role changes from WHu-1, alpha (B.1.1.7), and beta (B.1.351), to the delta (B.1.617.2), and omicron (BA.1 and BA.2.86) variants. More specifically, we find that the amphipathic nature of the N-glycan is instrumental to preserve the structural integrity of the RBD hydrophobic core and that loss of glycosylation at N343 triggers a specific and consistent conformational change. We show how this change allosterically regulates the conformation of the receptor binding motif (RBM) in the WHu-1, alpha, and beta RBDs, but not in the delta and omicron variants, due to mutations that reinforce the RBD architecture. In support of these findings, we show that the binding of the RBD to monosialylated ganglioside co-receptors is highly dependent on N343 glycosylation in the WHu-1, but not in the delta RBD, and that affinity changes significantly across VoCs. Ultimately, the molecular and functional insight we provide in this work reinforces our understanding of the role of glycosylation in protein structure and function and it also allows us to identify the structural constraints within which the glycosylation site at N343 can become a hotspot for mutations in the SARS-CoV-2 S glycan shield.
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Affiliation(s)
- Callum M Ives
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | - Linh Nguyen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Carl A Fogarty
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | | | - Yves Durocher
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council CanadaQuébecCanada
- Département de Biochimie et Médecine Moléculaire, Université de MontréalQuébecCanada
| | - John Klassen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Elisa Fadda
- School of Biological Sciences, University of SouthamptonSouthamptonUnited Kingdom
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7
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Liang L, Wang B, Zhang Q, Zhang S, Zhang S. Antibody drugs targeting SARS-CoV-2: Time for a rethink? Biomed Pharmacother 2024; 176:116900. [PMID: 38861858 DOI: 10.1016/j.biopha.2024.116900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) heavily burdens human health. Multiple neutralizing antibodies (nAbs) have been issued for emergency use or tested for treating infected patients in the clinic. However, SARS-CoV-2 variants of concern (VOC) carrying mutations reduce the effectiveness of nAbs by preventing neutralization. Uncoding the mutation profile and immune evasion mechanism of SARS-CoV-2 can improve the outcome of Ab-mediated therapies. In this review, we first outline the development status of anti-SARS-CoV-2 Ab drugs and provide an overview of SARS-CoV-2 variants and their prevalence. We next focus on the failure causes of anti-SARS-CoV-2 Ab drugs and rethink the design strategy for developing new Ab drugs against COVID-19. This review provides updated information for the development of therapeutic Ab drugs against SARS-CoV-2 variants.
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Affiliation(s)
- Likeng Liang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Bo Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Qing Zhang
- Department of Laboratory Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China.
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8
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Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Kit Tan T, Rijal P, Chen CP, Cheng SH, Lee WH, Chou YC, Townsend AR, Ma C, Huang KYA. The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. PLoS Pathog 2024; 20:e1012246. [PMID: 38857264 DOI: 10.1371/journal.ppat.1012246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/08/2024] [Indexed: 06/12/2024] Open
Abstract
Antibody-mediated immunity plays a key role in protection against SARS-CoV-2. We characterized B-cell-derived anti-SARS-CoV-2 RBD antibody repertoires from vaccinated and infected individuals and elucidate the mechanism of action of broadly neutralizing antibodies and dissect antibodies at the epitope level. The breadth and clonality of anti-RBD B cell response varies among individuals. The majority of neutralizing antibody clones lose or exhibit reduced activities against Beta, Delta, and Omicron variants. Nevertheless, a portion of anti-RBD antibody clones that develops after a primary series or booster dose of COVID-19 vaccination exhibit broad neutralization against emerging Omicron BA.2, BA.4, BA.5, BQ.1.1, XBB.1.5 and XBB.1.16 variants. These broadly neutralizing antibodies share genetic features including a conserved usage of the IGHV3-53 and 3-9 genes and recognize three clustered epitopes of the RBD, including epitopes that partially overlap the classically defined set identified early in the pandemic. The Fab-RBD crystal and Fab-Spike complex structures corroborate the epitope grouping of antibodies and reveal the detailed binding mode of broadly neutralizing antibodies. Structure-guided mutagenesis improves binding and neutralization potency of antibody with Omicron variants via a single amino-substitution. Together, these results provide an immunological basis for partial protection against severe COVID-19 by the ancestral strain-based vaccine and indicate guidance for next generation monoclonal antibody development and vaccine design.
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Affiliation(s)
- Xiaorui Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Hong Thuy Vy Nguyen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Lisa Schimanski
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Pramila Rijal
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Cheng-Pin Chen
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, and Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Hsing Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, and School of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Wen-Hsin Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Alain R Townsend
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuan-Ying A Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Immunology and Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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9
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Quarleri J, Delpino MV, Galvan V. Anticipating the future of the COVID-19 pandemic: insights into the emergence of SARS-CoV-2 variant JN.1 and its projected impact on older adults. GeroScience 2024; 46:2879-2883. [PMID: 38198026 PMCID: PMC11009205 DOI: 10.1007/s11357-024-01066-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Affiliation(s)
- Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Ciencias Médicas, Universidad de Buenos Aires-Consejo de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, Piso 11, C1121ABG, Buenos Aires, Argentina.
| | - M Victoria Delpino
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Ciencias Médicas, Universidad de Buenos Aires-Consejo de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, Piso 11, C1121ABG, Buenos Aires, Argentina
| | - Veronica Galvan
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Center for Geroscience and Healthy Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- US Department of Veterans Affairs, Oklahoma City VA Health Care System, Oklahoma City, OK, USA
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10
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Hattab D, Amer MFA, Al-Alami ZM, Bakhtiar A. SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants. Infection 2024; 52:767-786. [PMID: 38554253 PMCID: PMC11143066 DOI: 10.1007/s15010-024-02223-y] [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: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 04/01/2024]
Abstract
The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.
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Affiliation(s)
- Dima Hattab
- School of Pharmacy, The University of Jordan, Queen Rania Street, Amman, Jordan
| | - Mumen F A Amer
- Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Zina M Al-Alami
- Department of Basic Medical Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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11
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Cornish K, Huo J, Jones L, Sharma P, Thrush JW, Abdelkarim S, Kipar A, Ramadurai S, Weckener M, Mikolajek H, Liu S, Buckle I, Bentley E, Kirby A, Han X, Laidlaw SM, Hill M, Eyssen L, Norman C, Le Bas A, Clarke J, James W, Stewart JP, Carroll M, Naismith JH, Owens RJ. Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2. Open Biol 2024; 14:230252. [PMID: 38835241 DOI: 10.1098/rsob.230252] [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: 07/30/2023] [Accepted: 03/22/2024] [Indexed: 06/06/2024] Open
Abstract
The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. Therefore, in the 'arms race' with the virus, there is a continuing need to identify new biologics for the prevention or treatment of SARS-CoV-2 infections. Here, we report the isolation of nanobodies that bind to the Omicron BA.1 spike protein by screening nanobody phage display libraries previously generated from llamas immunized with either the Wuhan or Beta spike proteins. The structure and binding properties of three of these nanobodies (A8, H6 and B5-5) have been characterized in detail providing insight into their binding epitopes on the Omicron spike protein. Trimeric versions of H6 and B5-5 neutralized the SARS-CoV-2 variant of concern BA.5 both in vitro and in the hamster model of COVID-19 following nasal administration. Thus, either alone or in combination could serve as starting points for the development of new anti-viral immunotherapeutics.
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Affiliation(s)
- Katy Cornish
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
| | - Luke Jones
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - Parul Sharma
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Joseph W Thrush
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Sahar Abdelkarim
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
- Vetsuisse Faculty, Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, University of Zurich , Zurich, Switzerland
| | - Siva Ramadurai
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Miriam Weckener
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | | | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - Imogen Buckle
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Eleanor Bentley
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Ximeng Han
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Stephen M Laidlaw
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - Michelle Hill
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - Lauren Eyssen
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Chelsea Norman
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Audrey Le Bas
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - John Clarke
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - William James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - James P Stewart
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Miles Carroll
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
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12
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Raj ST, Bruce AW, Anbalagan M, Srinivasan H, Chinnappan S, Rajagopal M, Khanna K, Chandramoorthy HC, Mani RR. COVID-19 influenced gut dysbiosis, post-acute sequelae, immune regulation, and therapeutic regimens. Front Cell Infect Microbiol 2024; 14:1384939. [PMID: 38863829 PMCID: PMC11165100 DOI: 10.3389/fcimb.2024.1384939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) pandemic outbreak caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has garnered unprecedented global attention. It caused over 2.47 million deaths through various syndromes such as acute respiratory distress, hypercoagulability, and multiple organ failure. The viral invasion proceeds through the ACE2 receptor, expressed in multiple cell types, and in some patients caused serious damage to tissues, organs, immune cells, and the microbes that colonize the gastrointestinal tract (GIT). Some patients who survived the SARS-CoV-2 infection have developed months of persistent long-COVID-19 symptoms or post-acute sequelae of COVID-19 (PASC). Diagnosis of these patients has revealed multiple biological effects, none of which are mutually exclusive. However, the severity of COVID-19 also depends on numerous comorbidities such as obesity, age, diabetes, and hypertension and care must be taken with respect to other multiple morbidities, such as host immunity. Gut microbiota in relation to SARS-CoV-2 immunopathology is considered to evolve COVID-19 progression via mechanisms of biochemical metabolism, exacerbation of inflammation, intestinal mucosal secretion, cytokine storm, and immunity regulation. Therefore, modulation of gut microbiome equilibrium through food supplements and probiotics remains a hot topic of current research and debate. In this review, we discuss the biological complications of the physio-pathological effects of COVID-19 infection, GIT immune response, and therapeutic pharmacological strategies. We also summarize the therapeutic targets of probiotics, their limitations, and the efficacy of preclinical and clinical drugs to effectively inhibit the spread of SARS-CoV-2.
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Affiliation(s)
- Sterlin T. Raj
- Department of Molecular Biology, Ekka Diagnostics, Chennai, Tamil Nadu, India
| | - Alexander W. Bruce
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Muralidharan Anbalagan
- Department of Structural & Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Hemalatha Srinivasan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
| | - Sasikala Chinnappan
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
| | - Mogana Rajagopal
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
| | - Kushagra Khanna
- Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Harish C. Chandramoorthy
- Department of Microbiology and Clinical Parasitology, College of Medicine, King Khalid University, Abha, Saudi Arabia
- Center for Stem Cell Research, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Ravishankar Ram Mani
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
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13
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Hills FR, Eruera AR, Hodgkinson-Bean J, Jorge F, Easingwood R, Brown SHJ, Bouwer JC, Li YP, Burga LN, Bostina M. Variation in structural motifs within SARS-related coronavirus spike proteins. PLoS Pathog 2024; 20:e1012158. [PMID: 38805567 DOI: 10.1371/journal.ppat.1012158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments.
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Affiliation(s)
- Francesca R Hills
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alice-Roza Eruera
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James Hodgkinson-Bean
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Richard Easingwood
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Simon H J Brown
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - James C Bouwer
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yi-Ping Li
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Laura N Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
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14
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Zhang Y, Zhai S, Huang H, Qin S, Sun M, Chen Y, Lan X, Li G, Huang Z, Wang D, Luo Y, Xiao W, Li H, He X, Chen M, Peng X, Song X. Efficient signal sequence of mRNA vaccines enhances the antigen expression to expand the immune protection against viral infection. J Nanobiotechnology 2024; 22:295. [PMID: 38807131 PMCID: PMC11134928 DOI: 10.1186/s12951-024-02488-3] [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: 01/22/2024] [Accepted: 04/17/2024] [Indexed: 05/30/2024] Open
Abstract
The signal sequence played a crucial role in the efficacy of mRNA vaccines against virus pandemic by influencing antigen translation. However, limited research had been conducted to compare and analyze the specific mechanisms involved. In this study, a novel approach was introduced by substituting the signal sequence of the mRNA antigen to enhance its immune response. Computational simulations demonstrated that various signal peptides differed in their binding capacities with the signal recognition particle (SRP) 54 M subunit, which positively correlated with antigen translation efficiency. Our data revealed that the signal sequences of tPA and IL-6-modified receptor binding domain (RBD) mRNA vaccines sequentially led to higher antigen expression and elicited more robust humoral and cellular immune protection against the SARS-CoV-2 compared to the original signal sequence. By highlighting the importance of the signal sequence, this research provided a foundational and safe approach for ongoing modifications in signal sequence-antigen design, aiming to optimize the efficacy of mRNA vaccines.
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Affiliation(s)
- Yupei Zhang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Songhui Zhai
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hai Huang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shugang Qin
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Min Sun
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuting Chen
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xing Lan
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Guohong Li
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhiying Huang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Denggang Wang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yaoyao Luo
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wen Xiao
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hao Li
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xi He
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Meiwan Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
| | - Xingchen Peng
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Xiangrong Song
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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15
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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] [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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16
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Li X, Kulakova L, Jones K, Toth EA, Mitchell MK, Mendez Q, Weiner MP, Fuerst TR. Site-directed neutralizing antibodies targeting structural sites on SARS-CoV-2 spike protein. N Biotechnol 2024; 80:27-36. [PMID: 38128698 PMCID: PMC10954356 DOI: 10.1016/j.nbt.2023.12.004] [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: 07/03/2023] [Revised: 10/20/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023]
Abstract
'Epivolve' (epitope evolution) is an innovative paratope-evolving technology using a haptenated peptide or protein immunogen as a means of directing the in vivo immune response to specifically targeted sites at a one amino acid residue resolution. Guided by protein structural analysis, Epivolve technology was tested to develop site-directed neutralizing antibodies (nAbs) in a systematic fashion against the SARS-CoV-2 Receptor Binding Domain (RBD). Thirteen solvent-exposed sites covering the ACE2 receptor-binding interface were targeted. Immunogens composed of each targeted site were used to immunize rabbits in separate cohorts. In vivo site-directed immune responses against all 13 targets were demonstrated by B cell secreted IgG and recombinant IgG testing. One site, SL13 (Y505) which mutates from tyrosine to histidine in the SARS-CoV-2 Omicron variant, was chosen as a proof-of-concept (PoC) model for further functional monoclonal antibody development. Epivolve technology demonstrated the capabilities of generating pan-variant antibodies and nAbs against the SARS-CoV-2 primary strain and the Omicron variant.
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Affiliation(s)
- Xiaofeng Li
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA.
| | - Liudmila Kulakova
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Kezzia Jones
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Eric A Toth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | | | - Qiana Mendez
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Michael P Weiner
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Thomas R Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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17
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Chang YH, Hsu MF, Chen WN, Wu MH, Kong WL, Lu MYJ, Huang CH, Chang FJ, Chang LY, Tsai HY, Tung CP, Yu JH, Kuo Y, Chou YC, Bai LY, Chang YC, Chen AY, Chen CC, Chen YH, Liao CC, Chang CS, Liang JJ, Lin YL, Angata T, Hsu STD, Lin KI. Functional and structural investigation of a broadly neutralizing SARS-CoV-2 antibody. JCI Insight 2024; 9:e179726. [PMID: 38775156 PMCID: PMC11141937 DOI: 10.1172/jci.insight.179726] [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: 01/24/2024] [Accepted: 04/12/2024] [Indexed: 06/02/2024] Open
Abstract
Since its emergence, SARS-CoV-2 has been continuously evolving, hampering the effectiveness of current vaccines against COVID-19. mAbs can be used to treat patients at risk of severe COVID-19. Thus, the development of broadly protective mAbs and an understanding of the underlying protective mechanisms are of great importance. Here, we isolated mAbs from donors with breakthrough infection with Omicron subvariants using a single-B cell screening platform. We identified a mAb, O5C2, which possesses broad-spectrum neutralization and antibody-dependent cell-mediated cytotoxic activities against SARS-CoV-2 variants, including EG.5.1. Single-particle analysis by cryo-electron microscopy revealed that O5C2 targeted an unusually large epitope within the receptor-binding domain of spike protein that overlapped with the angiotensin-converting enzyme 2 binding interface. Furthermore, O5C2 effectively protected against BA.5 Omicron infection in vivo by mediating changes in transcriptomes enriched in genes involved in apoptosis and interferon responses. Our findings provide insights into the development of pan-protective mAbs against SARS-CoV-2.
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Affiliation(s)
- Yi-Hsuan Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | | | - Wei-Nan Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Wye-Lup Kong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Heng Huang
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Fang-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Ho-Yang Tsai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jou-Hui Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yali Kuo
- Biomedical Translation Research Center (BioTReC)
| | - Yu-Chi Chou
- Biomedical Translation Research Center (BioTReC)
| | - Li-Yang Bai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yuan-Chih Chang
- Institute of Biological Chemistry and
- Academia Sinica Cryo-EM Center, and
| | - An-Yu Chen
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
| | - Cheng-Cheung Chen
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Biomedical Translation Research Center (BioTReC)
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Takashi Angata
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry and
| | - Shang-Te Danny Hsu
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry and
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKC M2, ) Hiroshima University, Hiroshima, Japan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center (BioTReC)
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18
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Cohen AA, Keeffe JR, Schiepers A, Dross SE, Greaney AJ, Rorick AV, Gao H, Gnanapragasam PNP, Fan C, West AP, Ramsingh AI, Erasmus JH, Pata JD, Muramatsu H, Pardi N, Lin PJC, Baxter S, Cruz R, Quintanar-Audelo M, Robb E, Serrano-Amatriain C, Magneschi L, Fotheringham IG, Fuller DH, Victora GD, Bjorkman PJ. Mosaic sarbecovirus nanoparticles elicit cross-reactive responses in pre-vaccinated animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.576722. [PMID: 38370696 PMCID: PMC10871317 DOI: 10.1101/2024.02.08.576722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Immunization with mosaic-8b [60-mer nanoparticles presenting 8 SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs)] elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated effects of prior COVID-19 vaccinations in non-human primates and mice on anti-sarbecovirus responses elicited by mosaic-8b, admix-8b (8 homotypics), or homotypic SARS-CoV-2 immunizations, finding greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate-mapping in which antibodies from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b- and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced by mosaic-8b, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19 vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential.
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Affiliation(s)
- Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Ariën Schiepers
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Sandra E Dross
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Allison J Greaney
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Annie V Rorick
- 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
| | | | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | - Janice D Pata
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany, Albany, NY, 12201, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Scott Baxter
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Rita Cruz
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Martina Quintanar-Audelo
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
- Present address: Centre for Inflammation Research and Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Ellis Robb
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | | | - Leonardo Magneschi
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Ian G Fotheringham
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Deborah H Fuller
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Lead contact
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19
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Chi LA, Barnes JE, Suresh Patel J, Ytreberg FM. Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595230. [PMID: 38826284 PMCID: PMC11142147 DOI: 10.1101/2024.05.22.595230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and antibody-based therapies. The ability to predict these escape mutations with computer simulations would allow us to detect threats early and develop effective countermeasures, but a lack of large-scale experimental data has hampered the validation of these calculations. In this study, we evaluate the ability of the MD+FoldX molecular modeling method to predict escape mutations by leveraging a large deep mutational scanning dataset, focusing on the SARS-CoV-2 receptor binding domain. Our results show a positive correlation between predicted and experimental data, indicating that mutations with reduced predicted binding affinity correlate moderately with higher experimental escape fractions. We also demonstrate that better performance can be achieved using affinity cutoffs tailored to distinct antibody-antigen interactions rather than a one-size-fits-all approach. We find that 70% of the systems surpass the 50% precision mark, and demonstrate success in identifying mutations present in significant variants of concern and variants of interest. Despite promising results for some systems, our study highlights the challenges in comparing predicted and experimental values. It also emphasizes the need for new binding affinity methods with improved accuracy that are fast enough to estimate hundreds to thousands of antibody-antigen binding affinities.
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Affiliation(s)
- L. América Chi
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83843, USA
| | - Jonathan E. Barnes
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83843, USA
| | - Jagdish Suresh Patel
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83843, USA
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, ID 83843, USA
| | - F. Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83843, USA
- Department of Physics, University of Idaho, Moscow, ID 83843, USA
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20
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Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. Cell Rep Med 2024; 5:101553. [PMID: 38723626 PMCID: PMC11148769 DOI: 10.1016/j.xcrm.2024.101553] [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: 10/06/2023] [Revised: 01/10/2024] [Accepted: 04/11/2024] [Indexed: 05/24/2024]
Abstract
BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
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Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | | | - Piyada Supasa
- 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, Centre for Human Genetics, Oxford, UK
| | - Helen M Ginn
- Centre for Free Electron Laser Science, Hamburg, Germany
| | - Muneeswaran Selvaraj
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas G Ritter
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | | | - Lizzie Stafford
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Barbara Kronsteiner
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and University of Greenwich Chatham Maritime, Kent ME4 4TB, UK
| | - Yuan Lui
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Martin Fellermeyer
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Michael I Barton
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mikhail A Kutuzov
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Omer Dushek
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK; Sir William Dunn School of Pathology, Oxford, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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21
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Felbinger N, Ribeiro-Filho HV, Pierce BG. Proscan: a structure-based proline design web server. Nucleic Acids Res 2024:gkae408. [PMID: 38769060 DOI: 10.1093/nar/gkae408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/16/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The ability to control protein conformations and dynamics through structure-based design has been useful in various scenarios, including engineering of viral antigens for vaccines. One effective design strategy is the substitution of residues to proline amino acids, which due to its unique cyclic side chain can favor and rigidify key backbone conformations. To provide the community with a means to readily identify and explore proline designs for target proteins of interest, we developed the Proscan web server. Proscan provides assessment of backbone angles, energetic and deep learning-based favorability scores, and other parameters for proline substitutions at each position of an input structure, along with interactive visualization of backbone angles and candidate substitution sites on structures. It identifies known favorable proline substitutions for viral antigens, and was benchmarked against datasets of proline substitution stability effects from deep mutational scanning and thermodynamic measurements. This tool can enable researchers to identify and prioritize designs for prospective vaccine antigen targets, or other designs to favor stability of key protein conformations. Proscan is available at: https://proscan.ibbr.umd.edu.
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Affiliation(s)
- Nathaniel Felbinger
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Helder V Ribeiro-Filho
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas 13083-100, Brazil
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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22
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Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hällberg BM. Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies. Cell Rep Med 2024:101577. [PMID: 38761799 DOI: 10.1016/j.xcrm.2024.101577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 12/15/2023] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Descendants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant now account for almost all SARS-CoV-2 infections. The Omicron variant and its sublineages have spike glycoproteins that are highly diverged from the pandemic founder and first-generation vaccine strain, resulting in significant evasion from monoclonal antibody therapeutics and vaccines. Understanding how commonly elicited antibodies can broaden to cross-neutralize escape variants is crucial. We isolate IGHV3-53, using "public" monoclonal antibodies (mAbs) from an individual 7 months post infection with the ancestral virus and identify antibodies that exhibit potent and broad cross-neutralization, extending to the BA.1, BA.2, and BA.4/BA.5 sublineages of Omicron. Deep mutational scanning reveals these mAbs' high resistance to viral escape. Structural analysis via cryoelectron microscopy of a representative broadly neutralizing antibody, CAB-A17, in complex with the Omicron BA.1 spike highlights the structural underpinnings of this broad neutralization. By reintroducing somatic hypermutations into a germline-reverted CAB-A17, we delineate the role of affinity maturation in the development of cross-neutralization by a public class of antibodies.
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Affiliation(s)
- Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Hyllner
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Robert Dyrdak
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jimin Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pia Dosenovic
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - 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
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestraße 85, 22607 Hamburg, Germany.
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23
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Leducq V, Zafilaza K, Fauchois A, Ghidaoui E, Sayon S, Dorival C, Meledje ML, Lusivika-Nzinga C, Yordanov Y, Martin-Blondel G, Carrat F, Marcelin AG, Soulie C. Spike Protein Genetic Evolution in Patients at High Risk of Severe Coronavirus Disease 2019 Treated by Monoclonal Antibodies. J Infect Dis 2024; 229:1341-1351. [PMID: 37996072 DOI: 10.1093/infdis/jiad523] [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: 07/26/2023] [Revised: 10/16/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND High-risk patients, often immunocompromised and not responding to vaccine, continue to experience severe coronavirus disease 2019 (COVID-19) and death. Monoclonal antibodies (mAbs) were shown to be effective to prevent severe COVID-19 for these patients. Nevertheless, concerns about the emergence of resistance mutations were raised. METHODS We conducted a multicentric prospective cohort study, including 264 patients with mild to moderate COVID-19 at high risk for progression to severe COVID-19 and treated early with casirivimab/imdevimab, sotrovimab, or tixagevimab/cilgavimab. We sequenced the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during follow-up and searched for emerging spike mutations. RESULTS Immunocompromised patients have a 6-fold increased risk of developing mutations, which are associated with a prolonged duration of viral clearance but no clinical worsening. Emerging P337S/R/L/H, E340D/K/A/Q/V/G, and K356T/R substitutions in patients treated with sotrovimab are associated with higher viral RNA loads for up to 14 days post-treatment initiation. Tixagevimab/cilgavimab is associated with a 5-fold increased risk of developing mutations. R346K/I/T/S and K444R/N/M substitutions associated with tixagevimab/cilgavimab have been identified in multiple SARS-CoV-2 lineages, including BQ.1 and XBB. CONCLUSIONS The probability of emerging mutations arising in response to mAbs is significant, emphasizing the crucial need to investigate these mutations thoroughly and assess their impact on patients and the evolutionary trajectory of SARS-CoV-2.
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Affiliation(s)
- Valentin Leducq
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Karen Zafilaza
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Antoine Fauchois
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Emna Ghidaoui
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Sophie Sayon
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Céline Dorival
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Marie-Laure Meledje
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Clovis Lusivika-Nzinga
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Youri Yordanov
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Service d'Accueil des Urgences, Paris, France
| | - Guillaume Martin-Blondel
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Toulouse, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Inserm, Université Toulouse III, Toulouse, France
| | - Fabrice Carrat
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Département de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Cathia Soulie
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
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Mizuno Y, Nakasone W, Nakamura M, Otaki JM. In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development. Vaccines (Basel) 2024; 12:539. [PMID: 38793790 PMCID: PMC11125730 DOI: 10.3390/vaccines12050539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Spike protein sequences in SARS-CoV-2 have been employed for vaccine epitopes, but many short constituent sequences (SCSs) in the spike protein are present in the human proteome, suggesting that some anti-spike antibodies induced by infection or vaccination may be autoantibodies against human proteins. To evaluate this possibility of "molecular mimicry" in silico and in vitro, we exhaustively identified common SCSs (cSCSs) found both in spike and human proteins bioinformatically. The commonality of SCSs between the two systems seemed to be coincidental, and only some cSCSs were likely to be relevant to potential self-epitopes based on three-dimensional information. Among three antibodies raised against cSCS-containing spike peptides, only the antibody against EPLDVL showed high affinity for the spike protein and reacted with an EPLDVL-containing peptide from the human unc-80 homolog protein. Western blot analysis revealed that this antibody also reacted with several human proteins expressed mainly in the small intestine, ovary, and stomach. Taken together, these results showed that most cSCSs are likely incapable of inducing autoantibodies but that at least EPLDVL functions as a self-epitope, suggesting a serious possibility of infection-induced or vaccine-induced autoantibodies in humans. High-risk cSCSs, including EPLDVL, should be excluded from vaccine epitopes to prevent potential autoimmune disorders.
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Affiliation(s)
- Yuya Mizuno
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Wataru Nakasone
- Computer Science and Intelligent Systems Unit, Department of Engineering, Faculty of Engineering, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Morikazu Nakamura
- Computer Science and Intelligent Systems Unit, Department of Engineering, Faculty of Engineering, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Joji M. Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
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25
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Di H, Pusch EA, Jones J, Kovacs NA, Hassell N, Sheth M, Lynn KS, Keller MW, Wilson MM, Keong LM, Cui D, Park SH, Chau R, Lacek KA, Liddell JD, Kirby MK, Yang G, Johnson M, Thor S, Zanders N, Feng C, Surie D, DeCuir J, Lester SN, Atherton L, Hicks H, Tamin A, Harcourt JL, Coughlin MM, Self WH, Rhoads JP, Gibbs KW, Hager DN, Shapiro NI, Exline MC, Lauring AS, Rambo-Martin B, Paden CR, Kondor RJ, Lee JS, Barnes JR, Thornburg NJ, Zhou B, Wentworth DE, Davis CT. Antigenic Characterization of Circulating and Emerging SARS-CoV-2 Variants in the U.S. throughout the Delta to Omicron Waves. Vaccines (Basel) 2024; 12:505. [PMID: 38793756 PMCID: PMC11125585 DOI: 10.3390/vaccines12050505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into numerous lineages with unique spike mutations and caused multiple epidemics domestically and globally. Although COVID-19 vaccines are available, new variants with the capacity for immune evasion continue to emerge. To understand and characterize the evolution of circulating SARS-CoV-2 variants in the U.S., the Centers for Disease Control and Prevention (CDC) initiated the National SARS-CoV-2 Strain Surveillance (NS3) program and has received thousands of SARS-CoV-2 clinical specimens from across the nation as part of a genotype to phenotype characterization process. Focus reduction neutralization with various antisera was used to antigenically characterize 143 SARS-CoV-2 Delta, Mu and Omicron subvariants from selected clinical specimens received between May 2021 and February 2023, representing a total of 59 unique spike protein sequences. BA.4/5 subvariants BU.1, BQ.1.1, CR.1.1, CQ.2 and BA.4/5 + D420N + K444T; BA.2.75 subvariants BM.4.1.1, BA.2.75.2, CV.1; and recombinant Omicron variants XBF, XBB.1, XBB.1.5 showed the greatest escape from neutralizing antibodies when analyzed against post third-dose original monovalent vaccinee sera. Post fourth-dose bivalent vaccinee sera provided better protection against those subvariants, but substantial reductions in neutralization titers were still observed, especially among BA.4/5 subvariants with both an N-terminal domain (NTD) deletion and receptor binding domain (RBD) substitutions K444M + N460K and recombinant Omicron variants. This analysis demonstrated a framework for long-term systematic genotype to antigenic characterization of circulating and emerging SARS-CoV-2 variants in the U.S., which is critical to assessing their potential impact on the effectiveness of current vaccines and antigen recommendations for future updates.
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Affiliation(s)
- Han Di
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Elizabeth A. Pusch
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joyce Jones
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Nicholas A. Kovacs
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Norman Hassell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Mili Sheth
- Division of Core Laboratory Services and Response, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kelly Sabrina Lynn
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Matthew W. Keller
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Malania M. Wilson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Lisa M. Keong
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Dan Cui
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - So Hee Park
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Eagle Global Scientific, Inc., Atlanta, GA 30341, USA
| | - Reina Chau
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kristine A. Lacek
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jimma D. Liddell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Marie K. Kirby
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Genyan Yang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Monique Johnson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Sharmi Thor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Natosha Zanders
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Chenchen Feng
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Diya Surie
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jennifer DeCuir
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Sandra N. Lester
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Lydia Atherton
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Heather Hicks
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Synergy America, Inc., Duluth, GA 30329, USA
| | - Azaibi Tamin
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jennifer L. Harcourt
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Melissa M. Coughlin
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wesley H. Self
- Vanderbilt Institute for Clinical & Translational Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jillian P. Rhoads
- Vanderbilt Institute for Clinical & Translational Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kevin W. Gibbs
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - David N. Hager
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathan I. Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Matthew C. Exline
- Department of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Adam S. Lauring
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Benjamin Rambo-Martin
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Clinton R. Paden
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Rebecca J. Kondor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Justin S. Lee
- Division of Core Laboratory Services and Response, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Natalie J. Thornburg
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Bin Zhou
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - David E. Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Charles Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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26
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D'Arpino MC, Sineli PE, Goroso G, Watanabe W, Saavedra ML, Hebert EM, Martínez MA, Migliavacca J, Gerstenfeld S, Chahla RE, Bellomio A, Albarracín VH. Wastewater monitoring of SARS-CoV-2 gene for COVID-19 epidemiological surveillance in Tucumán, Argentina. J Basic Microbiol 2024:e202300773. [PMID: 38712352 DOI: 10.1002/jobm.202300773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/12/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024]
Abstract
Wastewater-based epidemiology provides temporal and spatial information about the health status of a population. The objective of this study was to analyze and report the epidemiological dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the province of Tucumán, Argentina during the second and third waves of coronavirus disease 2019 (COVID-19) between April 2021 and March 2022. The study aimed to quantify SARS-CoV-2 RNA in wastewater, correlating it with clinically reported COVID-19 cases. Wastewater samples (n = 72) were collected from 16 sampling points located in three cities of Tucumán (San Miguel de Tucumán, Yerba Buena y Banda del Río Salí). Detection of viral nucleocapsid markers (N1 gene) was carried out using one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Viral loads were determined for each positive sample using a standard curve. A positive correlation (p < 0.05) was observed between viral load (copies/mL) and the clinically confirmed COVID-19 cases reported at specific sampling points in San Miguel de Tucumán (SP4, SP7, and SP8) in both months, May and June. Indeed, the high viral load concurred with the peaks of COVID-19 cases. This method allowed us to follow the behavior of SARS-CoV-2 infection during epidemic outbreaks. Thus, wastewater monitoring is a valuable epidemiological indicator that enables the anticipation of increases in COVID-19 cases and tracking the progress of the pandemic. SARS-CoV-2 genome-based surveillance should be implemented as a routine practice to prepare for any future surge in infections.
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Affiliation(s)
- María Cecilia D'Arpino
- Laboratory of Molecular and Ultraestructural Microbiology, Centro Integral de Microscopía Electrónica, (CIME-UNT-CONICET), Facultad de Agronomía, Zootecnia y Veterinaria, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Pedro Eugenio Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Gustavo Goroso
- Laboratorio de Processamento de Sinais e Modelagem de Sistemas Biológicos. Núcleo de Pesquisas Tecnológicas, Universidade Mogi das Cruzes, Sao Paulo, Brasil
| | - William Watanabe
- Laboratorio de Processamento de Sinais e Modelagem de Sistemas Biológicos. Núcleo de Pesquisas Tecnológicas, Universidade Mogi das Cruzes, Sao Paulo, Brasil
| | | | | | | | | | | | | | - Augusto Bellomio
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-Universidad Nacional de Tucumán), Tucumán, Argentina
| | - Virginia Helena Albarracín
- Laboratory of Molecular and Ultraestructural Microbiology, Centro Integral de Microscopía Electrónica, (CIME-UNT-CONICET), Facultad de Agronomía, Zootecnia y Veterinaria, Universidad Nacional de Tucumán, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional Tucumán, Tucumán, Argentina
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27
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Rubio AA, Baharani VA, Dadonaite B, Parada M, Abernathy ME, Wang Z, Lee YE, Eso MR, Phung J, Ramos I, Chen T, Nesr GE, Bloom JD, Bieniasz PD, Nussenzweig MC, Barnes CO. Bispecific antibodies with broad neutralization potency against SARS-CoV-2 variants of concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592584. [PMID: 38766244 PMCID: PMC11100608 DOI: 10.1101/2024.05.05.592584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The ongoing emergence of SARS-CoV-2 variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized N-terminal domain (NTD) and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from COVID-19 convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-EM structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite. Given C1596's favorable binding profile, we designed a series of bispecific antibodies (bsAbs) termed CoV2-biRNs, that featured both NTD and RBD specificities. Notably, two of the C1596-inclusive bsAbs, CoV2-biRN5 and CoV2-biRN7, retained potent in vitro neutralization activity against all Omicron variants tested, including XBB.1.5, EG.5.1, and BA.2.86, contrasting the diminished potency of parental antibodies delivered as monotherapies or as a cocktail. Furthermore, prophylactic delivery of CoV2-biRN5 significantly reduced the viral load within the lungs of K18-hACE2 mice following challenge with SARS-CoV-2 XBB.1.5. In conclusion, our NTD-RBD bsAbs offer promising potential for the design of resilient, next-generation antibody therapeutics against SARS-CoV-2 VOCs.
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Affiliation(s)
- Adonis A. Rubio
- Stanford Biosciences, Stanford School of Medicine; Stanford, USA
- Department of Biology, Stanford University; Stanford, USA
| | - Viren A. Baharani
- Laboratory of Retrovirology, The Rockefeller University; New York, USA
- Laboratory of Molecular Immunology, The Rockefeller University; New York, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center; Seattle, USA
| | - Megan Parada
- Department of Biology, Stanford University; Stanford, USA
| | | | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University; New York, USA
| | - Yu E. Lee
- Department of Biology, Stanford University; Stanford, USA
| | - Michael R. Eso
- Department of Biology, Stanford University; Stanford, USA
| | - Jennie Phung
- Department of Biology, Stanford University; Stanford, USA
| | - Israel Ramos
- Department of Biology, Stanford University; Stanford, USA
| | - Teresia Chen
- Department of Biology, Stanford University; Stanford, USA
| | - Gina El Nesr
- Stanford Biosciences, Stanford School of Medicine; Stanford, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center; Seattle, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University; New York, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University; New York, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | - Christopher O. Barnes
- Department of Biology, Stanford University; Stanford, USA
- ChEM-H Institute, Stanford University; Stanford, CA
- Chan Zuckerberg Biohub; San Francisco, USA
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28
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Hills RA, Tan TK, Cohen AA, Keeffe JR, Keeble AH, Gnanapragasam PNP, Storm KN, Rorick AV, West AP, Hill ML, Liu S, Gilbert-Jaramillo J, Afzal M, Napier A, Admans G, James WS, Bjorkman PJ, Townsend AR, Howarth MR. Proactive vaccination using multiviral Quartet Nanocages to elicit broad anti-coronavirus responses. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01655-9. [PMID: 38710880 DOI: 10.1038/s41565-024-01655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/15/2024] [Indexed: 05/08/2024]
Abstract
Defending against future pandemics requires vaccine platforms that protect across a range of related pathogens. Nanoscale patterning can be used to address this issue. Here, we produce quartets of linked receptor-binding domains (RBDs) from a panel of SARS-like betacoronaviruses, coupled to a computationally designed nanocage through SpyTag/SpyCatcher links. These Quartet Nanocages, possessing a branched morphology, induce a high level of neutralizing antibodies against several different coronaviruses, including against viruses not represented in the vaccine. Equivalent antibody responses are raised to RBDs close to the nanocage or at the tips of the nanoparticle's branches. In animals primed with SARS-CoV-2 Spike, boost immunizations with Quartet Nanocages increase the strength and breadth of an otherwise narrow immune response. A Quartet Nanocage including the Omicron XBB.1.5 'Kraken' RBD induced antibodies with binding to a broad range of sarbecoviruses, as well as neutralizing activity against this variant of concern. Quartet nanocages are a nanomedicine approach with potential to confer heterotypic protection against emergent zoonotic pathogens and facilitate proactive pandemic protection.
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Affiliation(s)
- Rory A Hills
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | | | - Kaya N Storm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Annie V Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michelle L Hill
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Javier Gilbert-Jaramillo
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Madeeha Afzal
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Amy Napier
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gabrielle Admans
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - William S James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Alain R Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
| | - Mark R Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK.
- Department of Pharmacology, University of Cambridge, Cambridge, UK.
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29
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Das T, Luo S, Tang H, Fang J, Mao Y, Yen HH, Dash S, Shajahan A, Pepi L, Huang S, Jones VS, Xie S, Huang GF, Lu J, Anderson B, Zhang B, Azadi P, Huang RP. N-glycosylation of the SARS-CoV-2 spike protein at Asn331 and Asn343 is involved in spike-ACE2 binding, virus entry, and regulation of IL-6. Microbiol Immunol 2024; 68:165-178. [PMID: 38444370 DOI: 10.1111/1348-0421.13121] [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: 07/31/2023] [Revised: 12/06/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an ongoing global public health crisis. The causative agent, the SARS-CoV-2 virus, enters host cells via molecular interactions between the viral spike protein and the host cell ACE2 surface protein. The SARS-CoV-2 spike protein is extensively decorated with up to 66 N-linked glycans. Glycosylation of viral proteins is known to function in immune evasion strategies but may also function in the molecular events of viral entry into host cells. Here, we show that N-glycosylation at Asn331 and Asn343 of SARS-CoV-2 spike protein is required for it to bind to ACE2 and for the entry of pseudovirus harboring the SARS-CoV-2 spike protein into cells. Interestingly, high-content glycan binding screening data have shown that N-glycosylation of Asn331 and Asn343 of the RBD is important for binding to the specific glycan molecule G4GN (Galβ-1,4 GlcNAc), which is critical for spike-RBD-ACE2 binding. Furthermore, IL-6 was identified through antibody array analysis of conditioned media of the corresponding pseudovirus assay. Mutation of N-glycosylation of Asn331 and Asn343 sites of the spike receptor-binding domain (RBD) significantly reduced the transcriptional upregulation of pro-inflammatory signaling molecule IL-6. In addition, IL-6 levels correlated with spike protein levels in COVID-19 patients' serum. These findings establish the importance of RBD glycosylation in SARS-CoV-2 pathogenesis, which can be exploited for the development of novel therapeutics for COVID-19.
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Affiliation(s)
- Tuhin Das
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Shuhong Luo
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Hao Tang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Jianmin Fang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Yinging Mao
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Haw-Han Yen
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Sabyasachi Dash
- Department of Pathology, Center for Vascular Biology, Weill Cornell Medicine, New York, New York, USA
| | - Asif Shajahan
- Vaccine Research Center, Gaithersburg, Maryland, USA
| | - Lauren Pepi
- Vaccine Research Center, Gaithersburg, Maryland, USA
| | - Steven Huang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | | | - Shehuo Xie
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | | | - Jinqiao Lu
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | | | - Benyue Zhang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Ruo-Pan Huang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
- South China Biochip Research Center, Guangzhou, China
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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30
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Shukla N, Roelle SM, Snell JC, DelSignore O, Bruchez AM, Matreyek KA. Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage. PLoS Pathog 2024; 20:e1012044. [PMID: 38768238 PMCID: PMC11142672 DOI: 10.1371/journal.ppat.1012044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/31/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike's interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.
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Affiliation(s)
- Nidhi Shukla
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Sarah M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - John C. Snell
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Olivia DelSignore
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anna M. Bruchez
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
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31
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Guo H, Ha S, Botten JW, Xu K, Zhang N, An Z, Strohl WR, Shiver JW, Fu TM. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies. Viruses 2024; 16:697. [PMID: 38793580 PMCID: PMC11125895 DOI: 10.3390/v16050697] [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: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.
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Affiliation(s)
- Hailong Guo
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kai Xu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Park S, Choi J, Lee Y, Noh J, Kim N, Lee J, Cho G, Kim S, Yoo DK, Kang CK, Choe PG, Kim NJ, Park WB, Kim S, Oh MD, Kwon S, Chung J. An ancestral SARS-CoV-2 vaccine induces anti-Omicron variants antibodies by hypermutation. Nat Commun 2024; 15:3368. [PMID: 38643233 PMCID: PMC11032360 DOI: 10.1038/s41467-024-47743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/10/2024] [Indexed: 04/22/2024] Open
Abstract
The immune escape of Omicron variants significantly subsides by the third dose of an mRNA vaccine. However, it is unclear how Omicron variant-neutralizing antibodies develop under repeated vaccination. We analyze blood samples from 41 BNT162b2 vaccinees following the course of three injections and analyze their B-cell receptor (BCR) repertoires at six time points in total. The concomitant reactivity to both ancestral and Omicron receptor-binding domain (RBD) is achieved by a limited number of BCR clonotypes depending on the accumulation of somatic hypermutation (SHM) after the third dose. Our findings suggest that SHM accumulation in the BCR space to broaden its specificity for unseen antigens is a counterprotective mechanism against virus variant immune escape.
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Affiliation(s)
- Seoryeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Interdisciplinary Program in Cancer Biology Major, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jaewon Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Integrated Major in Innovative Medical Science, Seoul National University, Seoul, Republic of Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Namphil Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - JinAh Lee
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Geummi Cho
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sujeong Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam, Republic of Korea.
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Sunghoon Kwon
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea.
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea.
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Interdisciplinary Program in Cancer Biology Major, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Yang YL, Wang B, Li W, Cai HL, Qian QY, Qin Y, Shi FS, Bosch BJ, Huang YW. Functional dissection of the spike glycoprotein S1 subunit and identification of cellular cofactors for regulation of swine acute diarrhea syndrome coronavirus entry. J Virol 2024; 98:e0013924. [PMID: 38501663 PMCID: PMC11019839 DOI: 10.1128/jvi.00139-24] [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: 01/19/2024] [Accepted: 03/02/2024] [Indexed: 03/20/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel porcine enteric coronavirus, and the broad interspecies infection of SADS-CoV poses a potential threat to human health. This study provides experimental evidence to dissect the roles of distinct domains within the SADS-CoV spike S1 subunit in cellular entry. Specifically, we expressed the S1 and its subdomains, S1A and S1B. Cell binding and invasion inhibition assays revealed a preference for the S1B subdomain in binding to the receptors on the cell surface, and this unknown receptor is not utilized by the porcine epidemic diarrhea virus. Nanoparticle display demonstrated hemagglutination of erythrocytes from pigs, humans, and mice, linking the S1A subdomain to the binding of sialic acid (Sia) involved in virus attachment. We successfully rescued GFP-labeled SADS-CoV (rSADS-GFP) from a recombinant cDNA clone to track viral infection. Antisera raised against S1, S1A, or S1B contained highly potent neutralizing antibodies, with anti-S1B showing better efficiency in neutralizing rSADS-GFP infection compared to anti-S1A. Furthermore, depletion of heparan sulfate (HS) by heparinase treatment or pre-incubation of rSADS-GFP with HS or constituent monosaccharides could inhibit SADS-CoV entry. Finally, we demonstrated that active furin cleavage of S glycoprotein and the presence of type II transmembrane serine protease (TMPRSS2) are essential for SADS-CoV infection. These combined observations suggest that the wide cell tropism of SADS-CoV may be related to the distribution of Sia or HS on the cell surface, whereas the S1B contains the main protein receptor binding site. Specific host proteases also play important roles in facilitating SADS-CoV entry.IMPORTANCESwine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel pathogen infecting piglet, and its unique genetic evolution characteristics and broad species tropism suggest the potential for cross-species transmission. The virus enters cells through its spike (S) glycoprotein. In this study, we identify the receptor binding domain on the C-terminal part of the S1 subunit (S1B) of SADS-CoV, whereas the sugar-binding domain located at the S1 N-terminal part of S1 (S1A). Sialic acid, heparan sulfate, and specific host proteases play essential roles in viral attachment and entry. The dissection of SADS-CoV S1 subunit's functional domains and identification of cellular entry cofactors will help to explore the receptors used by SADS-CoV, which may contribute to exploring the mechanisms behind cross-species transmission and host tropism.
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Affiliation(s)
- Yong-Le Yang
- Xianghu Laboratory, Hangzhou, China
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Bin Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Wentao Li
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Qian-Yu Qian
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yu Qin
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Fang-Shu Shi
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Yao-Wei Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
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Tortorici MA, Addetia A, Seo AJ, Brown J, Sprouse K, Logue J, Clark E, Franko N, Chu H, Veesler D. Persistent immune imprinting occurs after vaccination with the COVID-19 XBB.1.5 mRNA booster in humans. Immunity 2024; 57:904-911.e4. [PMID: 38490197 DOI: 10.1016/j.immuni.2024.02.016] [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: 12/01/2023] [Revised: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Immune imprinting describes how the first exposure to a virus shapes immunological outcomes of subsequent exposures to antigenically related strains. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron breakthrough infections and bivalent COVID-19 vaccination primarily recall cross-reactive memory B cells induced by prior Wuhan-Hu-1 spike mRNA vaccination rather than priming Omicron-specific naive B cells. These findings indicate that immune imprinting occurs after repeated Wuhan-Hu-1 spike exposures, but whether it can be overcome remains unclear. To understand the persistence of immune imprinting, we investigated memory and plasma antibody responses after administration of the updated XBB.1.5 COVID-19 mRNA vaccine booster. We showed that the XBB.1.5 booster elicited neutralizing antibody responses against current variants that were dominated by recall of pre-existing memory B cells previously induced by the Wuhan-Hu-1 spike. Therefore, immune imprinting persists after multiple exposures to Omicron spikes through vaccination and infection, including post XBB.1.5 booster vaccination, which will need to be considered to guide future vaccination.
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Affiliation(s)
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaiti Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jenni Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Erica Clark
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Helen Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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35
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Addetia A, Stewart C, Seo AJ, Sprouse KR, Asiri AY, Al-Mozaini M, Memish ZA, Alshukairi A, Veesler D. Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.586409. [PMID: 38617298 PMCID: PMC11014493 DOI: 10.1101/2024.03.31.586409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Middle-East respiratory syndrome coronavirus (MERS-CoV) first emerged in 2012 and causes human infections in endemic regions. Most vaccines and therapeutics in development against MERS-CoV focus on the spike (S) glycoprotein to prevent viral entry into target cells. These efforts, however, are limited by a poor understanding of antibody responses elicited by infection along with their durability, fine specificity and contribution of distinct S antigenic sites to neutralization. To address this knowledge gap, we analyzed S-directed binding and neutralizing antibody titers in plasma collected from individuals infected with MERS-CoV in 2017-2019 (prior to the COVID-19 pandemic). We observed that binding and neutralizing antibodies peak 1 to 6 weeks after symptom onset/hospitalization, persist for at least 6 months, and broadly neutralize human and camel MERS-CoV strains. We show that the MERS-CoV S1 subunit is immunodominant and that antibodies targeting S1, particularly the RBD, account for most plasma neutralizing activity. Antigenic site mapping revealed that polyclonal plasma antibodies frequently target RBD epitopes, particularly a site exposed irrespective of the S trimer conformation, whereas targeting of S2 subunit epitopes is rare, similar to SARS-CoV-2. Our data reveal in unprecedented details the humoral immune responses elicited by MERS-CoV infection, which will guide vaccine and therapeutic design.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ayed Y Asiri
- Al-Hayat National Hospital, Riyadh, Saudi Arabia
| | - Maha Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ziad A Memish
- King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Kyung Hee University, Seoul, South Korea
| | - Abeer Alshukairi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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36
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Anzai I, Fujita J, Ono C, Kosaka Y, Miyamoto Y, Shichinohe S, Takada K, Torii S, Taguwa S, Suzuki K, Makino F, Kajita T, Inoue T, Namba K, Watanabe T, Matsuura Y. Characterization of a neutralizing antibody that recognizes a loop region adjacent to the receptor-binding interface of the SARS-CoV-2 spike receptor-binding domain. Microbiol Spectr 2024; 12:e0365523. [PMID: 38415660 PMCID: PMC10986471 DOI: 10.1128/spectrum.03655-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Although the global crisis caused by the coronavirus disease 2019 (COVID-19) pandemic is over, the global epidemic of the disease continues. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of COVID-19, initiates infection via the binding of the receptor-binding domain (RBD) of its spike protein to the human angiotensin-converting enzyme II (ACE2) receptor, and this interaction has been the primary target for the development of COVID-19 therapeutics. Here, we identified neutralizing antibodies against SARS-CoV-2 by screening mouse monoclonal antibodies and characterized an antibody, CSW1-1805, that targets a narrow region at the RBD ridge of the spike protein. CSW1-1805 neutralized several variants in vitro and completely protected mice from SARS-CoV-2 infection. Cryo-EM and biochemical analyses revealed that this antibody recognizes the loop region adjacent to the ACE2-binding interface with the RBD in both a receptor-inaccessible "down" state and a receptor-accessible "up" state and could stabilize the RBD conformation in the up-state. CSW1-1805 also showed different binding orientations and complementarity determining region properties compared to other RBD ridge-targeting antibodies with similar binding epitopes. It is important to continuously characterize neutralizing antibodies to address new variants that continue to emerge. Our characterization of this antibody that recognizes the RBD ridge of the spike protein will aid in the development of future neutralizing antibodies.IMPORTANCESARS-CoV-2 cell entry is initiated by the interaction of the viral spike protein with the host cell receptor. Therefore, mechanistic findings regarding receptor recognition by the spike protein help uncover the molecular mechanism of SARS-CoV-2 infection and guide neutralizing antibody development. Here, we characterized a SARS-CoV-2 neutralizing antibody that recognizes an epitope, a loop region adjacent to the receptor-binding interface, that may be involved in the conformational transition of the receptor-binding domain (RBD) of the spike protein from a receptor-inaccessible "down" state into a receptor-accessible "up" state, and also stabilizes the RBD in the up-state. Our mechanistic findings provide new insights into SARS-CoV-2 receptor recognition and guidance for neutralizing antibody development.
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Grants
- JP16H06429, JP16K21723, JP16H06432 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP16H06429, JP16K21723, JP16H06434 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15042 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP25K000013 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K22630 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP223fa627002, JP22am0401030, JP23fk0108659, JP20jk0210021, JP22gm1610010, JP19fk0108113 Japan Agency for Medical Research and Development (AMED)
- JP223fa627002 Japan Agency for Medical Research and Development (AMED)
- JP19fk0108113, JP20fk0108281, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP21am0101117, JP17pc0101020 Japan Agency for Medical Research and Development (AMED)
- JPMJOP1861 MEXT | Japan Science and Technology Agency (JST)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
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Affiliation(s)
- Itsuki Anzai
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Junso Fujita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Chikako Ono
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | | | | | - Shintaro Shichinohe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shiho Torii
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shuhei Taguwa
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
| | - Fumiaki Makino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- JEOL Ltd., Akishima, Tokyo, Japan
| | | | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research and Spring-8 Center, Suita, Osaka, Japan
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
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Nassiri M, Ghovvati S, Gharouni M, Tahmoorespur M, Bahrami AR, Dehghani H. Engineering Human Pancreatic RNase 1 as an Immunotherapeutic Agent for Cancer Therapy Through Computational and Experimental Studies. Protein J 2024; 43:316-332. [PMID: 38145445 DOI: 10.1007/s10930-023-10171-z] [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] [Accepted: 11/20/2023] [Indexed: 12/26/2023]
Abstract
Most plant and bacterial toxins are highly immunogenic with non-specific toxic effects. Human ribonucleases are thought to provide a promising basis for reducing the toxic agent's immunogenic properties, which are candidates for cancer therapy. In the cell, the ribonuclease inhibitor (RI) protein binds to the ribonuclease enzyme and forms a tight complex. This study aimed to engineer and provide a gene construct encoding an improved version of Human Pancreatic RNase 1 (HP-RNase 1) to reduce connection to RI and modulate the immunogenic effects of immunotoxins. To further characterize the interaction complex of HP-RNase 1 and RI, we established various in silico and in vitro approaches. These methods allowed us to specifically monitor interactions within native and engineered HP-RNase 1/RI complexes. In silico research involved molecular dynamics (MD) simulations of native and mutant HP-RNase 1 in their free form and when bound to RI. For HP-RNase 1 engineering, we designed five mutations (K8A/N72A/N89A/R92D/E112/A) based on literature studies, as this combination proved effective for the intended investigation. Then, the cDNA encoding HP-RNase 1 was generated by RT-PCR from blood and cloned into the pSYN2 expression vector. Consequently, wild-type and the engineered HP-RNase 1 were over-expressed in E. coli TG1 and purified using an IMAC column directed against a poly-his tag. The protein products were detected by SDS-PAGE and Western blot analysis. HP-RNase 1 catalytic activity, in the presence of various concentrations of RI, demonstrated that the mutated version of the protein is able to escape the ribonuclease inhibitor and target the RNA substrate 2.5 folds more than that of the wild type. From these data, we tend to suggest the engineered recombinant HP-RNase 1 potentially as a new immunotherapeutic agent for application in human cancer therapy.
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Affiliation(s)
- Mohammadreza Nassiri
- Department of Animal Science, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Shahrokh Ghovvati
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, 41635-1314, Rasht, Guilan, Iran.
| | - Marzieh Gharouni
- Department of Biochemistry, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mojtaba Tahmoorespur
- Department of Animal Science, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Reza Bahrami
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Molecular Cell Biology, College of Applied Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Physiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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38
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Tam EH, Peng Y, Cheah MXY, Yan C, Xiao T. Neutralizing antibodies to block viral entry and for identification of entry inhibitors. Antiviral Res 2024; 224:105834. [PMID: 38369246 DOI: 10.1016/j.antiviral.2024.105834] [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: 10/31/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Neutralizing antibodies (NAbs) are naturally produced by our immune system to combat viral infections. Clinically, neutralizing antibodies with potent efficacy and high specificity have been extensively used to prevent and treat a wide variety of viral infections, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Human Immunodeficiency Virus (HIV), Dengue Virus (DENV) and Hepatitis B Virus (HBV). An overwhelmingly large subset of clinically effective NAbs operates by targeting viral envelope proteins to inhibit viral entry into the host cell. Binding of viral envelope protein to the host receptor is a critical rate limiting step triggering a cascade of downstream events, including endocytosis, membrane fusion and pore formation to allow viral entry. In recent years, improved structural knowledge on these processes have allowed researchers to also leverage NAbs as an indispensable tool in guiding discovery of novel antiviral entry inhibitors, providing drug candidates with high efficacy and pan-genus specificity. This review will summarize the latest progresses on the applications of NAbs as effective entry inhibitors and as important tools to develop antiviral therapeutics by high-throughput drug screenings, rational design of peptidic entry inhibitor mimicking NAbs and in silico computational modeling approaches.
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Affiliation(s)
- Ee Hong Tam
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore
| | - Yu Peng
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore
| | - Megan Xin Yan Cheah
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research) 138673, Singapore
| | - Chuan Yan
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research) 138673, Singapore
| | - Tianshu Xiao
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore.
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39
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Kosik I, Da Silva Santos J, Angel M, Hu Z, Holly J, Gibbs JS, Gill T, Kosikova M, Li T, Bakhache W, Dolan PT, Xie H, Andrews SF, Gillespie RA, Kanekiyo M, McDermott AB, Pierson TC, Yewdell JW. C1q enables influenza hemagglutinin stem binding antibodies to block viral attachment and broadens the antibody escape repertoire. Sci Immunol 2024; 9:eadj9534. [PMID: 38517951 DOI: 10.1126/sciimmunol.adj9534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/14/2024] [Indexed: 03/24/2024]
Abstract
Antigenic drift, the gradual accumulation of amino acid substitutions in the influenza virus hemagglutinin (HA) receptor protein, enables viral immune evasion. Antibodies (Abs) specific for the drift-resistant HA stem region are a promising universal influenza vaccine target. Although anti-stem Abs are not believed to block viral attachment, here we show that complement component 1q (C1q), a 460-kilodalton protein with six Ab Fc-binding domains, confers attachment inhibition to anti-stem Abs and enhances their fusion and neuraminidase inhibition. As a result, virus neutralization activity in vitro is boosted up to 30-fold, and in vivo protection from influenza PR8 infection in mice is enhanced. These effects reflect increased steric hindrance and not increased Ab avidity. C1q greatly expands the anti-stem Ab viral escape repertoire to include residues throughout the HA, some of which cause antigenic alterations in the globular region or modulate HA receptor avidity. We also show that C1q enhances the neutralization activity of non-receptor binding domain anti-SARS-CoV-2 spike Abs, an effect dependent on spike density on the virion surface. These findings demonstrate that C1q can greatly expand Ab function and thereby contribute to viral evolution and immune escape.
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Affiliation(s)
- Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jefferson Da Silva Santos
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Mathew Angel
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jaroslav Holly
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - James S Gibbs
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Tanner Gill
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Martina Kosikova
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Tiansheng Li
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - William Bakhache
- Quantitative Virology and Evolution Unit, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Patrick T Dolan
- Quantitative Virology and Evolution Unit, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Hang Xie
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Sarah F Andrews
- Vaccine Immunology Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca A Gillespie
- Molecular Immunoengineering Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Masaru Kanekiyo
- Molecular Immunoengineering Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adrian B McDermott
- Vaccine Immunology Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Theodore C Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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40
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Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024; 15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [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: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
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Affiliation(s)
- Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | | | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Strauss van Graan
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | | | | | | | | | - Elizabeth Venter
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Monjurul Hoque
- KwaDabeka Community Health Centre, KwaDabeka, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombulelo Magula
- Department of Internal Medicine, Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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41
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Arevalo-Romero JA, Chingaté-López SM, Camacho BA, Alméciga-Díaz CJ, Ramirez-Segura CA. Next-generation treatments: Immunotherapy and advanced therapies for COVID-19. Heliyon 2024; 10:e26423. [PMID: 38434363 PMCID: PMC10907543 DOI: 10.1016/j.heliyon.2024.e26423] [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: 10/12/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in 2019 following prior outbreaks of coronaviruses like SARS and MERS in recent decades, underscoring their high potential of infectivity in humans. Insights from previous outbreaks of SARS and MERS have played a significant role in developing effective strategies to mitigate the global impact of SARS-CoV-2. As of January 7, 2024, there have been 774,075,242 confirmed cases of COVID-19 worldwide. To date, 13.59 billion vaccine doses have been administered, and there have been 7,012,986 documented fatalities (https://www.who.int/) Despite significant progress in addressing the COVID-19 pandemic, the rapid evolution of SARS-CoV-2 challenges human defenses, presenting ongoing global challenges. The emergence of new SARS-CoV-2 lineages, shaped by mutation and recombination processes, has led to successive waves of infections. This scenario reveals the need for next-generation vaccines as a crucial requirement for ensuring ongoing protection against SARS-CoV-2. This demand calls for formulations that trigger a robust adaptive immune response without leading the acute inflammation linked with the infection. Key mutations detected in the Spike protein, a critical target for neutralizing antibodies and vaccine design -specifically within the Receptor Binding Domain region of Omicron variant lineages (B.1.1.529), currently dominant worldwide, have intensified concerns due to their association with immunity evasion from prior vaccinations and infections. As the world deals with this evolving threat, the narrative extends to the realm of emerging variants, each displaying new mutations with implications that remain largely misunderstood. Notably, the JN.1 Omicron lineage is gaining global prevalence, and early findings suggest it stands among the immune-evading variants, a characteristic attributed to its mutation L455S. Moreover, the detrimental consequences of the novel emergence of SARS-CoV-2 lineages bear a particularly critical impact on immunocompromised individuals and older adults. Immunocompromised individuals face challenges such as suboptimal responses to COVID-19 vaccines, rendering them more susceptible to severe disease. Similarly, older adults have an increased risk of severe disease and the presence of comorbid conditions, find themselves at a heightened vulnerability to develop COVID-19 disease. Thus, recognizing these intricate factors is crucial for effectively tailoring public health strategies to protect these vulnerable populations. In this context, this review aims to describe, analyze, and discuss the current progress of the next-generation treatments encompassing immunotherapeutic approaches and advanced therapies emerging as complements that will offer solutions to counter the disadvantages of the existing options. Preliminary outcomes show that these strategies target the virus and address the immunomodulatory responses associated with COVID-19. Furthermore, the capacity to promote tissue repair has been demonstrated, which can be particularly noteworthy for immunocompromised individuals who stand as vulnerable actors in the global landscape of coronavirus infections. The emerging next-generation treatments possess broader potential, offering protection against a wide range of variants and enhancing the ability to counter the impact of the constant evolution of the virus. Furthermore, advanced therapies are projected as potential treatment alternatives for managing Chronic Post-COVID-19 syndromeand addressing its associated long-term complications.
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Affiliation(s)
- Jenny Andrea Arevalo-Romero
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
- Instituto de Errores Innatos del Metabolismo, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231, Bogotá, D.C., Colombia
| | - Sandra M. Chingaté-López
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
| | - Bernardo Armando Camacho
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
| | - Carlos Javier Alméciga-Díaz
- Instituto de Errores Innatos del Metabolismo, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231, Bogotá, D.C., Colombia
| | - Cesar A. Ramirez-Segura
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
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42
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Lebedin M, Ratswohl C, Garg A, Schips M, García CV, Spatt L, Thibeault C, Obermayer B, Weiner J, Velásquez IM, Gerhard C, Stubbemann P, Hanitsch LG, Pischon T, Witzenrath M, Sander LE, Kurth F, Meyer-Hermann M, de la Rosa K. Soluble ACE2 correlates with severe COVID-19 and can impair antibody responses. iScience 2024; 27:109330. [PMID: 38496296 PMCID: PMC10940809 DOI: 10.1016/j.isci.2024.109330] [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: 08/03/2023] [Revised: 11/25/2023] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
Identifying immune modulators that impact neutralizing antibody responses against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is of great relevance. We postulated that high serum concentrations of soluble angiotensin-converting enzyme 2 (sACE2) might mask the spike and interfere with antibody maturation toward the SARS-CoV-2-receptor-binding motif (RBM). We tested 717 longitudinal samples from 295 COVID-19 patients and showed a 2- to 10-fold increase of enzymatically active sACE2 (a-sACE2), with up to 1 μg/mL total sACE2 in moderate and severe patients. Fifty percent of COVID-19 sera inhibited ACE2 activity, in contrast to 1.3% of healthy donors and 4% of non-COVID-19 pneumonia patients. A mild inverse correlation of a-sACE2 with RBM-directed serum antibodies was observed. In silico, we show that sACE2 concentrations measured in COVID-19 sera can disrupt germinal center formation and inhibit timely production of high-affinity antibodies. We suggest that sACE2 is a biomarker for COVID-19 and that soluble receptors may contribute to immune suppression informing vaccine design.
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Affiliation(s)
- Mikhail Lebedin
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Ratswohl
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Free University of Berlin, Department of Biology, Chemistry and Pharmacy, 14195 Berlin, Berlin, Germany
| | - Amar Garg
- Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Schips
- Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Clara Vázquez García
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lisa Spatt
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - January Weiner
- Core Unit Bioinformatics, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Ilais Moreno Velásquez
- Molecular Epidemiology Research Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Cathrin Gerhard
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Paula Stubbemann
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Leif-Gunnar Hanitsch
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Tobias Pischon
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Molecular Epidemiology Research Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Biobank Technology Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Lung Research (DZL), 35392 Gießen, Germany
- CAPNETZ STIFTUNG, 30625 Hannover, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Lung Research (DZL), 35392 Gießen, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Lung Research (DZL), 35392 Gießen, Germany
| | - Michael Meyer-Hermann
- Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kathrin de la Rosa
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
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Chao CW, Sprouse KR, Miranda MC, Catanzaro NJ, Hubbard ML, Addetia A, Stewart C, Brown JT, Dosey A, Valdez A, Ravichandran R, Hendricks GG, Ahlrichs M, Dobbins C, Hand A, Treichel C, Willoughby I, Walls AC, McGuire AT, Leaf EM, Baric RS, Schäfer A, Veesler D, King NP. Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584735. [PMID: 38558973 PMCID: PMC10979991 DOI: 10.1101/2024.03.13.584735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that causes severe and often lethal respiratory illness in humans. The MERS-CoV spike (S) protein is the viral fusogen and the target of neutralizing antibodies, and has therefore been the focus of vaccine design efforts. Currently there are no licensed vaccines against MERS-CoV and only a few candidates have advanced to Phase I clinical trials. Here we developed MERS-CoV vaccines utilizing a computationally designed protein nanoparticle platform that has generated safe and immunogenic vaccines against various enveloped viruses, including a licensed vaccine for SARS-CoV-2. Two-component protein nanoparticles displaying MERS-CoV S-derived antigens induced robust neutralizing antibody responses and protected mice against challenge with mouse-adapted MERS-CoV. Electron microscopy polyclonal epitope mapping and serum competition assays revealed the specificities of the dominant antibody responses elicited by immunogens displaying the prefusion-stabilized S-2P trimer, receptor binding domain (RBD), or N-terminal domain (NTD). An RBD nanoparticle vaccine elicited antibodies targeting multiple non-overlapping epitopes in the RBD, whereas anti-NTD antibodies elicited by the S-2P- and NTD-based immunogens converged on a single antigenic site. Our findings demonstrate the potential of two-component nanoparticle vaccine candidates for MERS-CoV and suggest that this platform technology could be broadly applicable to betacoronavirus vaccine development.
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Affiliation(s)
- Cara W Chao
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Miranda L Hubbard
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adian Valdez
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Grace G Hendricks
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Isabelle Willoughby
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Andrew T McGuire
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth M Leaf
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Planas D, Staropoli I, Michel V, Lemoine F, Donati F, Prot M, Porrot F, Guivel-Benhassine F, Jeyarajah B, Brisebarre A, Dehan O, Avon L, Bolland WH, Hubert M, Buchrieser J, Vanhoucke T, Rosenbaum P, Veyer D, Péré H, Lina B, Trouillet-Assant S, Hocqueloux L, Prazuck T, Simon-Loriere E, Schwartz O. Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion. Nat Commun 2024; 15:2254. [PMID: 38480689 PMCID: PMC10938001 DOI: 10.1038/s41467-024-46490-7] [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: 12/14/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolate and characterize XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1 and JN.1 variants, representing >80% of circulating variants in January 2024. The XBB subvariants carry few but recurrent mutations in the spike, whereas BA.2.86.1 and JN.1 harbor >30 additional changes. These variants replicate in IGROV-1 but no longer in Vero E6 and are not markedly fusogenic. They potently infect nasal epithelial cells, with EG.5.1.3 exhibiting the highest fitness. Antivirals remain active. Neutralizing antibody (NAb) responses from vaccinees and BA.1/BA.2-infected individuals are markedly lower compared to BA.1, without major differences between variants. An XBB breakthrough infection enhances NAb responses against both XBB and BA.2.86 variants. JN.1 displays lower affinity to ACE2 and higher immune evasion properties compared to BA.2.86.1. Thus, while distinct, the evolutionary trajectory of these variants combines increased fitness and antibody evasion.
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Affiliation(s)
- Delphine Planas
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France.
- Vaccine Research Institute, Créteil, France.
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Vincent Michel
- Pathogenesis of Vascular Infections Unit, Institut Pasteur, INSERM, Paris, France
| | - Frederic Lemoine
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics Hub, Paris, France
| | - Flora Donati
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Francoise Porrot
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | | | - Banujaa Jeyarajah
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Angela Brisebarre
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Océane Dehan
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Léa Avon
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - William Henry Bolland
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Julian Buchrieser
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Thibault Vanhoucke
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Pierre Rosenbaum
- Humoral Immunology Laboratory, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris, France
| | - David Veyer
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Paris, France
- Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris, France
| | - Hélène Péré
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Paris, France
- Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Sophie Trouillet-Assant
- Laboratoire de Virologie, Institut des Agents Infectieux, Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | | | - Thierry Prazuck
- CHU d'Orléans, Service de Maladies Infectieuses, Orléans, France
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France.
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France.
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France.
- Vaccine Research Institute, Créteil, France.
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Wang Q, Guo Y, Bowen A, Mellis IA, Valdez R, Gherasim C, Gordon A, Liu L, Ho DD. XBB.1.5 monovalent mRNA vaccine booster elicits robust neutralizing antibodies against XBB subvariants and JN.1. Cell Host Microbe 2024; 32:315-321.e3. [PMID: 38377995 PMCID: PMC10948033 DOI: 10.1016/j.chom.2024.01.014] [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: 12/05/2023] [Revised: 01/04/2024] [Accepted: 01/26/2024] [Indexed: 02/22/2024]
Abstract
COVID-19 vaccines have recently been updated to specifically encode or contain the spike protein of the SARS-CoV-2 XBB.1.5 subvariant, but their immunogenicity in humans has yet to be fully evaluated and reported, particularly against emergent viruses that are rapidly expanding. We now report that administration of an updated monovalent mRNA vaccine booster (XBB.1.5 MV) to previously uninfected individuals boosted serum virus-neutralizing antibodies significantly against not only XBB.1.5 (27.0-fold increase) and EG.5.1 (27.6-fold increase) but also key emerging viruses such as HV.1, HK.3, JD.1.1, and JN.1 (13.3- to 27.4-fold increase). Individuals previously infected by an Omicron subvariant had the highest overall serum neutralizing titers (ID50 1,504-22,978) against all viral variants tested. While immunological imprinting was still evident with the updated vaccines, it was not nearly as severe as observed with the previously authorized bivalent BA.5 vaccine. Our findings strongly support the official recommendation to widely apply the updated COVID-19 vaccines.
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Affiliation(s)
- Qian Wang
- 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
| | - Anthony Bowen
- 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
| | - Ian A Mellis
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Riccardo Valdez
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carmen Gherasim
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Lihong Liu
- 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 D Ho
- 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; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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46
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Almubarak HF, Tan W, Hoffmann AD, Wei J, El-Shennawy L, Squires JR, Sun Y, Dashzeveg NK, Simonton B, Jia Y, Iyer R, Xu Y, Nicolaescu V, Elli D, Randall GC, Schipma MJ, Swaminathan S, Ison MG, Liu H, Fang D, Shen Y. Physics-driven structural docking and protein language models accelerate antibody screening and design for broad-spectrum antiviral therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582176. [PMID: 38496411 PMCID: PMC10942297 DOI: 10.1101/2024.03.01.582176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Therapeutic antibodies have become one of the most influential therapeutics in modern medicine to fight against infectious pathogens, cancer, and many other diseases. However, experimental screening for highly efficacious targeting antibodies is labor-intensive and of high cost, which is exacerbated by evolving antigen targets under selective pressure such as fast-mutating viral variants. As a proof-of-concept, we developed a machine learning-assisted antibody generation pipeline that greatly accelerates the screening and re-design of immunoglobulins G (IgGs) against a broad spectrum of SARS-CoV-2 coronavirus variant strains. These viruses infect human host cells via the viral spike protein binding to the host cell receptor angiotensin-converting enzyme 2 (ACE2). Using over 1300 IgG sequences derived from convalescent patient B cells that bind with spike's receptor binding domain (RBD), we first established protein structural docking models in assessing the RBD-IgG-ACE2 interaction interfaces and predicting the virus-neutralizing activity of each IgG with a confidence score. Additionally, employing Gaussian process regression (also known as Kriging) in a latent space of an antibody language model, we predicted the landscape of IgGs' activity profiles against individual coronaviral variants of concern. With functional analyses and experimental validations, we efficiently prioritized IgG candidates for neutralizing a broad spectrum of viral variants (wildtype, Delta, and Omicron) to prevent the infection of host cells in vitro and hACE2 transgenic mice in vivo. Furthermore, the computational analyses enabled rational redesigns of selective IgG clones with single amino acid substitutions at the RBD-binding interface to improve the IgG blockade efficacy for one of the severe, therapy-resistant strains - Delta (B.1.617). Our work expedites applications of artificial intelligence in antibody screening and re-design even in low-data regimes combining protein language models and Kriging for antibody sequence analysis, activity prediction, and efficacy improvement, in synergy with physics-driven protein docking models for antibody-antigen interface structure analyses and functional optimization.
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Affiliation(s)
- Hannah Faisal Almubarak
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Driskill Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
| | - Andrew D. Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Juncheng Wei
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Lamiaa El-Shennawy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Joshua R. Squires
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
| | - Nurmaa K. Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Brooke Simonton
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Radhika Iyer
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Yanan Xu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Vlad Nicolaescu
- Howard T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637
| | - Derek Elli
- Howard T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637
| | - Glenn C. Randall
- Howard T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637
| | - Matthew J. Schipma
- NUseq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Suchitra Swaminathan
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | | | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
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Xu Z, Wang H, Jiang S, Teng J, Zhou D, Chen Z, Wen C, Xu Z. Brain Pathology in COVID-19: Clinical Manifestations and Potential Mechanisms. Neurosci Bull 2024; 40:383-400. [PMID: 37715924 PMCID: PMC10912108 DOI: 10.1007/s12264-023-01110-0] [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: 01/12/2023] [Accepted: 05/25/2023] [Indexed: 09/18/2023] Open
Abstract
Neurological manifestations of coronavirus disease 2019 (COVID-19) are less noticeable than the respiratory symptoms, but they may be associated with disability and mortality in COVID-19. Even though Omicron caused less severe disease than Delta, the incidence of neurological manifestations is similar. More than 30% of patients experienced "brain fog", delirium, stroke, and cognitive impairment, and over half of these patients presented abnormal neuroimaging outcomes. In this review, we summarize current advances in the clinical findings of neurological manifestations in COVID-19 patients and compare them with those in patients with influenza infection. We also illustrate the structure and cellular invasion mechanisms of SARS-CoV-2 and describe the pathway for central SARS-CoV-2 invasion. In addition, we discuss direct damage and other pathological conditions caused by SARS-CoV-2, such as an aberrant interferon response, cytokine storm, lymphopenia, and hypercoagulation, to provide treatment ideas. This review may offer new insights into preventing or treating brain damage in COVID-19.
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Affiliation(s)
- Zhixing Xu
- First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Hui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Siya Jiang
- Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiao Teng
- Affiliated Lin'an People's Hospital of Hangzhou Medical College, First People's Hospital of Hangzhou Lin'an District, Lin'an, Hangzhou, 311300, China
| | - Dongxu Zhou
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Zhong Chen
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chengping Wen
- Laboratory of Rheumatology and Institute of TCM Clinical Basic Medicine, College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Zhenghao Xu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
- Laboratory of Rheumatology and Institute of TCM Clinical Basic Medicine, College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
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48
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Woodruff MC, Faliti CE, Sanz I. Systems biology of B cells in COVID-19. Semin Immunol 2024; 72:101875. [PMID: 38489999 DOI: 10.1016/j.smim.2024.101875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/17/2024]
Abstract
The integration of multi-'omic datasets into complex systems-wide assessments has become a mainstay in immunologic investigation. This focus on high-dimensional data collection and analysis was on full display in the investigation of COVID-19, the respiratory illness resulting from infection by the novel coronavirus SARS-CoV-2. Particularly in the area of B cell biology, tremendous efforts in both cellular and serologic investigation have resulted in an increasingly detailed mapping of the coordinated effector, memory, and antibody secreting cell responses that underpin the development of humoral immunity in response to primary viral infection. Further, the rapid development and deployment of effective vaccines has allowed for the assessment of developing memory responses across a wide variety of immune contexts, including in patients with compromised immune function. The result has been a period of rapid gains in the understanding of B cell biology unrestricted to the study of COVID-19. Here, we outline the systems-level technologies that have been routinely implemented in these investigations throughout the pandemic, and discuss how their use has led to clear and applicable gains in pursuance of the amelioration of human infectious disease and beyond.
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Affiliation(s)
- Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA; Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA.
| | - Caterina E Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA; Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA.
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA; Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
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49
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Jain A, Negi G, Kaur D, S V, Saxena V. Utility of COVID-19 Seropositive Plasma as Convalescent Plasma: An Immune and Neutralization Antibody Seroprevalence Analysis in Blood Donors for Future Potential Pandemic Readiness. Cureus 2024; 16:e57149. [PMID: 38681329 PMCID: PMC11055615 DOI: 10.7759/cureus.57149] [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] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
OBJECTIVES To analyze the seroprevalence of SARS-CoV-2 IgG antibodies and neutralizing antibodies in blood donors during the second wave of the pandemic and to explore the utility of COVID-19 seropositive plasma as convalescent plasma. MATERIALS AND METHODS In this study, 696 blood donors were tested for anti-SARS-CoV-2 IgG antibodies using a chemiluminescence assay. By blinding, 271 samples were chosen randomly for testing of neutralizing antibodies by enzyme-linked immunosorbent assay (ELISA) in duplicate among the 696 blood donors tested for anti-SARS-CoV-2 IgG antibodies, irrespective of the positivity or negativity of the result of the anti-SARS-CoV-2 IgG antibodies by chemiluminescence assay. IgG antibody levels were analyzed in signal-to-cutoff (S/Co), while neutralizing antibody levels were analyzed in percentage inhibition. RESULTS The seroprevalence of IgG antibodies based on the S/Co for the positive results ≥ 1.00 was 82.75%, while the seroprevalence of neutralizing antibodies based on the percentage inhibition for the positive results ≥ 30% was 89.59%. Frontline workers (FLWs) and Covishield-vaccinated individuals showed higher levels of the anti-SARS-CoV-2 IgG antibodies regarding higher S/Co. In comparison, levels of neutralization antibodies regarding percentage inhibition were higher only in FLWs. Covishield-vaccinated donors elicited a statistically higher seroprevalence of anti-SARS-CoV-2 IgG antibodies compared to the Covaxin-vaccinated, while the seroprevalence of neutralizing antibodies was not statistically different among this group. There was a positive correlation (0.762) between anti-SARS-CoV-2 IgG antibodies and neutralizing antibodies, and almost all donors' of S/Co ≥ 9.5 had neutralizing antibodies. CONCLUSION This study showed higher seroprevalence in the blood donor population compared to published seroprevalence in India's second wave of the pandemic. In the current study, 328 donors (47.12%) of the 696 screened donors were neither vaccinated nor had previous SARS-CoV-2 infection, but many had antibodies. The seroprevalence of neutralizing antibodies (96.42%) was higher than the seroprevalence of the anti-SARS-CoV-2 IgG antibodies (85.71%) in the donors who had previous infection of COVID-19. On the other hand, vaccinated donors showed similar immune responses for neutralizing antibodies and the anti-SARS-CoV-2 IgG antibodies. Higher IgG immune reactivity in S/Co showed a good correlation with neutralizing antibodies and can be used to screen whole blood donors for convalescent plasma donations.
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Affiliation(s)
- Ashish Jain
- Transfusion Medicine, All India Institute of Medical Sciences, Rishikesh, Rishikesh, IND
| | - Gita Negi
- Transfusion Medicine, All India Institute of Medical Sciences, Rishikesh, Rishikesh, IND
| | - Daljit Kaur
- Transfusion Medicine, All India Institute of Medical Sciences, Rishikesh, Rishikesh, IND
| | - Vivekanandhan S
- Biochemistry, All India Institute of Medical Sciences, Rishikesh, Rishikesh, IND
| | - Vartika Saxena
- Community and Family Medicine, All India Institute of Medical Sciences, Rishikesh, Rishikesh, IND
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Magazine N, Zhang T, Bungwon AD, McGee MC, Wu Y, Veggiani G, Huang W. Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development. Immunohorizons 2024; 8:214-226. [PMID: 38427047 PMCID: PMC10985062 DOI: 10.4049/immunohorizons.2400003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Despite the success of global vaccination programs in slowing the spread of COVID-19, these efforts have been hindered by the emergence of new SARS-CoV-2 strains capable of evading prior immunity. The mutation and evolution of SARS-CoV-2 have created a demand for persistent efforts in vaccine development. SARS-CoV-2 Spike protein has been the primary target for COVID-19 vaccine development, but it is also the hotspot of mutations directly involved in host susceptibility and virus immune evasion. Our ability to predict emerging mutants and select conserved epitopes is critical for the development of a broadly neutralizing therapy or a universal vaccine. In this article, we review the general paradigm of immune responses to COVID-19 vaccines, highlighting the immunological epitopes of Spike protein that are likely associated with eliciting protective immunity resulting from vaccination in humans. Specifically, we analyze the structural and evolutionary characteristics of the SARS-CoV-2 Spike protein related to immune activation and function via the TLRs, B cells, and T cells. We aim to provide a comprehensive analysis of immune epitopes of Spike protein, thereby contributing to the development of new strategies for broad neutralization or universal vaccination.
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Affiliation(s)
- Nicholas Magazine
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Tianyi Zhang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Anang D. Bungwon
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Michael C. McGee
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Yingying Wu
- Department of Mathematics, University of Houston, Houston, TX
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA
| | - Weishan Huang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
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