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Stafford P, Sherma ND, Peterson M, Diehnelt CW. A Peptide Microarray Platform Approach for Discovery of Immunodominant Antibody Epitopes. Anal Chem 2024; 96:14524-14530. [PMID: 39207871 DOI: 10.1021/acs.analchem.4c02806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Immunodominant epitope discovery platforms play an important role in identifying novel biomarkers for effective immunotherapies and diagnostics. Methods to analyze the B-cell repertoire have been improved both experimentally and computationally. We developed an enhanced peptide microarray platform to discover and subsequently screen immunodominant epitopes. We utilized SARS-Cov-2 IgG positive and negative samples as a proof-of-concept to demonstrate the power of these improved peptide microarrays. The method identified significantly discriminant epitopes that classify positive and negative samples with good performance both as single peptides and in combination. We provide the assay conditions and parameters that justify the use of peptide microarrays in the selection of high-affinity epitopes, and we directly compare peptide performance against proteins. The results suggest that this platform can be used to confidently identify immunodominant antiviral epitopes while also serving as a useful tool for high-volume screening.
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Affiliation(s)
- Phillip Stafford
- Robust Diagnostics, LLC, Chandler, Arizona 85226, United States of America
| | - Nisha D Sherma
- Robust Diagnostics, LLC, Chandler, Arizona 85226, United States of America
| | - Milene Peterson
- Robust Diagnostics, LLC, Chandler, Arizona 85226, United States of America
| | - Chris W Diehnelt
- Robust Diagnostics, LLC, Chandler, Arizona 85226, United States of America
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Davis SK, Jia F, Wright QG, Islam MT, Bean A, Layton D, Williams DT, Lynch SE. Defining correlates of protection for mammalian livestock vaccines against high-priority viral diseases. Front Immunol 2024; 15:1397780. [PMID: 39100679 PMCID: PMC11294087 DOI: 10.3389/fimmu.2024.1397780] [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: 03/08/2024] [Accepted: 06/28/2024] [Indexed: 08/06/2024] Open
Abstract
Enhancing livestock biosecurity is critical to safeguard the livelihoods of farmers, global and local economies, and food security. Vaccination is fundamental to the control and prevention of exotic and endemic high-priority infectious livestock diseases. Successful implementation of vaccination in a biosecurity plan is underpinned by a strong understanding of correlates of protection-those elements of the immune response that can reliably predict the level of protection from viral challenge. While correlates of protection have been successfully characterized for many human viral vaccines, for many high-priority livestock viral diseases, including African swine fever and foot and mouth disease, they remain largely uncharacterized. Current literature provides insights into potential correlates of protection that should be assessed during vaccine development for these high-priority mammalian livestock viral diseases. Establishment of correlates of protection for biosecurity purposes enables immune surveillance, rationale for vaccine development, and successful implementation of livestock vaccines as part of a biosecurity strategy.
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Affiliation(s)
- Samantha K. Davis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Centre for Disease Preparedness, Geelong, VIC, Australia
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Ramos FF, Pereira IAG, Cardoso MM, Bandeira RS, Lage DP, Scussel R, Anastacio RS, Freire VG, Melo MFN, Oliveira-da-Silva JA, Martins VT, Tavares GSV, Vale DL, Freitas CS, Chaves AT, Caporali JFM, Vassallo PF, Ravetti CG, Nobre V, Fonseca FG, Christodoulides M, Machado-de-Ávila RA, Coelho EAF, Ludolf F. B-Cell Epitopes-Based Chimeric Protein from SARS-CoV-2 N and S Proteins Is Recognized by Specific Antibodies in Serum and Urine Samples from Patients. Viruses 2023; 15:1877. [PMID: 37766284 PMCID: PMC10538162 DOI: 10.3390/v15091877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The impact of the COVID-19 pandemic caused by the SARS-CoV-2 virus underscored the crucial role of laboratorial tests as a strategy to control the disease, mainly to indicate the presence of specific antibodies in human samples from infected patients. Therefore, suitable recombinant antigens are relevant for the development of reliable tests, and so far, single recombinant proteins have been used. In this context, B-cell epitopes-based chimeric proteins can be an alternative to obtain tests with high accuracy through easier and cheaper production. The present study used bioinformatics tools to select specific B-cell epitopes from the spike (S) and the nucleocapsid (N) proteins from the SARS-CoV-2 virus, aiming to produce a novel recombinant chimeric antigen (N4S11-SC2). Eleven S and four N-derived B-cell epitopes were predicted and used to construct the N4S11-SC2 protein, which was analyzed in a recombinant format against serum and urine samples, by means of an in house-ELISA. Specific antibodies were detected in the serum and urine samples of COVID-19 patients, which were previously confirmed by qRT-PCR. Results showed that N4S11-SC2 presented 83.7% sensitivity and 100% specificity when using sera samples, and 91.1% sensitivity and 100% specificity using urine samples. Comparable findings were achieved with paired urine samples when compared to N and S recombinant proteins expressed in prokaryotic systems. However, better results were reached for N4S11-SC2 in comparison to the S recombinant protein when using paired serum samples. Anti-N4S11-SC2 antibodies were not clearly identified in Janssen Ad26.COV2.S COVID-19-vaccinated subjects, using serum or paired urine samples. In conclusion, this study presents a new chimeric recombinant antigen expressed in a prokaryotic system that could be considered as an alternative diagnostic marker for the SARS-CoV-2 infection, with the potential benefits to be used on serum or urine from infected patients.
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Affiliation(s)
- Fernanda F. Ramos
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Isabela A. G. Pereira
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Mariana M. Cardoso
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Raquel S. Bandeira
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Daniela P. Lage
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Rahisa Scussel
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma 88806-000, Santa Catarina, Brazil (R.A.M.-d.-Á.)
| | - Rafaela S. Anastacio
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma 88806-000, Santa Catarina, Brazil (R.A.M.-d.-Á.)
| | - Victor G. Freire
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma 88806-000, Santa Catarina, Brazil (R.A.M.-d.-Á.)
| | - Marina F. N. Melo
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Joao A. Oliveira-da-Silva
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Vivian T. Martins
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Grasiele S. V. Tavares
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Danniele L. Vale
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Camila S. Freitas
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Ana Thereza Chaves
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
| | - Júlia F. M. Caporali
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Paula F. Vassallo
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Cecilia G. Ravetti
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Vandack Nobre
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Flavio G. Fonseca
- Centro de Tecnologia de Vacinas (CT Vacinas), BH-Tec, UFMG, Belo Horizonte 31270-901, Minas Gerais, Brazil
- Laboratório de Virologia Molecular e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Myron Christodoulides
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Ricardo A. Machado-de-Ávila
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma 88806-000, Santa Catarina, Brazil (R.A.M.-d.-Á.)
| | - Eduardo A. F. Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
- Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Fernanda Ludolf
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil; (F.F.R.); (I.A.G.P.); (M.M.C.); (E.A.F.C.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte 30130-110, Minas Gerais, Brazil
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Frische A, Gunalan V, Krogfelt KA, Fomsgaard A, Lassaunière R. A Candidate DNA Vaccine Encoding the Native SARS-CoV-2 Spike Protein Induces Anti-Subdomain 1 Antibodies. Vaccines (Basel) 2023; 11:1451. [PMID: 37766128 PMCID: PMC10535225 DOI: 10.3390/vaccines11091451] [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: 07/24/2023] [Revised: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The ideal vaccine against viral infections should elicit antibody responses that protect against divergent strains. Designing broadly protective vaccines against SARS-CoV-2 and other divergent viruses requires insight into the specific targets of cross-protective antibodies on the viral surface protein(s). However, unlike therapeutic monoclonal antibodies, the B-cell epitopes of vaccine-induced polyclonal antibody responses remain poorly defined. Here we show that, through the combination of neutralizing antibody functional responses with B-cell epitope mapping, it is possible to identify unique antibody targets associated with neutralization breadth. The polyclonal antibody profiles of SARS-CoV-2 index-strain-vaccinated rabbits that demonstrated a low, intermediate, or high neutralization efficiency of different SARS-CoV-2 variants of concern (VOCs) were distinctly different. Animals with an intermediate and high cross-neutralization of VOCs targeted fewer antigenic sites on the spike protein and targeted one particular epitope, subdomain 1 (SD1), situated outside the receptor binding domain (RBD). Our results indicate that a targeted functional antibody response and an additional focus on non-RBD epitopes could be effective for broad protection against different SARS-CoV-2 variants. We anticipate that the approach taken in this study can be applied to other viral vaccines for identifying future epitopes that confer cross-neutralizing antibody responses, and that our findings will inform a rational vaccine design for SARS-CoV-2.
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Affiliation(s)
- Anders Frische
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
- Section of Molecular and Medicinal Biology, Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Vithiagaran Gunalan
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
| | - Karen Angeliki Krogfelt
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
- Section of Molecular and Medicinal Biology, Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Anders Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
- Infectious Diseases Unit, Clinical Institute, University of Southern Denmark, 5230 Odense, Denmark
| | - Ria Lassaunière
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
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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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Jiang HW, Li Y, Tao SC. SARS-CoV-2 peptides/epitopes for specific and sensitive diagnosis. Cell Mol Immunol 2023; 20:540-542. [PMID: 36973483 PMCID: PMC10040901 DOI: 10.1038/s41423-023-01001-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China.
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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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8
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Maghsood F, Ghorbani A, Yadegari H, Golsaz-Shirazi F, Amiri MM, Shokri F. SARS-CoV-2 nucleocapsid: Biological functions and implication for disease diagnosis and vaccine design. Rev Med Virol 2023; 33:e2431. [PMID: 36790816 DOI: 10.1002/rmv.2431] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/16/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is transmitted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has affected millions of people all around the world, leading to more than 6.5 million deaths. The nucleocapsid (N) phosphoprotein plays important roles in modulating viral replication and transcription, virus-infected cell cycle progression, apoptosis, and regulation of host innate immunity. As an immunodominant protein, N protein induces strong humoral and cellular immune responses in COVID-19 patients, making it a key marker for studying N-specific B cell and T cell responses and the development of diagnostic serological assays and efficient vaccines. In this review, we focus on the structural and functional features and the kinetic and epitope mapping of B cell and T cell responses against SARS-CoV-2 N protein to extend our understanding on the development of sensitive and specific diagnostic immunological tests and effective vaccines.
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Affiliation(s)
- Faezeh Maghsood
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Ghorbani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Yadegari
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Forough Golsaz-Shirazi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Amiri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fazel Shokri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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9
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Vashisht K, Goyal B, Pasupureddy R, Na BK, Shin HJ, Sahu D, De S, Chakraborti S, Pandey KC. Exploring the Immunodominant Epitopes of SARS-CoV-2 Nucleocapsid Protein as Exposure Biomarker. Cureus 2023; 15:e34827. [PMID: 36919074 PMCID: PMC10008226 DOI: 10.7759/cureus.34827] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 02/12/2023] Open
Abstract
Background The nucleocapsid protein (N protein) of SARS-CoV-2 is undeniably a potent target for the development of diagnostic tools due to its abundant expression and lower immune evasion pressure compared to spike (S) protein. Methods Blood samples of active COVID-19 infections (n=71) and post-COVID-19 (n=11) were collected from a tertiary care hospital in India; pre-COVID-19 (n=12) sera samples served as controls. Real-time reverse transcriptase-PCR (rRT-PCR) confirmed pooled sera samples (n=5) were used with PEPperCHIP® SARS-CoV-2 Proteome Microarray (PEPperPRINT GmbH, Germany) to screen immunodominant epitopes of SARS-CoV-2. Highly immunodominant epitopes were then commercially synthesized and further validated for their immunoreactivity by dot-blot and ELISA. Results The lowest detectable concentration (LDC) of the N1 peptide in the dot-blot assay was 12.5 µg demonstrating it to be fairly immunoreactive compared to control sera. IgG titers against the contiguous peptide (N2: 156AIVLQLPQGTTLPKGFYAEGS176) was found to be significantly higher (p=0.018) in post-COVID-19 compared to pre-COVID-19 control sera. These results suggested that N2-specific IgG titers buildup over time as expected in post-COVID-19 sera samples, while a non-significant immunoreactivity of the N2 peptide was also observed in active-COVID-19 sera samples. However, there were no significant differences in the total IgG titers between active COVID-19 infections, post-COVID-19 and pre-COVID-19 controls. Conclusion The N2-specific IgG titers in post-COVID-19 samples demonstrated the potential of N protein as an exposure biomarker, particularly in sero-surveillance studies.
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Affiliation(s)
- Kapil Vashisht
- Parasite-Host Biology, Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), Delhi, IND
| | - Bharti Goyal
- Parasite-Host Biology, Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), Delhi, IND.,Biological Sciences, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, IND
| | - Rahul Pasupureddy
- Parasite-Host Biology, Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), Delhi, IND
| | - Byoung-Kuk Na
- Parasitology and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, KOR
| | - Ho-Joon Shin
- Tropical Infectious Disease Cooperation Laboraory, Ajou University School of Medicine, Suwon, KOR
| | - Dibakar Sahu
- Pulmonology Department, All India Institute of Medical Sciences, Raipur, IND
| | - Sajal De
- Pulmonology Department, All India Institute of Medical Sciences, Raipur, IND
| | - Soumyananda Chakraborti
- Parasite-Host Biology, Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), Delhi, IND.,Biological Sciences, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, IND
| | - Kailash C Pandey
- Parasite-Host Biology, Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), Delhi, IND.,Biological Sciences, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, IND
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10
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Vengesai A, Naicker T, Midzi H, Kasambala M, Muleya V, Chipako I, Choto E, Moyo P, Mduluza T. Peptide microarray analysis of in-silico predicted B-cell epitopes in SARS-CoV-2 sero-positive healthcare workers in Bulawayo, Zimbabwe. Acta Trop 2023; 238:106781. [PMID: 36460093 PMCID: PMC9705268 DOI: 10.1016/j.actatropica.2022.106781] [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: 07/13/2022] [Revised: 10/31/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022]
Abstract
Immunogenic peptides that mimic linear B-cell epitopes coupled with immunoassay validation may improve serological tests for emerging diseases. This study reports a general approach for profiling linear B-cell epitopes derived from SARS-CoV-2 using an in-silico method and peptide microarray immunoassay, using healthcare workers' SARS-CoV-2 sero-positive sera. SARS-CoV-2 was tested using rapid chromatographic immunoassays and real-time reverse-transcriptase polymerase chain reaction. Immunogenic peptides mimicking linear B-cell epitopes were predicted in-silico using ABCpred. Peptides with the lowest sequence identity with human protein and proteins from other human pathogens were selected using the NCBI Protein BLAST. IgG and IgM antibodies against the SARS-CoV-2 spike protein, membrane glycoprotein and nucleocapsid derived peptides were measured in sera using peptide microarray immunoassay. Fifty-three healthcare workers included in the study were RT-PCR negative for SARS-CoV-2. Using rapid chromatographic immunoassays, 10 were SARS-CoV-2 IgM sero-positive and 7 were SARS-CoV-2 IgG sero-positive. From a total of 10 SARS-CoV-2 peptides contained on the microarray, 3 (QTH34388.1-1-14, QTN64908.1-135-148, and QLL35955.1-22-35) showed reactivity against IgG. Three peptides (QSM17284.1-76-89, QTN64908.1-135-148 and QPK73947.1-8-21) also showed reactivity against IgM. Based on the results we predicted one peptide (QSM17284.1-76-89) that had an acceptable diagnostic performance. Peptide QSM17284.1-76-89 was able to detect IgM antibodies against SARS-CoV-2 with area under the curve (AUC) 0.781 when compared to commercial antibody tests. In conclusion in silico peptide prediction and peptide microarray technology may provide a platform for the development of serological tests for emerging infectious diseases such as COVID-19. However, we recommend using at least three in-silico peptide prediction tools to improve the sensitivity and specificity of B-cell epitope prediction, to predict peptides with excellent diagnostic performances.
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Affiliation(s)
- Arthur Vengesai
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Midlands State University, Senga Road, Gweru, Zimbabwe.
| | - Thajasvarie Naicker
- Discipline of Optics and Imaging, Doris Duke Medical Research Institute, University of KwaZulu-Natal, College of Health Sciences Durban, ZA, South Africa
| | - Herald Midzi
- Department of Biotechnology and Biochemistry, Faculty of Science, University of Zimbabwe, Harare, Zimbabwe
| | - Maritha Kasambala
- Department of Biological Sciences and Ecology, Faculty of Science, University of Zimbabwe, Harare, Zimbabwe
| | - Victor Muleya
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Midlands State University, Senga Road, Gweru, Zimbabwe
| | - Isaac Chipako
- Aravas Pharmaceuticals Pvt LTD, Prospect Industrial Area, Harare, Zimbabwe
| | - Emilia Choto
- Immunology Department, Simon Mazorodze School of Medical and Health Sciences, Great Zimbabwe University, Masvingo, Zimbabwe
| | - Praise Moyo
- Department of Applied Biosciences and Biotechnology, Faculty of Science and Technology, Midlands State University, Senga Road, Gweru, Zimbabwe
| | - Takafira Mduluza
- Department of Biotechnology and Biochemistry, Faculty of Science, University of Zimbabwe, Harare, Zimbabwe
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11
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Watanabe Y, Hosokawa N, Yoshida M, Miura T, Kawano M. Identification of Closed Linear Epitopes in S1-RBD and S2-HR1/2 of SARS-CoV-2 Spike Protein Able to Induce Neutralizing Abs. Vaccines (Basel) 2023; 11:vaccines11020287. [PMID: 36851165 PMCID: PMC9966687 DOI: 10.3390/vaccines11020287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/15/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
SARS-CoV-2 has evolved as several variants. Immunization to boost the Ab response to Spike antigens is effective, but similar vaccines could not enhance Ab efficacy enough. Effective Ab responses against the human ACE2 (hACE2)-mediated infection of the emerging SARS-CoV-2 variants are needed. We identified closed linear epitopes of the SARS-CoV-2 Spike molecule that induced neutralizing Abs (nAbs) against both S1-RBD, responsible for attachment to hACE2, and S2-HR1/2, in convalescents and vaccine recipients. They inhibited a pseudo-virus infection mediated by the hACE2 pathway. The epitope sequences included epitopes #7 (aa411-432), #11 (aa459-480) and #111 (aa1144-1161), in S1-RBD and S2-HR2. Epitope #111 was conserved in Wuhan and variant strains, whereas #7 and #11 were conserved in Wuhan carried mutations K417N and S477N/T478K in Omicron BA.4/5. These mutations were recognized by the original epitope-specific Abs. These epitopes in RBD and HR2 neither contained, nor overlapped with, those responsible for the antibody-dependent enhancement of the SARS-CoV-2 infection. The sublingual administration of multiple epitope-conjugated antigens increased the IgG and IgA Abs specific to the neutralizing epitopes in mice pre-immunized subcutaneously. The findings indicated that S1-RBD and S2-HR2 epitopes were responsible for pseudo-virus SARS-CoV-2 infections and that sublingual boosts with multiple epitope-conjugated antigens could enhance the protection by nAbs of IgG and IgA against infection by a wide range of variants.
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Affiliation(s)
- Yoshihiro Watanabe
- Innovative Clinical Research Center of Kanazawa University Hospital, Kanazawa 920-8641, Japan
- Correspondence: ; Tel.: +81-76-265-2871
| | - Natsuko Hosokawa
- Rheumatology of Kanazawa University Hospital, Kanazawa 920-8641, Japan
| | - Misaki Yoshida
- Rheumatology of Kanazawa University Hospital, Kanazawa 920-8641, Japan
| | - Tomoyuki Miura
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Mitsuhiro Kawano
- Rheumatology of Kanazawa University Hospital, Kanazawa 920-8641, Japan
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12
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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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13
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Acharjee A, Ray A, Salkar A, Bihani S, Tuckley C, Shastri J, Agrawal S, Duttagupta S, Srivastava S. Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray. Viruses 2023; 15:248. [PMID: 36680289 PMCID: PMC9866125 DOI: 10.3390/v15010248] [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: 11/26/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
The amaranthine scale of the COVID-19 pandemic and unpredictable disease severity is of grave concern. Serological diagnostic aids are an excellent choice for clinicians for rapid and easy prognosis of the disease. To this end, we studied the humoral immune response to SARS-CoV-2 infection to map immunogenic regions in the SARS-CoV-2 proteome at amino acid resolution using a high-density SARS-CoV-2 proteome peptide microarray. The microarray has 4932 overlapping peptides printed in duplicates spanning the entire SARS-CoV-2 proteome. We found 204 and 676 immunogenic peptides against IgA and IgG, corresponding to 137 and 412 IgA and IgG epitopes, respectively. Of these, 6 and 307 epitopes could discriminate between disease severity. The emergence of variants has added to the complexity of the disease. Using the mutation panel available, we could detect 5 and 10 immunogenic peptides against IgA and IgG with mutations belonging to SAR-CoV-2 variants. The study revealed severity-based epitopes that could be presented as potential prognostic serological markers. Further, the mutant epitope immunogenicity could indicate the putative use of these markers for diagnosing variants responsible for the infection.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arka Ray
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | | | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Mumbai 400011, India
| | - Siddhartha Duttagupta
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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14
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Wey L, Masetto T, Spaeth A, Brehm J, Kochem C, Reinhart M, Müller H, Kempin U, Lorenz F, Peter C, Grimmler M. Bioinformatical Design and Performance Evaluation of a Nucleocapsid- and an RBD-Based Particle Enhanced Turbidimetric Immunoassay (PETIA) to Quantify the Wild Type and Variants of Concern-Derived Immunoreactivity of SARS-CoV-2. Biomedicines 2023; 11:160. [PMID: 36672668 PMCID: PMC9855841 DOI: 10.3390/biomedicines11010160] [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: 12/02/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
Since SARS-CoV-2 emerged in December 2019 in Wuhan, the resulting pandemic has paralyzed the economic and cultural life of the world. Variants of concern (VOC) strongly increase pressure on public health systems. Rapid, easy-to-use, and cost-effective assays are essential to manage the pandemic. Here we present a bioinformatical approach for the fast and efficient design of two innovative serological Particle Enhanced Turbidimetric Immunoassays (PETIA) to quantify the SARS-CoV-2 immunoresponse. To confirm bioinformatical assumptions, an S-RBD- and a Nucleocapsid-based PETIA were produced. Sensitivity and specificity were compared for 95 patient samples using a BioMajesty™ fully automated analyzer. The S-RBD-based PETIA showed necessary specificity (98%) over the N protein-based PETIA (21%). Further, the reactivity and cross-reactivity of the RBD-based PETIA towards variant-derived antibodies of SARS-CoV-2 were assessed by a quenching inhibition test. The inhibition kinetics of the S-RBD variants Alpha, Beta, Delta, Gamma, Kappa, and Omicron were evaluated. In summary, we showed that specific and robust PETIA immunoassays can be rapidly designed and developed. The quantification of the SARS-CoV-2-related immunoresponse of variants (Alpha to Kappa) is possible using specific RBD assays. In contrast, Omicron revealed lower cross-reactivity (approx. 50%). To ensure the quantification of the Omicron variant, modified immunoassays appear to be necessary.
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Affiliation(s)
- Leoni Wey
- DiaSys Diagnostic Systems GmbH, Alte Str. 9, 65558 Holzheim, Germany
- Hochschule Fresenius Gem. Trägergesellschaft mbH, University of Applied Sciences, Limburger Str. 2, 65510 Idstein, Germany
| | - Thomas Masetto
- DiaSys Diagnostic Systems GmbH, Alte Str. 9, 65558 Holzheim, Germany
- Institut für Molekulare Medizin I, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Alexander Spaeth
- MVZ Medizinische Labore Dessau Kassel GmbH, Bauhüttenstr. 6, 06847 Dessau-Roßlau, Germany
| | - Jessica Brehm
- MVZ Medizinische Labore Dessau Kassel GmbH, Bauhüttenstr. 6, 06847 Dessau-Roßlau, Germany
| | - Christian Kochem
- DiaSys Diagnostic Systems GmbH, Alte Str. 9, 65558 Holzheim, Germany
| | | | - Holger Müller
- DiaSys Diagnostic Systems GmbH, Alte Str. 9, 65558 Holzheim, Germany
| | - Uwe Kempin
- pes Medizinische Diagnosesysteme GmbH, Hauptstr. 103, 04416 Markkleeberg, Germany
| | - Franziska Lorenz
- MVZ Medizinische Labore Dessau Kassel GmbH, Bauhüttenstr. 6, 06847 Dessau-Roßlau, Germany
| | - Christoph Peter
- Institut für Molekulare Medizin I, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Matthias Grimmler
- DiaSys Diagnostic Systems GmbH, Alte Str. 9, 65558 Holzheim, Germany
- Hochschule Fresenius Gem. Trägergesellschaft mbH, University of Applied Sciences, Limburger Str. 2, 65510 Idstein, Germany
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15
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Venkatakrishnan AJ, Anand P, Lenehan PJ, Ghosh P, Suratekar R, Silvert E, Pawlowski C, Siroha A, Chowdhury DR, O'Horo JC, Yao JD, Pritt BS, Norgan AP, Hurt RT, Badley AD, Halamka J, Soundararajan V. Expanding repertoire of SARS-CoV-2 deletion mutations contributes to evolution of highly transmissible variants. Sci Rep 2023; 13:257. [PMID: 36604461 PMCID: PMC9815892 DOI: 10.1038/s41598-022-26646-5] [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: 08/13/2021] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
The emergence of highly transmissible SARS-CoV-2 variants and vaccine breakthrough infections globally mandated the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed 2.13 million SARS-CoV-2 genomes from 188 countries/territories (up to June 2021) and performed whole-genome viral sequencing from 102 COVID-19 patients, including 43 vaccine breakthrough infections. We identified 92 Spike protein mutations that increased in prevalence during at least one surge in SARS-CoV-2 test positivity in any country over a 3-month window. Deletions in the Spike protein N-terminal domain were highly enriched for these 'surge-associated mutations' (Odds Ratio = 14.19, 95% CI 6.15-32.75, p value = 3.41 × 10-10). Based on a longitudinal analysis of mutational prevalence globally, we found an expanding repertoire of Spike protein deletions proximal to an antigenic supersite in the N-terminal domain that may be one of the key contributors to the evolution of highly transmissible variants. Finally, we generated clinically annotated SARS-CoV-2 whole genome sequences from 102 patients and identified 107 unique mutations, including 78 substitutions and 29 deletions. In five patients, we identified distinct deletions between residues 85-90, which reside within a linear B cell epitope. Deletions in this region arose contemporaneously on a diverse background of variants across the globe since December 2020. Overall, our findings based on genomic-epidemiology and clinical surveillance suggest that the genomic deletion of dispensable antigenic regions in SARS-CoV-2 may contribute to the evasion of immune responses and the evolution of highly transmissible variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Venky Soundararajan
- nference, Cambridge, MA, 02139, USA.
- nference Labs, Bengaluru, Karnataka, India.
- Anumana, Cambridge, MA, 02139, USA.
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16
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Frigerio R, Musicò A, Strada A, Mussida A, Gagni P, Bergamaschi G, Chiari M, Barzon L, Gori A, Cretich M. Epitope Mapping on Microarrays Highlights a Sequence on the N Protein with Strong Immune Response in SARS-CoV-2 Patients. Methods Mol Biol 2023; 2578:209-217. [PMID: 36152290 DOI: 10.1007/978-1-0716-2732-7_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In SARS-CoV-2 pandemic scenario, the identification of rapid methods to detect antibodies against coronavirus has been a wide and urgent issue. Epitope mapping on peptide microarrays is a rapid way to identify sequences with a high immunoreactivity. The process begins with a proteome-wide screening, based on immune affinity; the use of a high-density microarray is followed by a validation phase, where a restricted panel of probes is tested using peptide microarrays; peptide sequences are immobilized through a click-based strategy.COVID-19-positive sera are tested and immuno-domains regions are identified on SARS-CoV-2 spike (S), nucleocapsid (N) protein, and Orf1ab polyprotein. An epitope on N protein (region 155-171) provided good diagnostic performance in discriminating COVID-19-positive vs. healthy individuals. Using this sequence, 92% sensitivity and 100% specificity are reached for IgG detection in COVID-19 samples, and no cross-reactivity with common cold coronaviruses is detected. Overall, epitope 155-171 from N protein represents a promising candidate for further development and rapid implementation in serological tests.
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Affiliation(s)
- Roberto Frigerio
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy.
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
| | - Angelo Musicò
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandro Strada
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Alessandro Mussida
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
- Dipartimento di Scienze Farmaceutiche (DISFARM), Università degli Studi di Milano, Milan, Italy
| | - Paola Gagni
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Greta Bergamaschi
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Marcella Chiari
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Alessandro Gori
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Marina Cretich
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
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17
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Akimoto J, Kashiwagi H, Morishima N, Obuse S, Isoshima T, Kageyama T, Nakajima H, Ito Y. Rapid and quantitative detection of multiple antibodies against SARS-CoV-2 mutant proteins by photo-immobilized microarray. ANAL SCI 2022; 38:1313-1321. [PMID: 35917106 PMCID: PMC9343572 DOI: 10.1007/s44211-022-00161-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/30/2022] [Indexed: 11/21/2022]
Abstract
A rapid automatic quantitative diagnostic system for multiple SARS-CoV-2 mutant protein-specific antibodies was developed using a microarray with photoreactive polymers. Two types of photoreactive polymers, phenylazide and polyoxyethylene, were prepared. The polymers were coated on a plastic plate. Aqueous solutions of mutant virus proteins were microspotted on the coated plate and immobilized by photoirradiation. Virus-specific IgG in the serum or blood was automatically assayed using an instrument that we developed for pipetting, reagent stirring, and washing. The results highly correlated with those of the conventional enzyme-linked immunoassay or immunochromatography. This system was successfully used to test the sera or blood from the patients recovered from the infection and the vaccinated individuals. The recovered individuals had antibodies against the nucleoprotein, in contrast to the vaccinated individuals. The amount of antibodies produced decreased with an increase in virus mutation. Blood collected from the fingertip (5 μL) and a test period of 8 min were sufficient conditions for conducting multiple antibody assays. We believe that our system would facilitate rapid and quantitative automatic assays and aid in the diagnosis of various viral infectious diseases and assessment of the immune status for clinical applications.
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Affiliation(s)
- Jun Akimoto
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
- R-NanoBio Co., Ltd., Wako-RIKEN Incubation Plaza, 3-13 Minami, Wako-shi, Saitama, 351-0104, Japan
| | - Hiroharu Kashiwagi
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Nobuhiro Morishima
- R-NanoBio Co., Ltd., Wako-RIKEN Incubation Plaza, 3-13 Minami, Wako-shi, Saitama, 351-0104, Japan
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Sei Obuse
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
- R-NanoBio Co., Ltd., Wako-RIKEN Incubation Plaza, 3-13 Minami, Wako-shi, Saitama, 351-0104, Japan
| | - Takashi Isoshima
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Takahiro Kageyama
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba City, Chiba, 260-8670, Japan
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba City, Chiba, 260-8670, Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.
- R-NanoBio Co., Ltd., Wako-RIKEN Incubation Plaza, 3-13 Minami, Wako-shi, Saitama, 351-0104, Japan.
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.
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18
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Abd El-Baky N, Amara AAAF. Depending on Epitope Profile of COVID-19 mRNA Vaccine Recipients: Are They More Efficient Against the Arising Viral Variants? An Opinion Article. Front Med (Lausanne) 2022; 9:903876. [PMID: 35795625 PMCID: PMC9251123 DOI: 10.3389/fmed.2022.903876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/01/2022] [Indexed: 12/02/2022] Open
Affiliation(s)
- Nawal Abd El-Baky
- Department of Protein Research, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Amro Abd Al Fattah Amara
- Department of Protein Research, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
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19
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Akinshina YA, Mardanly SG, Rotanov SV, Pomazanov VV, Kiseleva VA, Ermolaev III. Features of the humoral response to immunization "Gam-COVID-Vac" and in patients with COVID-19. Klin Lab Diagn 2022; 67:227-233. [PMID: 35575396 DOI: 10.51620/0869-2084-2022-67-4-227-233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The paper present the results of a survey of people who have undergone immunization with a combined vector vaccine for the prevention of coronavirus infection COVID-19 «Sputnik V - Gam-COVID-Vac», as well as COVID-19 recovalents. Using a quantitative enzyme-linked immunosorbent assay, the levels of specific IgG were determined in persons who had had different degrees of severity before vaccination, in persons who were immuno-negative before immunization, as well as in convalescents who had undergone coronavirus infection of varying severity. The immunological targeting of antibodies against various SARS-CoV-2 proteins is considered.
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Affiliation(s)
| | - S G Mardanly
- CJSC «EKOlab».,«First Moscow State Medical University after I.M. Sechenov» of the Ministry of Healthcare of the Russian Federation (1st MSMU after I.M. Sechenov).,State educational institution of higher education of the Moscow region «State Humanitarian University of Technology» (GGTU)
| | - S V Rotanov
- CJSC «EKOlab».,State budgetary healthcare institution оf Moscow region «Liuberetskiy kozhno-venerologicheskiy dispanser»
| | - V V Pomazanov
- CJSC «EKOlab».,State educational institution of higher education of the Moscow region «State Humanitarian University of Technology» (GGTU)
| | - V A Kiseleva
- State educational institution of higher education of the Moscow region «State Humanitarian University of Technology» (GGTU)
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20
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Tajuelo A, López-Siles M, Más V, Pérez-Romero P, Aguado JM, Briz V, McConnell MJ, Martín-Galiano AJ, López D. Cross-Recognition of SARS-CoV-2 B-Cell Epitopes with Other Betacoronavirus Nucleoproteins. Int J Mol Sci 2022; 23:ijms23062977. [PMID: 35328398 PMCID: PMC8955325 DOI: 10.3390/ijms23062977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/08/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
The B and T lymphocytes of the adaptive immune system are important for the control of most viral infections, including COVID-19. Identification of epitopes recognized by these cells is fundamental for understanding how the immune system detects and removes pathogens, and for antiviral vaccine design. Intriguingly, several cross-reactive T lymphocyte epitopes from SARS-CoV-2 with other betacoronaviruses responsible for the common cold have been identified. In addition, antibodies that cross-recognize the spike protein, but not the nucleoprotein (N protein), from different betacoronavirus have also been reported. Using a consensus of eight bioinformatic methods for predicting B-cell epitopes and the collection of experimentally detected epitopes for SARS-CoV and SARS-CoV-2, we identified four surface-exposed, conserved, and hypothetical antigenic regions that are exclusive of the N protein. These regions were analyzed using ELISA assays with two cohorts: SARS-CoV-2 infected patients and pre-COVID-19 samples. Here we describe four epitopes from SARS-CoV-2 N protein that are recognized by the humoral response from multiple individuals infected with COVID-19, and are conserved in other human coronaviruses. Three of these linear surface-exposed sequences and their peptide homologs in SARS-CoV-2 and HCoV-OC43 were also recognized by antibodies from pre-COVID-19 serum samples, indicating cross-reactivity of antibodies against coronavirus N proteins. Different conserved human coronaviruses (HCoVs) cross-reactive B epitopes against SARS-CoV-2 N protein are detected in a significant fraction of individuals not exposed to this pandemic virus. These results have potential clinical implications.
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Affiliation(s)
- Ana Tajuelo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Mireia López-Siles
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Vicente Más
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Pilar Pérez-Romero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | | | - Verónica Briz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Michael J. McConnell
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
- Correspondence: (M.J.M.); (D.L.)
| | - Antonio J. Martín-Galiano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Daniel López
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
- Correspondence: (M.J.M.); (D.L.)
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21
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Acharjee A, Stephen Kingsly J, Kamat M, Kurlawala V, Chakraborty A, Vyas P, Vaishnav R, Srivastava S. Rise of the SARS-CoV-2 Variants: can proteomics be the silver bullet? Expert Rev Proteomics 2022; 19:197-212. [PMID: 35655386 DOI: 10.1080/14789450.2022.2085564] [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] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The challenges posed by emergent strains of SARS-CoV-2 need to be tackled by contemporary scientific approaches, with proteomics playing a significant role. AREAS COVERED In this review, we provide a brief synthesis of the impact of proteomics technologies in elucidating disease pathogenesis and classifiers for the prognosis of COVID-19 and propose proteomics methodologies that could play a crucial role in understanding emerging variants and their altered disease pathology. From aiding the design of novel drug candidates to facilitating the identification of T cell vaccine targets, we have discussed the impact of proteomics methods in COVID-19 research. Techniques varied as mass spectrometry, single-cell proteomics, multiplexed ELISA arrays, high-density proteome arrays, surface plasmon resonance, immunopeptidomics, and in silico docking studies that have helped augment the fight against existing diseases were useful in preparing us to tackle SARS-CoV-2 variants. We also propose an action plan for a pipeline to combat emerging pandemics using proteomics technology by adopting uniform standard operating procedures and unified data analysis paradigms. EXPERT OPINION The knowledge about the use of diverse proteomics approaches for COVID-19 investigation will provide a framework for future basic research, better infectious disease prevention strategies, improved diagnostics, and targeted therapeutics.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Madhura Kamat
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | - Vishakha Kurlawala
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | | | - Priyanka Vyas
- Department of Biotechnology and Botany, Mahila PG Mahavidyalaya, J. N. V University, Jodhpur, India
| | - Radhika Vaishnav
- Department of Life Sciences, Ivy Tech Community College, Indianapolis, Indiana, USA
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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22
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Bergamaschi G, Musicò A, Frigerio R, Strada A, Pizzi A, Talone B, Ghezzi J, Gautieri A, Chiari M, Metrangolo P, Vanna R, Baldelli Bombelli F, Cretich M, Gori A. Composite Peptide-Agarose Hydrogels for Robust and High-Sensitivity 3D Immunoassays. ACS APPLIED MATERIALS & INTERFACES 2022; 14:4811-4822. [PMID: 35060693 DOI: 10.1021/acsami.1c18466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Canonical immunoassays rely on highly sensitive and specific capturing of circulating biomarkers by interacting biomolecular baits. In this frame, bioprobe immobilization in spatially discrete three-dimensional (3D) spots onto analytical surfaces by hydrogel encapsulation was shown to provide relevant advantages over conventional two-dimensional (2D) platforms. Yet, the broad application of 3D systems is still hampered by hurdles in matching their straightforward fabrication with optimal functional properties. Herein, we report on a composite hydrogel obtained by combining a self-assembling peptide (namely, Q3 peptide) with low-temperature gelling agarose that is proved to have simple and robust application in the fabrication of microdroplet arrays, overcoming hurdles and limitations commonly associated with 3D hydrogel assays. We demonstrate the real-case scenario feasibility of our 3D system in the profiling of Covid-19 patients' serum IgG immunoreactivity, which showed remarkably improved signal-to-noise ratio over canonical assays in the 2D format and exquisite specificity. Overall, the new two-component hydrogel widens the perspectives of hydrogel-based arrays and represents a step forward towards their routine use in analytical practices.
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Affiliation(s)
- Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Angelo Musicò
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Roberto Frigerio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Alessandro Strada
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Benedetta Talone
- Physics Department, Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Jacopo Ghezzi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
- Biomolecular Engineering Lab, Dept. Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dept. Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Renzo Vanna
- Istituto di Fotonica e Nanotecnologie─National Research Council of Italy (IFN-CNR), 20133 Milan, Italy
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Marina Cretich
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
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23
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ELISA-Based Analysis Reveals an Anti-SARS-CoV-2 Protein Immune Response Profile Associated with Disease Severity. J Clin Med 2022; 11:jcm11020405. [PMID: 35054099 PMCID: PMC8781066 DOI: 10.3390/jcm11020405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 01/01/2023] Open
Abstract
Since the start of the COVID-19 pandemic, many studies have investigated the humoral response to SARS-CoV-2 during infection. Studies with native viral proteins constitute a first-line approach to assessing the overall immune response, but small peptides are an accurate and valuable tool for the fine characterization of B-cell epitopes, despite the restriction of this approach to the determination of linear epitopes. In this study, we used ELISA and peptides covering a selection of structural and non-structural SARS-CoV-2 proteins to identify key epitopes eliciting a strong immune response that could serve as a biological signature of disease characteristics, such as severity, in particular. We used 213 plasma samples from a cohort of patients well-characterized clinically and biologically and followed for COVID-19 infection. We found that patients developing severe disease had higher titers of antibodies mapping to multiple specific epitopes than patients with mild to moderate disease. These data are potentially important as they could be used for immunological profiling to improve our knowledge of the quantitative and qualitative characteristics of the humoral response in relation to patient outcome.
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24
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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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25
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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: 15] [Impact Index Per Article: 5.0] [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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26
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Kashiwagi H, Morishima N, Obuse S, Isoshima T, Akimoto J, Ito Y. SARS-CoV-2 Proteins Microarray by Photoimmobilization for Serodiagnosis of the Antibodies. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hiroharu Kashiwagi
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- R-NanoBio Co., Ltd., Wako-RIKEN Incubation Plaza, 3-13 Minami, Wako, Saitama 351-0104, Japan
| | - Nobuhiro Morishima
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Sei Obuse
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- R-NanoBio Co., Ltd., Wako-RIKEN Incubation Plaza, 3-13 Minami, Wako, Saitama 351-0104, Japan
| | - Takashi Isoshima
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Jun Akimoto
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- R-NanoBio Co., Ltd., Wako-RIKEN Incubation Plaza, 3-13 Minami, Wako, Saitama 351-0104, Japan
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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27
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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; 0:10.2217/fvl-2021-0062. [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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28
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Uttamrao PP, Sathyaseelan C, Patro LPP, Rathinavelan T. Revelation of Potent Epitopes Present in Unannotated ORF Antigens of SARS-CoV-2 for Epitope-Based Polyvalent Vaccine Design Using Immunoinformatics Approach. Front Immunol 2021; 12:692937. [PMID: 34497604 PMCID: PMC8419283 DOI: 10.3389/fimmu.2021.692937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/31/2021] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kills thousands of people worldwide every day, thus necessitating rapid development of countermeasures. Immunoinformatics analyses carried out here in search of immunodominant regions in recently identified SARS-CoV-2 unannotated open reading frames (uORFs) have identified eight linear B-cell, one conformational B-cell, 10 CD4+ T-cell, and 12 CD8+ T-cell promising epitopes. Among them, ORF9b B-cell and T-cell epitopes are the most promising followed by M.ext and ORF3c epitopes. ORF9b40-48 (CD8+ T-cell epitope) is found to be highly immunogenic and antigenic with the highest allele coverage. Furthermore, it has overlap with four potent CD4+ T-cell epitopes. Structure-based B-cell epitope prediction has identified ORF9b61-68 to be immunodominant, which partially overlaps with one of the linear B-cell epitopes (ORF9b65-69). ORF3c CD4+ T-cell epitopes (ORF3c2-16, ORF3c3-17, and ORF3c4-18) and linear B-cell epitope (ORF3c14-22) have also been identified as the candidate epitopes. Similarly, M.ext and 7a.iORF1 (overlap with M and ORF7a) proteins have promising immunogenic regions. By considering the level of antigen expression, four ORF9b and five M.ext epitopes are finally shortlisted as potent epitopes. Mutation analysis has further revealed that the shortlisted potent uORF epitopes are resistant to recurrent mutations. Additionally, four N-protein (expressed by canonical ORF) epitopes are found to be potent. Thus, SARS-CoV-2 uORF B-cell and T-cell epitopes identified here along with canonical ORF epitopes may aid in the design of a promising epitope-based polyvalent vaccine (when connected through appropriate linkers) against SARS-CoV-2. Such a vaccine can act as a bulwark against SARS-CoV-2, especially in the scenario of emergence of variants with recurring mutations in the spike protein.
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29
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Perkmann T, Perkmann-Nagele N, Koller T, Mucher P, Radakovics A, Marculescu R, Wolzt M, Wagner OF, Binder CJ, Haslacher H. Anti-Spike Protein Assays to Determine SARS-CoV-2 Antibody Levels: a Head-to-Head Comparison of Five Quantitative Assays. Microbiol Spectr 2021; 9:e0024721. [PMID: 34190591 PMCID: PMC8552734 DOI: 10.1128/spectrum.00247-21] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Reliable quantification of the antibody response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly relevant, e.g., for identifying possible vaccine failure and estimating the time of protection. Therefore, we evaluated five different anti-SARS-CoV-2 antibody assays regarding the quantification of anti-spike (S) antibodies. Sera from 69 SARS-CoV-2-naive individuals 21 ± 1 days after vaccination with a single dose of BNT162b2 (Pfizer/BioNTech) were tested using the following quantitative assays: Roche S total antibody, DiaSorin trimeric spike IgG, DiaSorin S1/S2 IgG, Abbott II IgG, and Serion/Virion IgG. Results were further compared to the percent inhibition calculated from a surrogate virus neutralization test (sVNT). Individual values were distributed over several orders of magnitude for all assays. Although the assays were in good overall agreement (ρ = 0.80 to 0.94), Passing-Bablok regression revealed systematic constant and proportional differences, which could not be eliminated by converting the results to binding antibody units (BAU) per milliliter, as suggested by the manufacturers. Seven (10%) individuals had negative sVNT results (i.e., <30% inhibition). These samples were identified by most assays and yielded significantly lower binding antibody levels. Although all assays showed good correlation, they were not interchangeable, even when converted to BAU per milliliter using the WHO international standard for SARS-CoV-2 immunoglobulin. This highlights the need for further standardization of SARS-CoV-2 serology. IMPORTANCE Reliable quantification of the antibody response to SARS-CoV-2 is highly relevant, e.g., for identifying possible vaccine failure and estimating the time of protection. We compared the performance of five CE marked tests that quantify antibodies against the viral spike protein. Our findings suggest that, although all assays showed good correlation, their results were not interchangeable, even when converted to BAU per milliliter using the WHO international standard for SARS-CoV-2 immunoglobulin. This highlights the need for further standardization of SARS-CoV-2 serology.
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Affiliation(s)
- Thomas Perkmann
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Thomas Koller
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Patrick Mucher
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Astrid Radakovics
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Rodrig Marculescu
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Michael Wolzt
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Oswald F. Wagner
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christoph J. Binder
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Helmuth Haslacher
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
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30
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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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31
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Heggestad JT, Kinnamon DS, Olson LB, Liu J, Kelly G, Wall SA, Oshabaheebwa S, Quinn Z, Fontes CM, Joh DY, Hucknall AM, Pieper C, Anderson JG, Naqvi IA, Chen L, Que LG, Oguin T, Nair SK, Sullenger BA, Woods CW, Burke TW, Sempowski GD, Kraft BD, Chilkoti A. Multiplexed, quantitative serological profiling of COVID-19 from blood by a point-of-care test. SCIENCE ADVANCES 2021; 7:eabg4901. [PMID: 34172447 PMCID: PMC8232907 DOI: 10.1126/sciadv.abg4901] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/12/2021] [Indexed: 05/08/2023]
Abstract
Highly sensitive, specific, and point-of-care (POC) serological assays are an essential tool to manage coronavirus disease 2019 (COVID-19). Here, we report on a microfluidic POC test that can profile the antibody response against multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens-spike S1 (S1), nucleocapsid (N), and the receptor binding domain (RBD)-simultaneously from 60 μl of blood, plasma, or serum. We assessed the levels of antibodies in plasma samples from 31 individuals (with longitudinal sampling) with severe COVID-19, 41 healthy individuals, and 18 individuals with seasonal coronavirus infections. This POC assay achieved high sensitivity and specificity, tracked seroconversion, and showed good concordance with a live virus microneutralization assay. We can also detect a prognostic biomarker of severity, IP-10 (interferon-γ-induced protein 10), on the same chip. Because our test requires minimal user intervention and is read by a handheld detector, it can be globally deployed to combat COVID-19.
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Affiliation(s)
- Jacob T Heggestad
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - David S Kinnamon
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Lyra B Olson
- Duke Medical Scientist Training Program, Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jason Liu
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Garrett Kelly
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Simone A Wall
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Solomon Oshabaheebwa
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Zachary Quinn
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Cassio M Fontes
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Daniel Y Joh
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
- Division of Plastic, Maxillofacial, and Oral Surgery, Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Angus M Hucknall
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Carl Pieper
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27708, USA
| | - Jack G Anderson
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Ibtehaj A Naqvi
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lingye Chen
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Loretta G Que
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Thomas Oguin
- Department of Medicine and Duke Human Vaccine Institute, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Smita K Nair
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Neurosurgery and Pathology, Duke University School of Medicine, Duke University, Durham, NC 27710, USA
| | - Bruce A Sullenger
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Department of Medicine and Duke Human Vaccine Institute, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Gregory D Sempowski
- Department of Medicine and Duke Human Vaccine Institute, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Bryan D Kraft
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA.
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32
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Immunoinformatics and Pepscan strategies on the path of a peptide-based serological diagnosis of COVID19. J Immunol Methods 2021; 495:113071. [PMID: 33991531 PMCID: PMC8116314 DOI: 10.1016/j.jim.2021.113071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/21/2021] [Accepted: 05/10/2021] [Indexed: 01/13/2023]
Abstract
Several diagnostic tools have been developed for clinical and epidemiological assays. RT-PCR and antigen detection tests are more useful for diagnosis of acute disease, while antibody tests allow the estimation of exposure in the population. Currently, there is an urgent need for the development of diagnostic tests for COVID-19 that can be used for large-scale epidemiological sampling. Through a comprehensive strategy, potential 16 mer antigenic peptides suited for antibody-based SARS-CoV-2 diagnosis were identified. A systematic scan of the three structural proteins (S,N and M) and the non-structural proteins (ORFs) present in the SARS-CoV-2 virus was conducted through the combination of immunoinformatic methods, peptide SPOT synthesis and an immunoassay with cellulose-bound peptides (Pepscan). The Pepscan filter paper sheets with synthetic peptides were tested against pools of sera of COVID-19 patients. Antibody recognition showed a strong signal for peptides corresponding to the S, N and M proteins of SARS-CoV-2 virus, but not for the ORFs proteins. The peptides exhibiting higher signal intensity were found in the C-terminal region of the N protein. Several peptides of this region showed strong recognition with all three immunoglobulins in the pools of sera. The differential reactivity observed between the different immunoglobulin isotypes (IgA, IgM and IgG) within different regions of the S and N proteins, can be advantageous for ensuring accurate diagnosis of all infected patients, with different times of exposure to infection. Few peptides of the M protein showed antibody recognition and no recognition was observed for peptides of the ORFs proteins.
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33
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Sen SR, Sanders EC, Gabriel KN, Miller BM, Isoda HM, Salcedo GS, Garrido JE, Dyer RP, Nakajima R, Jain A, Caldaruse AM, Santos AM, Bhuvan K, Tifrea DF, Ricks-Oddie JL, Felgner PL, Edwards RA, Majumdar S, Weiss GA. Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score. mSphere 2021; 6:e00203-21. [PMID: 33910993 PMCID: PMC8092137 DOI: 10.1128/msphere.00203-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/14/2022] Open
Abstract
Effective methods for predicting COVID-19 disease trajectories are urgently needed. Here, enzyme-linked immunosorbent assay (ELISA) and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide range of disease states. The experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including admission to the intensive care unit (ICU), requirement for ventilators, or death. Importantly, anti-Ep9 antibodies can be detected within 6 days post-symptom onset and sometimes within 1 day. Furthermore, anti-Ep9 antibodies correlate with various comorbidities and hallmarks of immune hyperactivity. We introduce a simple-to-calculate, disease risk factor score to quantitate each patient's comorbidities and age. For patients with anti-Ep9 antibodies, scores above 3.0 predict more severe disease outcomes with a 13.42 likelihood ratio (96.7% specificity). The results lay the groundwork for a new type of COVID-19 prognostic to allow early identification and triage of high-risk patients. Such information could guide more effective therapeutic intervention.IMPORTANCE The COVID-19 pandemic has resulted in over two million deaths worldwide. Despite efforts to fight the virus, the disease continues to overwhelm hospitals with severely ill patients. Diagnosis of COVID-19 is readily accomplished through a multitude of reliable testing platforms; however, prognostic prediction remains elusive. To this end, we identified a short epitope from the SARS-CoV-2 nucleocapsid protein and also a disease risk factor score based upon comorbidities and age. The presence of antibodies specifically binding to this epitope plus a score cutoff can predict severe COVID-19 outcomes with 96.7% specificity.
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Affiliation(s)
- Sanjana R Sen
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
| | - Emily C Sanders
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Kristin N Gabriel
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
| | - Brian M Miller
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Hariny M Isoda
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Gabriela S Salcedo
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Jason E Garrido
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
| | - Rebekah P Dyer
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
| | - Rie Nakajima
- Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Aarti Jain
- Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Ana-Maria Caldaruse
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA
| | - Alicia M Santos
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Keertna Bhuvan
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, USA
| | - Joni L Ricks-Oddie
- Center for Statistical Consulting, Department of Statistics, University of California Irvine, Irvine, California, USA
- Biostatics, Epidemiology and Research Design Unit, Institute for Clinical and Translational Sciences, University of California Irvine, Irvine, California, USA
| | - Philip L Felgner
- Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, USA
| | - Sudipta Majumdar
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Gregory A Weiss
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
- Department of Chemistry, University of California Irvine, Irvine, California, USA
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA
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34
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Ryzhikov AB, Ryzhikov ЕА, Bogryantseva MP, Usova SV, Danilenko ED, Nechaeva EA, Pyankov OV, Pyankova OG, Gudymo AS, Bodnev SA, Onkhonova GS, Sleptsova ES, Kuzubov VI, Ryndyuk NN, Ginko ZI, Petrov VN, Moiseeva AA, Torzhkova PY, Pyankov SA, Tregubchak TV, Antonec DV, Gavrilova EV, Maksyutov RA. A single blind, placebo-controlled randomized study of the safety, reactogenicity and immunogenicity of the “EpiVacCorona” Vaccine for the prevention of COVID-19, in volunteers aged 18–60 years (phase I–II). ACTA ACUST UNITED AC 2021. [DOI: 10.15789/2220-7619-asb-1699] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Vaccination of the population is one of the most effective countermeasures in responding to the pandemic caused by novel coronavirus infection. Therefore, scientists all over the world have been working to develop effective and safe vaccines. We have developed a synthetic peptide vaccine, EpiVacCorona, against novel SARS-CoV-2 coronavirus, which is a suspension for intramuscular administration containing a composition of chemically synthesized peptide immunogens of the S protein of SARS-CoV-2 coronavirus conjugated to a carrier protein and adsorbed on aluminum hydroxide. Phase I–II clinical trials of the vaccine have started that consist of two stages: Stage 1 is an open study of the safety, reactogenicity, and immunological activity of the vaccine with the involvement of 14 volunteers aged 18–30 years; Stage 2 is a single blind, comparative, randomized placebo-controlled study with the involvement of 86 volunteers. The study involved volunteers aged 18–60 years; the vaccine was injected intramuscularly twice, spaced 21 days apart between injections. All local reactions in response to vaccine administration were mild, such as a short-term pain at the injection site. There were no signs of development of local or systemic adverse reactions. The two-dose vaccination scheme induced the production of antibodies, specific to the antigens that make up the vaccine, in 100% of the volunteers. Seroconversion with a neutralizing antibody titer ≥ 1:20 was reported in 100% of the volunteers 21 days following the second immunization dose. No seroconversion was reported in the groups of volunteers vaccinated with a placebo. The peptide-based EpiVacCorona Vaccine has low reactogenicity and is a safe, immunogenic product. Clinical Trials Identifier: NCT04527575.
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Affiliation(s)
- A. B. Ryzhikov
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | | | - M. P. Bogryantseva
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - S. V. Usova
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - E. D. Danilenko
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - E. A. Nechaeva
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - O. V. Pyankov
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - O. G. Pyankova
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - A. S. Gudymo
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - S. A. Bodnev
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - G. S. Onkhonova
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | | | - V. I. Kuzubov
- Medical Unit No. 163 of the Federal Medical and Biological Agency of Russia
| | - N. N. Ryndyuk
- Medical Unit No. 163 of the Federal Medical and Biological Agency of Russia
| | - Z. I. Ginko
- Medical Unit No. 163 of the Federal Medical and Biological Agency of Russia
| | - V. N. Petrov
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - A. A. Moiseeva
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - P. Yu. Torzhkova
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - S. A. Pyankov
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - T. V. Tregubchak
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - D. V. Antonec
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - E. V. Gavrilova
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
| | - R. A. Maksyutov
- State Scientific Center of Virology and Biotechnology “Vector” of Rospotrebnadzor
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