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Maje Bello A, Chaimongkolnukul K, Poomputsa K, Mekvichitsaeng P, Maprang Roshorm Y. Immunogenicity and immunodominant linear B-cell epitopes of a new DNA-based tetravalent vaccine against four major enteroviruses causing hand, foot, and mouth disease. Vaccine 2024; 42:3733-3743. [PMID: 38705805 DOI: 10.1016/j.vaccine.2024.04.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
Hand, foot, and mouth disease (HFMD) poses a significant public health threat primarily caused by four major enteroviruses: enterovirus 71 (EV71), coxsackieviruses A16, A10, and A6. Broadly protective immune responses are essential for complete protection against these major enteroviruses. In this study, we designed a new tetravalent immunogen for HFMD, validated it in silico, in vivo evaluated the immunogenicity of the DNA-based tetravalent vaccine in mice, and identified immunogenic B-cell and T-cell epitopes. A new tetravalent immunogen, VP1me, was designed based on the chimeric protein and epitope-based vaccine principles. It contains a complete EV71 VP1 protein and six reported neutralizing B-cell epitopes derived from the four major enteroviruses causing HFMD. In silico validation using multiple immunoinformatic tools indicated good attributes of the VP1me immunogen suitable for vaccine development. The VP1me-based DNA vaccine efficiently induced both humoral and cellular immune responses in BALB/cAJcl mice. A combination of in silico prediction and immunoassays enabled the identification of immunogenic linear B-cell and CD8 T-cell epitopes within the VP1me immunogen. Immunodominant linear B-cell epitopes were identified in six regions of VP1me, with one epitope located at the N-terminus of the VP1 protein (aa 9-23) regarded as a novel epitope. Interestingly, some B-cell epitopes could also induce the CD8 T-cell response, suggesting their dual functions in immune stimulation. These results lay the groundwork for further development of VP1me as a new vaccine candidate.
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MESH Headings
- Animals
- Vaccines, DNA/immunology
- Epitopes, B-Lymphocyte/immunology
- Hand, Foot and Mouth Disease/prevention & control
- Hand, Foot and Mouth Disease/immunology
- Mice, Inbred BALB C
- Mice
- Viral Vaccines/immunology
- Immunodominant Epitopes/immunology
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Female
- Epitopes, T-Lymphocyte/immunology
- Capsid Proteins/immunology
- Capsid Proteins/genetics
- Enterovirus/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Enterovirus A, Human/immunology
- Enterovirus A, Human/genetics
- Immunogenicity, Vaccine
- Immunity, Cellular
- Immunity, Humoral
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Affiliation(s)
- Aliyu Maje Bello
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand; Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Bayero University Kano, Kano Nigeria
| | | | - Kanokwan Poomputsa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand; Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Phenjun Mekvichitsaeng
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Yaowaluck Maprang Roshorm
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand; Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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2
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Coria LM, Rodriguez JM, Demaria A, Bruno LA, Medrano MR, Castro CP, Castro EF, Del Priore SA, Hernando Insua AC, Kaufmann IG, Saposnik LM, Stone WB, Prado L, Notaro US, Amweg AN, Diaz PU, Avaro M, Ortega H, Ceballos A, Krum V, Zurvarra FM, Sidabra JE, Drehe I, Baqué JA, Li Causi M, De Nichilo AV, Payes CJ, Southard T, Vega JC, Auguste AJ, Álvarez DE, Flo JM, Pasquevich KA, Cassataro J. A Gamma-adapted subunit vaccine induces broadly neutralizing antibodies against SARS-CoV-2 variants and protects mice from infection. Nat Commun 2024; 15:997. [PMID: 38307851 PMCID: PMC10837449 DOI: 10.1038/s41467-024-45180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/17/2024] [Indexed: 02/04/2024] Open
Abstract
In the context of continuous emergence of SARS-CoV-2 variants of concern (VOCs), one strategy to prevent the severe outcomes of COVID-19 is developing safe and effective broad-spectrum vaccines. Here, we present preclinical studies of a RBD vaccine derived from the Gamma SARS-CoV-2 variant adjuvanted with Alum. The Gamma-adapted RBD vaccine is more immunogenic than the Ancestral RBD vaccine in terms of inducing broader neutralizing antibodies. The Gamma RBD presents more immunogenic B-cell restricted epitopes and induces a higher proportion of specific-B cells and plasmablasts than the Ancestral RBD version. The Gamma-adapted vaccine induces antigen specific T cell immune responses and confers protection against Ancestral and Omicron BA.5 SARS-CoV-2 challenge in mice. Moreover, the Gamma RBD vaccine induces higher and broader neutralizing antibody activity than homologous booster vaccination in mice previously primed with different SARS-CoV-2 vaccine platforms. Our study indicates that the adjuvanted Gamma RBD vaccine is highly immunogenic and a broad-spectrum vaccine candidate.
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Affiliation(s)
- Lorena M Coria
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina.
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina.
| | - Juan Manuel Rodriguez
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
- Fundación Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Agostina Demaria
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - Laura A Bruno
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - Mayra Rios Medrano
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - Celeste Pueblas Castro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - Eliana F Castro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - Sabrina A Del Priore
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Andres C Hernando Insua
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
- Fundación Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Ingrid G Kaufmann
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Lucas M Saposnik
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - William B Stone
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Lineia Prado
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - Ulises S Notaro
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Ayelen N Amweg
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Pablo U Diaz
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Martin Avaro
- Servicio Virosis Respiratorias, Laboratorio de Referencia de Influenza, SARS-CoV-2 y otros Virus Respiratorios, Centro Nacional de Influenza de OPS/OMS, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas - ANLIS "Dr. Carlos G. Malbrán". Ciudad Autónoma de Buenos Aires, Buenos Aires, C1282AFF, Argentina
| | - Hugo Ortega
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Ana Ceballos
- Facultad de Medicina UBA, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, INBIRS-CONICET, Buenos Aires, Argentina
| | - Valeria Krum
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Francisco M Zurvarra
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
- Fundación Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Johanna E Sidabra
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Ignacio Drehe
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Jonathan A Baqué
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Mariana Li Causi
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Analia V De Nichilo
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
- Fundación Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Cristian J Payes
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Teresa Southard
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Julio C Vega
- Laboratorio Pablo Cassará - I+D+i, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1408GBV, Argentina
| | - Albert J Auguste
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Diego E Álvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - Juan M Flo
- Laboratorio Pablo Cassará, Unidad de I+D de Biofármacos, Ciudad Autónoma de Buenos Aires, Buenos Aires, C1440FFX, Argentina
| | - Karina A Pasquevich
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina
| | - Juliana Cassataro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín (1650), Buenos Aires, Argentina.
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín (1650), Buenos Aires, Argentina.
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Poh CL, Yahaya AAAFB, Cheong HT, Lim HX. Identification and Validation of Peptides Specifying SARS-CoV-2 B-Cell Epitopes Eliciting Neutralizing Antibodies. Methods Mol Biol 2024; 2821:165-177. [PMID: 38997488 DOI: 10.1007/978-1-0716-3914-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Vaccination is an effective means of inducing immune protection to prevent transmissible diseases. During the Covid-19 pandemic, immunizations using traditional and novel vaccine platforms such as the inactivated SARSCo-V-2 vaccine, adenoviral-vectored, and nucleic acid-based mRNA vaccines have been relatively successful in controlling the rates of infection and hospitalizations. Nevertheless, the danger posed by the emergence of SARS-CoV-2 variants would set the stage for the design of next generation vaccines. To overcome the lack of efficacy of current vaccines against emerging SARS-CoV-2 variants, new vaccines must be able to overcome the reduced effectiveness of the current vaccines. Since the current Covid-19 vaccines are dependent on the whole S-protein of Wuhan strain as the antigen, mutations have rendered the current Covid-19 vaccines less effective against variants of concern (VoCs). Instead of using the whole S-protein, peptide-based epitopes could be predicted using immunoinformatic approaches, simulation of the 3D structures, overlapping peptides covering the whole length of the S-protein or peptide arrays based on synthetic peptide combinatorial libraries comprising peptides recognizable by monoclonal antibodies. B-cell epitopes were predicted, and immunogenicity of peptides was validated in mice by immunizing mice with peptides conjugated to keyhole limpet hemocyanin (KLH) mixed with Montanide 51 as an adjuvant. The immunogenicity of epitopes that could elicit peptide specific IgGs was determined by peptide-based ELISA. Neutralizing activities were determined by cPass and pseudovirus-based neutralization assays.
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Affiliation(s)
- Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Selangor, Malaysia.
| | | | - Huey Tyng Cheong
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Selangor, Malaysia
| | - Hui Xuan Lim
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Selangor, Malaysia
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Shaprova ON, Shanshin DV, Kolosova EA, Borisevich SS, Soroka AA, Merkuleva IA, Nikitin AO, Volosnikova EA, Ushkalenko ND, Zaykovskaya AV, Pyankov OV, Elchaninova SA, Shcherbakov DN, Ilyicheva TN. Pre-Pandemic Cross-Reactive Immunity against SARS-CoV-2 among Siberian Populations. Antibodies (Basel) 2023; 12:82. [PMID: 38131804 PMCID: PMC10741209 DOI: 10.3390/antib12040082] [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: 09/28/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
In December 2019, a new coronavirus, SARS-CoV-2, was found to in Wuhan, China. Cases of infection were subsequently detected in other countries in a short period of time, resulting in the declaration of the COVID-19 pandemic by the World Health Organization (WHO) on 11 March 2020. Questions about the impact of herd immunity of pre-existing immune reactivity to SARS-CoV-2 on COVID-19 severity, associated with the immunity to seasonal manifestation, are still to be resolved and may be useful for understanding some processes that precede the emergence of a pandemic virus. Perhaps this will contribute to understanding some of the processes that precede the emergence of a pandemic virus. We assessed the specificity and virus-neutralizing capacity of antibodies reacting with the nucleocapsid and spike proteins of SARS-CoV-2 in a set of serum samples collected in October and November 2019, before the first COVID-19 cases were documented in this region. Blood serum samples from 799 residents of several regions of Siberia, Russia, (the Altai Territory, Irkutsk, Kemerovo and Novosibirsk regions, the Republic of Altai, Buryatia, and Khakassia) were analyzed. Sera of non-infected donors were collected within a study of seasonal influenza in the Russian Federation. The sample collection sites were located near the flyways and breeding grounds of wild waterfowl. The performance of enzyme-linked immunosorbent assay (ELISA) for the collected sera included the usage of recombinant SARS-CoV-2 protein antigens: full-length nucleocapsid protein (CoVN), receptor binding domain (RBD) of S-protein and infection fragment of the S protein (S5-6). There were 183 (22.9%) sera reactive to the S5-6, 270 (33.8%) sera corresponding to the full-length N protein and 128 (16.2%) sera simultaneously reactive to both these proteins. Only 5 out of 799 sera had IgG antibodies reactive to the RBD. None of the sera exhibited neutralizing activity against the nCoV/Victoria/1/2020 SARS-CoV-2 strain in Vero E6 cell culture. The data obtained in this study suggest that some of the population of the analyzed regions of Russia had cross-reactive humoral immunity against SARS-CoV-2 before the COVID-19 pandemic started. Moreover, among individuals from relatively isolated regions, there were significantly fewer reliably cross-reactive sera. The possible significance of these data and impact of cross-immunity to SARS-CoV-2 on the prevalence and mortality of COVID-19 needs further assessment.
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Affiliation(s)
- Olga N. Shaprova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Daniil V. Shanshin
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Evgeniia A. Kolosova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 450078 Ufa, Russia;
- Institute of Intelligent Cybernetic Systems, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia;
| | - Artem A. Soroka
- Institute of Intelligent Cybernetic Systems, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia;
| | - Iuliia A. Merkuleva
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Artem O. Nikitin
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Ekaterina A. Volosnikova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Nikita D. Ushkalenko
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Svetlana A. Elchaninova
- Department of Biochemistry and Clinical Laboratory Diagnostics, Altai State Medical University, 656038 Barnaul, Russia;
| | - Dmitry N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Tatiana N. Ilyicheva
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
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5
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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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6
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Khalid K, Poh CL. The development of DNA vaccines against SARS-CoV-2. Adv Med Sci 2023; 68:213-226. [PMID: 37364379 PMCID: PMC10290423 DOI: 10.1016/j.advms.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND The COVID-19 pandemic exerted significant impacts on public health and global economy. Research efforts to develop vaccines at warp speed against SARS-CoV-2 led to novel mRNA, viral vectored, and inactivated vaccines being administered. The current COVID-19 vaccines incorporate the full S protein of the SARS-CoV-2 Wuhan strain but rapidly emerging variants of concern (VOCs) have led to significant reductions in protective efficacies. There is an urgent need to develop next-generation vaccines which could effectively prevent COVID-19. METHODS PubMed and Google Scholar were systematically reviewed for peer-reviewed papers up to January 2023. RESULTS A promising solution to the problem of emerging variants is a DNA vaccine platform since it can be easily modified. Besides expressing whole protein antigens, DNA vaccines can also be constructed to include specific nucleotide genes encoding highly conserved and immunogenic epitopes from the S protein as well as from other structural/non-structural proteins to develop effective vaccines against VOCs. DNA vaccines are associated with low transfection efficiencies which could be enhanced by chemical, genetic, and molecular adjuvants as well as delivery systems. CONCLUSIONS The DNA vaccine platform offers a promising solution to the design of effective vaccines. The challenge of limited immunogenicity in humans might be solved through the use of genetic modifications such as the addition of nuclear localization signal (NLS) peptide gene, strong promoters, MARs, introns, TLR agonists, CD40L, and the development of appropriate delivery systems utilizing nanoparticles to increase uptake by APCs in enhancing the induction of potent immune responses.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia.
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7
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Lerner A, Benzvi C, Vojdani A. SARS-CoV-2 Gut-Targeted Epitopes: Sequence Similarity and Cross-Reactivity Join Together for Molecular Mimicry. Biomedicines 2023; 11:1937. [PMID: 37509576 PMCID: PMC10376948 DOI: 10.3390/biomedicines11071937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The gastrointestinal tract can be heavily infected by SARS-CoV-2. Being an auto-immunogenic virus, SARS-CoV-2 represents an environmental factor that might play a role in gut-associated autoimmune diseases. However, molecular mimicry between the virus and the intestinal epitopes is under-investigated. The present study aims to elucidate sequence similarity between viral antigens and human enteric sequences, based on known cross-reactivity. SARS-CoV-2 epitopes that cross-react with human gut antigens were explored, and sequence alignment was performed against self-antigens implicated in enteric autoimmune conditions. Experimental SARS-CoV-2 epitopes were aggregated from the Immune Epitope Database (IEDB), while enteric antigens were obtained from the UniProt Knowledgebase. A Pairwise Local Alignment tool, EMBOSS Matcher, was employed for the similarity search. Sequence similarity and targeted cross-reactivity were depicted between 10 pairs of immunoreactive epitopes. Similar pairs were found in four viral proteins and seven enteric antigens related to ulcerative colitis, primary biliary cholangitis, celiac disease, and autoimmune hepatitis. Antibodies made against the viral proteins that were cross-reactive with human gut antigens are involved in several essential cellular functions. The relationship and contribution of those intestinal cross-reactive epitopes to SARS-CoV-2 or its potential contribution to gut auto-immuno-genesis are discussed.
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Affiliation(s)
- Aaron Lerner
- Chaim Sheba Medical Center, The Zabludowicz Research Center for Autoimmune Diseases, Ramat Gan 52621, Israel
- Research Department, Ariel University, Ariel 40700, Israel
| | - Carina Benzvi
- Chaim Sheba Medical Center, The Zabludowicz Research Center for Autoimmune Diseases, Ramat Gan 52621, Israel
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8
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Peptide microarray IgM and IgG screening of pre-SARS-CoV-2 human serum samples from Zimbabwe for reactivity with peptides from all seven human coronaviruses: a cross-sectional study. THE LANCET MICROBE 2023. [PMCID: PMC9931394 DOI: 10.1016/s2666-5247(22)00295-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
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9
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State of the art in epitope mapping and opportunities in COVID-19. Future Sci OA 2023; 16:FSO832. [PMID: 36897962 PMCID: PMC9987558 DOI: 10.2144/fsoa-2022-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
The understanding of any disease calls for studying specific biological structures called epitopes. One important tool recently drawing attention and proving efficiency in both diagnosis and vaccine development is epitope mapping. Several techniques have been developed with the urge to provide precise epitope mapping for use in designing sensitive diagnostic tools and developing rpitope-based vaccines (EBVs) as well as therapeutics. In this review, we will discuss the state of the art in epitope mapping with a special emphasis on accomplishments and opportunities in combating COVID-19. These comprise SARS-CoV-2 variant analysis versus the currently available immune-based diagnostic tools and vaccines, immunological profile-based patient stratification, and finally, exploring novel epitope targets for potential prophylactic, therapeutic or diagnostic agents for COVID-19.
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10
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Muacevic A, Adler JR. Mitogen Activated Protein Kinase (MAPK) Activation, p53, and Autophagy Inhibition Characterize the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike Protein Induced Neurotoxicity. Cureus 2022; 14:e32361. [PMID: 36514706 PMCID: PMC9733976 DOI: 10.7759/cureus.32361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 12/13/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and prions use common pathogenic pathways to induce toxicity in neurons. Infectious prions rapidly activate the p38 mitogen activated protein kinase (MAPK) pathway, and SARS-CoV-2 spike proteins rapidly activate both the p38 MAPK and c-Jun NH2-terminal kinase (JNK) pathways through toll-like receptor signaling, indicating the potential for similar neurotoxicity, causing prion and prion-like disease. In this review, we analyze the roles of autophagy inhibition, molecular mimicry, elevated intracellular p53 levels and reduced Wild-type p53-induced phosphatase 1 (Wip1) and dual-specificity phosphatase (DUSP) expression in neurons in the disease process. The pathways induced by the spike protein via toll-like receptor activation induce both the upregulation of PrPC (the normal isoform of the prion protein, PrP) and the expression of β amyloid. Through the spike-protein-dependent elevation of p53 levels via β amyloid metabolism, increased PrPC expression can lead to PrP misfolding and impaired autophagy, generating prion disease. We conclude that, according to the age of the spike protein-exposed patient and the state of their cellular autophagy activity, excess sustained activity of p53 in neurons may be a catalytic factor in neurodegeneration. An autoimmune reaction via molecular mimicry likely also contributes to neurological symptoms. Overall results suggest that neurodegeneration is in part due to the intensity and duration of spike protein exposure, patient advanced age, cellular autophagy activity, and activation, function and regulation of p53. Finally, the neurologically damaging effects can be cumulatively spike-protein dependent, whether exposure is by natural infection or, more substantially, by repeated mRNA vaccination.
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11
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Chao CH, Cheng D, Huang SW, Chuang YC, Yeh TM, Wang JR. Serological responses triggered by different SARS-CoV-2 vaccines against SARS-CoV-2 variants in Taiwan. Front Immunol 2022; 13:1023943. [PMID: 36458016 PMCID: PMC9705976 DOI: 10.3389/fimmu.2022.1023943] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/31/2022] [Indexed: 09/05/2023] Open
Abstract
Broadly neutralizing ability is critical for developing the next-generation SARS-CoV-2 vaccine. We collected sera samples between December 2021-January 2022 from 113 Taiwan naïve participants after their second dose of homologous vaccine (AZD1222, mRNA-1273, BNT162-b2, and MVC-COV1901) and compared the differences in serological responses of various SARS-CoV-2 vaccines. Compared to AZD1222, the two mRNA vaccines could elicit a higher level of anti-S1-RBD binding antibodies with higher broadly neutralizing ability evaluated using pseudoviruses of various SARS-CoV-2 lineages. The antigenic maps produced from the neutralization data implied that Omicron represents very different antigenic characteristics from the ancestral lineage. These results suggested that constantly administering the vaccine with ancestral Wuhan spike is insufficient for the Omicron outbreak. In addition, we found that anti-ACE2 autoantibodies were significantly increased in all four vaccinated groups compared to the unvaccinated pre-pandemic group, which needed to be investigated in the future.
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Affiliation(s)
- Chiao-Hsuan Chao
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Dayna Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | | | - Trai-Ming Yeh
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
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12
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Pacheco-Olvera DL, Saint Remy-Hernández S, García-Valeriano MG, Rivera-Hernández T, López-Macías C. Bioinformatic Analysis of B- and T-cell Epitopes from SARS-CoV-2 Structural Proteins and their Potential Cross-reactivity with Emerging Variants and other Human Coronaviruses. Arch Med Res 2022; 53:694-710. [PMID: 36336501 PMCID: PMC9633039 DOI: 10.1016/j.arcmed.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/23/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Background The mutations in SARS-CoV-2 variants of concern (VOC) facilitate the virus’ escape from the neutralizing antibodies induced by vaccines. However, the protection from hospitalization and death is not significantly diminished. Both vaccine boosters and infection improve immune responses and provide protection, suggesting that conserved and/or cross-reactive epitopes could be involved. While several important T- and B-cell epitopes have been identified, mainly in the S protein, the M and N proteins and their potential cross-reactive epitopes with other coronaviruses remain largely unexplored. Aims To identify and map new potential B- and T-cell epitopes within the SARS-CoV-2 S, M and N proteins, as well as cross-reactive epitopes with human coronaviruses. Methods Different bioinformatics tools were used to: i) Identify new and compile previously-reported B-and T-cell epitopes from SARS-CoV-2 S, M and N proteins; ii) Determine the mutations in S protein from VOC that affect B- and T-cell epitopes, and; iii) Identify cross-reactive epitopes with coronaviruses relevant to human health. Results New, potential B- and T-cell epitopes from S, M and N proteins as well as cross-reactive epitopes with other coronaviruses were found and mapped within the proteins’ structures. Conclusion Numerous potential B- and T-cell epitopes were found in S, M and N proteins, some of which are conserved between coronaviruses. VOCs present mutations within important epitopes in the S protein; however, a significant number of other epitopes remain unchanged. The epitopes identified here may contribute to augmenting the protective response to SARS-CoV-2 and its variants induced by infection and/or vaccination, and may also be used for the rational design of novel broad-spectrum coronavirus vaccines.
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Affiliation(s)
- Diana Laura Pacheco-Olvera
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Stephanie Saint Remy-Hernández
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - María Guadalupe García-Valeriano
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Tania Rivera-Hernández
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México,Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México,Address reprint requests to: Constantino López-Macías or Tania Rivera-Hern..ndez, UMAE, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, IMSS, Av. Cuahutémoc 330, 06720, Ciudad de México, México; Phone: (+52) (55) 5627 6900 ext. 21476
| | - Constantino López-Macías
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México,Address reprint requests to: Constantino López-Macías or Tania Rivera-Hern..ndez, UMAE, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, IMSS, Av. Cuahutémoc 330, 06720, Ciudad de México, México; Phone: (+52) (55) 5627 6900 ext. 21476
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13
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Wang A, Tian Y, Liu H, Ding P, Chen Y, Liang C, Du Y, Jiang D, Zhu X, Yin J, Zhang G. Identification of three conserved linear B cell epitopes on the SARS-CoV-2 spike protein. Emerg Microbes Infect 2022; 11:2120-2131. [PMID: 35916768 PMCID: PMC9487943 DOI: 10.1080/22221751.2022.2109515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Spike (S) glycoproteins is the most significant structural protein of SARS-CoV-2 and a key target for neutralizing antibodies. In light of the ongoing SARS-CoV-2 pandemic, identification and screening of epitopes of spike glycoproteins will provide vital progress in the development of sensitive and specific diagnostic tools. In the present study, NTD, RBD and S2 gene were inserted to the pcDNA3.1(+) vector and designed with N-terminal 6×His-tag for fusion expression in HEK293F cells by transient transfection. Six monoclonal antibodies (4G, 9E, 4B, 7D, 8F, 3D) were prepared using the expressed proteins by cell fusion technique. The characterization of mAbs were performed by indirect -ELISA, western blot and IFA. We designed 49 overlapping synthetized peptides cover the extracellular region of S protein which 6 amino acid residues were offset between adjacent (S1-S49). Peptides S12, S19 and S49 were identified as the immunodominant epitopes regions by the mAbs. These regions were further truncated and the peptides S12.2 286TDAVDCALDPLS297, S19.2 464FERDISTEIYQA475 and S49.4 1202ELGKYEQYIKWP1213 were identified as B- cell linear epitopes for the first time. Alanine scans showed that, the D467, I468, E471, Q474, A475 of the epitope S19.2 and K1205, Q1208, Y1209 of the epitope S49.4 were the core sites involved in the mAbs binding. Multiple sequence alignment analysis showed that these three epitopes were highly conserved among the variants of concern (VOCs) and variants of interest (VOIs). Taken together, the findings provide a potential material for rapid diagnosis methods of COVID-19.
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Affiliation(s)
- Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Yuanyuan Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Hongliang Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Peiyang Ding
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Chao Liang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Yongkun Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Dawei Jiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Xifang Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Jiajia Yin
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Gaiping Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China.,College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, P.R. China
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14
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Diebold O, Gonzalez V, Venditti L, Sharp C, Blake RA, Tan WS, Stevens J, Caddy S, Digard P, Borodavka A, Gaunt E. Using Species a Rotavirus Reverse Genetics to Engineer Chimeric Viruses Expressing SARS-CoV-2 Spike Epitopes. J Virol 2022; 96:e0048822. [PMID: 35758692 PMCID: PMC9327695 DOI: 10.1128/jvi.00488-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/31/2022] [Indexed: 02/02/2023] Open
Abstract
Species A rotavirus (RVA) vaccines based on live attenuated viruses are used worldwide in humans. The recent establishment of a reverse genetics system for rotoviruses (RVs) has opened the possibility of engineering chimeric viruses expressing heterologous peptides from other viral or microbial species in order to develop polyvalent vaccines. We tested the feasibility of this concept by two approaches. First, we inserted short SARS-CoV-2 spike peptides into the hypervariable region of the simian RV SA11 strain viral protein (VP) 4. Second, we fused the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, or the shorter receptor binding motif (RBM) nested within the RBD, to the C terminus of nonstructural protein (NSP) 3 of the bovine RV RF strain, with or without an intervening Thosea asigna virus 2A (T2A) peptide. Mutating the hypervariable region of SA11 VP4 impeded viral replication, and for these mutants, no cross-reactivity with spike antibodies was detected. To rescue NSP3 mutants, we established a plasmid-based reverse genetics system for the bovine RV RF strain. Except for the RBD mutant that demonstrated a rescue defect, all NSP3 mutants delivered endpoint infectivity titers and exhibited replication kinetics comparable to that of the wild-type virus. In ELISAs, cell lysates of an NSP3 mutant expressing the RBD peptide showed cross-reactivity with a SARS-CoV-2 RBD antibody. 3D bovine gut enteroids were susceptible to infection by all NSP3 mutants, but cross-reactivity with SARS-CoV-2 RBD antibody was only detected for the RBM mutant. The tolerance of large SARS-CoV-2 peptide insertions at the C terminus of NSP3 in the presence of T2A element highlights the potential of this approach for the development of vaccine vectors targeting multiple enteric pathogens simultaneously. IMPORTANCE We explored the use of rotaviruses (RVs) to express heterologous peptides, using SARS-CoV-2 as an example. Small SARS-CoV-2 peptide insertions (<34 amino acids) into the hypervariable region of the viral protein 4 (VP4) of RV SA11 strain resulted in reduced viral titer and replication, demonstrating a limited tolerance for peptide insertions at this site. To test the RV RF strain for its tolerance for peptide insertions, we constructed a reverse genetics system. NSP3 was C-terminally tagged with SARS-CoV-2 spike peptides of up to 193 amino acids in length. With a T2A-separated 193 amino acid tag on NSP3, there was no significant effect on the viral rescue efficiency, endpoint titer, and replication kinetics. Tagged NSP3 elicited cross-reactivity with SARS-CoV-2 spike antibodies in ELISA. We highlight the potential for development of RV vaccine vectors targeting multiple enteric pathogens simultaneously.
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Affiliation(s)
- Ola Diebold
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Victoria Gonzalez
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Luca Venditti
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Colin Sharp
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Rosemary A. Blake
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Wenfang S. Tan
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Joanne Stevens
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Sarah Caddy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul Digard
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eleanor Gaunt
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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15
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Lim HX, Masomian M, Khalid K, Kumar AU, MacAry PA, Poh CL. Identification of B-Cell Epitopes for Eliciting Neutralizing Antibodies against the SARS-CoV-2 Spike Protein through Bioinformatics and Monoclonal Antibody Targeting. Int J Mol Sci 2022; 23:ijms23084341. [PMID: 35457159 PMCID: PMC9029629 DOI: 10.3390/ijms23084341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global public health crisis. Effective COVID-19 vaccines developed by Pfizer-BioNTech, Moderna, and Astra Zeneca have made significant impacts in controlling the COVID-19 burden, especially in reducing the transmission of SARS-CoV-2 and hospitalization incidences. In view of the emergence of new SARS-CoV-2 variants, vaccines developed against the Wuhan strain were less effective against the variants. Neutralizing antibodies produced by B cells are a critical component of adaptive immunity, particularly in neutralizing viruses by blocking virus attachment and entry into cells. Therefore, the identification of protective linear B-cell epitopes can guide epitope-based peptide designs. This study reviews the identification of SARS-CoV-2 B-cell epitopes within the spike, membrane and nucleocapsid proteins that can be incorporated as potent B-cell epitopes into peptide vaccine constructs. The bioinformatic approach offers a new in silico strategy for the mapping and identification of potential B-cell epitopes and, upon in vivo validation, would be useful for the rapid development of effective multi-epitope-based vaccines. Potent B-cell epitopes were identified from the analysis of three-dimensional structures of monoclonal antibodies in a complex with SARS-CoV-2 from literature mining. This review provides significant insights into the elicitation of potential neutralizing antibodies by potent B-cell epitopes, which could advance the development of multi-epitope peptide vaccines against SARS-CoV-2.
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Affiliation(s)
- Hui Xuan Lim
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
| | - Malihe Masomian
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
| | - Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
| | - Asqwin Uthaya Kumar
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
| | - Paul A. MacAry
- Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore;
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
- Correspondence:
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16
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Chen J, Deng Y, Huang B, Han D, Wang W, Huang M, Zhai C, Zhao Z, Yang R, Zhao Y, Wang W, Zhai D, Tan W. DNA Vaccines Expressing the Envelope and Membrane Proteins Provide Partial Protection Against SARS-CoV-2 in Mice. Front Immunol 2022; 13:827605. [PMID: 35281016 PMCID: PMC8907653 DOI: 10.3389/fimmu.2022.827605] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a public health emergency of international concern, and an effective vaccine is urgently needed to control the pandemic. Envelope (E) and membrane (M) proteins are highly conserved structural proteins among SARS-CoV-2 and SARS-CoV and have been proposed as potential targets for the development of cross-protective vaccines. Here, synthetic DNA vaccines encoding SARS-CoV-2 E/M proteins (called p-SARS-CoV-2-E/M) were developed, and mice were immunised with three doses via intramuscular injection and electroporation. Significant cellular immune responses were elicited, whereas no robust humoral immunity was detected. In addition, novel H-2d-restricted T-cell epitopes were identified. Notably, although no drop in lung tissue virus titre was detected in DNA-vaccinated mice post-challenge with SARS-CoV-2, immunisation with either p-SARS-CoV-2-E or p-SARS-CoV-2-M provided minor protection and co-immunisation with p-SARS-CoV-2-E+M increased protection. Therefore, E/M proteins should be considered as vaccine candidates as they may be valuable in the optimisation of vaccination strategies against COVID-19.
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Affiliation(s)
- Jinni Chen
- School of Public Health, Xinxiang Medical University, Xinxiang, China.,National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yao Deng
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Baoying Huang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Di Han
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.,Basic Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Wen Wang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Mengjing Huang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.,Basic Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Chengcheng Zhai
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.,School of Public Health, Baotou Medical College, Baotou, China
| | - Zhimin Zhao
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Ren Yang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Ying Zhao
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Wenling Wang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Desheng Zhai
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Wenjie Tan
- School of Public Health, Xinxiang Medical University, Xinxiang, China.,National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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17
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Pack SM, Peters PJ. SARS-CoV-2-Specific Vaccine Candidates; the Contribution of Structural Vaccinology. Vaccines (Basel) 2022; 10:236. [PMID: 35214693 PMCID: PMC8877865 DOI: 10.3390/vaccines10020236] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2 vaccine production has taken us by storm. We aim to fill in the history of concepts and the work of pioneers and provide a framework of strategies employing structural vaccinology. Cryo-electron microscopy became crucial in providing three-dimensional (3D) structures and creating candidates eliciting T and B cell-mediated immunity. It also determined structural changes in the emerging mutants in order to design new constructs that can be easily, quickly and safely added to the vaccines. The full-length spike (S) protein, the S1 subunit and its receptor binding domain (RBD) of the virus are the best candidates. The vaccine development to cease this COVID-19 pandemic sets a milestone for the pan-coronavirus vaccine's designing and manufacturing. By employing structural vaccinology, we propose that the mRNA and the protein sequences of the currently approved vaccines should be modified rapidly to keep up with the more infectious new variants.
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Affiliation(s)
| | - Peter J. Peters
- The Maastricht Multimodal Molecular Imaging Institute (M4i), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, 6229 ER Maastricht, The Netherlands;
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18
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Polyiam K, Ruengjitchatchawalya M, Mekvichitsaeng P, Kaeoket K, Hoonsuwan T, Joiphaeng P, Roshorm YM. Immunodominant and Neutralizing Linear B-Cell Epitopes Spanning the Spike and Membrane Proteins of Porcine Epidemic Diarrhea Virus. Front Immunol 2022; 12:785293. [PMID: 35126354 PMCID: PMC8807655 DOI: 10.3389/fimmu.2021.785293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is the causative agent of PED, an enteric disease that causes high mortality rates in piglets. PEDV is an alphacoronavirus that has high genetic diversity. Insights into neutralizing B-cell epitopes of all genetically diverse PEDV strains are of importance, particularly for designing a vaccine that can provide broad protection against PEDV. In this work, we aimed to explore the landscape of linear B-cell epitopes on the spike (S) and membrane (M) proteins of global PEDV strains. All amino acid sequences of the PEDV S and M proteins were retrieved from the NCBI database and grouped. Immunoinformatics-based methods were next developed and used to identify putative linear B-cell epitopes from 14 and 5 consensus sequences generated from distinct groups of the S and M proteins, respectively. ELISA testing predicted peptides with PEDV-positive sera revealed nine novel immunodominant epitopes on the S protein. Importantly, seven of these novel immunodominant epitopes and other subdominant epitopes were demonstrated to be neutralizing epitopes by neutralization–inhibition assay. Our findings unveil important roles of the PEDV S2 subunit in both immune stimulation and virus neutralization. Additionally, our study shows the first time that the M protein is also the target of PEDV neutralization with seven neutralizing epitopes identified. Conservancy profiles of the epitopes are also provided. In this study, we offer immunoinformatics-based methods for linear B-cell epitope identification and a more complete profile of linear B-cell epitopes across the PEDV S and M proteins, which may contribute to the development of a greater next-generation PEDV vaccine as well as peptide-based immunoassays.
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Affiliation(s)
- Kanokporn Polyiam
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Marasri Ruengjitchatchawalya
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Phenjun Mekvichitsaeng
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Kampon Kaeoket
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Sciences, Mahidol University, Salaya, Thailand
| | | | | | - Yaowaluck Maprang Roshorm
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- *Correspondence: Yaowaluck Maprang Roshorm,
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