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Timofeeva AM, Sedykh SE, Litvinova EA, Dolgushin SA, Matveev AL, Tikunova NV, Nevinsky GA. Binding of Natural Antibodies Generated after COVID-19 and Vaccination with Individual Peptides Corresponding to the SARS-CoV-2 S-Protein. Vaccines (Basel) 2024; 12:426. [PMID: 38675808 PMCID: PMC11053827 DOI: 10.3390/vaccines12040426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The rapid development of vaccines is a crucial objective in modern biotechnology and molecular pharmacology. In this context, conducting research to expedite the selection of a potent immunogen is imperative. The candidate vaccine should induce the production of antibodies that can recognize the immunogenic epitopes of the target protein, resembling the ones found in recovered patients. One major challenge in vaccine development is the absence of straightforward and reliable techniques to determine the extent to which the spectrum of antibodies produced after vaccination corresponds to antibodies found after recovery. This paper describes a newly developed method to detect antibodies specific to immunogenic epitopes of the target protein in blood plasma and to compare them with antibody spectra generated post vaccination. Comparing the antibody pool generated in the human body after recovering from an infectious disease with the pool formed through vaccination can become a universal method for screening candidate vaccines. This method will enable the identification of candidate vaccines that can induce the production of antibodies similar to those generated in response to a natural infection. Implementing this approach will facilitate the rapid development of new vaccines, even when faced with a pandemic.
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Affiliation(s)
- Anna M. Timofeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina A. Litvinova
- Physical Engineering Faculty, Novosibirsk State Technical University, Novosibirsk 630073, Russia
| | | | - Andrey L. Matveev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
| | - Nina V. Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
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2
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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3
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Carzaniga T, Casiraghi L, Nava G, Zanchetta G, Inzani T, Chiari M, Bollati V, Epis S, Bandi C, Lai A, Zehender G, Bellini T, Buscaglia M. Serum antibody fingerprinting of SARS-CoV-2 variants in infected and vaccinated subjects by label-free microarray biosensor. Front Immunol 2024; 15:1323406. [PMID: 38476234 PMCID: PMC10927789 DOI: 10.3389/fimmu.2024.1323406] [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: 10/17/2023] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Both viral infection and vaccination affect the antibody repertoire of a person. Here, we demonstrate that the analysis of serum antibodies generates information not only on the virus type that caused the infection but also on the specific virus variant. We developed a rapid multiplex assay providing a fingerprint of serum antibodies against five different SARS-CoV-2 variants based on a microarray of virus antigens immobilized on the surface of a label-free reflectometric biosensor. We analyzed serum from the plasma of convalescent subjects and vaccinated volunteers and extracted individual antibody profiles of both total immunoglobulin Ig and IgA fractions. We found that Ig level profiles were strongly correlated with the specific variant of infection or vaccination and that vaccinated subjects displayed a larger quantity of total Ig and a lower fraction of IgA relative to the population of convalescent unvaccinated subjects.
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Affiliation(s)
- Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Tommaso Inzani
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, National Research Council of Italy (SCITEC-CNR), Milano, Italy
| | - Valentina Bollati
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milano, Italy
| | - Sara Epis
- Dipartimento di Bioscienze and Pediatric Clinical Research Center (CRC) ‘Fondazione Romeo ed Enrica Invernizzi’, Università degli Studi di Milano, Milano, Italy
| | - Claudio Bandi
- Dipartimento di Bioscienze and Pediatric Clinical Research Center (CRC) ‘Fondazione Romeo ed Enrica Invernizzi’, Università degli Studi di Milano, Milano, Italy
| | - Alessia Lai
- Dipartimento di Scienze Biomediche e Cliniche, Università degli Studi di Milano, Milano, Italy
| | - Gianguglielmo Zehender
- Dipartimento di Scienze Biomediche e Cliniche, Università degli Studi di Milano, Milano, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
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4
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Elko EA, Mead HL, Nelson GA, Zaia JA, Ladner JT, Altin JA. Recurrent SARS-CoV-2 mutations at Spike D796 evade antibodies from pre-Omicron convalescent and vaccinated subjects. Microbiol Spectr 2024; 12:e0329123. [PMID: 38189279 PMCID: PMC10871546 DOI: 10.1128/spectrum.03291-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/03/2023] [Indexed: 01/09/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages of the Omicron variant rapidly became dominant in early 2022 and frequently cause human infections despite vaccination or prior infection with other variants. In addition to antibody-evading mutations in the receptor-binding domain, Omicron features amino acid mutations elsewhere in the Spike protein; however, their effects generally remain ill defined. The Spike D796Y substitution is present in all Omicron sub-variants and occurs at the same site as a mutation (D796H) selected during viral evolution in a chronically infected patient. Here, we map antibody reactivity to a linear epitope in the Spike protein overlapping position 796. We show that antibodies binding this region arise in pre-Omicron SARS-CoV-2 convalescent and vaccinated subjects but that both D796Y and D796H abrogate their binding. These results suggest that D796Y contributes to the fitness of Omicron in hosts with pre-existing immunity to other variants of SARS-CoV-2 by evading antibodies targeting this site.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved substantially through the coronavirus disease 2019 (COVID-19) pandemic: understanding the drivers and consequences of this evolution is essential for projecting the course of the pandemic and developing new countermeasures. Here, we study the immunological effects of a particular mutation present in the Spike protein of all Omicron strains and find that it prevents the efficient binding of a class of antibodies raised by pre-Omicron vaccination and infection. These findings reveal a novel consequence of a poorly understood Omicron mutation and shed light on the drivers and effects of SARS-CoV-2 evolution.
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Affiliation(s)
- Evan A. Elko
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Heather L. Mead
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - Georgia A. Nelson
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - John A. Zaia
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - John A. Altin
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
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5
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Guo C, Wu JY. Pathogen Discovery in the Post-COVID Era. Pathogens 2024; 13:51. [PMID: 38251358 PMCID: PMC10821006 DOI: 10.3390/pathogens13010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/22/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Pathogen discovery plays a crucial role in the fields of infectious diseases, clinical microbiology, and public health. During the past four years, the global response to the COVID-19 pandemic highlighted the importance of early and accurate identification of novel pathogens for effective management and prevention of outbreaks. The post-COVID era has ushered in a new phase of infectious disease research, marked by accelerated advancements in pathogen discovery. This review encapsulates the recent innovations and paradigm shifts that have reshaped the landscape of pathogen discovery in response to the COVID-19 pandemic. Primarily, we summarize the latest technology innovations, applications, and causation proving strategies that enable rapid and accurate pathogen discovery for both acute and historical infections. We also explored the significance and the latest trends and approaches being employed for effective implementation of pathogen discovery from various clinical and environmental samples. Furthermore, we emphasize the collaborative nature of the pandemic response, which has led to the establishment of global networks for pathogen discovery.
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Affiliation(s)
- Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Jian-Yong Wu
- School of Public Health, Xinjiang Medical University, Urumqi 830017, China
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6
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Hoefges A, McIlwain SJ, Erbe AK, Mathers N, Xu A, Melby D, Tetreault K, Le T, Kim K, Pinapati RS, Garcia BH, Patel J, Heck M, Feils AS, Tsarovsky N, Hank JA, Morris ZS, Ong IM, Sondel PM. Antibody landscape of C57BL/6 mice cured of B78 melanoma via a combined radiation and immunocytokine immunotherapy regimen. Front Immunol 2023; 14:1221155. [PMID: 38077403 PMCID: PMC10701281 DOI: 10.3389/fimmu.2023.1221155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Sera of immune mice that were previously cured of their melanoma through a combined radiation and immunocytokine immunotherapy regimen consisting of 12 Gy of external beam radiation and the intratumoral administration of an immunocytokine (anti-GD2 mAb coupled to IL-2) with long-term immunological memory showed strong antibody-binding against melanoma tumor cell lines via flow cytometric analysis. Using a high-density whole-proteome peptide array (of 6.090.593 unique peptides), we assessed potential protein-targets for antibodies found in immune sera. Sera from 6 of these cured mice were analyzed with this high-density, whole-proteome peptide array to determine specific antibody-binding sites and their linear peptide sequence. We identified thousands of peptides that were targeted by these 6 mice and exhibited strong antibody binding only by immune (after successful cure and rechallenge), not naïve (before tumor implantation) sera and developed a robust method to detect these differentially targeted peptides. Confirmatory studies were done to validate these results using 2 separate systems, a peptide ELISA and a smaller scale peptide array utilizing a slightly different technology. To the best of our knowledge, this is the first study of the full set of germline encoded linear peptide-based proteome epitopes that are recognized by immune sera from mice cured of cancer via radio-immunotherapy. We furthermore found that although the generation of B-cell repertoire in immune development is vastly variable, and numerous epitopes are identified uniquely by immune serum from each of these 6 immune mice evaluated, there are still several epitopes and proteins that are commonly recognized by at least half of the mice studied. This suggests that every mouse has a unique set of antibodies produced in response to the curative therapy, creating an individual "fingerprint." Additionally, certain epitopes and proteins stand out as more immunogenic, as they are recognized by multiple mice in the immune group.
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Affiliation(s)
- Anna Hoefges
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Sean J. McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - Amy K. Erbe
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Nicholas Mathers
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Angie Xu
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Drew Melby
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Kaitlin Tetreault
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - Trang Le
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - Kyungmann Kim
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | | | | | - Jigar Patel
- Nimble Therapeutics, Inc., Madison, WI, United States
| | - Mackenzie Heck
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Arika S. Feils
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Noah Tsarovsky
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Jacquelyn Ann Hank
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Zachary Scott Morris
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Irene M. Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
- Department of Obstetrics and Gynecology, University of Wisconsin, Madison, WI, United States
| | - Paul Mark Sondel
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
- Department of Pediatrics, University of Wisconsin, Madison, WI, United States
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7
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Alshamrani S, Mashraqi MM, Alzamami A, Alturki NA, Almasoudi HH, Alshahrani MA, Basharat Z. Mining Autoimmune-Disorder-Linked Molecular-Mimicry Candidates in Clostridioides difficile and Prospects of Mimic-Based Vaccine Design: An In Silico Approach. Microorganisms 2023; 11:2300. [PMID: 37764144 PMCID: PMC10536613 DOI: 10.3390/microorganisms11092300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Molecular mimicry, a phenomenon in which microbial or environmental antigens resemble host antigens, has been proposed as a potential trigger for autoimmune responses. In this study, we employed a bioinformatics approach to investigate the role of molecular mimicry in Clostridioides difficile-caused infections and the induction of autoimmune disorders due to this phenomenon. Comparing proteomes of host and pathogen, we identified 23 proteins that exhibited significant sequence homology and were linked to autoimmune disorders. The disorders included rheumatoid arthritis, psoriasis, Alzheimer's disease, etc., while infections included viral and bacterial infections like HIV, HCV, and tuberculosis. The structure of the homologous proteins was superposed, and RMSD was calculated to find the maximum deviation, while accounting for rigid and flexible regions. Two sequence mimics (antigenic, non-allergenic, and immunogenic) of ≥10 amino acids from these proteins were used to design a vaccine construct to explore the possibility of eliciting an immune response. Docking analysis of the top vaccine construct C2 showed favorable interactions with HLA and TLR-4 receptor, indicating potential efficacy. The B-cell and T-helper cell activity was also simulated, showing promising results for effective immunization against C. difficile infections. This study highlights the potential of C. difficile to trigger autoimmunity through molecular mimicry and vaccine design based on sequence mimics that trigger a defensive response.
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Affiliation(s)
- Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (S.A.); (H.H.A.); (M.A.A.)
| | - Mutaib M. Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (S.A.); (H.H.A.); (M.A.A.)
| | - Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, AlQuwayiyah 11961, Saudi Arabia;
| | - Norah A. Alturki
- Clinical Laboratory Science Department, College of Applied Medical Science, King Saud University, Riyadh 11433, Saudi Arabia;
| | - Hassan H. Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (S.A.); (H.H.A.); (M.A.A.)
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (S.A.); (H.H.A.); (M.A.A.)
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8
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Lundin SB, Kann H, Fulurija A, Andersson B, Nakka SS, Andersson LM, Gisslén M, Harandi AM. A novel precision-serology assay for SARS-CoV-2 infection based on linear B-cell epitopes of Spike protein. Front Immunol 2023; 14:1166924. [PMID: 37251407 PMCID: PMC10213285 DOI: 10.3389/fimmu.2023.1166924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction The COVID-19 pandemic illustrates the need for serology diagnostics with improved accuracy. While conventional serology based on recognition of entire proteins or subunits thereof has made significant contribution to the antibody assessment space, it often suffers from sub-optimal specificity. Epitope-based, high-precision, serology assays hold potential to capture the high specificity and diversity of the immune system, hence circumventing the cross-reactivity with closely related microbial antigens. Methods We herein report mapping of linear IgG and IgA antibody epitopes of the SARS-CoV-2 Spike (S) protein in samples from SARS-CoV-2 exposed individuals along with certified SARS-CoV-2 verification plasma samples using peptide arrays. Results We identified 21 distinct linear epitopes. Importantly, we showed that pre-pandemic serum samples contain IgG antibodies reacting to the majority of protein S epitopes, most likely as a result of prior infection with seasonal coronaviruses. Only 4 of the identified SARS-CoV-2 protein S linear epitopes were specific for SARS-CoV-2 infection. These epitopes are located at positions 278-298 and 550-586, just proximal and distal to the RBD, as well as at position 1134-1156 in the HR2 subdomain and at 1248-1271 in the C-terminal subdomain of protein S. To substantiate the applicability of our findings, we tested three of the high-accuracy protein S epitopes in a Luminex assay, using a certified validation plasma sample set from SARS-CoV-2 infected individuals. The Luminex results were well aligned with the peptide array results, and correlated very well with in-house and commercial immune assays for RBD, S1 and S1/S2 domains of protein S. Conclusion We present a comprehensive mapping of linear B-cell epitopes of SARS-CoV-2 protein S, that identifies peptides suitable for a precision serology assay devoid of cross-reactivity. These results have implications for development of highly specific serology test for exposure to SARS-CoV-2 and other members of the coronaviridae family, as well as for rapid development of serology tests for future emerging pandemic threats.
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Affiliation(s)
- Samuel B. Lundin
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Biotome Pty Ltd, Perth, WA, Australia
- Biotome AB, Kullavik, Sweden
| | - Hanna Kann
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Alma Fulurija
- Biotome Pty Ltd, Perth, WA, Australia
- Biotome AB, Kullavik, Sweden
- School of Biomedical Sciences, Marshall Centre, University of Western Australia, Perth, WA, Australia
| | - Björn Andersson
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sravya S. Nakka
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Lars-Magnus Andersson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden
| | - Ali M. Harandi
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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9
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Lorenz P, Steinbeck F, Mai F, Reisinger EC, Müller-Hilke B. A linear B-cell epitope close to the furin cleavage site within the S1 domain of SARS-CoV-2 Spike protein discriminates the humoral immune response of nucleic acid- and protein-based vaccine cohorts. Front Immunol 2023; 14:1192395. [PMID: 37228598 PMCID: PMC10203960 DOI: 10.3389/fimmu.2023.1192395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
Background Understanding the humoral immune response towards viral infection and vaccination is instrumental in developing therapeutic tools to fight and restrict the viral spread of global pandemics. Of particular interest are the specificity and breadth of antibody reactivity in order to pinpoint immune dominant epitopes that remain immutable in viral variants. Methods We used profiling with peptides derived from the Spike surface glycoprotein of SARS-CoV-2 to compare the antibody reactivity landscapes between patients and different vaccine cohorts. Initial screening was done with peptide microarrays while detailed results and validation data were obtained using peptide ELISA. Results Overall, antibody patterns turned out to be individually distinct. However, plasma samples of patients conspicuously recognized epitopes covering the fusion peptide region and the connector domain of Spike S2. Both regions are evolutionarily conserved and are targets of antibodies that were shown to inhibit viral infection. Among vaccinees, we discovered an invariant Spike region (amino acids 657-671) N-terminal to the furin cleavage site that elicited a significantly stronger antibody response in AZD1222- and BNT162b2- compared to NVX-CoV2373-vaccinees. Conclusions Understanding the exact function of antibodies recognizing amino acid region 657-671 of SARS-CoV-2 Spike glycoprotein and why nucleic acid-based vaccines elicit different responses from protein-based ones will be helpful for future vaccine design.
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Affiliation(s)
- Peter Lorenz
- Institute of Immunology, Rostock University Medical Center, Rostock, Germany
| | - Felix Steinbeck
- Institute of Immunology, Rostock University Medical Center, Rostock, Germany
| | - Franz Mai
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Rostock, Germany
| | - Emil C. Reisinger
- Division of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Brigitte Müller-Hilke
- Institute of Immunology, Rostock University Medical Center, Rostock, Germany
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Rostock, Germany
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10
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Hoefges A, McIlwain SJ, Erbe AK, Mathers N, Xu A, Melby D, Tetreault K, Le T, Kim K, Pinapati RS, Garcia B, Patel J, Heck M, Feils AS, Tsarovsky N, Hank JA, Morris ZS, Ong IM, Sondel PM. Antibody landscape of C57BL/6 mice cured of B78 melanoma via immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529012. [PMID: 36896021 PMCID: PMC9996675 DOI: 10.1101/2023.02.24.529012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Hoefges et al. utilized a whole-proteome peptide array approach to show that C57BL/6 mice develop a large repertoire of antibodies against linear peptide sequences of their melanoma after receiving a curative immunotherapy regimen consisting of radiation and an immunocytokine. Antibodies can play an important role in innate and adaptive immune responses against cancer, and in preventing infectious disease. Flow cytometry analysis of sera of immune mice that were previously cured of their melanoma through a combined immunotherapy regimen with long-term memory showed strong antibody-binding against melanoma tumor cell lines. Using a high-density whole-proteome peptide array, we assessed potential protein-targets for antibodies found in immune sera. Sera from 6 of these cured mice were analyzed with this high-density, whole-proteome peptide array to determine specific antibody-binding sites and their linear peptide sequence. We identified thousands of peptides that were targeted by 2 or more of these 6 mice and exhibited strong antibody binding only by immune, not naive sera. Confirmatory studies were done to validate these results using 2 separate ELISA-based systems. To the best of our knowledge, this is the first study of the "immunome" of protein-based epitopes that are recognized by immune sera from mice cured of cancer via immunotherapy.
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Affiliation(s)
- A Hoefges
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - S J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - A K Erbe
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - N Mathers
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - A Xu
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - D Melby
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - K Tetreault
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - T Le
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - K Kim
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | | | - B Garcia
- Nimble Therapeutics, Inc., Madison, WI, USA
| | - J Patel
- Nimble Therapeutics, Inc., Madison, WI, USA
| | - M Heck
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - A S Feils
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - N Tsarovsky
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - J A Hank
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Z S Morris
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - I M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin, Madison, WI, USA
| | - P M Sondel
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
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11
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Felbinger N, Trudil D, Loomis L, Ascione R, Siragusa G, Haba S, Rastogi S, Mucci A, Claycomb M, Snowberger S, Luke B, Francesconi S, Tsang S. Epitope mapping of SARS-CoV-2 spike protein differentiates the antibody binding activity in vaccinated and infected individuals. FRONTIERS IN VIROLOGY 2023. [DOI: 10.3389/fviro.2023.988109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Previous studies have attempted to characterize the antibody response of individuals to the SARS-CoV-2 virus on a linear peptide level by utilizing peptide microarrays. These studies have helped to identify epitopes that have potential to be used for diagnostic tests to identify infected individuals. The immunological responses of individuals who have received the two most popular vaccines available in the US, the Moderna mRNA-1273 or the Pfizer BNT162b2 mRNA vaccines, have not been characterized. We aimed to identify linear peptides of the SARS-CoV-2 spike protein that elicited high IgG or IgA binding activity and to compare the immunoreactivity of infected individuals to those who received both doses of either vaccine by utilizing peptide microarrays. Our results revealed peptide epitopes of significant IgG binding among recently infected individuals. Some of these peptides are located near variable regions of the receptor binding domains as well as the conserved region in the c-terminal of the spike protein implicated in the high infectivity of SARS-CoV-2. Vaccinated individuals lacked a response to these distinct markers despite the overall antibody binding activity being similar.
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12
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Al-Tamimi M, Tarifi AA, Qaqish A, Abbas MM, Albalawi H, Abu-Raideh J, Salameh M, Khasawneh AI. Immunoglobulins response of COVID-19 patients, COVID-19 vaccine recipients, and random individuals. PLoS One 2023; 18:e0281689. [PMID: 36787317 PMCID: PMC9928079 DOI: 10.1371/journal.pone.0281689] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/29/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND The development of specific immunoglobulins to COVID-19 after natural infection or vaccination has been proposed. The efficacy and dynamics of this response are not clear yet. AIM This study aims to analyze the immunoglobulins response among COVID-19 patients, COVID-19 vaccine recipients and random individuals. METHODS A total of 665 participants including 233 COVID-19 patients, 288 COVID-19 vaccine recipients, and 144 random individuals were investigated for anti-COVID-19 immunoglobulins (IgA, IgG, IgM). RESULTS Among COVID-19 patients, 22.7% had detectable IgA antibodies with a mean of 27.3±57.1 ng/ml, 29.6% had IgM antibodies with a mean of 188.4±666.0 BAU/ml, while 59.2% had IgG antibodies with a mean of 101.7±139.7 BAU/ml. Pfizer-BioNTech vaccine recipients had positive IgG in 99.3% with a mean of 515.5±1143.5 BAU/ml while 85.7% of Sinopharm vaccine recipients had positive IgG with a mean of 170.0±230.0 BAU/ml. Regarding random individuals, 54.9% had positive IgG with a mean of 164.3±214 BAU/ml. The peak IgM response in COVID-19 patients was detected early at 15-22 days, followed by IgG peak at 16-30 days, and IgA peak at 0-60 days. IgM antibodies disappeared at 61-90 days, while IgG and IgA antibodies decreased slowly after the peak and remained detectable up to 300 days. The frequency of IgG positivity among patients was significantly affected by increased age, admission department (inpatient or outpatient), symptoms, need for oxygen therapy, and increased duration between positive COVID-19 RT PCR test and serum sampling (p˂0.05). Positive correlations were noted between different types of immunoglobulins (IgG, IgM, and IgA) among patients. CONCLUSIONS Natural infection and COIVD-19 vaccines provide IgG-mediated immunity. The class, positivity, mean, efficacy, and duration of immunoglobulins response are affected by the mechanism of immunity and host related variables. Random community individuals had detectable COVID-19 IgG at ~55%, far from reaching herd immunity levels.
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Affiliation(s)
- Mohammad Al-Tamimi
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Amjed A. Tarifi
- Department of Specialized Surgery, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Arwa Qaqish
- Department of Biology and Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Manal M. Abbas
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
- Pharmacological and Diagnostic Research Lab, Al-Ahliyya Amman University, Amman, Jordan
| | - Hadeel Albalawi
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Jumanah Abu-Raideh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Muna Salameh
- Department of Basic Medical Sciences, Faculty of Medicine, AlBalqa Applied University, Alsalt, Jordan
| | - Ashraf I. Khasawneh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
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13
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Tornesello AL, Botti C, Micillo A, Labonia F, Arpino S, Isgrò MA, Meola S, Russo L, Cavalcanti E, Sale S, Nicastro C, Atripaldi L, Starita N, Cerasuolo A, Reimer U, Holenya P, Buonaguro L, Buonaguro FM, Tornesello ML. Immune profiling of SARS-CoV-2 epitopes in asymptomatic and symptomatic pediatric and adult patients. J Transl Med 2023; 21:123. [PMID: 36788606 PMCID: PMC9927035 DOI: 10.1186/s12967-023-03963-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND The infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has unpredictable manifestations of coronavirus disease (COVID-19) and variable clinical course with some patients being asymptomatic whereas others experiencing severe respiratory distress, or even death. We aimed to evaluate the immunoglobulin G (IgG) response towards linear peptides on a peptide array containing sequences from SARS-CoV-2, Middle East respiratory syndrome-related coronavirus (MERS) and common-cold coronaviruses 229E, OC43, NL63 and HKU1 antigens, in order to identify immunological indicators of disease outcome in SARS-CoV-2 infected patients. METHODS We included in the study 79 subjects, comprising 19 pediatric and 30 adult SARS-CoV-2 infected patients with increasing disease severity, from mild to critical illness, and 30 uninfected subjects who were vaccinated with one dose of SARS-CoV-2 spike mRNA BNT162b2 vaccine. Serum samples were analyzed by a peptide microarray containing 5828 overlapping 15-mer synthetic peptides corresponding to the full SARS-CoV-2 proteome and selected linear epitopes of spike (S), envelope (E) and membrane (M) glycoproteins as well as nucleoprotein (N) of MERS, SARS and coronaviruses 229E, OC43, NL63 and HKU1 (isolates 1, 2 and 5). RESULTS All patients exhibited high IgG reactivity against the central region and C-terminus peptides of both SARS-CoV-2 N and S proteins. Setting the threshold value for serum reactivity above 25,000 units, 100% and 81% of patients with severe disease, 36% and 29% of subjects with mild symptoms, and 8% and 17% of children younger than 8-years reacted against N and S proteins, respectively. Overall, the total number of peptides in the SARS-CoV-2 proteome targeted by serum samples was much higher in children compared to adults. Notably, we revealed a differential antibody response to SARS-CoV-2 peptides of M protein between adults, mainly reacting against the C-terminus epitopes, and children, who were highly responsive to the N-terminus of M protein. In addition, IgG signals against NS7B, NS8 and ORF10 peptides were found elevated mainly among adults with mild (63%) symptoms. Antibodies towards S and N proteins of other coronaviruses (MERS, 229E, OC43, NL63 and HKU1) were detected in all groups without a significant correlation with SARS-CoV-2 antibody levels. CONCLUSIONS Overall, our results showed that antibodies elicited by specific linear epitopes of SARS-CoV-2 proteome are age dependent and related to COVID-19 clinical severity. Cross-reaction of antibodies to epitopes of other human coronaviruses was evident in all patients with distinct profiles between children and adult patients. Several SARS-CoV-2 peptides identified in this study are of particular interest for the development of vaccines and diagnostic tests to predict the clinical outcome of SARS-CoV-2 infection.
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Affiliation(s)
- Anna Lucia Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", 80131, Naples, Italy.
| | - Chiara Botti
- grid.415247.10000 0004 1756 8081Laboratory of Clinical Pathology, Santobono-Pausilipon Children’s Hospital, 80129 Napoli, Italy
| | - Alberto Micillo
- grid.415247.10000 0004 1756 8081Laboratory of Clinical Pathology, Santobono-Pausilipon Children’s Hospital, 80129 Napoli, Italy
| | - Francesco Labonia
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Sergio Arpino
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Maria Antonietta Isgrò
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Serena Meola
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Luigi Russo
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Ernesta Cavalcanti
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Silvia Sale
- UOC Biochimica Chimica, AORN Ospedali dei Colli P.O. Monaldi, Naples, Italy
| | - Carmine Nicastro
- UOC Biochimica Chimica, AORN Ospedali dei Colli P.O. Monaldi, Naples, Italy
| | - Luigi Atripaldi
- UOC Biochimica Chimica, AORN Ospedali dei Colli P.O. Monaldi, Naples, Italy
| | - Noemy Starita
- grid.508451.d0000 0004 1760 8805Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Andrea Cerasuolo
- grid.508451.d0000 0004 1760 8805Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Ulf Reimer
- grid.435562.3JPT Peptide Technologies GmbH, Berlin, Germany
| | - Pavlo Holenya
- grid.435562.3JPT Peptide Technologies GmbH, Berlin, Germany
| | - Luigi Buonaguro
- grid.508451.d0000 0004 1760 8805Innovative Immunological Models, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, Via Mariano Semmola, 80131 Naples, Italy
| | - Franco M. Buonaguro
- grid.508451.d0000 0004 1760 8805Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Maria Lina Tornesello
- grid.508451.d0000 0004 1760 8805Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
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14
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Vigan-Womas I, Spadoni JL, Poiret T, Taïeb F, Randrianarisaona F, Faye R, Mbow AA, Gaye A, Dia N, Loucoubar C, Ny Mioramalala DJ, Ratovoson R, Randremanana RV, Sall AA, Seydi M, Noirel J, Moreau G, Simon A, Holenya P, Meyniel JP, Zagury JF, Schoenhals M. Linear epitope mapping of the humoral response against SARS-CoV-2 in two independent African cohorts. Sci Rep 2023; 13:782. [PMID: 36646780 PMCID: PMC9842613 DOI: 10.1038/s41598-023-27810-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Profiling of the antibody responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) proteins in African populations is scarce. Here, we performed a detailed IgM and IgG epitope mapping study against 487 peptides covering SARS-CoV-2 wild-type structural proteins. A panel of 41 pre-pandemic and 82 COVID-19 RT-PCR confirmed sera from Madagascar and Senegal were used. We found that the main 36 immunodominant linear epitopes identified were (i) similar in both countries, (ii) distributed mainly in the Spike and the Nucleocapsid proteins, (iii) located outside the RBD and NTD regions where most of the reported SARS-CoV-2 variant mutations occur, and (iv) identical to those reported in European, North American, and Asian studies. Within the severe group, antibody levels were inversely correlated with the viral load. This first antibody epitope mapping study performed in patients from two African countries may be helpful to guide rational peptide-based diagnostic assays or vaccine development.
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Affiliation(s)
- Inès Vigan-Womas
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal.
| | - Jean-Louis Spadoni
- Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris, France
| | - Thomas Poiret
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Fabien Taïeb
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Rokhaya Faye
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Adji Astou Mbow
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Rila Ratovoson
- Institut Pasteur de Madagascar, BP 1274, 101, Antananarivo, Madagascar
| | | | - Amadou Alpha Sall
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa Seydi
- Service des Maladies Infectieuses et Tropicales, Fann University Hospital Center, Dakar, Senegal
| | - Josselin Noirel
- Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris, France
| | - Gabriel Moreau
- Bioinformatics Team, Peptinov, Hôpital Cochin, 27 Rue du Fbg Saint-Jacques, 75014, Paris, France
| | - Arnaud Simon
- Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris, France
| | | | - Jean-Philippe Meyniel
- Bioinformatics Department, ISoft, Parc des Algorithmes, Bâtiment Euclide, Route de l'Orme, 91190, Saint-Aubin, France
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris, France.
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15
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Rak A, Gorbunov N, Kostevich V, Sokolov A, Prokopenko P, Rudenko L, Isakova-Sivak I. Assessment of Immunogenic and Antigenic Properties of Recombinant Nucleocapsid Proteins of Five SARS-CoV-2 Variants in a Mouse Model. Viruses 2023; 15:230. [PMID: 36680269 PMCID: PMC9861333 DOI: 10.3390/v15010230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
COVID-19 cases caused by new variants of highly mutable SARS-CoV-2 continue to be identified worldwide. Effective control of the spread of new variants can be achieved through targeting of conserved viral epitopes. In this regard, the SARS-CoV-2 nucleocapsid (N) protein, which is much more conserved than the evolutionarily influenced spike protein (S), is a suitable antigen. The recombinant N protein can be considered not only as a screening antigen but also as a basis for the development of next-generation COVID-19 vaccines, but little is known about induction of antibodies against the N protein via different SARS-CoV-2 variants. In addition, it is important to understand how antibodies produced against the antigen of one variant can react with the N proteins of other variants. Here, we used recombinant N proteins from five SARS-CoV-2 strains to investigate their immunogenicity and antigenicity in a mouse model and to obtain and characterize a panel of hybridoma-derived monoclonal anti-N antibodies. We also analyzed the variable epitopes of the N protein that are potentially involved in differential recognition of antiviral antibodies. These results will further deepen our knowledge of the cross-reactivity of the humoral immune response in COVID-19.
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Affiliation(s)
- Alexandra Rak
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Nikolay Gorbunov
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Valeria Kostevich
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Alexey Sokolov
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Polina Prokopenko
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Larisa Rudenko
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Irina Isakova-Sivak
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
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16
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Abstract
The diversity of the antigen-specific humoral immune response reflects the interaction of the immune system with pathogens and autoantigens. Peptide microarray analysis opens up new perspectives for the use of antibodies as diagnostic biomarkers and provides unique access to a more differentiated view on humoral responses to disease. This review focuses on the latest applications of peptide microarrays for the serologic medical diagnosis of autoimmunity, infectious diseases (including COVID-19), and cancer.
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Affiliation(s)
- Carsten Grötzinger
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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17
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Hotop SK, Reimering S, Shekhar A, Asgari E, Beutling U, Dahlke C, Fathi A, Khan F, Lütgehetmann M, Ballmann R, Gerstner A, Tegge W, Cicin-Sain L, Bilitewski U, McHardy AC, Brönstrup M. Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2. Emerg Microbes Infect 2022; 11:1037-1048. [PMID: 35320064 PMCID: PMC9009950 DOI: 10.1080/22221751.2022.2057874] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The coronavirus SARS-CoV-2 is the causative agent for the disease COVID-19. To capture the IgA, IgG, and IgM antibody response of patients infected with SARS-CoV-2 at individual epitope resolution, we constructed planar microarrays of 648 overlapping peptides that cover the four major structural proteins S(pike), N(ucleocapsid), M(embrane), and E(nvelope). The arrays were incubated with sera of 67 SARS-CoV-2 positive and 22 negative control samples. Specific responses to SARS-CoV-2 were detectable, and nine peptides were associated with a more severe course of the disease. A random forest model disclosed that antibody binding to 21 peptides, mostly localized in the S protein, was associated with higher neutralization values in cellular anti-SARS-CoV-2 assays. For antibodies addressing the N-terminus of M, or peptides close to the fusion region of S, protective effects were proven by antibody depletion and neutralization assays. The study pinpoints unusual viral binding epitopes that might be suited as vaccine candidates.
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Affiliation(s)
| | - Susanne Reimering
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Aditya Shekhar
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ehsaneddin Asgari
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Partner Site Hannover-Braunschweig, German Centre for Infection Research (DZIF), Germany
| | - Ulrike Beutling
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christine Dahlke
- University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research, Germany
| | - Anahita Fathi
- University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research, Germany
| | - Fawad Khan
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marc Lütgehetmann
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research, Germany.,Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie du Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Andreas Gerstner
- Klinikum Braunschweig, Hals-, Nasen-, Ohrenklinik, Braunschweig, Germany
| | - Werner Tegge
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Luka Cicin-Sain
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Partner Site Hannover-Braunschweig, German Centre for Infection Research (DZIF), Germany
| | | | - Alice C McHardy
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Partner Site Hannover-Braunschweig, German Centre for Infection Research (DZIF), Germany
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Partner Site Hannover-Braunschweig, German Centre for Infection Research (DZIF), Germany.,Biomolecular Drug Research Center (BMWZ), Hannover, Germany
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18
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Wang Q, Ning J, Chen Y, Li B, Shi L, He T, Zhang F, Chen X, Zhai A, Wu C. The BBIBP-CorV inactivated COVID-19 vaccine induces robust and persistent humoral responses to SARS-CoV-2 nucleocapsid, besides spike protein in healthy adults. Front Microbiol 2022; 13:1008420. [PMID: 36406456 PMCID: PMC9672472 DOI: 10.3389/fmicb.2022.1008420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/17/2022] [Indexed: 01/15/2024] Open
Abstract
Vaccination is one of the best ways to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic. Among the various SARS-CoV-2 vaccines approved for use, the BBIBP-CorV inactivated vaccine has been widely used in 93 countries. In order to understand deeply the protective mechanism of inactivated vaccine, which retains all antigenic components of live virus, the analysis of humoral responses triggered by multiple proteins is necessary. In this research, antibody responses were generated with 6 selected recombinant proteins and 68 overlapping peptides that completely covered SARS-CoV-2 nucleocapsid (N) protein in 254 healthy volunteers vaccinated with BBIBP-CorV. As a result, antibody responses to the receptor binding domain (RBD), N, and non-structural protein 8 (NSP8) were induced following immunization by BBIBP-CorV. The antibody responses detected in donors after the 2nd dose vaccination can be maintained for about 6 months. Moreover, specific antibody levels can be restored after the boosting vaccination measured by ELISA. Furthermore, the level of SARS-CoV-2 specific IgG response is independent of age and gender. Moreover, N391-408 was identified as a dominant peptide after vaccination of BBIBP-CorV through peptide screening. Understanding the overview of humoral reactivity of the vaccine will contribute to further research on the protective mechanism of the SARS-CoV-2 inactivated vaccine and provide potential biomarkers for the related application of inactivated vaccine.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Aixia Zhai
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Chao Wu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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19
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Schuettenberg A, Piña A, Metrailer M, Peláez-Sánchez RG, Agudelo-Flórez P, Lopez JÁ, Ryle L, Monroy FP, Altin JA, Ladner JT. Highly Multiplexed Serology for Nonhuman Mammals. Microbiol Spectr 2022; 10:e0287322. [PMID: 36125316 PMCID: PMC9602771 DOI: 10.1128/spectrum.02873-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/06/2022] [Indexed: 01/04/2023] Open
Abstract
Emerging infectious diseases represent a serious and ongoing threat to humans. Most emerging viruses are maintained in stable relationships with other species of animals, and their emergence within the human population results from cross-species transmission. Therefore, if we want to be prepared for the next emerging virus, we need to broadly characterize the diversity and ecology of viruses currently infecting other animals (i.e., the animal virosphere). High-throughput metagenomic sequencing has accelerated the pace of virus discovery. However, molecular assays can detect only active infections and only if virus is present within the sampled fluid or tissue at the time of collection. In contrast, serological assays measure long-lived antibody responses to infections, which can be detected within the blood, regardless of the infected tissues. Therefore, serological assays can provide a complementary approach for understanding the circulation of viruses, and while serological assays have historically been limited in scope, recent advancements allow thousands to hundreds of thousands of antigens to be assessed simultaneously using <1 μL of blood (i.e., highly multiplexed serology). The application of highly multiplexed serology for the characterization of the animal virosphere is dependent on the availability of reagents that can be used to capture or label antibodies of interest. Here, we evaluate the utility of commercial immunoglobulin-binding proteins (protein A and protein G) to enable highly multiplexed serology in 25 species of nonhuman mammals, and we describe a competitive fluorescence-linked immunosorbent assay (FLISA) that can be used as an initial screen for choosing the most appropriate capture protein for a given host species. IMPORTANCE Antibodies are generated in response to infections with viruses and other pathogens, and they help protect against future exposures. Mature antibodies are long lived, are highly specific, and can bind to their protein targets with high affinity. Thus, antibodies can also provide information about an individual's history of viral exposures, which has important applications for understanding the epidemiology and etiology of disease. In recent years, there have been large advances in the available methods for broadly characterizing antibody-binding profiles, but thus far, these have been utilized primarily with human samples only. Here, we demonstrate that commercial antibody-binding reagents can facilitate modern antibody assays for a wide variety of mammalian species, and we describe an inexpensive and fast approach for choosing the best reagent for each animal species. By studying antibody-binding profiles in captive and wild animals, we can better understand the distribution and prevalence of viruses that could spill over into humans.
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Affiliation(s)
- Alexa Schuettenberg
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alejandra Piña
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Morgan Metrailer
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | | | | | - Juan Álvaro Lopez
- Microbiology School, Primary Immunodeficiencies Group, University of Antioquia, Medellín, Colombia
| | - Luke Ryle
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Fernando P. Monroy
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - John A. Altin
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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20
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Kakkanas A, Karamichali E, Koufogeorgou EI, Kotsakis SD, Georgopoulou U, Foka P. Targeting the YXXΦ Motifs of the SARS Coronaviruses 1 and 2 ORF3a Peptides by In Silico Analysis to Predict Novel Virus-Host Interactions. Biomolecules 2022; 12:1052. [PMID: 36008946 PMCID: PMC9405953 DOI: 10.3390/biom12081052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/08/2023] Open
Abstract
The emerging SARS-CoV and SARS-CoV-2 belong to the family of "common cold" RNA coronaviruses, and they are responsible for the 2003 epidemic and the current pandemic with over 6.3 M deaths worldwide. The ORF3a gene is conserved in both viruses and codes for the accessory protein ORF3a, with unclear functions, possibly related to viral virulence and pathogenesis. The tyrosine-based YXXΦ motif (Φ: bulky hydrophobic residue-L/I/M/V/F) was originally discovered to mediate clathrin-dependent endocytosis of membrane-spanning proteins. Many viruses employ the YXXΦ motif to achieve efficient receptor-guided internalisation in host cells, maintain the structural integrity of their capsids and enhance viral replication. Importantly, this motif has been recently identified on the ORF3a proteins of SARS-CoV and SARS-CoV-2. Given that the ORF3a aa sequence is not fully conserved between the two SARS viruses, we aimed to map in silico structural differences and putative sequence-driven alterations of regulatory elements within and adjacently to the YXXΦ motifs that could predict variations in ORF3a functions. Using robust bioinformatics tools, we investigated the presence of relevant post-translational modifications and the YXXΦ motif involvement in protein-protein interactions. Our study suggests that the predicted YXXΦ-related features may confer specific-yet to be discovered-functions to ORF3a proteins, significant to the new virus and related to enhanced propagation, host immune regulation and virulence.
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Affiliation(s)
- Athanassios Kakkanas
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Eirini Karamichali
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Efthymia Ioanna Koufogeorgou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Stathis D. Kotsakis
- Laboratory of Bacteriology, Hellenic Pasteur Institute, 115-21 Athens, Greece;
| | - Urania Georgopoulou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Pelagia Foka
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
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21
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Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins. Viruses 2022; 14:v14071415. [PMID: 35891400 PMCID: PMC9318917 DOI: 10.3390/v14071415] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 01/08/2023] Open
Abstract
Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. The coronavirus SARS-CoV-2 causes COVID-19, a disease curiously resulting in varied symptoms and outcomes, ranging from asymptomatic to fatal. Autoimmunity due to cross-reacting antibodies resulting from molecular mimicry between viral antigens and host proteins may provide an explanation. Thus, we computationally investigated molecular mimicry between SARS-CoV-2 Spike and known epitopes. We discovered molecular mimicry hotspots in Spike and highlight two examples with tentative high autoimmune potential and implications for understanding COVID-19 complications. We show that a TQLPP motif in Spike and thrombopoietin shares similar antibody binding properties. Antibodies cross-reacting with thrombopoietin may induce thrombocytopenia, a condition observed in COVID-19 patients. Another motif, ELDKY, is shared in multiple human proteins, such as PRKG1 involved in platelet activation and calcium regulation, and tropomyosin, which is linked to cardiac disease. Antibodies cross-reacting with PRKG1 and tropomyosin may cause known COVID-19 complications such as blood-clotting disorders and cardiac disease, respectively. Our findings illuminate COVID-19 pathogenesis and highlight the importance of considering autoimmune potential when developing therapeutic interventions to reduce adverse reactions.
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22
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IgG targeting distinct seasonal coronavirus- conserved SARS-CoV-2 spike subdomains correlates with differential COVID-19 disease outcomes. Cell Rep 2022; 39:110904. [PMID: 35617962 PMCID: PMC9108089 DOI: 10.1016/j.celrep.2022.110904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/25/2022] [Accepted: 05/11/2022] [Indexed: 11/20/2022] Open
Abstract
Despite SARS-CoV-2 being a "novel" virus, early detection of anti-spike IgG in severe COVID-19 patients may be caused by the amplification of humoral memory responses against seasonal coronaviruses. Here, we examine this phenomenon by characterizing anti-spike IgG responses in non-hospitalized convalescent individuals across a spectrum of COVID-19 severity. We observe that disease severity positively correlates with anti-spike IgG levels, IgG cross-reactivity against other betacoronaviruses (β-CoVs), and FcγR activation. Analysis of IgG targeting β-CoV-conserved and non-conserved immunodominant epitopes within the SARS-CoV-2 spike protein revealed epitope-specific relationships: IgG targeting the conserved heptad repeat (HR) 2 region significantly correlates with milder disease, while targeting the conserved S2'FP region correlates with more severe disease. Furthermore, a lower HR2-to-S2'FP IgG-binding ratio correlates with greater disease severity, with ICU-hospitalized COVID-19 patients showing the lowest HR2/S2'FP ratios. These findings suggest that HR2/S2'FP IgG profiles may predict disease severity and offer insight into protective versus deleterious humoral recall responses.
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23
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Mishra M, Zahra A, Chauhan LV, Thakkar R, Ng J, Joshi S, Spitzer ED, Marcos LA, Lipkin WI, Mishra N. A Short Series of Case Reports of COVID-19 in Immunocompromised Patients. Viruses 2022; 14:v14050934. [PMID: 35632677 PMCID: PMC9145915 DOI: 10.3390/v14050934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 01/08/2023] Open
Abstract
Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the immune responses elicited by SARS-CoV-2 infection, reinfections, and vaccinations with emerging variants in immunocompromised patients. We analyzed clinical samples that were opportunistically collected from eight immunocompromised individuals for mutations in SARS-CoV-2 genomes, neutralizing antibody (NAb) titers against different SARS-CoV-2 variants, and the identification of immunoreactive epitopes using a high-throughput coronavirus peptide array. The viral genome analysis revealed two SARS-CoV-2 variants (20A from a deceased patient and an Alpha variant from a recovered patient) with an eight amino-acid (aa) deletion within the N-terminal domain (NTD) of the surface glycoprotein. A higher NAb titer was present against the prototypic USA/WA1/2020 strain in vaccinated immunocompromised patients. NAb titer was absent against the Omicron variant and the cultured virus of the 20A variant with eight aa deletions in non-vaccinated patients. Our data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination. Moreover, persistent SARS-CoV-2 infection may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the SARS-CoV-2 surface glycoprotein.
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Affiliation(s)
- Mitali Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Aleena Zahra
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - Lokendra V. Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Shreyas Joshi
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Eric D. Spitzer
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - Luis A. Marcos
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
- Correspondence: (W.I.L.); (N.M.)
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
- Correspondence: (W.I.L.); (N.M.)
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24
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Chen L, Pang P, Qi H, Yan K, Ren Y, Ma M, Cao R, Li H, Hu C, Li Y, Xia J, Lai D, Dong Y, Jiang H, Zhang H, Shan H, Tao S, Liu S. Evaluation of Spike Protein Epitopes by Assessing the Dynamics of Humoral Immune Responses in Moderate COVID-19. Front Immunol 2022; 13:770982. [PMID: 35371042 PMCID: PMC8971992 DOI: 10.3389/fimmu.2022.770982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike protein (S) of SARS-CoV-2 is a major target for diagnosis and vaccine development because of its essential role in viral infection and host immunity. Currently, time-dependent responses of humoral immune system against various S protein epitopes are poorly understood. In this study, enzyme-linked immunosorbent assay (ELISA), peptide microarray, and antibody binding epitope mapping (AbMap) techniques were used to systematically analyze the dynamic changes of humoral immune responses against the S protein in a small cohort of moderate COVID-19 patients who were hospitalized for approximately two months after symptom onset. Recombinant truncated S proteins, target S peptides, and random peptides were used as antigens in the analyses. The assays demonstrated the dynamic IgM- and IgG recognition and reactivity against various S protein epitopes with patient-dependent patterns. Comprehensive analysis of epitope distribution along the spike gene sequence and spatial structure of the homotrimer S protein demonstrated that most IgM- and IgG-reactive peptides were clustered into similar genomic regions and were located at accessible domains. Seven S peptides were generally recognized by IgG antibodies derived from serum samples of all COVID-19 patients. The dynamic immune recognition signals from these seven S peptides were comparable to those of the entire S protein or truncated S1 protein. This suggested that the humoral immune system recognized few conserved S protein epitopes in most COVID-19 patients during the entire duration of humoral immune response after symptom onset. Furthermore, in this cohort, individual patients demonstrated stable immune recognition to certain S protein epitopes throughout their hospitalization period. Therefore, the dynamic characteristics of humoral immune responses to S protein have provided valuable information for accurate diagnosis and immunotherapy of COVID-19 patients.
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Affiliation(s)
- Lingyun Chen
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Pengfei Pang
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Huan Qi
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Keqiang Yan
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Yan Ren
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Mingliang Ma
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Ruyin Cao
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Hua Li
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Jun Xia
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Danyun Lai
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Yuliang Dong
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Hewei Jiang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Hainan Zhang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Hong Shan
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
| | - Siqi Liu
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
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25
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Immunodominant Linear B-Cell Epitopes of SARS-CoV-2 Spike, Identified by Sera from K18-hACE2 Mice Infected with the WT or Variant Viruses. Vaccines (Basel) 2022; 10:vaccines10020251. [PMID: 35214711 PMCID: PMC8875268 DOI: 10.3390/vaccines10020251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 surface spike protein mediates the viral entry into the host cell and represents the primary immunological target of COVID-19 vaccines as well as post-exposure immunotherapy. Establishment of the highly immunogenic B-cell epitope profile of SARS-CoV-2 proteins in general, and that of the spike protein in particular, may contribute to the development of sensitive diagnostic tools and identification of vaccine` candidate targets. In the current study, the anti-viral antibody response in transgenic K18-hACE-2 mice was examined by implementing an immunodominant epitope mapping approach of the SARS-CoV-2 spike. Serum samples for probing an epitope array covering the entire spike protein were collected from mice following infection with the original SARS-CoV-2 strain as well as the B.1.1.7 Alpha and B.1.351 Beta genetic variants of concern. The analysis resulted in distinction of six linear epitopes common to the humoral response against all virus variants inspected at a frequency of more than 20% of the serum samples. Finally, the universality of the response was probed by cross-protective in vitro experiments using plaque-reducing neutralization tests. The data presented here has important implications for prediction of the efficacy of immune countermeasures against emerging SARS-CoV-2 variants.
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26
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Wang Z, Morrissey JJ, Liu L, Wang Y, Zhou Q, Naik RR, Singamaneni S. Plasmonically Enhanced Ultrasensitive Epitope-Specific Serologic Assay for COVID-19. Anal Chem 2022; 94:909-917. [PMID: 34935364 PMCID: PMC8782240 DOI: 10.1021/acs.analchem.1c03676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly spread and resulted in the global pandemic of COVID-19. Although IgM/IgG serology assay has been widely used, with the entire spike or nucleocapsid antigens, they only indicate the presence or absence of antibodies against these proteins but are not specific to the neutralization antibodies, therefore providing only generic information about infection stage and possible future immune protection. Novel technologies enabling easy-to-use and sensitive detection of multiple specific antibodies simultaneously will facilitate precise diagnosis of infection stage, prediction of clinical outcomes, and evaluation of future immune protection upon viral exposure or vaccination. Here, we demonstrate a rapid and ultrasensitive quantification method for epitope-specific antibodies, including different isotypes and subclasses, in a multiplexed manner. Using an ultrabright fluorescent nanolabel, plasmonic-fluor, this novel assay can be completed in 20 min and more importantly, the limit of detection of the plasmon-enhanced immunoassay for SARS-CoV-2 antibodies is as much as 100-fold lower compared to the assays relying on enzymatic amplification of colorimetric signals. Using convalescent patient plasma, we demonstrate that this biodetection method reveals the patient-to-patient variability in immune response as evidenced by the variations in whole protein and epitope-specific antibodies. This cost-effective, rapid, and ultrasensitive plasmonically enhanced multiplexed epitope-specific serological assay has the potential to be broadly employed in the detection of specific antibodies, which may benefit the advanced epidemiology studies and enable improvement of the clinical outcomes and prediction of the future protection against the SARS-CoV-2.
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Affiliation(s)
- Zheyu Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Jeremiah J. Morrissey
- Department of Anesthesiology, Division of Clinical and Translational Research, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lin Liu
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Yixuan Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Qingjun Zhou
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Rajesh R. Naik
- 711 Human Performance Wing, Air Force Research Laboratory, Wright Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
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27
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Francino-Urdaniz IM, Whitehead TA. An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies. RSC Chem Biol 2021; 2:1580-1589. [PMID: 34977572 PMCID: PMC8637828 DOI: 10.1039/d1cb00169h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/25/2021] [Indexed: 12/20/2022] Open
Abstract
This mini-review presents a critical survey of techniques used for epitope mapping on the SARS-CoV-2 Spike protein. The sequence and structures for common neutralizing and non-neutralizing epitopes on the Spike protein are described as determined by X-ray crystallography, electron microscopy and linear peptide epitope mapping, among other methods. An additional focus of this mini-review is an analytical appraisal of different deep mutational scanning workflows for conformational epitope mapping and identification of mutants on the Spike protein which escape antibody neutralization. Such a focus is necessary as a critical review of deep mutational scanning for conformational epitope mapping has not been published. A perspective is presented on the use of different epitope determination methods for development of broadly potent antibody therapies and vaccines against SARS-CoV-2.
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Affiliation(s)
- Irene M Francino-Urdaniz
- Department of Chemical and Biological Engineering, University of Colorado JSC Biotechnology Building, 3415 Colorado Avenue Boulder CO 80305 USA +1 303-735-2145
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado JSC Biotechnology Building, 3415 Colorado Avenue Boulder CO 80305 USA +1 303-735-2145
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28
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Hein S, Benz NI, Eisert J, Herrlein ML, Oberle D, Dreher M, Stingl JC, Hildt C, Hildt E. Comirnaty-Elicited and Convalescent Sera Recognize Different Spike Epitopes. Vaccines (Basel) 2021; 9:1419. [PMID: 34960165 PMCID: PMC8708883 DOI: 10.3390/vaccines9121419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/09/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022] Open
Abstract
Many of the approved SARS-CoV-2 vaccines are based on a stabilized variant of the spike protein. This raises the question of whether the immune response against the stabilized spike is identical to the immune response that is elicited by the native spike in the case of a SARS-CoV-2 infection. Using a peptide array-based approach, we analysed the binding of antibodies from Comirnaty-elicited, convalescent, and control sera to the peptides covering the spike protein. A total of 37 linear epitopes were identified. A total of 26 of these epitopes were almost exclusively recognized by the convalescent sera. Mapping these epitopes to the spike structures revealed that most of these 26 epitopes are masked in the pre-fusion structure. In particular, in the conserved central helix, three epitopes that are only exposed in the post-fusion conformation were identified. This indicates a higher spike-specific antibody diversity in convalescent sera. These differences could be relevant for the breadth of spike-specific immune response.
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Affiliation(s)
- Sascha Hein
- Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich Street 51–59, D-63225 Langen, Germany; (N.I.B.); (J.E.); (M.-L.H.)
| | - Nuka Ivalu Benz
- Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich Street 51–59, D-63225 Langen, Germany; (N.I.B.); (J.E.); (M.-L.H.)
| | - Jonathan Eisert
- Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich Street 51–59, D-63225 Langen, Germany; (N.I.B.); (J.E.); (M.-L.H.)
| | - Marie-Luise Herrlein
- Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich Street 51–59, D-63225 Langen, Germany; (N.I.B.); (J.E.); (M.-L.H.)
| | - Doris Oberle
- Division of Pharmacovigilance, Paul-Ehrlich-Institut, Paul-Ehrlich Street 51–59, D-63325 Langen, Germany;
| | - Michael Dreher
- Department of Pneumology and Intensive Care Medicine, RWTH Aachen University Hospital Aachen, Pauwelsstraße 30, D-52074 Aachen, Germany;
| | - Julia C. Stingl
- Institute of Clinical Pharmacology, RWTH Aachen University Hospital Aachen, Pauwelsstraße 30, D-52074 Aachen, Germany;
| | - Christoph Hildt
- Main-Kinzig-Kliniken, Herzbachweg 14, D-63571 Gelnhausen, Germany;
| | - Eberhard Hildt
- Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich Street 51–59, D-63225 Langen, Germany; (N.I.B.); (J.E.); (M.-L.H.)
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29
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Laha S, Chatterjee R. Temporal variations of country-specific mutational profile of SARS-CoV-2: effect on vaccine efficacy. Future Virol 2021; 0. [PMID: 34824595 PMCID: PMC8603786 DOI: 10.2217/fvl-2021-0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022]
Abstract
Aim: In order to curb the transmission of SARS-CoV-2, nation-wide travel restrictions at different levels were implemented in different countries. Country-specific mutational profile may exist and have an impact on vaccine efficacy. Materials & methods: We identified nonsynonymous mutations in approximately 215,000 SARS-CoV-2 sequences during the 1st year of the pandemic in 35 countries. Mutational profiles on a bimonthly basis were traced over time. We also examined the mutations that overlapped with the spike protein vaccine epitopes. Results: Several new mutations emerged over time and were dominating in specific countries. Many nonsynonymous mutations were within multiple spike protein epitopes that might impact the vaccine efficacy. Conclusion: Our study advocates requirement of active monitoring of country-specific mutations and vaccine efficacies in respective countries.
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Affiliation(s)
- Sayantan Laha
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
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30
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Sherman AC, Smith T, Zhu Y, Taibl K, Howard-Anderson J, Landay T, Pisanic N, Kleinhenz J, Simon TW, Espinoza D, Edupuganti N, Hammond S, Rouphael N, Shen H, Fairley JK, Edupuganti S, Cardona-Ospina JA, Rodriguez-Morales AJ, Premkumar L, Wrammert J, Tarleton R, Fridkin S, Heaney CD, Scherer EM, Collins MH. Application of SARS-CoV-2 Serology to Address Public Health Priorities. Front Public Health 2021; 9:744535. [PMID: 34888282 PMCID: PMC8650110 DOI: 10.3389/fpubh.2021.744535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Antibodies against SARS-CoV-2 can be detected by various testing platforms, but a detailed understanding of assay performance is critical. Methods: We developed and validated a simple enzyme-linked immunosorbent assay (ELISA) to detect IgG binding to the receptor-binding domain (RBD) of SARS-CoV-2, which was then applied for surveillance. ELISA results were compared to a set of complimentary serologic assays using a large panel of clinical research samples. Results: The RBD ELISA exhibited robust performance in ROC curve analysis (AUC> 0.99; Se = 89%, Sp = 99.3%). Antibodies were detected in 23/353 (6.5%) healthcare workers, 6/9 RT-PCR-confirmed mild COVID-19 cases, and 0/30 non-COVID-19 cases from an ambulatory site. RBD ELISA showed a positive correlation with neutralizing activity (p = <0.0001, R2 = 0.26). Conclusions: We applied a validated SARS-CoV-2-specific IgG ELISA in multiple contexts and performed orthogonal testing on samples. This study demonstrates the utility of a simple serologic assay for detecting prior SARS-CoV-2 infection, particularly as a tool for efficiently testing large numbers of samples as in population surveillance. Our work also highlights that precise understanding of SARS-CoV-2 infection and immunity at the individual level, particularly with wide availability of vaccination, may be improved by orthogonal testing and/or more complex assays such as multiplex bead assays.
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Affiliation(s)
- Amy C. Sherman
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, United States
| | - Teresa Smith
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Yerun Zhu
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Kaitlin Taibl
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | | | - Taylor Landay
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Nora Pisanic
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Jennifer Kleinhenz
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
- Division of Infectious, Diseases, Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - Trevor W. Simon
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Daniel Espinoza
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Neena Edupuganti
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Skyler Hammond
- Department of Anthropology, Emory University, Atlanta, GA, United States
| | - Nadine Rouphael
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Huifeng Shen
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Jessica K. Fairley
- Division of Infectious Diseases, Emory University, Atlanta, GA, United States
| | - Srilatha Edupuganti
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Jaime A. Cardona-Ospina
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Colombia
- Emerging Infectious Diseases and Tropical Medicine Research Group, Sci-Help, Pereira, Colombia
| | - Alfonso J. Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Colombia
- Master of Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima, Peru
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Jens Wrammert
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Rick Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Scott Fridkin
- Division of Infectious Diseases, Emory University, Atlanta, GA, United States
- Georgia Emerging Infections Program, Atlanta, GA, United States
| | | | - Erin M. Scherer
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Matthew H. Collins
- Division of Infectious Diseases, The Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
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31
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Wang J, Guo C, Cai L, Liao C, Yi H, Li Q, Hu H, Deng Q, Lu Y, Guo Z, Chen Z, Lu J. Pre-Existing Cross-Reactive Antibody Responses Do Not Significantly Impact Inactivated COVID-19 Vaccine-Induced Neutralization. Front Immunol 2021; 12:772511. [PMID: 34868035 PMCID: PMC8640209 DOI: 10.3389/fimmu.2021.772511] [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: 09/09/2021] [Accepted: 11/03/2021] [Indexed: 11/24/2022] Open
Abstract
Recent exposure to seasonal coronaviruses (sCoVs) may stimulate cross-reactive antibody responses against severe acute respiratory syndrome CoV 2 (SARS-CoV-2). However, previous studies have produced divergent results regarding protective or damaging immunity induced by prior sCoV exposure. It remains unknown whether pre-existing humoral immunity plays a role in vaccine-induced neutralization and antibody responses. In this study, we collected 36 paired sera samples from 36 healthy volunteers before and after immunization with inactivated whole-virion SARS-CoV-2 vaccines for COVID-19, and analyzed the distribution and intensity of pre-existing antibody responses at the epitope level pre-vaccination as well as the relationship between pre-existing sCoV immunity and vaccine-induced neutralization. We observed large amounts of pre-existing cross-reactive antibodies in the conserved regions among sCoVs, especially the S2 subunit. Excep t for a few peptides, the IgG and IgM fluorescence intensities against S, M and N peptides did not differ significantly between pre-vaccination and post-vaccination sera of vaccinees who developed a neutralization inhibition rate (%inhibition) <40 and %inhibition ≥40 after two doses of the COVID-19 vaccine. Participants with strong and weak pre-existing cross-reactive antibodies (strong pre-CRA; weak pre-CRA) had similar %inhibition pre-vaccination (10.9% ± 2.9% vs. 12.0% ± 2.2%, P=0.990) and post-vaccination (43.8% ± 25.1% vs. 44.6% ± 21.5%, P=0.997). Overall, the strong pre-CRA group did not show a significantly greater increase in antibody responses to the S protein linear peptides post-vaccination compared with the weak pre-CRA group. Therefore, we found no evidence for a significant impact of pre-existing antibody responses on inactivated vaccine-induced neutralization and antibody responses. Our research provides an important basis for inactivated SARS-CoV-2 vaccine use in the context of high sCoV seroprevalence.
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Affiliation(s)
- Jin Wang
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Lin Cai
- Futian District Center for Disease Control and Prevention, Shenzhen, China
| | - Conghui Liao
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Huaimin Yi
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Qianlin Li
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Huan Hu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Qiang Deng
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Yuying Lu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Zhongmin Guo
- Laboratory Animal Center, Sun Yat-sen University, Guangzhou, China
| | - Zeliang Chen
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Jiahai Lu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou, China
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32
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Wolfe M, Webb S, Chushak Y, Krabacher R, Liu Y, Swami N, Harbaugh S, Chávez J. A high-throughput pipeline for design and selection of peptides targeting the SARS-Cov-2 Spike protein. Sci Rep 2021; 11:21768. [PMID: 34741099 PMCID: PMC8571316 DOI: 10.1038/s41598-021-01225-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/22/2021] [Indexed: 12/23/2022] Open
Abstract
Rapid design, screening, and characterization of biorecognition elements (BREs) is essential for the development of diagnostic tests and antiviral therapeutics needed to combat the spread of viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To address this need, we developed a high-throughput pipeline combining in silico design of a peptide library specific for SARS-CoV-2 spike (S) protein and microarray screening to identify binding sequences. Our optimized microarray platform allowed the simultaneous screening of ~ 2.5 k peptides and rapid identification of binding sequences resulting in selection of four peptides with nanomolar affinity to the SARS-CoV-2 S protein. Finally, we demonstrated the successful integration of one of the top peptides into an electrochemical sensor with a clinically relevant limit of detection for S protein in spiked saliva. Our results demonstrate the utility of this novel pipeline for the selection of peptide BREs in response to the SARS-CoV-2 pandemic, and the broader application of such a platform in response to future viral threats.
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Affiliation(s)
- Monica Wolfe
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
- UES, Inc., Dayton, OH, 45432, USA
| | - Sean Webb
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
- UES, Inc., Dayton, OH, 45432, USA
| | - Yaroslav Chushak
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
- Henry M. Jackson Foundation, Dayton, OH, 45433, USA
| | - Rachel Krabacher
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
- Materials & Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Yi Liu
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, 22904, USA
| | - Nathan Swami
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, 22904, USA
| | - Svetlana Harbaugh
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Jorge Chávez
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA.
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33
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Polyiam K, Phoolcharoen W, Butkhot N, Srisaowakarn C, Thitithanyanont A, Auewarakul P, Hoonsuwan T, Ruengjitchatchawalya M, Mekvichitsaeng P, Roshorm YM. Immunodominant linear B cell epitopes in the spike and membrane proteins of SARS-CoV-2 identified by immunoinformatics prediction and immunoassay. Sci Rep 2021; 11:20383. [PMID: 34650130 PMCID: PMC8516869 DOI: 10.1038/s41598-021-99642-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/29/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 continues to infect an ever-expanding number of people, resulting in an increase in the number of deaths globally. With the emergence of new variants, there is a corresponding decrease in the currently available vaccine efficacy, highlighting the need for greater insights into the viral epitope profile for both vaccine design and assessment. In this study, three immunodominant linear B cell epitopes in the SARS-CoV-2 spike receptor-binding domain (RBD) were identified by immunoinformatics prediction, and confirmed by ELISA with sera from Macaca fascicularis vaccinated with a SARS-CoV-2 RBD subunit vaccine. Further immunoinformatics analyses of these three epitopes gave rise to a method of linear B cell epitope prediction and selection. B cell epitopes in the spike (S), membrane (M), and envelope (E) proteins were subsequently predicted and confirmed using convalescent sera from COVID-19 infected patients. Immunodominant epitopes were identified in three regions of the S2 domain, one region at the S1/S2 cleavage site and one region at the C-terminus of the M protein. Epitope mapping revealed that most of the amino acid changes found in variants of concern are located within B cell epitopes in the NTD, RBD, and S1/S2 cleavage site. This work provides insights into B cell epitopes of SARS-CoV-2 as well as immunoinformatics methods for B cell epitope prediction, which will improve and enhance SARS-CoV-2 vaccine development against emergent variants.
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Affiliation(s)
- Kanokporn Polyiam
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Waranyoo Phoolcharoen
- Research Unit for Plant-Produced Pharmaceuticals and Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Namphueng Butkhot
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Chanya Srisaowakarn
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tawatchai Hoonsuwan
- B.F. Feed Company Limited, Prachachuen Road, Thung Song Hong, Lak Si, Bangkok, Thailand
| | - Marasri Ruengjitchatchawalya
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Phenjun Mekvichitsaeng
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Yaowaluck Maprang Roshorm
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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34
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Loyal L, Braun J, Henze L, Kruse B, Dingeldey M, Reimer U, Kern F, Schwarz T, Mangold M, Unger C, Dörfler F, Kadler S, Rosowski J, Gürcan K, Uyar-Aydin Z, Frentsch M, Kurth F, Schnatbaum K, Eckey M, Hippenstiel S, Hocke A, Müller MA, Sawitzki B, Miltenyi S, Paul F, Mall MA, Wenschuh H, Voigt S, Drosten C, Lauster R, Lachman N, Sander LE, Corman VM, Röhmel J, Meyer-Arndt L, Thiel A, Giesecke-Thiel C. Cross-reactive CD4 + T cells enhance SARS-CoV-2 immune responses upon infection and vaccination. Science 2021; 374:eabh1823. [PMID: 34465633 PMCID: PMC10026850 DOI: 10.1126/science.abh1823] [Citation(s) in RCA: 182] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The functional relevance of preexisting cross-immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a subject of intense debate. Here, we show that human endemic coronavirus (HCoV)–reactive and SARS-CoV-2–cross-reactive CD4+ T cells are ubiquitous but decrease with age. We identified a universal immunodominant coronavirus-specific spike peptide (S816-830) and demonstrate that preexisting spike- and S816-830–reactive T cells were recruited into immune responses to SARS-CoV-2 infection and their frequency correlated with anti–SARS-CoV-2-S1-IgG antibodies. Spike–cross-reactive T cells were also activated after primary BNT162b2 COVID-19 messenger RNA vaccination and displayed kinetics similar to those of secondary immune responses. Our results highlight the functional contribution of preexisting spike–cross-reactive T cells in SARS-CoV-2 infection and vaccination. Cross-reactive immunity may account for the unexpectedly rapid induction of immunity after primary SARS-CoV-2 immunization and the high rate of asymptomatic or mild COVID-19 disease courses.
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Affiliation(s)
- Lucie Loyal
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Julian Braun
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Larissa Henze
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Beate Kruse
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Manuela Dingeldey
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Florian Kern
- JPT Peptide Technologies GmbH, Berlin, Germany
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Tatjana Schwarz
- Institute of Virology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Maike Mangold
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Clara Unger
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Friederike Dörfler
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Shirin Kadler
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Medical Biotechnology, Institute for Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Jennifer Rosowski
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Medical Biotechnology, Institute for Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Kübrah Gürcan
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Medical Biotechnology, Institute for Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Zehra Uyar-Aydin
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Medical Biotechnology, Institute for Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Marco Frentsch
- Department of Hematology, Oncology and Tumor Immunology, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Therapy-Induced Remodeling in Immuno-Oncology, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, and Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Maren Eckey
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Marcel A. Müller
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Virology, Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Partner Site Charité, Berlin, Germany
| | - Birgit Sawitzki
- Institute of Medical Immunology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | | | - Friedemann Paul
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine, and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Clinical Neuroimmunology, NeuroCure Clinical Research Center, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner, Berlin, Germany
| | | | - Sebastian Voigt
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
- Institute for Virology, Universitätsklinikum Essen, Essen, Germany
| | - Christian Drosten
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Virology, Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Partner Site Charité, Berlin, Germany
| | - Roland Lauster
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Medical Biotechnology, Institute for Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Nils Lachman
- Institute for Transfusion Medicine, Tissue Typing Laboratory, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Leif-Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Victor M. Corman
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Virology, Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Partner Site Charité, Berlin, Germany
| | - Jobst Röhmel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Lil Meyer-Arndt
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine, and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Clinical Neuroimmunology, NeuroCure Clinical Research Center, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Thiel
- Si-M/“Der Simulierte Mensch,” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Corresponding author. (A.T.); (C.G.-T.)
| | - Claudia Giesecke-Thiel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Corresponding author. (A.T.); (C.G.-T.)
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35
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Cheng L, Zhang X, Chen Y, Wang D, Zhang D, Yan S, Wang H, Xiao M, Liang T, Li H, Xu M, Hou X, Dai J, Wu X, Li M, Lu M, Wu D, Tian R, Zhao J, Zhang Y, Cao W, Wang J, Yan X, Zhou X, Liu Z, Xu Y, He F, Li Y, Yu X, Zhang S. Dynamic landscape mapping of humoral immunity to SARS-CoV-2 identifies non-structural protein antibodies associated with the survival of critical COVID-19 patients. Signal Transduct Target Ther 2021; 6:304. [PMID: 34404759 PMCID: PMC8368053 DOI: 10.1038/s41392-021-00718-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/19/2021] [Accepted: 08/01/2021] [Indexed: 12/12/2022] Open
Abstract
A comprehensive analysis of the humoral immune response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential in understanding COVID-19 pathogenesis and developing antibody-based diagnostics and therapy. In this work, we performed a longitudinal analysis of antibody responses to SARS-CoV-2 proteins in 104 serum samples from 49 critical COVID-19 patients using a peptide-based SARS-CoV-2 proteome microarray. Our data show that the binding epitopes of IgM and IgG antibodies differ across SARS-CoV-2 proteins and even within the same protein. Moreover, most IgM and IgG epitopes are located within nonstructural proteins (nsps), which are critical in inactivating the host's innate immune response and enabling SARS-CoV-2 replication, transcription, and polyprotein processing. IgM antibodies are associated with a good prognosis and target nsp3 and nsp5 proteases, whereas IgG antibodies are associated with high mortality and target structural proteins (Nucleocapsid, Spike, ORF3a). The epitopes targeted by antibodies in patients with a high mortality rate were further validated using an independent serum cohort (n = 56) and using global correlation mapping analysis with the clinical variables that are associated with COVID-19 severity. Our data provide fundamental insight into humoral immunity during SARS-CoV-2 infection. SARS-CoV-2 immunogenic epitopes identified in this work could also help direct antibody-based COVID-19 treatment and triage patients.
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Affiliation(s)
- Linlin Cheng
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Yu Chen
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Dan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Dong Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Songxin Yan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Te Liang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Haolong Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Meng Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Xin Hou
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jiayu Dai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Xian Wu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Mingyuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Minya Lu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Dong Wu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ran Tian
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jing Zhao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yan Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei Cao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jinglan Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaowei Yan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiang Zhou
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Zhengyin Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China.
| | - Yongzhe Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China.
| | - Shuyang Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
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36
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Heffron AS, McIlwain SJ, Amjadi MF, Baker DA, Khullar S, Armbrust T, Halfmann PJ, Kawaoka Y, Sethi AK, Palmenberg AC, Shelef MA, O’Connor DH, Ong IM. The landscape of antibody binding in SARS-CoV-2 infection. PLoS Biol 2021; 19:e3001265. [PMID: 34143766 PMCID: PMC8245122 DOI: 10.1371/journal.pbio.3001265] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/30/2021] [Accepted: 05/06/2021] [Indexed: 02/08/2023] Open
Abstract
The search for potential antibody-based diagnostics, vaccines, and therapeutics for pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has focused almost exclusively on the spike (S) and nucleocapsid (N) proteins. Coronavirus membrane (M), ORF3a, and ORF8 proteins are humoral immunogens in other coronaviruses (CoVs) but remain largely uninvestigated for SARS-CoV-2. Here, we use ultradense peptide microarray mapping to show that SARS-CoV-2 infection induces robust antibody responses to epitopes throughout the SARS-CoV-2 proteome, particularly in M, in which 1 epitope achieved excellent diagnostic accuracy. We map 79 B cell epitopes throughout the SARS-CoV-2 proteome and demonstrate that antibodies that develop in response to SARS-CoV-2 infection bind homologous peptide sequences in the 6 other known human CoVs. We also confirm reactivity against 4 of our top-ranking epitopes by enzyme-linked immunosorbent assay (ELISA). Illness severity correlated with increased reactivity to 9 SARS-CoV-2 epitopes in S, M, N, and ORF3a in our population. Our results demonstrate previously unknown, highly reactive B cell epitopes throughout the full proteome of SARS-CoV-2 and other CoV proteins.
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Affiliation(s)
- Anna S. Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sean J. McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Maya F. Amjadi
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David A. Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Tammy Armbrust
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter J. Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ajay K. Sethi
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ann C. Palmenberg
- Department of Biochemistry, Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Miriam A. Shelef
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Irene M. Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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37
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Cimolai N. Passive Immunity Should and Will Work for COVID-19 for Some Patients. Clin Hematol Int 2021; 3:47-68. [PMID: 34595467 PMCID: PMC8432400 DOI: 10.2991/chi.k.210328.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
In the absence of effective antiviral chemotherapy and still in the context of emerging vaccines for severe acute respiratory syndrome-CoV-2 infections, passive immunotherapy remains a key treatment and possible prevention strategy. What might initially be conceived as a simplified donor-recipient process, the intricacies of donor plasma, IV immunoglobulins, and monoclonal antibody modality applications are becoming more apparent. Key targets of such treatment have largely focused on virus neutralization and the specific viral components of the attachment Spike protein and its constituents (e.g., receptor binding domain, N-terminal domain). The cumulative laboratory and clinical experience suggests that beneficial protective and treatment outcomes are possible. Both a dose- and a time-dependency emerge. Lesser understood are the concepts of bioavailability and distribution. Apart from direct antigen binding from protective immunoglobulins, antibody effector functions have potential roles in outcome. In attempting to mimic the natural but variable response to infection or vaccination, a strong functional polyclonal approach attracts the potential benefits of attacking antigen diversity, high antibody avidity, antibody persistence, and protection against escape viral mutation. The availability and ease of administration for any passive immunotherapy product must be considered in the current climate of need. There is never a perfect product, but yet there is considerable room for improving patient outcomes. Given the variability of human genetics, immunity, and disease, and given the nuances of the virus and its potential for change, passive immunotherapy can be developed that will be effective for some but not all patients. An understanding of such patient variability and limitations is just as important as the understanding of the direct interactions between immunotherapy and virus.
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Affiliation(s)
- Nevio Cimolai
- Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Children’s and Women’s Health Centre of British Columbia, 4480 Oak Street, Vancouver, BC, Canada V6H 3V4
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