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Larsen DN, Kaczmarek JZ, Palarasah Y, Graversen JH, Højrup P. Epitope mapping of SARS-CoV-2 RBDs by hydroxyl radical protein footprinting reveals the importance of including negative antibody controls. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141011. [PMID: 38499233 DOI: 10.1016/j.bbapap.2024.141011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024]
Abstract
Understanding protein-protein interactions is crucial for drug design and investigating biological processes. Various techniques, such as CryoEM, X-ray spectroscopy, linear epitope mapping, and mass spectrometry-based methods, can be employed to map binding regions on proteins. Commonly used mass spectrometry-based techniques are cross-linking and hydrogen‑deuterium exchange (HDX). Another approach, hydroxyl radical protein footprinting (HRPF), identifies binding residues on proteins but faces challenges due to high initial costs and complex setups. This study introduces a generally applicable method using Fenton chemistry for epitope mapping in a standard mass spectrometry laboratory. It emphasizes the importance of controls, particularly the inclusion of a negative antibody control, not widely utilized in HRPF epitope mapping. Quantification by TMT labelling is introduced to reduce false positives, enabling direct comparison between sample conditions and biological triplicates. Additionally, six technical replicates were incorporated to enhance the depth of analysis. Observations on the receptor-binding domain (RBD) of SARS-CoV-2 Spike Protein, Alpha and Delta variants, revealed both binding and opening regions. Significantly changed peptides upon mixing with a negative control antibody suggested structural alterations or nonspecific binding induced by the antibody alone. Integration of negative control antibody experiments and high overlap between biological triplicates led to the exclusion of 40% of significantly changed regions. The final identified binding region correlated with existing literature on neutralizing antibodies against RBD. The presented method offers a straightforward implementation for HRPF analysis in a generic mass spectrometry-based laboratory. Enhanced data reliability was achieved through increased technical and biological replicates alongside negative antibody controls.
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Affiliation(s)
- Daniel Nyberg Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark; Ovodan Biotech A/S, Havnegade 36, DK-5000 Odense, Denmark
| | | | - Yaseelan Palarasah
- Department of Inflammation, Institute of Molecular Medicine, Faculty of Health and Medical Sciences, University of Southern Denmark, Odense, Denmark
| | - Jonas Heilskov Graversen
- Department of Inflammation, Institute of Molecular Medicine, Faculty of Health and Medical Sciences, University of Southern Denmark, Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark; Ovodan Biotech A/S, Havnegade 36, DK-5000 Odense, Denmark.
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2
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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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3
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Metzdorf K, Jacobsen H, Kim Y, Teixeira Alves LG, Kulkarni U, Eschke K, Chaudhry MZ, Hoffmann M, Bertoglio F, Ruschig M, Hust M, Cokarić Brdovčak M, Materljan J, Šustić M, Krmpotić A, Jonjić S, Widera M, Ciesek S, Pöhlmann S, Landthaler M, Čičin-Šain L. A single-dose MCMV-based vaccine elicits long-lasting immune protection in mice against distinct SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.11.25.517953. [PMID: 36482969 PMCID: PMC9727759 DOI: 10.1101/2022.11.25.517953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Current vaccines against COVID-19 elicit immune responses that are overall strong but wane rapidly. As a consequence, the necessary booster shots have led to vaccine fatigue. Hence, vaccines that would provide lasting protection against COVID-19 are needed, but are still unavailable. Cytomegaloviruses (CMV) elicit lasting and uniquely strong immune responses. Used as vaccine vectors, they may be attractive tools that obviate the need for boosters. Therefore, we tested the murine CMV (MCMV) as a vaccine vector against COVID-19 in relevant preclinical models of immunization and challenge. We have previously developed a recombinant murine CMV (MCMV) vaccine vector expressing the spike protein of the ancestral SARS-CoV-2 (MCMVS). In this study, we show that the MCMVS elicits a robust and lasting protection in young and aged mice. Notably, S-specific humoral and cellular immunity was not only maintained but even increased over a period of at least 6 months. During that time, antibody avidity continuously increased and expanded in breadth, resulting in neutralization of genetically distant variants, like Omicron BA.1. A single dose of MCMVS conferred rapid virus clearance upon challenge. Moreover, MCMVS vaccination controlled two immune-evading variants of concern (VoCs), the Beta (B.1.135) and the Omicron (BA.1) variants. Thus, CMV vectors provide unique advantages over other vaccine technologies, eliciting broadly reactive and long-lasting immune responses against COVID-19.
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Affiliation(s)
- Kristin Metzdorf
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yeonsu Kim
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Upasana Kulkarni
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kathrin Eschke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - M. Zeeshan Chaudhry
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Federico Bertoglio
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maximilian Ruschig
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Jelena Materljan
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marko Šustić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Astrid Krmpotić
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Stipan Jonjić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
- German Centre for Infection Research (DZIF), External partner site Frankfurt, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine (CiiM), a joint venture of HZI and MHH, Hannover, Germany
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Teng S, Hu Y, Wang Y, Tang Y, Wu Q, Zheng X, Lu R, Pan D, Liu F, Xie T, Wu C, Li YP, Liu W, Qu X. SARS-CoV-2 spike-reactive naïve B cells and pre-existing memory B cells contribute to antibody responses in unexposed individuals after vaccination. Front Immunol 2024; 15:1355949. [PMID: 38420128 PMCID: PMC10899457 DOI: 10.3389/fimmu.2024.1355949] [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: 12/14/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction Since December 2019, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) has presented considerable public health challenges. Multiple vaccines have been used to induce neutralizing antibodies (nAbs) and memory B-cell responses against the viral spike (S) glycoprotein, and many essential epitopes have been defined. Previous reports have identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike-reactive naïve B cells and preexisting memory B cells in unexposed individuals. However, the role of these spike-reactive B cells in vaccine-induced immunity remains unknown. Methods To elucidate the characteristics of preexisting SARS-CoV-2 S-reactive B cells as well as their maturation after antigen encounter, we assessed the relationship of spike-reactive B cells before and after vaccination in unexposed human individuals. We further characterized the sequence identity, targeting domain, broad-spectrum binding activity and neutralizing activity of these SARS-CoV-2 S-reactive B cells by isolating monoclonal antibodies (mAbs) from these B cells. Results The frequencies of both spike-reactive naïve B cells and preexisting memory B cells before vaccination correlated with the frequencies of spike-reactive memory B cells after vaccination. Isolated mAbs from spike-reactive naïve B cells before vaccination had fewer somatic hypermutations (SHMs) than mAbs isolated from spike-reactive memory B cells before and after vaccination, but bound SARS-CoV-2 spike in vitro. Intriguingly, these germline-like mAbs possessed broad binding profiles for SARS-CoV-2 and its variants, although with low or no neutralizing capacity. According to tracking of the evolution of IGHV4-4/IGKV3-20 lineage antibodies from a single donor, the lineage underwent SHMs and developed increased binding activity after vaccination. Discussion Our findings suggest that spike-reactive naïve B cells can be expanded and matured by vaccination and cocontribute to vaccine-elicited antibody responses with preexisting memory B cells. Selectively and precisely targeting spike-reactive B cells by rational antigen design may provide a novel strategy for next-generation SARS-CoV-2 vaccine development.
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Affiliation(s)
- Shishan Teng
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Yabin Hu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - You Wang
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Yinggen Tang
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Qian Wu
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Xingyu Zheng
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Rui Lu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Dong Pan
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Fen Liu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Tianyi Xie
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Chanfeng Wu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, Hengyang Medical School, University of South China, Chenzhou, China
| | - Yi-Ping Li
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Wenpei Liu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
| | - Xiaowang Qu
- School of Public Health & School of Basic Medicine Sciences, Hengyang Medical School & Ministry of Education Key Laboratory of Rare Pediatric Diseases, University of South China, Hengyang, China
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5
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Rosas-Murrieta NH, Rodríguez-Enríquez A, Herrera-Camacho I, Millán-Pérez-Peña L, Santos-López G, Rivera-Benítez JF. Comparative Review of the State of the Art in Research on the Porcine Epidemic Diarrhea Virus and SARS-CoV-2, Scope of Knowledge between Coronaviruses. Viruses 2024; 16:238. [PMID: 38400014 PMCID: PMC10892376 DOI: 10.3390/v16020238] [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: 12/13/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
This review presents comparative information corresponding to the progress in knowledge of some aspects of infection by the porcine epidemic diarrhea virus (PEDV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronaviruses. PEDV is an alphacoronavirus of great economic importance due to the million-dollar losses it generates in the pig industry. PEDV has many similarities to the SARS-CoV-2 betacoronavirus that causes COVID-19 disease. This review presents possible scenarios for SARS-CoV-2 based on the collected literature on PEDV and the tools or strategies currently developed for SARS-CoV-2 that would be useful in PEDV research. The speed of the study of SARS-CoV-2 and the generation of strategies to control the pandemic was possible due to the knowledge derived from infections caused by other human coronaviruses such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS). Therefore, from the information obtained from several coronaviruses, the current and future behavior of SARS-CoV-2 could be inferred and, with the large amount of information on the virus that causes COVID-19, the study of PEDV could be improved and probably that of new emerging and re-emerging coronaviruses.
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Affiliation(s)
- Nora H. Rosas-Murrieta
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Alan Rodríguez-Enríquez
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
- Posgrado en Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Irma Herrera-Camacho
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Lourdes Millán-Pérez-Peña
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Gerardo Santos-López
- Centro de Investigación Biomédica de Oriente, Laboratorio de Biología Molecular y Virología, Instituto Mexicano del Seguro Social (IMSS), Metepec 74360, Mexico;
| | - José F. Rivera-Benítez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ciudad de México 38110, Mexico;
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Dübel S. Can antibodies be "vegan"? A guide through the maze of today's antibody generation methods. MAbs 2024; 16:2343499. [PMID: 38634488 PMCID: PMC11028021 DOI: 10.1080/19420862.2024.2343499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
There is no doubt that today's life sciences would look very different without the availability of millions of research antibody products. Nevertheless, the use of antibody reagents that are poorly characterized has led to the publication of false or misleading results. The use of laboratory animals to produce research antibodies has also been criticized. Surprisingly, both problems can be addressed with the same technology. This review charts today's maze of different antibody formats and the various methods for antibody production and their interconnections, ultimately concluding that sequence-defined recombinant antibodies offer a clear path to both improved quality of experimental data and reduced use of animals.
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Affiliation(s)
- Stefan Dübel
- Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
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7
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Gressett TE, Hossen ML, Talkington G, Volic M, Perez H, Tiwari PB, Chapagain P, Bix G. Molecular interactions between perlecan LG3 and the SARS-CoV-2 spike protein receptor binding domain. Protein Sci 2024; 33:e4843. [PMID: 37996967 PMCID: PMC10731540 DOI: 10.1002/pro.4843] [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: 06/18/2023] [Revised: 10/14/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global health crisis with significant clinical morbidity and mortality. While angiotensin-converting enzyme 2 (ACE2) is the primary receptor for viral entry, other cell surface and extracellular matrix proteins may also bind to the viral receptor binding domain (RBD) within the SARS-CoV-2 spike protein. Recent studies have implicated heparan sulfate proteoglycans, specifically perlecan LG3, in facilitating SARS-CoV-2 binding to ACE2. However, the role of perlecan LG3 in SARS-CoV-2 pathophysiology is not well understood. In this study, we investigated the binding interactions between the SARS-CoV-2 spike protein RBD and perlecan LG3 through molecular modeling simulations and surface plasmon resonance (SPR) experiments. Our results indicate stable binding between LG3 and SARS-CoV-2 spike protein RBD, which may potentially enhance RBD-ACE2 interactions. These findings shed light on the role of perlecan LG3 in SARS-CoV-2 infection and provide insight into SARS-CoV-2 pathophysiology and potential therapeutic strategy for COVID-19.
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Affiliation(s)
- Timothy E. Gressett
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Md Lokman Hossen
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Department of PhysicsUniversity of BarishalKornokathiBangladesh
| | - Grant Talkington
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Milla Volic
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
| | - Hugo Perez
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
| | | | - Prem Chapagain
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Biomolecular Sciences InstituteFlorida International UniversityMiamiFloridaUSA
| | - Gregory Bix
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
- Department of NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
- Department of Microbiology and ImmunologyTulane University School of MedicineNew OrleansLouisianaUSA
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8
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Almazán NM, Rahbar A, Carlsson M, Hoffman T, Kolstad L, Rönnberg B, Pantalone MR, Fuchs IL, Nauclér A, Ohlin M, Sacharczuk M, Religa P, Amér S, Molnár C, Lundkvist Å, Susrud A, Sörensen B, Söderberg-Nauclér C. Influenza-A mediated pre-existing immunity levels to SARS-CoV-2 could predict early COVID-19 outbreak dynamics. iScience 2023; 26:108441. [PMID: 38144451 PMCID: PMC10746369 DOI: 10.1016/j.isci.2023.108441] [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: 05/10/2023] [Revised: 09/14/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023] Open
Abstract
Susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is highly variable and could be mediated by a cross-protective pre-immunity. We identified 14 cross-reactive peptides between SARS-CoV-2 and influenza A H1N1, H3N2, and human herpesvirus (HHV)-6A/B with potential relevance. The H1N1 peptide NGVEGF was identical to a peptide in the most critical receptor binding motif in SARS-CoV-2 spike protein that interacts with the angiotensin converting enzyme 2 receptor. About 62%-73% of COVID-19-negative blood donors in Stockholm had antibodies to this peptide in the early pre-vaccination phase of the pandemic. Seasonal flu vaccination enhanced neutralizing capacity to SARS-CoV-2 and T cell immunity to this peptide. Mathematical modeling taking the estimated pre-immunity levels to flu into account could fully predict pre-Omicron SARS-CoV-2 outbreaks in Stockholm and India. This cross-immunity provides mechanistic explanations to the epidemiological observation that influenza vaccination protected people against early SARS-CoV-2 infections and implies that flu-mediated cross-protective immunity significantly dampened the first SARS-CoV-2 outbreaks.
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Affiliation(s)
- Nerea Martín Almazán
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 86 Huddinge Stockholm, Sweden
| | - Afsar Rahbar
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
| | - Marcus Carlsson
- Centre for the Mathematical Sciences, Lund University, 223 62 Lund, Sweden
| | - Tove Hoffman
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Linda Kolstad
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Bengt Rönnberg
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Mattia Russel Pantalone
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
| | - Ilona Lewensohn Fuchs
- Department of Labortory Medicine, Division of Clinical Microbiology, Karolinska Institutet, 141 86 Huddinge Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, 141 86 Huddinge Stockholm, Sweden
| | - Anna Nauclér
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology and SciLifeLab Human Antibody Therapeutics Infrastructure Unit, Lund University, 223 62 Lund, Sweden
| | - Mariusz Sacharczuk
- Faculty of Pharmacy with the Laboratory Medicine Division, Department of Pharmacodynamics, Medical University of Warsaw, Centre for Preclinical Research and Technology, Banacha 1B, 02-091 Warsaw, Poland
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Piotr Religa
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Stefan Amér
- Familjeläkarna Saltsjöbaden, 133 34 Saltsjöbaden, Sweden
| | - Christian Molnár
- Familjeläkarna Saltsjöbaden, 133 34 Saltsjöbaden, Sweden
- Department of Neurobiology, Care Sciences and Society, NVS, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | | | | | - Cecilia Söderberg-Nauclér
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Institute of Biomedicine, Unit for Infection and Immunology, MediCity Research Laboratory, University of Turku, FI-20014 Turku, Finland
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9
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Wang X, Shao S, Ye H, Li S, Gu B, Tang B. Development of a quantum dot-based lateral flow immunoassay strip for rapid and sensitive detection of SARS-CoV-2 neutralizing antibodies. Sci Rep 2023; 13:22253. [PMID: 38097611 PMCID: PMC10721894 DOI: 10.1038/s41598-023-49244-5] [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: 03/06/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
To a certain extent, the development and vaccination of COVID-19 vaccine have reduced the alarming rate of transmission speed and mortality rate. At present, vaccine coverage is quite high in countries around the world. Since individual differences are unavoidable, it is necessary to assess the efficacy of the vaccine in each vaccinated person in order to reflect the protective effect of the vaccine in different populations. In this study, we developed a novel COVID-19 neutralizing antibody detection kit combining lateral flow immunochromatography and novel quantum dot technology with 85.23% sensitivity, 92.50% specificity. The novel QD-ICA could achieve an accurate detection of SARS-CoV-2 neutralizing antibodies with 10 minutes, two steps, small equipment size, and broad testing application, suggesting its capability to assess vaccine effectiveness on a large scale in areas of world that currently affected by the pandemic.
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Affiliation(s)
- Xirong Wang
- Medical Technology School of Xuzhou Medical University, Xuzhou, 221004, China
| | - Shulin Shao
- Department of Laboratory, Nanjing Pukou Hospital of Traditional Chinese Medicine, Nanjing, 211800, China
| | - Huan Ye
- Nanjing Vazyme Medical Technology Co. Ltd., Nanjing, 210046, China
| | - Sen Li
- Nanjing Vazyme Medical Technology Co. Ltd., Nanjing, 210046, China
- Nanjing Vazyme Biotechnology Co. Ltd., Nanjing, 210046, China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People's Hospital, 106 Zhongshan 2nd Rd, Yuexiu District, Guangzhou, Guangdong, 510000, China.
| | - Bo Tang
- Medical Technology School of Xuzhou Medical University, Xuzhou, 221004, China.
- Nanjing Vazyme Medical Technology Co. Ltd., Nanjing, 210046, China.
- Nanjing Vazyme Biotechnology Co. Ltd., Nanjing, 210046, China.
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10
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Mattsson J, Ljungars A, Carlsson A, Svensson C, Nilsson B, Ohlin M, Frendéus B. Sequence enrichment profiles enable target-agnostic antibody generation for a broad range of antigens. CELL REPORTS METHODS 2023; 3:100475. [PMID: 37323567 PMCID: PMC10261905 DOI: 10.1016/j.crmeth.2023.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/27/2023] [Accepted: 04/17/2023] [Indexed: 06/17/2023]
Abstract
Phenotypic drug discovery (PDD) enables the target-agnostic generation of therapeutic drugs with novel mechanisms of action. However, realizing its full potential for biologics discovery requires new technologies to produce antibodies to all, a priori unknown, disease-associated biomolecules. We present a methodology that helps achieve this by integrating computational modeling, differential antibody display selection, and massive parallel sequencing. The method uses the law of mass action-based computational modeling to optimize antibody display selection and, by matching computationally modeled and experimentally selected sequence enrichment profiles, predict which antibody sequences encode specificity for disease-associated biomolecules. Applied to a phage display antibody library and cell-based antibody selection, ∼105 antibody sequences encoding specificity for tumor cell surface receptors expressed at 103-106 receptors/cell were discovered. We anticipate that this approach will be broadly applicable to molecular libraries coupling genotype to phenotype and to the screening of complex antigen populations for identification of antibodies to unknown disease-associated targets.
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Affiliation(s)
- Jenny Mattsson
- BioInvent, Research, Lund, Sweden
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anne Ljungars
- BioInvent, Research, Lund, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Carolin Svensson
- BioInvent, Research, Lund, Sweden
- Section of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Björn Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Broad Institute, 415 Main Street, Cambridge, MA, USA
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
- SciLifeLab Human Antibody Therapeutics, Lund University, Lund, Sweden
| | - Björn Frendéus
- BioInvent, Research, Lund, Sweden
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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11
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Development of an inhibiting antibody against equine interleukin 5 to treat insect bite hypersensitivity of horses. Sci Rep 2023; 13:4029. [PMID: 36899044 PMCID: PMC10000358 DOI: 10.1038/s41598-023-31173-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Insect bite hypersensitivity (IBH) is the most common allergic skin disease of horses. It is caused by insect bites of the Culicoides spp. which mediate a type I/IVb allergy with strong involvement of eosinophil cells. No specific treatment option is available so far. One concept could be the use of a therapeutic antibody targeting equine interleukin 5, the main activator and regulator of eosinophils. Therefore, antibodies were selected by phage display using the naïve human antibody gene libraries HAL9/10, tested in a cellular in vitro inhibition assay and subjected to an in vitro affinity maturation. In total, 28 antibodies were selected by phage display out of which eleven have been found to be inhibiting in the final format as chimeric immunoglobulin G with equine constant domains. The two most promising candidates were further improved by in vitro affinity maturation up to factor 2.5 regarding their binding activity and up to factor 2.0 regarding their inhibition effect. The final antibody named NOL226-2-D10 showed a strong inhibition of the interleukin 5 binding to its receptor (IC50 = 4 nM). Furthermore, a nanomolar binding activity (EC50 = 8.8 nM), stable behavior and satisfactory producibility were demonstrated. This antibody is an excellent candidate for in vivo studies for the treatment of equine IBH.
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12
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Erasmus MF, Dovner M, Ferrara F, D'Angelo S, Teixeira AA, Leal-Lopes C, Spector L, Hopkins E, Bradbury ARM. Determining the affinities of high-affinity antibodies using KinExA and surface plasmon resonance. MAbs 2023; 15:2291209. [PMID: 38088807 DOI: 10.1080/19420862.2023.2291209] [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: 10/26/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Accurate and efficient affinity measurement techniques are essential for the biophysical characterization of therapeutic monoclonal antibodies, one of the fastest growing drug classes. Surface plasmon resonance (SPR) is widely used for determining antibody affinity, but does not perform well with extremely high affinity (low picomolar to femtomolar range) molecules. In this study, we compare the SPR-based Carterra LSA and the kinetic exclusion assay (KinExA) for measuring the affinities of 48 antibodies generated against the SARS-CoV-2 receptor-binding domain. These data reveal that high-affinity antibodies can be generated straight from selections using high-quality in vitro library platforms with 54% correspondence between affinities measured using LSA and KinExA. Generally, where there was a 2-fold or greater difference between LSA and KinExA, KinExA reported that affinities were tighter. We highlight the differences between LSA and KinExA, identifying the benefits and pitfalls of each in terms of dynamic range and throughput. Furthermore, we demonstrate for the first time that single-point screening with KinExA can significantly improve throughput while maintaining a strong correlation with full binding curve equilibrium measurements, enabling the accurate rank-ordering of clones with exceptionally tight binding properties.
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Affiliation(s)
| | | | | | - Sara D'Angelo
- Specifica, LLC, a Q2 Solutions Company, Santa Fe, NM, USA
| | | | | | - Laura Spector
- Specifica, LLC, a Q2 Solutions Company, Santa Fe, NM, USA
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13
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Steinke S, Roth KDR, Englick R, Langreder N, Ballmann R, Fühner V, Zilkens KJK, Moreira GMSG, Koch A, Azzali F, Russo G, Schubert M, Bertoglio F, Heine PA, Hust M. Mapping Epitopes by Phage Display. Methods Mol Biol 2023; 2702:563-585. [PMID: 37679639 DOI: 10.1007/978-1-0716-3381-6_28] [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] [Indexed: 09/09/2023]
Abstract
Monoclonal antibodies (mAbs) are valuable biological molecules, serving for many applications. Therefore, it is advantageous to know the interaction pattern between antibodies and their antigens. Regions on the antigen which are recognized by the antibodies are called epitopes, and the respective molecular counterpart of the epitope on the mAbs is called paratope. These epitopes can have many different compositions and/or structures. Knowing the epitope is a valuable information for the development or improvement of biological products, e.g., diagnostic assays, therapeutic mAbs, and vaccines, as well as for the elucidation of immune responses. Most of the techniques for epitope mapping rely on the presentation of the target, or parts of it, in a way that it can interact with a certain mAb. Among the techniques used for epitope mapping, phage display is a versatile technology that allows the display of a library of oligopeptides or fragments from a single gene product on the phage surface, which then can interact with several antibodies to define epitopes. In this chapter, a protocol for the construction of a single-target oligopeptide phage library, as well as for the panning procedure for epitope mapping using phage display is given.
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Affiliation(s)
- Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ruben Englick
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Gustavo Marçal Schmidt Garcia Moreira
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Sector for Antibody and Protein Biochemistry, Tacalyx GmbH, Berlin, Germany
| | - Allan Koch
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Innovationszentrum Niedersachsen GmbH, startup.niedersachsen, Hannover, Germany
| | - Filippo Azzali
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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14
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Heine PA, Ruschig M, Langreder N, Wenzel EV, Schubert M, Bertoglio F, Hust M. Antibody Selection in Solution Using Magnetic Beads. Methods Mol Biol 2023; 2702:261-274. [PMID: 37679624 DOI: 10.1007/978-1-0716-3381-6_13] [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] [Indexed: 09/09/2023]
Abstract
Antibody phage display is a valuable in vitro technology to generate recombinant, sequence-defined antibodies for research, diagnostics, and therapy. Up to now (autumn 2022), 14 FDA/EMA-approved therapeutic antibodies were developed using phage display, including the world best-selling antibody adalimumab. Additionally, recombinant, sequence-defined antibodies have significant advantages over their polyclonal counterparts.For a successful in vitro antibody generation by phage display, a suitable panning strategy is highly important. We present in this book chapter the panning in solution and its advantages over panning with immobilized antigens and give detailed protocols for the panning and screening procedure.
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Affiliation(s)
- Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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15
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Ballmann R, Schneider KT, Roth KDR, Dübel S. Antibody Batch Cloning. Methods Mol Biol 2023; 2702:411-417. [PMID: 37679632 DOI: 10.1007/978-1-0716-3381-6_21] [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] [Indexed: 09/09/2023]
Abstract
The antigen-binding ability of each antibody clone selected by phage display is usually initially ranked by a screening ELISA using monovalent scFv antibody fragments. Further characterization often requires bivalent antibody molecules such as IgG or scFv-Fc fusions. To produce these, the V region encoding genes of selected hits have to be cloned into a mammalian expression vector and analyzed as a bivalent molecule, requiring a laborious cloning procedure. We established a high-throughput procedure allowing rapid screening of candidates in bivalent formats. This protocol allows for the parallelized cloning of all selected antibody fragments into a mammalian expression vector in the 96-well plate format. The bivalent antibody molecules can then be produced and purified in 96-well plates for further analysis in microtiter plate assays.
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Affiliation(s)
- Rico Ballmann
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig, Germany
| | - Kai-Thomas Schneider
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig, Germany
| | - Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig, Germany.
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16
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Steinke S, Roth KDR, Ruschig M, Langreder N, Polten S, Schneider KT, Ballmann R, Russo G, Zilkens KJK, Schubert M, Bertoglio F, Hust M. Antibody Selection via Phage Display in Microtiter Plates. Methods Mol Biol 2023; 2702:247-260. [PMID: 37679623 DOI: 10.1007/978-1-0716-3381-6_12] [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] [Indexed: 09/09/2023]
Abstract
The most common and robust in vitro technology to generate monoclonal human antibodies is phage display. This technology is a widely used and powerful key technology for recombinant antibody selection. Phage display-derived antibodies are used as research tools, in diagnostic assays, and by 2022, 14 phage display-derived therapeutic antibodies were approved. In this review, we describe a fast high-throughput antibody (scFv) selection procedure in 96-well microtiter plates. The given detailed protocol allows the antibody selection ("panning"), screening, and identification of monoclonal antibodies in less than 2 weeks. Furthermore, we describe an on-rate panning approach for the selection of monoclonal antibodies with fast on-rates.
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Affiliation(s)
- Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Saskia Polten
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kai-Thomas Schneider
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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17
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Tulika T, Ljungars A. Deep Mining of Complex Antibody Phage Pools. Methods Mol Biol 2023; 2702:419-431. [PMID: 37679633 DOI: 10.1007/978-1-0716-3381-6_22] [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] [Indexed: 09/09/2023]
Abstract
An important, and rapidly growing class of drugs are antibodies which can be discovered through phage display technology. In this technique, antibodies are typically first enriched through consecutive rounds of selection on a target antigen with amplification in bacteria between each selection round. Thereafter, a subset of random individual clones is analyzed for binding in a screening procedure. This results in discovery of the most abundant antibodies in the pool. However, there are multiple factors affecting the enrichment of antibodies during the selection resulting in a very complex output pool of antibodies. A few antibodies are present in many copies and others only in a few copies, where the most abundant antibodies are not necessarily the functionally best ones. In order to utilize the full potential of the output from a phage display selection, and enable discovery of low abundant, potentially functionally important clones, deep mining technologies are needed. In this chapter, two methods for deep mining of an antibody pool are described, protein depletion and antibody blocking. The methods can be applied both when the target is a single antigen and on complex antigen mixtures such as whole cells and tissues.
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Affiliation(s)
- Tulika Tulika
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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18
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Testing of Diamond Electrodes as Biosensor for Antibody-Based Detection of Immunoglobulin Protein with Electrochemical Impedance Spectroscopy. Mol Vis 2022. [DOI: 10.3390/c8040074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To control the increasing virus pandemics, virus detection methods are essential. Today’s standard virus detections methods are fast (immune assays) or precise (PCR). A method that is both fast and precise would enable more efficient mitigation measures and better life comfort. According to recent papers, electrochemical impedance spectroscopy (EIS) has proven to detect viruses fast and precise. Boron-doped diamond (BDD) was used as a high-performance electrode material in these works. The aim of this work was to perform an initial test of BDD-based EIS for biosensing. As an easily available standard biomaterial, human immunoglobulin G (IgG) was used as analyte. Niobium plates were coated via hot-filament activated chemical vapor deposition with polycrystalline diamond, and doped with boron for electrical conductivity. An anti-human IgG antibody was immobilised on the BDD electrodes as a biosensing component. Four different analyte concentrations up to 1.1 µg per litre were tested. During EIS measurements, both impedance over frequency curves and Nyquist plot demonstrated no clear sign of a change of the charge transfer resistance. Thus, no positive statement about a successful biosensing could be made so far. It is assumed that these issues need to be investigated and improved, including the relation of BDD electrode size to electrolyte volume, termination of the BDD electrodes (H, O) for a successful functionalisation and EIS frequency range. The work will be continued concerning these improvement issues in order to finally use virus materials as analyte.
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19
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Pang YT, Acharya A, Lynch DL, Pavlova A, Gumbart JC. SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact. Commun Biol 2022; 5:1170. [PMID: 36329138 PMCID: PMC9631587 DOI: 10.1038/s42003-022-04138-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer's receptor binding domain (RBD) switching from a "down" (closed) to an "up" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 μs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally, we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody's epitope is continuously exposed, explaining its high efficacy.
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Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,BioInspired Syracuse and Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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20
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Engineered multivalent self-assembled binder protein against SARS-CoV-2 RBD. Biochem Eng J 2022; 187:108596. [PMID: 36034180 PMCID: PMC9396458 DOI: 10.1016/j.bej.2022.108596] [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: 06/13/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 02/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic since December 2019, and with it, a push for innovations in rapid testing and neutralizing antibody treatments in an effort to solve the spread and fatality of the disease. One such solution to both of these prevailing issues is targeting the interaction of SARS-CoV-2 spike receptor binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2) receptor protein. Structural studies have shown that the N-terminal alpha-helix comprised of the first 23 residues of ACE2 plays an important role in this interaction. Where it is typical to design a binding domain to fit a target, we have engineered a protein that relies on multivalency rather than the sensitivity of a monomeric ligand to provide avidity to its target by fusing the N-terminal helix of ACE2 to the coiled-coil domain of the cartilage oligomeric matrix protein. The resulting ACE-MAP is able to bind to the SARS-CoV-2 RBD with improved binding affinity, is expressible in E. coli, and is thermally stable and relatively small (62 kDa). These properties suggest ACE-MAP and the MAP scaffold to be a promising route towards developing future diagnostics and therapeutics to SARS-CoV-2.
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21
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Xie L, Xu QY, Zheng XQ, Xue JH, Niu JJ, Yang TC. Evaluation of the efficacy of four anti-SARS-CoV-2 antibodies after vaccination using kits from two manufacturers: A prospective, longitudinal, cohort study at 11 serial time points within 160 days. Int Immunopharmacol 2022; 112:109285. [PMID: 36182874 PMCID: PMC9515333 DOI: 10.1016/j.intimp.2022.109285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
PURPOSE The accuracy of level of anti- severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies is a great concern. We aimed to compare the efficacy of anti-SARS-CoV-2 antibody detection kits from two manufacturers in evaluating the efficacy of SARS-CoV-2 vaccines. METHODS The immune responses and consistency of four anti-SARS-CoV-2 antibodies were evaluated using two manufacturers' antibody kits (A and B) in 61 subjects within 160 days after vaccination with the CoronaVac vaccine. RESULTS The total seropositivity rates of neutralizing antibodies and IgM antibodies detected by kit A were higher than those detected by kit B (P = 0.003 and P < 0.001, respectively). Conversely, the total seropositivity rates of total antibodies and IgG antibodies were higher in kit B than kit A (P < 0.001 and P < 0.001, respectively). The consistency rates showed less than 90% agreement between the kits for the detection of the four antibodies, and the κ score showed moderate or substantial consistency. The half-lives of neutralizing antibodies, total antibodies, and IgG antibodies within 160 days after vaccination, detected by kit A were 63.88 days, 80.50 days, and 63.70 days, respectively and by kit B were 97.06 days, 65.41 days, and 77.99 days, respectively. CONCLUSION The efficacy of antibody detection differed between the two commercial anti-SARS-CoV-2 antibody kits, although there was moderate consistency, which may affect the clinical application and formulation of the vaccine strategy.
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Affiliation(s)
- Lin Xie
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Qiu-Yan Xu
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Xin-Qi Zheng
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Jian-Hang Xue
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jian-Jun Niu
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China.
| | - Tian-Ci Yang
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China.
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22
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022. [PMID: 36298643 DOI: 10.3390/v14102087/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical "Corona" aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
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23
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022; 14:v14102087. [PMID: 36298643 PMCID: PMC9606917 DOI: 10.3390/v14102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical “Corona” aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
- Correspondence:
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24
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Arnold F, Huzly D, Tanriver Y, Welte T. Response to SARS-CoV-2 vaccines in patients receiving B-cell modulating antibodies for renal autoimmune disease. BMC Infect Dis 2022; 22:734. [PMID: 36104663 PMCID: PMC9472190 DOI: 10.1186/s12879-022-07722-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Background Effective SARS-CoV-2 vaccination in patients receiving treatment with B-cell depleting agents is challenging. Information on vaccination responses in these patients are a valuable tool to develop efficient vaccination regimens. Methods In this single-center retrospective observational study, we report the humoral and cellular response in 34 patients receiving anti-CD20 antibody treatment for renal immune disease. Results After base immunization with SARS-CoV-2-vaccines, 92.0% developed a cellular, 32.4% a humoral response. Humoral immunity correlated with B-cell counts and the timespan between anti-CD20 antibody treatment and vaccination. All patients with > 21/µl B-cells, or > 197 days after treatment showed humoral response. Conclusions Adequate timing of SARS-CoV-2-vaccinations after anti-CD20 antibody treatment and CD19 measurements are crucial to generate immunity. Awaiting partial B-cell recovery by postponing regularly scheduled anti-CD20 treatment should be considered in patients with stable immune disease. Trial registration: This study has been retrospectively registered in the German Clinical Trials Register (DRKS00027049) on 29/10/2021. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07722-7.
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25
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Wang T, Xu J, Wang B, Wang Y, Zhao W, Xiang B, Xue Y, Yuan Q, Wang Y. Receptor-binding domain-anchored peptides block binding of severe acute respiratory syndrome coronavirus 2 spike proteins with cell surface angiotensin-converting enzyme 2. Front Microbiol 2022; 13:910343. [PMID: 36177466 PMCID: PMC9513850 DOI: 10.3389/fmicb.2022.910343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022] Open
Abstract
Background The COVID-19 pandemic has killed over 6 million people worldwide. Despite the accumulation of knowledge about the causative pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the pathogenesis of this disease, cures remain to be discovered. We searched for certain peptides that might interfere with spike protein (S protein)-angiotensin-converting enzyme 2 (ACE2) interactions. Methods Phage display (PhD)-12 peptide library was screened against recombinant spike trimer (S-trimer) or receptor-binding domain (S-RBD) proteins. The resulting enriched peptide sequences were obtained, and their potential binding sites on S-trimer and S-RBD 3D structure models were searched. Synthetic peptides corresponding to these and other reference sequences were tested for their efficacy in blocking the binding of S-trimer protein onto recombinant ACE2 proteins or ACE2-overexpressing cells. Results After three rounds of phage selections, two peptide sequences (C2, DHAQRYGAGHSG; C6, HWKAVNWLKPWT) were enriched by S-RBD, but only C2 was present in S-trimer selected phages. When the 3D structures of static monomeric S-RBD (6M17) and S-trimer (6ZGE, 6ZGG, 7CAI, and 7CAK, each with different status of S-RBDs in the three monomer S proteins) were scanned for potential binding sites of C2 and C6 peptides, C6 opt to bind the saddle of S-RBD in both 6M17 and erected S-RBD in S-trimers, but C2 failed to cluster there in the S-trimers. In the competitive S-trimer-ACE2-binding experiments, synthetic C2 and C6 peptides inhibited S-trimer binding onto 293T-ACE2hR cells at high concentrations (50 μM) but not at lower concentrations (10 μM and below), neither for the settings of S-trimer binding onto recombinant ACE2 proteins. Conclusion Using PhD methodology, two peptides were generated bearing potentials to interfere with S protein-ACE2 interaction, which might be further exploited to produce peptidomimetics that block the attachment of SARS-CoV-2 virus onto host cells, hence diminishing the pathogenesis of COVID-19.
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Affiliation(s)
- Ting Wang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jie Xu
- Central Laboratory, Xiang’an Hospital of Xiamen University, Xiang’an University Medical Center, Xiamen University, Xiamen, Fujian, China
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Beibei Wang
- Center for Advanced Materials Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong, China
| | - Yulian Wang
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Wei Zhao
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Bin Xiang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yuhua Xue
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Yiqiang Wang
- Central Laboratory, Xiang’an Hospital of Xiamen University, Xiang’an University Medical Center, Xiamen University, Xiamen, Fujian, China
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- *Correspondence: Yiqiang Wang,
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26
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Garg S, Raj N, Lukose A, Jamwal D, Parray HA, Kumar S, Dhyani S, Jakhar K, Sonar S, Tiwari M, Reema, Mani S, Bhattacharyya S, Sharma C, Shrivastava T, Kumar R. Characterization of a broadly cross reactive tetravalent human monoclonal antibody, recognizing conformational epitopes in receptor binding domain of SARS-CoV-2. 3 Biotech 2022; 12:202. [PMID: 35928502 PMCID: PMC9345016 DOI: 10.1007/s13205-022-03272-6] [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: 04/27/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
We used human semi-synthetic phage antibody gene libraries to select anti-SARS-CoV-2 RBD scFv antibody fragment and subsequent characterization of this novel tetravalent monoclonal antibody targeting conformational epitopes in the receptor binding domain of SARS-CoV-2. Binding studies suggest that II62 tetravalent antibody cross-reacts with RBD protein of SARS-CoV2 and its different variants of concerns. The epitope mapping data reveals that II62 tetravalent antibody targets an epitope that does not directly interferes with RBD: ACE2 interaction. Neutralization studies with live authentic SARS-CoV2 virus suggests that increase in valency of II62 mAb from monovalent to tetravalent doesn’t perturbate virus interactions with the ACE2 expressing host cells in cytopathic effect-based (CPE) assay.
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Affiliation(s)
- Sonal Garg
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Nisha Raj
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Asha Lukose
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Deepti Jamwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Hilal Ahmed Parray
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Sandeep Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Samridhi Dhyani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Kamini Jakhar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Sudipta Sonar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Mahima Tiwari
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Reema
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Chandresh Sharma
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India.,Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, India
| | - Tripti Shrivastava
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India
| | - Rajesh Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box # 04, Faridabad, Haryana 121001 India.,Institute of Advanced Virology, Bio 360 Life Science Park, Trivandrum, India
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27
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Geisen UM, Rose R, Neumann F, Ciripoi M, Vullriede L, Reid HM, Berner DK, Bertoglio F, Hoff P, Hust M, Longardt AC, Lorentz T, Martini GR, Saggau C, Schirmer JH, Schubert M, Sümbül M, Tran F, Voß M, Zeuner R, Morrison PJ, Bacher P, Fickenscher H, Gerdes S, Peipp M, Schreiber S, Krumbholz A, Hoyer BF. The long term vaccine-induced anti-SARS-CoV-2 immune response is impaired in quantity and quality under TNFα blockade. J Med Virol 2022; 94:5780-5789. [PMID: 35945627 PMCID: PMC9538219 DOI: 10.1002/jmv.28063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/03/2022] [Accepted: 08/06/2022] [Indexed: 01/06/2023]
Abstract
The humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination in patients with chronic inflammatory disease (CID) declines more rapidly with tumor necrosis factor-α (TNF-α) inhibition. Furthermore, the efficacy of current vaccines against Omicron variants of concern (VOC) including BA.2 is limited. Alterations within immune cell populations, changes in IgG affinity, and the ability to neutralize a pre-VOC strain and the BA.2 virus were investigated in these at-risk patients. Serum levels of anti-SARS-CoV-2 IgG, IgG avidity, and neutralizing antibodies (NA) were determined in anti-TNF-α patients (n = 10) and controls (n = 24 healthy individuals; n = 12 patients under other disease-modifying antirheumatic drugs, oDMARD) before and after the second and third vaccination by ELISA, immunoblot and live virus neutralization assay. SARS-CoV-2-specific B- and T cell subsets were analysed by multicolor flow cytometry. Six months after the second vaccination, anti-SARS-CoV-2 IgG levels, IgG avidity and anti-pre-VOC NA titres were significantly reduced in anti-TNF-α recipients compared to controls (healthy individuals: avidity: p ≤ 0.0001; NA: p = 0.0347; oDMARDs: avidity: p = 0.0012; NA: p = 0.0293). The number of plasma cells was increased in anti-TNF-α patients (Healthy individuals: p = 0.0344; oDMARDs: p = 0.0254), while the absolute number of SARS-CoV-2-specific plasma cells 7 days after 2nd vaccination were comparable. Even after a third vaccination, these patients had lower anti-BA.2 NA titres compared to both other groups. We show a reduced SARS-CoV-2 neutralizing capacity in patients under TNF-α blockade. In this cohort, the plasma cell response appears to be less specific and shows stronger bystander activation. While these effects were observable after the first two vaccinations and with older VOC, the differences in responses to BA.2 were enhanced.
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Affiliation(s)
- Ulf Martin Geisen
- Medical Department I, Rheumatology and Clinical ImmunologyUniversity Medical Center Schleswig‐Holstein Campus KielKielGermany
| | - Ruben Rose
- Institute for Infection Medicine, Christian‐Albrecht University of Kiel and University Medical Center Schleswig‐HolsteinKielGermany
| | | | - Maria Ciripoi
- Medical Department I, Rheumatology and Clinical ImmunologyUniversity Medical Center Schleswig‐Holstein Campus KielKielGermany
| | - Lena Vullriede
- Medical Department I, Rheumatology and Clinical ImmunologyUniversity Medical Center Schleswig‐Holstein Campus KielKielGermany
| | - Hayley M. Reid
- Medical Department I, Rheumatology and Clinical ImmunologyUniversity Medical Center Schleswig‐Holstein Campus KielKielGermany
| | - Dennis Kristopher Berner
- Medical Department I, Rheumatology and Clinical ImmunologyUniversity Medical Center Schleswig‐Holstein Campus KielKielGermany
| | - Federico Bertoglio
- Department of BiotechnologyInstitute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität BraunschweigBraunschweigGermany
| | - Paula Hoff
- Department of Rheumatology, Endokrinologikum‐GruppeBerlinGermany
| | - Michael Hust
- Department of BiotechnologyInstitute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität BraunschweigBraunschweigGermany
| | | | | | - Gabriela Rios Martini
- Institute of ImmunologyUniversity Medical Center Schleswig‐HolsteinKielGermany,Department for DermatologyUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Carina Saggau
- Institute of ImmunologyUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Jan Henrik Schirmer
- Medical Department I, Rheumatology and Clinical ImmunologyUniversity Medical Center Schleswig‐Holstein Campus KielKielGermany
| | - Maren Schubert
- Department of BiotechnologyInstitute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität BraunschweigBraunschweigGermany
| | - Melike Sümbül
- Department for DermatologyUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Florian Tran
- Institute of Clinical Molecular BiologyChristian‐Albrecht University of KielKielGermany,Department for Internal Medicine IUniversity Medical Center Schleswig‐HolsteinKiel
| | - Mathias Voß
- Institute for Infection Medicine, Christian‐Albrecht University of Kiel and University Medical Center Schleswig‐HolsteinKielGermany
| | - Rainald Zeuner
- Medical Department I, Rheumatology and Clinical ImmunologyUniversity Medical Center Schleswig‐Holstein Campus KielKielGermany
| | - Peter J. Morrison
- Department for DermatologyUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Petra Bacher
- Institute of ImmunologyUniversity Medical Center Schleswig‐HolsteinKielGermany,Institute of Clinical Molecular BiologyChristian‐Albrecht University of KielKielGermany
| | - Helmut Fickenscher
- Institute for Infection Medicine, Christian‐Albrecht University of Kiel and University Medical Center Schleswig‐HolsteinKielGermany
| | - Sascha Gerdes
- Department for DermatologyUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Matthias Peipp
- Department of Internal Medicine II, Division of Antibody‐Based ImmunotherapyUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Stefan Schreiber
- Institute of Clinical Molecular BiologyChristian‐Albrecht University of KielKielGermany,Department for Internal Medicine IUniversity Medical Center Schleswig‐HolsteinKiel
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian‐Albrecht University of Kiel and University Medical Center Schleswig‐HolsteinKielGermany,Labor Dr. Krause und Kollegen MVZ GmbHKielGermany
| | - Bimba Franziska Hoyer
- Medical Department I, Rheumatology and Clinical ImmunologyUniversity Medical Center Schleswig‐Holstein Campus KielKielGermany
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Puerta-Guardo H, Parra-Cardeña M, Peña-Miranda F, Flores-Quintal F, Granja-Pérez P, Villanueva-Jorge S, González-Losa R, Conde-Ferraez L, Gómez-Carballo J, Vazquez-Prokopec G, Earnest JT, Manrique-Saide P, Ayora-Talavera G. Human IgG antibody responses to severe acute respiratory syndrome coronavirus 2 viral antigens receptor-binding domain, spike, and nucleocapsid, in vaccinated adults from Merida, Mexico. Front Med (Lausanne) 2022; 9:916241. [PMID: 35935758 PMCID: PMC9354829 DOI: 10.3389/fmed.2022.916241] [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: 04/08/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Several vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been approved for controlling the coronavirus disease 2019 (COVID-19) pandemic worldwide. Antibody response is essential to understand the immune response to different viral targets after vaccination with different vaccine platforms. Thus, the main aim of this study was to describe how vaccination with two distinct SARS-CoV-2 vaccine preparations elicit IgG antibody specific responses against two antigenically relevant SARS-CoV-2 viral proteins: the receptor-binding domain (RBD) and the full-length spike (S). To do so, SARS-CoV-2 protein specific in-house enzyme-linked immunosorbent assays (ELISAs) were standardized and tested against serum samples collected from 89 adults, recipients of either a single-dose of the Spike-encoding mRNA-based Pfizer/BioNTech (Pf-BNT) (70%, 62/89) or the Spike-encoding-Adenovirus-5-based CanSino Biologics Inc. (CSBIO) (30%, 27/89) in Merida, Mexico. Overall, we identified an IgG seroconversion rate of 88% (68/78) in all vaccinees after more than 25 days post-vaccination (dpv). Anti-RBD IgG-specific responses ranged from 90% (46/51) in the Pf-BNT vaccine at 25 dpv to 74% (20/27) in the CSBIO vaccine at 42 dpv. Compared to the S, the RBD IgG reactivity was significantly higher in both Pf-BNT (p < 0.004) and CSBIO (p < 0.003) vaccinees. Interestingly, in more than 50% of vaccine recipients, with no history of COVID-19 infection, antibodies against the nucleocapsid (N) protein were detected. Thus, participants were grouped either as naïve or pre-exposed vaccinees. Seroconversion rates after 25 and more dpv varies between 100% in Pf-BNT (22/22) and 75% (9/12) in CSBIO pre-exposed vaccinees, and 89% (26/29) and 73% (11/15) in Pf-BNT and CSBIO naïve vaccine recipients, respectively. In summary, observed seroconversion rates varied depending on the type of vaccine, previous infection with SARS-CoV-2, and the target viral antigen. Our results indicate that both vaccine preparations can induce detectable levels of IgG against the RBD or Spike in both naïve and SARS-CoV-2 pre-exposed vaccinees. Our study provides valuable and novel information about the serodiagnosis and the antibody response to vaccines in Mexico.
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Affiliation(s)
- Henry Puerta-Guardo
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
- Unidad Colaborativa para Bioensayos Entomológicos, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Manuel Parra-Cardeña
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | | | | | - Pilar Granja-Pérez
- Laboratorio Estatal de Salud Pública, Servicios de Salud de Yucatán, Mérida, Mexico
| | | | - Refugio González-Losa
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Laura Conde-Ferraez
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Jesus Gómez-Carballo
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | | | - James T. Earnest
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States
| | - Pablo Manrique-Saide
- Unidad Colaborativa para Bioensayos Entomológicos, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Guadalupe Ayora-Talavera
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
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Virus Infection and Systemic Inflammation: Lessons Learnt from COVID-19 and Beyond. Cells 2022; 11:cells11142198. [PMID: 35883640 PMCID: PMC9316821 DOI: 10.3390/cells11142198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 07/09/2022] [Indexed: 02/06/2023] Open
Abstract
Respiratory infections with newly emerging zoonotic viruses such as SARS-CoV-2, the etiological agent of COVID-19, often lead to the perturbation of the human innate and adaptive immune responses causing severe disease with high mortality. The responsible mechanisms are commonly virus-specific and often include either over-activated or delayed local interferon responses, which facilitate efficient viral replication in the primary target organ, systemic viral spread, and rapid onset of organ-specific and harmful inflammatory responses. Despite the distinct replication strategies, human infections with SARS-CoV-2 and highly pathogenic avian influenza viruses demonstrate remarkable similarities and differences regarding the mechanisms of immune induction, disease dynamics, as well as the long-term sequelae, which will be discussed in this review. In addition, we will highlight some important lessons about the effectiveness of antiviral and immunomodulatory therapeutic strategies that this pandemic has taught us.
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30
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Xue JH, Wang YJ, Li W, Li QL, Xu QY, Niu JJ, Liu LL. Anti-Receptor-Binding Domain Immunoglobulin G Antibody as a Predictor of Seropositivity for Anti-SARS-CoV-2 Neutralizing Antibody. Arch Pathol Lab Med 2022; 146:814-821. [PMID: 35380612 DOI: 10.5858/arpa.2022-0041-sa] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/24/2022]
Abstract
CONTEXT.— Neutralizing antibody detection can assess the incidence of COVID-19 and the effectiveness of vaccines. However, commercial reagents for neutralizing antibodies were developed after the anti-SARS-CoV-2 immunoglobulin (Ig) G and IgM antibodies. Therefore, some laboratories did not perform neutralizing antibody testing services because of multiple factors. OBJECTIVE.— To find a fast, accurate, and economic alternative for the detection of neutralizing antibodies for the development of COVID-19 screening programs. DESIGN.— The response and correlation of 3 antibodies (anti-spike protein neutralizing antibody, total anti-receptor-binding domain [RBD] antibody, and anti-RBD IgG) were determined by observing the dynamics in 61 participants for 160 days after vaccination. RESULTS.— The levels of neutralizing and anti-RBD IgG antibodies reached their peak values on day 42 after vaccination (120.75 IU/mL and 14.38 signal-to-cutoff ratio [S/CO], respectively). The total antibody levels peaked at 138.47 S/CO on day 35 after vaccination. The strongest correlation was found between neutralizing and anti-RBD IgG antibody levels (r = 0.894, P < .001). The area under the receiver operating characteristic curve for total antibody levels for the prediction of seropositivity for neutralizing antibodies was 0.881 (P < .001), and that for anti-RBD IgG antibody levels was 0.937 (P < .001). CONCLUSIONS.— Neutralizing and anti-RBD IgG antibody levels were strongly correlated, and thus anti-RBD IgG antibody levels can be used for the accurate assessment of immunity following SARS-CoV-2 infection or vaccination.
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Affiliation(s)
- Jian-Hang Xue
- From the Clinical Laboratory Center, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China (Xue, Wang, W. Li, Q.L. Li, Xu, Niu, Liu).,From the Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China (Xue)
| | - Yong-Jing Wang
- From the Clinical Laboratory Center, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China (Xue, Wang, W. Li, Q.L. Li, Xu, Niu, Liu)
| | - Wei Li
- From the Clinical Laboratory Center, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China (Xue, Wang, W. Li, Q.L. Li, Xu, Niu, Liu)
| | - Qiu-Ling Li
- From the Clinical Laboratory Center, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China (Xue, Wang, W. Li, Q.L. Li, Xu, Niu, Liu)
| | - Qiu-Yan Xu
- From the Clinical Laboratory Center, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China (Xue, Wang, W. Li, Q.L. Li, Xu, Niu, Liu)
| | - Jian-Jun Niu
- From the Clinical Laboratory Center, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China (Xue, Wang, W. Li, Q.L. Li, Xu, Niu, Liu)
| | - Li-Li Liu
- From the Clinical Laboratory Center, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China (Xue, Wang, W. Li, Q.L. Li, Xu, Niu, Liu).,From the Xiamen Clinical Laboratory Quality Control Center, Xiamen, China (Liu)
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31
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Ballmann R, Hotop SK, Bertoglio F, Steinke S, Heine PA, Chaudhry MZ, Jahn D, Pucker B, Baldanti F, Piralla A, Schubert M, Čičin-Šain L, Brönstrup M, Hust M, Dübel S. ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein. Viruses 2022; 14:1326. [PMID: 35746797 PMCID: PMC9229677 DOI: 10.3390/v14061326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of the spike, and therefore lose neutralization efficacy against emerging SARS-CoV-2 variants, which frequently mutate in the RBD region. Previously, phage display has been used to identify epitopes of antibody responses against several diseases. Such epitopes have been applied to design vaccines or neutralize antibodies. Here, we constructed an ORFeome phage display library for the SARS-CoV-2 genome. Open reading frames (ORFs) representing the SARS-CoV-2 genome were displayed on the surface of phage particles in order to identify enriched immunogenic epitopes from COVID-19 patients. Library quality was assessed by both NGS and epitope mapping of a monoclonal antibody with a known binding site. The most prominent epitope captured represented parts of the fusion peptide (FP) of the spike. It is associated with the cell entry mechanism of SARS-CoV-2 into the host cell; the serine protease TMPRSS2 cleaves the spike within this sequence. Blocking this mechanism could be a potential target for non-RBD binding therapeutic anti-SARS-CoV-2 antibodies. As mutations within the FP amino acid sequence have been rather rare among SARS-CoV-2 variants so far, this may provide an advantage in the fight against future virus variants.
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Affiliation(s)
- Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Sven-Kevin Hotop
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - M. Zeeshan Chaudhry
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany;
| | - Boas Pucker
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstr 1, 38106 Braunschweig, Germany;
| | - Fausto Baldanti
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy;
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Fondazione Policlinico, 27100 Pavia, Italy;
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Fondazione Policlinico, 27100 Pavia, Italy;
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Luka Čičin-Šain
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
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Li L, Gao M, Jiao P, Zu S, Deng YQ, Wan D, Cao Y, Duan J, Aliyari SR, Li J, Shi Y, Rao Z, Qin CF, Guo Y, Cheng G, Yang H. Antibody engineering improves neutralization activity against K417 spike mutant SARS-CoV-2 variants. Cell Biosci 2022; 12:63. [PMID: 35581593 PMCID: PMC9113379 DOI: 10.1186/s13578-022-00794-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neutralizing antibodies are approved drugs to treat coronavirus disease-2019 (COVID-19) patients, yet mutations in severe acute respiratory syndrome coronavirus (SARS-CoV-2) variants may reduce the antibody neutralizing activity. New monoclonal antibodies (mAbs) and antibody remolding strategies are recalled in the battle with COVID-19 epidemic. RESULTS We identified multiple mAbs from antibody phage display library made from COVID-19 patients and further characterized the R3P1-E4 clone, which effectively suppressed SARS-CoV-2 infection and rescued the lethal phenotype in mice infected with SARS-CoV-2. Crystal structural analysis not only explained why R3P1-E4 had selectively reduced binding and neutralizing activity to SARS-CoV-2 variants carrying K417 mutations, but also allowed us to engineer mutant antibodies with improved neutralizing activity against these variants. Thus, we screened out R3P1-E4 mAb which inhibits SARS-CoV-2 and related mutations in vitro and in vivo. Antibody engineering improved neutralizing activity of R3P1-E4 against K417 mutations. CONCLUSION Our studies have outlined a strategy to identify and engineer neutralizing antibodies against SARS-CoV-2 variants.
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Affiliation(s)
- Lili Li
- Institute of Systems Medicine, Chinese Academy of Medical Science & Peking Union College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Meiling Gao
- Institute of Systems Medicine, Chinese Academy of Medical Science & Peking Union College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Peng Jiao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Shulong Zu
- Institute of Systems Medicine, Chinese Academy of Medical Science & Peking Union College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Yong-Qiang Deng
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China
| | - Dingyi Wan
- AtaGenix Laboratories (Wuhan) Co., Ltd, Wuhan, 430075, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jing Duan
- AtaGenix Laboratories (Wuhan) Co., Ltd, Wuhan, 430075, China
| | - Saba R Aliyari
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Jie Li
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Yueyue Shi
- Institute of Systems Medicine, Chinese Academy of Medical Science & Peking Union College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, 300071, China
- Guangzhou Laboratory, B1, Standard Property Unite 4, Guangzhou international bio-island, Guangzhou, 510320, China
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, 100071, China.
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Genhong Cheng
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Heng Yang
- Institute of Systems Medicine, Chinese Academy of Medical Science & Peking Union College, Beijing, 100005, China.
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
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Velappan N, Nguyen HB, Micheva-Viteva S, Bedinger D, Ye C, Mangadu B, Watts AJ, Meagher R, Bradfute S, Hu B, Waldo GS, Lillo AM. Healthy humans can be a source of antibodies countering COVID-19. Bioengineered 2022; 13:12598-12624. [PMID: 35599623 PMCID: PMC9275966 DOI: 10.1080/21655979.2022.2076390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/13/2022] [Accepted: 05/06/2022] [Indexed: 11/05/2022] Open
Abstract
Here, we describe the isolation of 18 unique anti SARS-CoV-2 human single-chain antibodies from an antibody library derived from healthy donors. The selection used a combination of phage and yeast display technologies and included counter-selection strategies meant to direct the selection of the receptor-binding motif (RBM) of SARS-CoV-2 spike protein's receptor binding domain (RBD2). Selected antibodies were characterized in various formats including IgG, using flow cytometry, ELISA, high throughput SPR, and fluorescence microscopy. We report antibodies' RBD2 recognition specificity, binding affinity, and epitope diversity, as well as ability to block RBD2 binding to the human receptor angiotensin-converting enzyme 2 (ACE2) and to neutralize authentic SARS-CoV-2 virus infection in vitro. We present evidence supporting that: 1) most of our antibodies (16 out of 18) selectively recognize RBD2; 2) the best performing 8 antibodies target eight different epitopes of RBD2; 3) one of the pairs tested in sandwich assays detects RBD2 with sub-picomolar sensitivity; and 4) two antibody pairs inhibit SARS-CoV-2 infection at low nanomolar half neutralization titers. Based on these results, we conclude that our antibodies have high potential for therapeutic and diagnostic applications. Importantly, our results indicate that readily available non immune (naïve) antibody libraries obtained from healthy donors can be used to select high-quality monoclonal antibodies, bypassing the need for blood of infected patients, and offering a widely accessible and low-cost alternative to more sophisticated and expensive antibody selection approaches (e.g. single B cell analysis and natural evolution in humanized mice).
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Affiliation(s)
- Nileena Velappan
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
| | - Hau B. Nguyen
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
| | | | - Daniel Bedinger
- Experimental division, Carterra Inc, Walnut Creek, CA, 94568, USA
| | - Chunyan Ye
- Center for Global Health and Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Betty Mangadu
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Austin J. Watts
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
- Experimental division, Carterra Inc, Walnut Creek, CA, 94568, USA
- Center for Global Health and Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Robert Meagher
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Steven Bradfute
- Center for Global Health and Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Bin Hu
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
| | - Geoffrey S. Waldo
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
| | - Antonietta M. Lillo
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM87547, USA
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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35
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Xiao C, Mao L, Wang Z, Gao L, Zhu G, Su J, Chen X, Yuan J, Hu Y, Yin Z, Xie J, Ji W, Niu H, Gao F, Luo OJ, Xiao L, Wang P, Chen G. SARS-CoV-2 variant B.1.1.7 caused HLA-A2 + CD8 + T cell epitope mutations for impaired cellular immune response. iScience 2022; 25:103934. [PMID: 35194575 PMCID: PMC8851741 DOI: 10.1016/j.isci.2022.103934] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/29/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Here, we evaluated the immune properties of the HLA-A2 restricted CD8+ T cell epitopes containing mutations from B.1.1.7, and furthermore performed a comprehensive analysis of the SARS-CoV-2 specific CD8+ T cell responses from COVID-19 convalescent patients and SARS-CoV-2 vaccinees recognizing the ancestral Wuhan strain compared to B.1.1.7. First, most of the predicted CD8+ T cell epitopes showed proper binding with HLA-A2, whereas epitopes from B.1.1.7 had lower binding capability than those from the ancestral strain. In addition, these peptides could effectively induce the activation and cytotoxicity of CD8+ T cells. Our results further showed that at least two site mutations in B.1.1.7 resulted in a decrease in CD8+ T cell activation and a possible immune evasion, namely A1708D mutation in ORF1ab1707-1716 and I2230T mutation in ORF1ab2230-2238. Our current analysis provides information that contributes to the understanding of SARS-CoV-2-specific CD8+ T cell responses elicited by infection of mutated strains or vaccination.
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Affiliation(s)
- Chanchan Xiao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
| | - Lipeng Mao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
| | - Zhigang Wang
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou 510000, China
| | - Lijuan Gao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
| | - Guodong Zhu
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
- Department of Geriatrics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510000, China
| | - Jun Su
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou 510000, China
| | - Xiongfei Chen
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510000, China
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510000, China
| | - Yutian Hu
- Meng Yi Center Limited, Macau 999078, China
| | - Zhinan Yin
- Biomedical Translational Research Institute, Jinan University, Guangzhou 510000, China
| | - Jun Xie
- ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 200052, China
- Arthritis Institute of Integrated Traditional Chinese and Western Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai University of Chinese Traditional Medicine, Shanghai 200052, China
| | - Weiqing Ji
- ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 200052, China
- Arthritis Institute of Integrated Traditional Chinese and Western Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai University of Chinese Traditional Medicine, Shanghai 200052, China
| | - Haitao Niu
- School of Medicine & Institute of Laboratory Animal Sciences, Jinan University, Guangzhou 510000, China
| | - Feng Gao
- School of Medicine, Jinan University, Guangzhou 510000, China
| | - Oscar Junhong Luo
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou 510000, China
| | - Lianbo Xiao
- ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 200052, China
- Arthritis Institute of Integrated Traditional Chinese and Western Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai University of Chinese Traditional Medicine, Shanghai 200052, China
| | - Pengcheng Wang
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
| | - Guobing Chen
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou 510000, China
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Ercanoglu MS, Gieselmann L, Dähling S, Poopalasingam N, Detmer S, Koch M, Korenkov M, Halwe S, Klüver M, Di Cristanziano V, Janicki H, Schlotz M, Worczinski J, Gathof B, Gruell H, Zehner M, Becker S, Vanshylla K, Kreer C, Klein F. No substantial preexisting B cell immunity against SARS-CoV-2 in healthy adults. iScience 2022; 25:103951. [PMID: 35224466 PMCID: PMC8857777 DOI: 10.1016/j.isci.2022.103951] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 11/29/2022] Open
Abstract
Preexisting immunity against SARS-CoV-2 may have critical implications for our understanding of COVID-19 susceptibility and severity. The presence and clinical relevance of a preexisting B cell immunity remain to be fully elucidated. Here, we provide a detailed analysis of the B cell immunity to SARS-CoV-2 in unexposed individuals. To this end, we extensively investigated SARS-CoV-2 humoral immunity in 150 adults sampled pre-pandemically. Comprehensive screening of donor plasma and purified IgG samples for binding and neutralization in various functional assays revealed no substantial activity against SARS-CoV-2 but broad reactivity to endemic betacoronaviruses. Moreover, we analyzed antibody sequences of 8,174 putatively SARS-CoV-2-reactive B cells at a single cell level and generated and tested 158 monoclonal antibodies. None of these antibodies displayed relevant binding or neutralizing activity against SARS-CoV-2. Taken together, our results show no evidence of competent preexisting antibody and B cell immunity against SARS-CoV-2 in unexposed adults. Comprehensive analysis of the B cell response to SARS-CoV-2 in pre-pandemic samples No substantial plasma and IgG reactivity against SARS-CoV-2 MAbs isolated from pre-pandemic samples showed no SARS-CoV-2 neutralizing activity No indication of competent preexisting B cell immunity against SARS-CoV-2
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Affiliation(s)
- Meryem Seda Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Sabrina Dähling
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nareshkumar Poopalasingam
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Susanne Detmer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.,Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, University of Cologne, 50931 Cologne, Germany
| | - Michael Korenkov
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sandro Halwe
- Institute of Virology, Philipps University Marburg, Hans-Meerwein-Straße 2, 35042 Marburg, Germany.,German Center for Infection Research, Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Michael Klüver
- Institute of Virology, Philipps University Marburg, Hans-Meerwein-Straße 2, 35042 Marburg, Germany.,German Center for Infection Research, Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Veronica Di Cristanziano
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Maike Schlotz
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Johanna Worczinski
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Birgit Gathof
- Institute of Transfusion Medicine, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Matthias Zehner
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Stephan Becker
- Institute of Virology, Philipps University Marburg, Hans-Meerwein-Straße 2, 35042 Marburg, Germany.,German Center for Infection Research, Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
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37
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Schubert M, Bertoglio F, Steinke S, Heine PA, Ynga-Durand MA, Maass H, Sammartino JC, Cassaniti I, Zuo F, Du L, Korn J, Milošević M, Wenzel EV, Krstanović F, Polten S, Pribanić-Matešić M, Brizić I, Baldanti F, Hammarström L, Dübel S, Šustić A, Marcotte H, Strengert M, Protić A, Piralla A, Pan-Hammarström Q, Čičin-Šain L, Hust M. Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. BMC Med 2022; 20:102. [PMID: 35236358 PMCID: PMC8890955 DOI: 10.1186/s12916-022-02312-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/21/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic is caused by the betacoronavirus SARS-CoV-2. In November 2021, the Omicron variant was discovered and immediately classified as a variant of concern (VOC), since it shows substantially more mutations in the spike protein than any previous variant, especially in the receptor-binding domain (RBD). We analyzed the binding of the Omicron RBD to the human angiotensin-converting enzyme-2 receptor (ACE2) and the ability of human sera from COVID-19 patients or vaccinees in comparison to Wuhan, Beta, or Delta RBD variants. METHODS All RBDs were produced in insect cells. RBD binding to ACE2 was analyzed by ELISA and microscale thermophoresis (MST). Similarly, sera from 27 COVID-19 patients, 81 vaccinated individuals, and 34 booster recipients were titrated by ELISA on RBDs from the original Wuhan strain, Beta, Delta, and Omicron VOCs. In addition, the neutralization efficacy of authentic SARS-CoV-2 wild type (D614G), Delta, and Omicron by sera from 2× or 3× BNT162b2-vaccinated persons was analyzed. RESULTS Surprisingly, the Omicron RBD showed a somewhat weaker binding to ACE2 compared to Beta and Delta, arguing that improved ACE2 binding is not a likely driver of Omicron evolution. Serum antibody titers were significantly lower against Omicron RBD compared to the original Wuhan strain. A 2.6× reduction in Omicron RBD binding was observed for serum of 2× BNT162b2-vaccinated persons. Neutralization of Omicron SARS-CoV-2 was completely diminished in our setup. CONCLUSION These results indicate an immune escape focused on neutralizing antibodies. Nevertheless, a boost vaccination increased the level of anti-RBD antibodies against Omicron, and neutralization of authentic Omicron SARS-CoV-2 was at least partially restored. This study adds evidence that current vaccination protocols may be less efficient against the Omicron variant.
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Affiliation(s)
- Maren Schubert
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Federico Bertoglio
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Stephan Steinke
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Philip Alexander Heine
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Mario Alberto Ynga-Durand
- Helmholtz Centre for Infection Research, Department of Viral Immunology, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Henrike Maass
- Helmholtz Centre for Infection Research, Department of Viral Immunology, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Josè Camilla Sammartino
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Irene Cassaniti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Fanglei Zuo
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Likun Du
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Janin Korn
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany.,Abcalis GmbH, Science Campus Braunschweig-Süd, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Marko Milošević
- Department of Anesthesiology, Reanimation, Intensive Care and Emergency Medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Esther Veronika Wenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany.,Abcalis GmbH, Science Campus Braunschweig-Süd, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Fran Krstanović
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saskia Polten
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | | | - Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Stefan Dübel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Alan Šustić
- Department of Anesthesiology, Reanimation, Intensive Care and Emergency Medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Alen Protić
- Department of Anesthesiology, Reanimation, Intensive Care and Emergency Medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | | | - Luka Čičin-Šain
- Helmholtz Centre for Infection Research, Department of Viral Immunology, Inhoffenstr. 7, 38124, Braunschweig, Germany.,Centre for Individualised Infection Medicine (CIIM), a joint venture of Helmholtz Centre for Infection Research and Medical School Hannover, Hannover, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany.
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38
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Collection of Monoclonal Antibodies Targeting SARS-CoV-2 Proteins. Viruses 2022; 14:v14020443. [PMID: 35216036 PMCID: PMC8875891 DOI: 10.3390/v14020443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/03/2022] [Accepted: 02/19/2022] [Indexed: 12/25/2022] Open
Abstract
In early 2020, the COVID-19 pandemic sparked a global crisis that continues to pose a serious threat to human health and the economy. Further advancement in research is necessary and requires the availability of quality molecular tools, including monoclonal antibodies. Here, we present the development and characterization of a collection of over 40 new monoclonal antibodies directed against different SARS-CoV-2 proteins. Recombinant SARS-CoV-2 proteins were expressed, purified, and used as immunogens. Upon development of specific hybridomas, the obtained monoclonal antibody (mAb) clones were tested for binding to recombinant proteins and infected cells. We generated mAbs against structural proteins, the Spike and Nucleocapsid protein, several non-structural proteins (nsp1, nsp7, nsp8, nsp9, nsp10, nsp16) and accessory factors (ORF3a, ORF9b) applicable in flow cytometry, immunofluorescence, or Western blot. Our collection of mAbs provides a set of novel, highly specific tools that will allow a comprehensive analysis of the viral proteome, which will allow further understanding of SARS-CoV-2 pathogenesis and the design of therapeutic strategies.
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39
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Ma X, Guo S, Ruan S, Liu Y, Zang J, Yang Y, Dong H, Li Y, Ren T, An M, Li Y. HACE2-Exosome-Based Nano-Bait for Concurrent SARS-CoV-2 Trapping and Antioxidant Therapy. ACS APPLIED MATERIALS & INTERFACES 2022; 14:4882-4891. [PMID: 35067058 PMCID: PMC8805705 DOI: 10.1021/acsami.1c19541] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/12/2022] [Indexed: 05/22/2023]
Abstract
Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is seriously threatening human health. Following SARS-CoV-2 infection, immune cell infiltration creates an inflammatory and oxidative microenvironment, which can cause pneumonia, severe acute respiratory syndrome, kidney failure, and even death. Clinically, a safe and effective treatment strategy remains to be established. Herein, a nano-bait strategy for inhibition of SARS-CoV-2 infection by redirecting viral attack while simultaneously relieving inflammation is developed. Specifically, the nano-bait was based on the exosome-sheathed polydopamine (PDA@Exosome) nanoparticles, which were generated by exocytosis of the PDA nanoparticles from H293T cells. In this approach, PDA@Exosome inherits from the source cells of H293T cells a surface display of ACE2 through pre-engineered expression. The resulting PDA@Exosome can compete with ACE2-expressing epithelial cells for S protein binding, in either the pre-exposure or post-exposure route. Moreover, relying on the ability of PDA to intercept and deactivate radical species, the PDA@Exosome can significantly attenuate the level of inflammatory cytokines by mediating oxidative stress, a major cause of organ injury. Due to its high trapping, multiple antioxidant ability, and good biocompatibility, the HACE2-exosome based nano-bait is a promising robust antiviral nanotherapeutics for the ongoing COVID-19 pandemic.
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Affiliation(s)
- Xiaoyi Ma
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
| | - Shiyu Guo
- Department
of Pharmacology, Tongji University School of Medicine, Shanghai Tenth People’s Hospital, Shanghai 200092, P. R. China
| | - Shuangrong Ruan
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
| | - Yao Liu
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
| | - Jie Zang
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
| | - Yushan Yang
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
| | - Haiqing Dong
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
| | - Yan Li
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
| | - Tianbin Ren
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
| | - Maomao An
- Department
of Pharmacology, Tongji University School of Medicine, Shanghai Tenth People’s Hospital, Shanghai 200092, P. R. China
| | - Yongyong Li
- Shanghai
Skin Disease Hospital, The Institute for Biomedical Engineering &
Nano Science, Tongji University School of
Medicine, Shanghai 200092, P. R. China
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40
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Ferrara F, Erasmus MF, D'Angelo S, Leal-Lopes C, Teixeira AA, Choudhary A, Honnen W, Calianese D, Huang D, Peng L, Voss JE, Nemazee D, Burton DR, Pinter A, Bradbury ARM. A pandemic-enabled comparison of discovery platforms demonstrates a naïve antibody library can match the best immune-sourced antibodies. Nat Commun 2022; 13:462. [PMID: 35075126 PMCID: PMC8786865 DOI: 10.1038/s41467-021-27799-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
As a result of the SARS-CoV-2 pandemic numerous scientific groups have generated antibodies against a single target: the CoV-2 spike antigen. This has provided an unprecedented opportunity to compare the efficacy of different methods and the specificities and qualities of the antibodies generated by those methods. Generally, the most potent neutralizing antibodies have been generated from convalescent patients and immunized animals, with non-immune phage libraries usually yielding significantly less potent antibodies. Here, we show that it is possible to generate ultra-potent (IC50 < 2 ng/ml) human neutralizing antibodies directly from a unique semisynthetic naïve antibody library format with affinities, developability properties and neutralization activities comparable to the best from hyperimmune sources. This demonstrates that appropriately designed and constructed naïve antibody libraries can effectively compete with immunization to directly provide therapeutic antibodies against a viral pathogen, without the need for immune sources or downstream optimization. The most potent neutralizing antibodies are typically generated from convalescent patients and immunized animals. Here, the authors show it is possible to generate highly potent human neutralizing antibodies against the SARS-CoV-2 spike protein directly from a semisynthetic naïve antibody library.
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Affiliation(s)
| | | | | | - Camila Leal-Lopes
- Bioscience Division, New Mexico Consortium, Los Alamos, NM, 87544, USA
| | - André A Teixeira
- Bioscience Division, New Mexico Consortium, Los Alamos, NM, 87544, USA
| | - Alok Choudhary
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - William Honnen
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - David Calianese
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - Deli Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Linghan Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Abraham Pinter
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
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41
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Hwang YC, Lu RM, Su SC, Chiang PY, Ko SH, Ke FY, Liang KH, Hsieh TY, Wu HC. Monoclonal antibodies for COVID-19 therapy and SARS-CoV-2 detection. J Biomed Sci 2022; 29:1. [PMID: 34983527 PMCID: PMC8724751 DOI: 10.1186/s12929-021-00784-w] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an exceptional public health crisis that demands the timely creation of new therapeutics and viral detection. Owing to their high specificity and reliability, monoclonal antibodies (mAbs) have emerged as powerful tools to treat and detect numerous diseases. Hence, many researchers have begun to urgently develop Ab-based kits for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ab drugs for use as COVID-19 therapeutic agents. The detailed structure of the SARS-CoV-2 spike protein is known, and since this protein is key for viral infection, its receptor-binding domain (RBD) has become a major target for therapeutic Ab development. Because SARS-CoV-2 is an RNA virus with a high mutation rate, especially under the selective pressure of aggressively deployed prophylactic vaccines and neutralizing Abs, the use of Ab cocktails is expected to be an important strategy for effective COVID-19 treatment. Moreover, SARS-CoV-2 infection may stimulate an overactive immune response, resulting in a cytokine storm that drives severe disease progression. Abs to combat cytokine storms have also been under intense development as treatments for COVID-19. In addition to their use as drugs, Abs are currently being utilized in SARS-CoV-2 detection tests, including antigen and immunoglobulin tests. Such Ab-based detection tests are crucial surveillance tools that can be used to prevent the spread of COVID-19. Herein, we highlight some key points regarding mAb-based detection tests and treatments for the COVID-19 pandemic.
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Affiliation(s)
- Yu-Chyi Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Ruei-Min Lu
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Chieh Su
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Pao-Yin Chiang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Han Ko
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Feng-Yi Ke
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Kang-Hao Liang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Tzung-Yang Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan.
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Yuan TZ, Garg P, Wang L, Willis JR, Kwan E, Hernandez AGL, Tuscano E, Sever EN, Keane E, Soto C, Mucker EM, Fouch ME, Davidson E, Doranz BJ, Kailasan S, Aman MJ, Li H, Hooper JW, Saphire EO, Crowe JE, Liu Q, Axelrod F, Sato AK. Rapid discovery of diverse neutralizing SARS-CoV-2 antibodies from large-scale synthetic phage libraries. MAbs 2022; 14:2002236. [PMID: 34967699 PMCID: PMC8726723 DOI: 10.1080/19420862.2021.2002236] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/12/2021] [Accepted: 11/01/2021] [Indexed: 12/22/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an evolving global public health crisis in need of therapeutic options. Passive immunization of monoclonal antibodies (mAbs) represents a promising therapeutic strategy capable of conferring immediate protection from SARS-CoV-2 infection. Herein, we describe the discovery and characterization of neutralizing SARS-CoV-2 IgG and VHH antibodies from four large-scale phage libraries. Each library was constructed synthetically with shuffled complementarity-determining region loops from natural llama and human antibody repertoires. While most candidates targeted the receptor-binding domain of the S1 subunit of SARS-CoV-2 spike protein, we also identified a neutralizing IgG candidate that binds a unique epitope on the N-terminal domain. A select number of antibodies retained binding to SARS-CoV-2 variants Alpha, Beta, Gamma, Kappa and Delta. Overall, our data show that synthetic phage libraries can rapidly yield SARS-CoV-2 S1 antibodies with therapeutically desirable features, including high affinity, unique binding sites, and potent neutralizing activity in vitro, and a capacity to limit disease in vivo.
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MESH Headings
- Animals
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Neutralizing/pharmacology
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antibody Specificity
- Binding Sites, Antibody
- COVID-19/immunology
- COVID-19/metabolism
- COVID-19/prevention & control
- COVID-19/virology
- Cell Surface Display Techniques
- Chlorocebus aethiops
- Disease Models, Animal
- Epitopes
- Female
- Host-Pathogen Interactions
- Immunoglobulin G/genetics
- Immunoglobulin G/immunology
- Immunoglobulin G/metabolism
- Immunoglobulin G/pharmacology
- Mesocricetus
- Peptide Library
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Single-Domain Antibodies/genetics
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/immunology
- Vero Cells
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Affiliation(s)
- Tom Z. Yuan
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | | | - Linya Wang
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Jordan R. Willis
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, USA
| | - Eric Kwan
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | | | - Emily Tuscano
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Emily N. Sever
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Erica Keane
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Cinque Soto
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric M. Mucker
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | | | | | | | | | | | - Haoyang Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jay W. Hooper
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiang Liu
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Fumiko Axelrod
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Aaron K. Sato
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
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43
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Blanco OR, Dorta D, Hernández CA, Abreu D, Domínguez AG, Luna Y, Valdivia O, Pérez-Bernal M, Tamayo C, Lemos G, Pasarón IM, Pérez JJ, Benítez L, Bequet-Romero M, Fragas A, Cabrera Y, Pérez ER. Murine monoclonal antibodies against RBD of the SARS-CoV-2 spike protein as useful analytical tools for subunit vaccine development and clinical trials. J Immunol Methods 2022; 500:113195. [PMID: 34843713 PMCID: PMC8619880 DOI: 10.1016/j.jim.2021.113195] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/16/2022]
Abstract
COVID-19 pandemic poses a serious threat to human health; it has completely disrupted global stability, making vaccine development an important goal to achieve. Monoclonal antibodies play an important role in subunit vaccines strategies. In this work, nine murine MAbs against the RBD of the SARS-CoV-2 spike protein were obtained by hybridoma technology. Characterization of purified antibodies demonstrated that five of them have affinities in the order of 108 L/mol. Six MAbs showed specific recognition of different recombinant RBD-S antigens in solution. Studies of the additivity index of anti-RBD antibodies, by using a novel procedure to determine the additivity cut point, showed recognition of at least five different epitopes. The MAbs CBSSRBD-S.11 and CBSSRBD-S.8 revealed significant neutralizing capacity against SARS-CoV-2 in an ACE2-RBD binding inhibition assay (IC50 = 85.5pM and IC50 = 122.7pM, respectively) and in a virus neutralizing test with intact SARS-CoV-2 (VN50 = 0.552 nM and VN50 = 4.854 nM, respectively) when D614G strain was used to infect Vero cells. Also CBSSRBD-S.11 neutralized the SARS-CoV-2 strains Alpha and Beta: VN50 = 0.707 nM and VN50 = 0.132 nM, respectively. The high affinity CBSSRBD-S.8 and CBSSRBD-S.7 recognized different epitopes, so they are suitable for the development of a sandwich ELISA to quantitate RBD-S recombinant antigens in biomanufacturing processes, as well as in pharmacokinetic studies in clinical and preclinical trials.
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Affiliation(s)
- Omar R Blanco
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Dayamí Dorta
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Carlos A Hernández
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Daymí Abreu
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Andy G Domínguez
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Yaramis Luna
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Onel Valdivia
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Maylín Pérez-Bernal
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Celia Tamayo
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Gilda Lemos
- Center for Genetic Engineering and Biotechnology, Ave. 31 e/ 158 y 190, Playa, Havana, Cuba
| | - Ivis M Pasarón
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Joel J Pérez
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Liudmila Benítez
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
| | - Mónica Bequet-Romero
- Center for Genetic Engineering and Biotechnology, Ave. 31 e/ 158 y 190, Playa, Havana, Cuba
| | - Anitza Fragas
- Civilian Defense Scientific Research Center, Carretera de Jamaica y Autopista 15 Nacional, San José de las Lajas, Mayabeque, Cuba
| | - Yeosvany Cabrera
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba.
| | - Enrique R Pérez
- Center for Genetic Engineering and Biotechnology of Sancti Spíritus, Circunvalante Norte, Olivos III, Sancti Spíritus, Cuba
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44
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Alfaleh MA, Zawawi A, Al-Amri SS, Hashem AM. David versus goliath: ACE2-Fc receptor traps as potential SARS-CoV-2 inhibitors. MAbs 2022; 14:2057832. [PMID: 35380919 PMCID: PMC8986284 DOI: 10.1080/19420862.2022.2057832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Anti-SARS-CoV-2 monoclonal antibodies and vaccines have shown improvement in lowering viral burden and hospitalization. However, emerging SARS-CoV-2 variants contain neutralizing antibody-escape mutations. Therefore, several reports have suggested the administration of recombinant angiotensin-converting enzyme 2 (rACE2) as a soluble receptor trap to block SARS-CoV-2 infection and limit viral escape potential. Several strategies have been implemented to enhance the efficacy of rACE2 as a therapeutic agent. Fc fusions have been used to improve pharmacokinetics and boost the affinity and avidity of ACE2 decoys for the virus spike protein. Furthermore, the intrinsic catalytic activity of ACE2 can be eliminated by introducing point mutations on the catalytic site of ACE2 to obtain an exclusive antiviral activity. This review summarizes different evolution platforms that have been used to enhance ACE2-Fc (i.e., immunoadhesins) as potential therapeutics for the current pandemic or future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Mohamed A Alfaleh
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia
| | - Ayat Zawawi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia.,Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah Saudi Arabia
| | - Sawsan S Al-Amri
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah Saudi Arabia
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45
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Qiang M, Ma P, Li Y, Liu H, Harding A, Min C, Wang F, Liu L, Yuan M, Ji Q, Tao P, Shi X, Li Z, Li T, Wang X, Zhang Y, Wu NC, Lee CD, Zhu X, Gilbert‐Jaramillo J, Zhang C, Saxena A, Huang X, Wang H, James W, Dwek RA, Wilson IA, Yang G, Lerner RA. Neutralizing Antibodies to SARS-CoV-2 Selected from a Human Antibody Library Constructed Decades Ago. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2102181. [PMID: 34716683 PMCID: PMC8646600 DOI: 10.1002/advs.202102181] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Combinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, a combinatorial human antibody library constructed 20 years before the coronavirus disease 2019 (COVID-19) pandemic is used to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these three antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in their crystal structures with SARS-CoV-2 spike receptor binding domain. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of these antibodies with respect to their reactivity with SARS-CoV-2.
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MESH Headings
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Neutralizing/pharmacology
- Antibodies, Viral/immunology
- Binding Sites
- Binding, Competitive
- Cell Surface Display Techniques
- Chlorocebus aethiops
- HEK293 Cells
- Humans
- Peptide Library
- SARS-CoV-2/drug effects
- SARS-CoV-2/immunology
- Somatic Hypermutation, Immunoglobulin
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Vero Cells
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46
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Schneider KT, Kirmann T, Wenzel EV, Grosch JH, Polten S, Meier D, Becker M, Matejtschuk P, Hust M, Russo G, Dübel S. Shelf-Life Extension of Fc-Fused Single Chain Fragment Variable Antibodies by Lyophilization. Front Cell Infect Microbiol 2021; 11:717689. [PMID: 34869052 PMCID: PMC8634725 DOI: 10.3389/fcimb.2021.717689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/25/2021] [Indexed: 11/18/2022] Open
Abstract
Generation of sequence defined antibodies from universal libraries by phage display has been established over the past three decades as a robust method to cope with the increasing market demand in therapy, diagnostics and research. For applications requiring the bivalent antigen binding and an Fc part for detection, phage display generated single chain Fv (scFv) antibody fragments can rapidly be genetically fused to the Fc moiety of an IgG for the production in eukaryotic cells of antibodies with IgG-like properties. In contrast to conversion of scFv into IgG format, the conversion to scFv-Fc requires only a single cloning step, and provides significantly higher yields in transient cell culture production than IgG. ScFv-Fcs can be effective as neutralizing antibodies in vivo against a panel of pathogens and toxins. However, different scFv fragments are more heterologous in respect of stability than Fab fragments. While some scFv fragments can be made extremely stable, this may change due to few mutations, and is not predictable from the sequence of a newly selected antibody. To mitigate the necessity to assess the stability for every scFv-Fc antibody, we developed a generic lyophilization protocol to improve their shelf life. We compared long-term stability and binding activity of phage display-derived antibodies in the scFv-Fc and IgG format, either stored in liquid or lyophilized state. Conversion of scFv-Fcs into the full IgG format reduced protein degradation and aggregation, but in some cases compromised binding activity. Comparably to IgG conversion, lyophilization of scFv-Fc resulted in the preservation of the antibodies' initial properties after storage, without any drop in affinity for any of the tested antibody clones.
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Affiliation(s)
- Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Toni Kirmann
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Esther Veronika Wenzel
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Abcalis GmbH, Braunschweig, Germany
| | - Jan-Hendrik Grosch
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Saskia Polten
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Doris Meier
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marlies Becker
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Paul Matejtschuk
- Standardisation Science, National Institute for Biological Standards & Control (NIBSC), Hertfordshire, United Kingdom
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Abcalis GmbH, Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
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47
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Tan TH, Patton E, Munro CA, Corzo-Leon DE, Porter AJ, Palliyil S. Monoclonal Human Antibodies That Recognise the Exposed N and C Terminal Regions of the Often-Overlooked SARS-CoV-2 ORF3a Transmembrane Protein. Viruses 2021; 13:2201. [PMID: 34835009 PMCID: PMC8624585 DOI: 10.3390/v13112201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/15/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022] Open
Abstract
ORF3a has been identified as a viroporin of SARS-CoV-2 and is known to be involved in various pathophysiological activities including disturbance of cellular calcium homeostasis, inflammasome activation, apoptosis induction and disruption of autophagy. ORF3a-targeting antibodies may specifically and favorably modulate these viroporin-dependent pathological activities. However, suitable viroporin-targeting antibodies are difficult to generate because of the well-recognized technical challenge associated with isolating antibodies to complex transmembrane proteins. Here we exploited a naïve human single chain antibody phage display library, to isolate binders against carefully chosen ORF3a recombinant epitopes located towards the extracellular N terminal and cytosolic C terminal domains of the protein using peptide antigens. These binders were subjected to further characterization using enzyme-linked immunosorbent assays and surface plasmon resonance analysis to assess their binding affinities to the target epitopes. Binding to full-length ORF3a protein was evaluated by western blot and fluorescent microscopy using ORF3a transfected cells and SARS-CoV-2 infected cells. Co-localization analysis was also performed to evaluate the "pairing potential" of the selected binders as possible alternative diagnostic or prognostic biomarkers for COVID-19 infections. Both ORF3a N and C termini, epitope-specific monoclonal antibodies were identified in our study. Whilst the linear nature of peptides might not always represent their native conformations in the context of full protein, with carefully designed selection protocols, we have been successful in isolating anti-ORF3a binders capable of recognising regions of the transmembrane protein that are exposed either on the "inside" or "outside" of the infected cell. Their therapeutic potential will be discussed.
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Affiliation(s)
- Tyng Hwey Tan
- Scottish Biologics Facility, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZP, UK; (T.H.T.); (E.P.)
- Aberdeen Fungal Group, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (C.A.M.); (D.E.C.-L.)
| | - Elizabeth Patton
- Scottish Biologics Facility, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZP, UK; (T.H.T.); (E.P.)
| | - Carol A. Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (C.A.M.); (D.E.C.-L.)
| | - Dora E. Corzo-Leon
- Aberdeen Fungal Group, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (C.A.M.); (D.E.C.-L.)
| | - Andrew J. Porter
- Scottish Biologics Facility, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZP, UK; (T.H.T.); (E.P.)
| | - Soumya Palliyil
- Scottish Biologics Facility, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZP, UK; (T.H.T.); (E.P.)
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48
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Laurini E, Marson D, Aulic S, Fermeglia A, Pricl S. Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Sci Rep 2021; 11:20274. [PMID: 34642465 PMCID: PMC8511038 DOI: 10.1038/s41598-021-99827-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022] Open
Abstract
The purpose of this work is to provide an in silico molecular rationale of the role eventually played by currently circulating mutations in the receptor binding domain of the SARS-CoV-2 spike protein (S-RBDCoV‑2) in evading the immune surveillance effects elicited by the two Eli Lilly LY-CoV555/bamlanivimab and LY-CoV016/etesevimab monoclonal antibodies. The main findings from this study show that, compared to the wild-type SARS-CoV-2 spike protein, mutations E484A/G/K/Q/R/V, Q493K/L/R, S494A/P/R, L452R and F490S are predicted to be markedly resistant to neutralization by LY-CoV555, while mutations K417E/N/T, D420A/G/N, N460I/K/S/T, T415P, and Y489C/S are predicted to confer LY-CoV016 escaping advantage to the viral protein. A challenge of our global in silico results against relevant experimental data resulted in an overall 90% agreement. Thus, the results presented provide a molecular-based rationale for all relative experimental findings, constitute a fast and reliable tool for identifying and prioritizing all present and newly reported circulating spike SARS-CoV-2 variants with respect to antibody neutralization, and yield substantial structural information for the development of next-generation vaccines and monoclonal antibodies more resilient to viral evolution.
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Affiliation(s)
- Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy.
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-136, Lodz, Poland.
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49
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Qu Y, Zhang X, Wang M, Sun L, Jiang Y, Li C, Wu W, Chen Z, Yin Q, Jiang X, Liu Y, Li C, Li J, Ying T, Li D, Zhan F, Wang Y, Guan W, Wang S, Liang M. Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Virol Sin 2021; 36:934-947. [PMID: 34224110 PMCID: PMC8255729 DOI: 10.1007/s12250-021-00409-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/06/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has precipitated multiple variants resistant to therapeutic antibodies. In this study, 12 high-affinity antibodies were generated from convalescent donors in early outbreaks using immune antibody phage display libraries. Of them, two RBD-binding antibodies (F61 and H121) showed high-affinity neutralization against SARS-CoV-2, whereas three S2-target antibodies failed to neutralize SARS-CoV-2. Following structure analysis, F61 identified a linear epitope located in residues G446-S494, which overlapped with angiotensin-converting enzyme 2 (ACE2) binding sites, while H121 recognized a conformational epitope located on the side face of RBD, outside from ACE2 binding domain. Hence the cocktail of the two antibodies achieved better performance of neutralization to SARS-CoV-2. Importantly, these two antibodies also showed efficient neutralizing activities to the variants including B.1.1.7 and B.1.351, and reacted with mutations of N501Y, E484K, and L452R, indicated that it may also neutralize the recent India endemic strain B.1.617. The unchanged binding activity of F61 and H121 to RBD with multiple mutations revealed a broad neutralizing activity against variants, which mitigated the risk of viral escape. Our findings revealed the therapeutic basis of cocktail antibodies against constantly emerging SARS-CoV-2 variants and provided promising candidate antibodies to clinical treatment of COVID-19 patients infected with broad SARS-CoV-2 variants.
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Affiliation(s)
- Yuanyuan Qu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xueyan Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyu Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China
- Peking Union Medical College, Beijing, 100730, China
| | - Lina Sun
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yongzhong Jiang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430065, China
| | - Cheng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wei Wu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Qiangling Yin
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaolin Jiang
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Yang Liu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Chuan Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jiandong Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Dexin Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Faxian Zhan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430065, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China
- Peking Union Medical College, Beijing, 100730, China
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
| | - Shiwen Wang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Mifang Liang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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50
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Hsiao WWW, Le TN, Pham DM, Ko HH, Chang HC, Lee CC, Sharma N, Lee CK, Chiang WH. Recent Advances in Novel Lateral Flow Technologies for Detection of COVID-19. BIOSENSORS 2021; 11:295. [PMID: 34562885 PMCID: PMC8466143 DOI: 10.3390/bios11090295] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/21/2021] [Accepted: 08/22/2021] [Indexed: 02/07/2023]
Abstract
The development of reliable and robust diagnostic tests is one of the most efficient methods to limit the spread of coronavirus disease 2019 (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, most laboratory diagnostics for COVID-19, such as enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR), are expensive, time-consuming, and require highly trained professional operators. On the other hand, the lateral flow immunoassay (LFIA) is a simpler, cheaper device that can be operated by unskilled personnel easily. Unfortunately, the current technique has some limitations, mainly inaccuracy in detection. This review article aims to highlight recent advances in novel lateral flow technologies for detecting SARS-CoV-2 as well as innovative approaches to achieve highly sensitive and specific point-of-care testing. Lastly, we discuss future perspectives on how smartphones and Artificial Intelligence (AI) can be integrated to revolutionize disease detection as well as disease control and surveillance.
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Affiliation(s)
- Wesley Wei-Wen Hsiao
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; (T.-N.L.); (H.-C.C.); (N.S.); (C.-K.L.)
| | - Trong-Nghia Le
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; (T.-N.L.); (H.-C.C.); (N.S.); (C.-K.L.)
| | - Dinh Minh Pham
- GENTIS JSC, 249A, Thuy Khue, Tay Ho, Hanoi 100000, Vietnam;
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Hui-Hsin Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; (H.-H.K.); (C.-C.L.)
| | - Huan-Cheng Chang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; (T.-N.L.); (H.-C.C.); (N.S.); (C.-K.L.)
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; (H.-H.K.); (C.-C.L.)
| | - Neha Sharma
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; (T.-N.L.); (H.-C.C.); (N.S.); (C.-K.L.)
| | - Cheng-Kang Lee
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; (T.-N.L.); (H.-C.C.); (N.S.); (C.-K.L.)
| | - Wei-Hung Chiang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; (T.-N.L.); (H.-C.C.); (N.S.); (C.-K.L.)
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