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Safitri IA, Sugijo Y, Puspasari F, Masduki FF, Ihsanawati, Giri-Rachman EA, Artarini AA, Tan MI, Natalia D. Immunogenicity studies of recombinant RBD SARS-CoV-2 as a COVID-19 vaccine candidate produced in Escherichia coli. Vaccine X 2024; 16:100443. [PMID: 38304876 PMCID: PMC10832452 DOI: 10.1016/j.jvacx.2024.100443] [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: 07/03/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 -related global COVID-19 pandemic has been impacting millions of people since its outbreak in 2020. COVID-19 vaccination has proven highly efficient in reducing illness severity and preventing infection-related fatalities. The World Health Organization has granted emergency use approval to multiple, including protein subunit technology-based, COVID-19 vaccines. Foreseeably, additional COVID-19 subunit vaccine development would be essential to meet the accessible and growing demand for effective vaccines, especially for Low-Middle-Income Countries (LMIC). The SARS-CoV-2 spike protein receptor binding domain (RBD), as the primary target for neutralizing antibodies, holds significant potential for future COVID-19 subunit vaccine development. In this study, we developed a recombinant Escherichia coli-expressed RBD (rRBD) as a vaccine candidate and evaluated its immunogenicity and preliminary toxicity in BALB/c mice. The rRBD induced humoral immune response from day 7 post-vaccination and, following the booster doses, the IgG levels increased dramatically in mice. Interestingly, our vaccine candidate also significantly induced cellular immune response, indicated by the incrased IFN-ɣ-producing cell numbers. We observed no adverse effect or local reactogenicity either in control or treated mice. Taken together, our discoveries could potentially support efficient and cost-effective vaccine antigen production, from which LMICs could particularly benefit.
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Affiliation(s)
- Intan Aghniya Safitri
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
| | - Yovin Sugijo
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Fernita Puspasari
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Fifi Fitriyah Masduki
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Ihsanawati
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Ernawati Arifin Giri-Rachman
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Aluicia Anita Artarini
- Pharmaceutical Biotechnology Laboratory, Pharmaceutics Department, School of Pharmacy, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Marselina Irasonia Tan
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Dessy Natalia
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
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Shikha S, Jogi MK, Jha R, Kumar RA, Sah T, Singh P, Sagar R, Kumar A, Marwal R, Ponnusamy K, Agarwal SM, Kumar RS, Arif N, Bharadwaj M, Singh S, Kumar P. Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein. Front Immunol 2023; 14:1209513. [PMID: 37849762 PMCID: PMC10577267 DOI: 10.3389/fimmu.2023.1209513] [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: 04/20/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike's mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes.
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Affiliation(s)
- Sristy Shikha
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Mukesh Kumar Jogi
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Ruchika Jha
- Department of Biotechnology, Vinoba Bhave University, Hazaribagh, Jharkhand, India
| | - Rana Amit Kumar
- Department of Biotechnology, Anugrah Narayan College, Patna, Bihar, India
| | - Tathagat Sah
- Department of Chemical Engineering and Biotechnology, Beant College of Engineering and Technology, Gurdaspur, Punjab, India
| | - Pushpendra Singh
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Ritu Sagar
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Anuj Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control, Delhi, India
| | | | - Subhash Mohan Agarwal
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - R. Suresh Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Nazneen Arif
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Mausumi Bharadwaj
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Shalini Singh
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Pramod Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
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3
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Jiang M, Wang A, Sun Y, Li Y, Chen Y, Zhou J, Liu H, Ding P, Qi Y, Li N, Zhang G. Development of a Gold Nanoparticle-Based Immunochromatographic Strip for Rapid Detection of Porcine Circovirus Type 2. Microbiol Spectr 2023; 11:e0195322. [PMID: 37466437 PMCID: PMC10434270 DOI: 10.1128/spectrum.01953-22] [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: 05/31/2022] [Accepted: 05/15/2023] [Indexed: 07/20/2023] Open
Abstract
Porcine circovirus type 2 (PCV2) is an important swine infectious pathogen that seriously threatens the global swine industry. PCV2 Cap protein is the only structural and the main immunogenic protein constituting the viral capsid. In this study, a gold nanoparticle-based immunochromatographic strip with high sensitivity and specificity was developed which could be used for rapid detection of PCV2 virions or Cap protein in research. The visual detection limit of the strip was 103.18 50% tissue culture infective does (TCID50)/mL for PCV2, and 2.03 μg/mL for PCV2 Cap protein. No cross-reactivity was observed with the PCV1 and PCV3 Cap proteins and other common swine pathogens such as porcine reproductive and respiratory syndrome virus, classical swine fever virus, pseudorabies virus, porcine epidemic diarrhea virus, porcine parvovirus, and swine influenza virus. The repeatability of the strip was good. The stability of the strip was perfect for 12 months in a dry state at room temperature. Visual results could be obtained within 5 min by simply inserting the strip into the diluted sample. The strip is a time-saving, labor-saving, and reliable tool for testing of PCV2 virions or Cap protein in research. The idea of this study might open a new perspective for the application of the strip. IMPORTANCE Porcine circovirus type 2 (PCV2) Cap protein is the only structural and the main immunogenic protein constituting the viral capsid. Although many methods can be used to identify PCV2 or PCV2 Cap protein in vaccine research, they usually require high workload and time. The developed strip can specifically detect PCV2 virions or Cap protein, and visual qualitative results can be obtained within 5 min by simply diluting the sample and inserting the strip into the sample. The final value of the strip is providing a simple and time-saving method for real-time monitoring of PCV2 antigen in vaccine research with reliable results, such as the different stages of PCV2 Cap protein expression and purification, as well as the different stages of PCV2 reproduction and purification.
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Affiliation(s)
- Min Jiang
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Provincial Key Laboratory of Immunobiology, Zhengzhou, China
| | - Aiping Wang
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Agricultural University, Zhengzhou, Henan, China
- Henan Provincial Key Laboratory of Immunobiology, Zhengzhou, China
| | - Yaning Sun
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
| | - Yuan Li
- School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yumei Chen
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Provincial Key Laboratory of Immunobiology, Zhengzhou, China
| | - Jingming Zhou
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Provincial Key Laboratory of Immunobiology, Zhengzhou, China
| | - Hongliang Liu
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Provincial Key Laboratory of Immunobiology, Zhengzhou, China
| | - Peiyang Ding
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Provincial Key Laboratory of Immunobiology, Zhengzhou, China
| | - Yanhua Qi
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Provincial Key Laboratory of Immunobiology, Zhengzhou, China
| | - Ning Li
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
| | - Gaiping Zhang
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
- Henan Agricultural University, Zhengzhou, Henan, China
- Henan Provincial Key Laboratory of Immunobiology, Zhengzhou, China
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Kaewchim K, Glab-ampai K, Mahasongkram K, Saenlom T, Thepsawat W, Chulanetra M, Choowongkomon K, Sookrung N, Chaicumpa W. Neutralizing and Enhancing Epitopes of the SARS-CoV-2 Receptor-Binding Domain (RBD) Identified by Nanobodies. Viruses 2023; 15:1252. [PMID: 37376552 PMCID: PMC10301551 DOI: 10.3390/v15061252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Engineered nanobodies (VHs) to the SARS-CoV-2 receptor-binding domain (RBD) were generated using phage display technology. A recombinant Wuhan RBD served as bait in phage panning to fish out nanobody-displaying phages from a VH/VHH phage display library. Sixteen phage-infected E. coli clones produced nanobodies with 81.79-98.96% framework similarity to human antibodies; thus, they may be regarded as human nanobodies. Nanobodies of E. coli clones 114 and 278 neutralized SARS-CoV-2 infectivity in a dose-dependent manner; nanobodies of clones 103 and 105 enhanced the virus's infectivity by increasing the cytopathic effect (CPE) in an infected Vero E6 monolayer. These four nanobodies also bound to recombinant Delta and Omicron RBDs and native SARS-CoV-2 spike proteins. The neutralizing VH114 epitope contains the previously reported VYAWN motif (Wuhan RBD residues 350-354). The linear epitope of neutralizing VH278 at Wuhan RBD 319RVQPTESIVRFPNITN334 is novel. In this study, for the first time, we report SARS-CoV-2 RBD-enhancing epitopes, i.e., a linear VH103 epitope at RBD residues 359NCVADVSVLYNSAPFFTFKCYG380, and the VH105 epitope, most likely conformational and formed by residues in three RBD regions that are spatially juxtaposed upon the protein folding. Data obtained in this way are useful for the rational design of subunit SARS-CoV-2 vaccines that should be devoid of enhancing epitopes. VH114 and VH278 should be tested further for clinical use against COVID-19.
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Affiliation(s)
- Kanasap Kaewchim
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand;
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kittirat Glab-ampai
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kodchakorn Mahasongkram
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Thanatsaran Saenlom
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Watayagorn Thepsawat
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Monrat Chulanetra
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Sciences, Kasetsart University, Bangkok 10900, Thailand;
| | - Nitat Sookrung
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
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5
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Piubelli C, Ruggiero A, Calciano L, Mazzi C, Castilletti C, Tiberti N, Caldrer S, Verzè M, Longoni SS, Accordini S, Bisoffi Z, Zipeto D. Subjects who developed SARS-CoV-2 specific IgM after vaccination show a longer humoral immunity and a lower frequency of infection. EBioMedicine 2023; 89:104471. [PMID: 36796232 PMCID: PMC9925293 DOI: 10.1016/j.ebiom.2023.104471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND We have previously shown that eliciting SARS-CoV-2-specific IgM after vaccination is associated with higher levels of SARS-CoV-2 neutralizing IgG. This study aims to assess whether IgM development is also associated with longer-lasting immunity. METHODS We analysed anti-SARS-CoV-2 spike protein IgG and IgM (IgG-S, IgM-S), and anti-nucleocapsid IgG (IgG-N) in 1872 vaccinees at different time points: before the first dose (D1; w0), before the second dose (D2; w3) at three (w6) and 23 weeks (w29) after D2; moreover, 109 subjects were further tested at the booster dose (D3, w44), at 3 weeks (w47) and 6 months (w70) after D3. Two-level linear regression models were used to evaluate the differences in IgG-S levels. FINDINGS In subjects who had no evidence of a previous infection at D1 (non-infected, NI), IgM-S development after D1 and D2 was associated with higher IgG-S levels at short (w6, p < 0.0001) and long (w29, p < 0.001) follow-up. Similar IgG-S levels were observed after D3. The majority (28/33, 85%) of the NI subjects who had developed IgM-S in response to vaccination did not experience infection. INTERPRETATION The development of anti-SARS-CoV-2 IgM-S following D1 and D2 is associated with higher IgG-S levels. Most individuals who developed IgM-S never became infected, suggesting that IgM elicitation may be associated with a lower risk of infection. FUNDING "Fondi Ricerca Corrente" and "Progetto Ricerca Finalizzata" COVID-2020 (Italian Ministry of Health); FUR 2020 Department of Excellence 2018-2022 (MIUR, Italy); the Brain Research Foundation Verona.
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Affiliation(s)
- Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Alessandra Ruggiero
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Lucia Calciano
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Cristina Mazzi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Concetta Castilletti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Natalia Tiberti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Sara Caldrer
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Matteo Verzè
- Health Department, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Silvia Stefania Longoni
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Simone Accordini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Donato Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy.
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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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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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8
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Wang D, Chen Y, Xiang S, Hu H, Zhan Y, Yu Y, Zhang J, Wu P, Liu FY, Kai T, Ding P. Recent advances in immunoassay technologies for the detection of human coronavirus infections. Front Cell Infect Microbiol 2023; 12:1040248. [PMID: 36683684 PMCID: PMC9845787 DOI: 10.3389/fcimb.2022.1040248] [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: 09/09/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the seventh coronavirus (CoV) that has spread in humans and has become a global pandemic since late 2019. Efficient and accurate laboratory diagnostic methods are one of the crucial means to control the development of the current pandemic and to prevent potential future outbreaks. Although real-time reverse transcription-polymerase chain reaction (rRT-PCR) is the preferred laboratory method recommended by the World Health Organization (WHO) for diagnosing and screening SARS-CoV-2 infection, the versatile immunoassays still play an important role for pandemic control. They can be used not only as supplemental tools to identify cases missed by rRT-PCR, but also for first-line screening tests in areas with limited medical resources. Moreover, they are also indispensable tools for retrospective epidemiological surveys and the evaluation of the effectiveness of vaccination. In this review, we summarize the mainstream immunoassay methods for human coronaviruses (HCoVs) and address their benefits, limitations, and applications. Then, technical strategies based on bioinformatics and advanced biosensors were proposed to improve the performance of these methods. Finally, future suggestions and possibilities that can lead to higher sensitivity and specificity are provided for further research.
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Affiliation(s)
- Danqi Wang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Yuejun Chen
- Breast Surgery Department I, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Shan Xiang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Huiting Hu
- Breast Surgery Department I, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Yujuan Zhan
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ying Yu
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Jingwen Zhang
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Pian Wu
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Fei Yue Liu
- Department of Economics and Management, ChangSha University, Changsha, Hunan, China
| | - Tianhan Kai
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping Ding
- Xiang Ya School of Public Health, Central South University, Changsha, Hunan, China
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9
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Bajoria S, Kaur K, Kumru OS, Van Slyke G, Doering J, Novak H, Rodriguez Aponte SA, Dalvie NC, Naranjo CA, Johnston RS, Silverman JM, Kleanthous H, Love JC, Mantis NJ, Joshi SB, Volkin DB. Antigen-adjuvant interactions, stability, and immunogenicity profiles of a SARS-CoV-2 receptor-binding domain (RBD) antigen formulated with aluminum salt and CpG adjuvants. Hum Vaccin Immunother 2022; 18:2079346. [PMID: 35666264 PMCID: PMC9621007 DOI: 10.1080/21645515.2022.2079346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023] Open
Abstract
Low-cost, refrigerator-stable COVID-19 vaccines will facilitate global access and improve vaccine coverage in low- and middle-income countries. To this end, subunit-based approaches targeting the receptor-binding domain (RBD) of SARS-CoV-2 Spike protein remain attractive. Antibodies against RBD neutralize SARS-CoV-2 by blocking viral attachment to the host cell receptor, ACE2. Here, a yeast-produced recombinant RBD antigen (RBD-L452K-F490W or RBD-J) was formulated with various combinations of aluminum-salt (Alhydrogel®, AH; AdjuPhos®, AP) and CpG 1018 adjuvants. We assessed the effect of antigen-adjuvant interactions on the stability and mouse immunogenicity of various RBD-J preparations. While RBD-J was 50% adsorbed to AH and <15% to AP, addition of CpG resulted in complete AH binding, yet no improvement in AP adsorption. ACE2 competition ELISA analyses of formulated RBD-J stored at varying temperatures (4, 25, 37°C) revealed that RBD-J was destabilized by AH, an effect exacerbated by CpG. DSC studies demonstrated that aluminum-salt and CpG adjuvants decrease the conformational stability of RBD-J and suggest a direct CpG-RBD-J interaction. Although AH+CpG-adjuvanted RBD-J was the least stable in vitro, the formulation was most potent at eliciting SARS-CoV-2 pseudovirus neutralizing antibodies in mice. In contrast, RBD-J formulated with AP+CpG showed minimal antigen-adjuvant interactions, a better stability profile, but suboptimal immune responses. Interestingly, the loss of in vivo potency associated with heat-stressed RBD-J formulated with AH+CpG after one dose was abrogated by a booster. Our findings highlight the importance of elucidating the key interrelationships between antigen-adjuvant interactions, storage stability, and in vivo performance to enable successful formulation development of stable and efficacious subunit vaccines.
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Affiliation(s)
- Sakshi Bajoria
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Ozan S. Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Greta Van Slyke
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jennifer Doering
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Hayley Novak
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Sergio A. Rodriguez Aponte
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Neil C. Dalvie
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Christopher A. Naranjo
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan S. Johnston
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - J. Christopher Love
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Nicholas J. Mantis
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
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10
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Maghsood F, Amiri MM, Zarnani AH, Salimi V, Kardar GA, Khoshnoodi J, Mobini M, Ahmadi Zare H, Ghaderi A, Jeddi-Tehrani M, Schmidt S, Laumond G, Moog C, Shokri F. Epitope mapping of severe acute respiratory syndrome coronavirus 2 neutralizing receptor binding domain-specific monoclonal antibodies. Front Med (Lausanne) 2022; 9:973036. [PMID: 36148457 PMCID: PMC9485472 DOI: 10.3389/fmed.2022.973036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the outbreak led to the coronavirus disease 2019 (COVID-19) pandemic. Receptor binding domain (RBD) of spike (S) protein of SARS-CoV-2 is considered as a major target for immunotherapy and vaccine design. Here, we generated and characterized a panel of anti-RBD monoclonal antibodies (MAbs) isolated from eukaryotic recombinant RBD-immunized mice by hybridoma technology. Epitope mapping was performed using a panel of 20-mer overlapping peptides spanning the entire sequence of the RBD protein from wild-type (WT) Wuhan strain by enzyme-linked immunosorbent assay (ELISA). Several hybridomas showed reactivity toward restricted RBD peptide pools by Pepscan analysis, with more focus on peptides encompassing aa 76-110 and 136-155. However, our MAbs with potent neutralizing activity which block SARS-CoV-2 spike pseudovirus as well as the WT virus entry into angiotensin-converting enzyme-2 (ACE2) expressing HEK293T cells showed no reactivity against these peptides. These findings, largely supported by the Western blotting results suggest that the neutralizing MAbs recognize mainly conformational epitopes. Moreover, our neutralizing MAbs recognized the variants of concern (VOC) currently in circulation, including alpha, beta, gamma, and delta by ELISA, and neutralized alpha and omicron variants at different levels by conventional virus neutralization test (CVNT). While the neutralization of MAbs to the alpha variant showed no substantial difference as compared with the WT virus, their neutralizing activity was lower on omicron variant, suggesting the refractory effect of mutations in emerging variants against this group of neutralizing MAbs. Also, the binding reactivity of our MAbs to delta variant showed a modest decline by ELISA, implying that our MAbs are insensitive to the substitutions in the RBD of delta variant. Our data provide important information for understanding the immunogenicity of RBD, and the potential application of the novel neutralizing MAbs for passive immunotherapy of SARS-CoV-2 infection.
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Affiliation(s)
- Faezeh Maghsood
- 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
| | - Amir-Hassan Zarnani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholam Ali Kardar
- Immunology, Asthma and Allergy Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalal Khoshnoodi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mobini
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hengameh Ahmadi Zare
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran
| | - Mahmood Jeddi-Tehrani
- Monoclonal Antibody Research Center, Avicenna Research Institute, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Sylvie Schmidt
- Laboratoire d’ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Géraldine Laumond
- Laboratoire d’ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Christiane Moog
- Laboratoire d’ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Fazel Shokri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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11
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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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12
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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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13
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Designing and characterization of a SARS-CoV-2 immunogen with receptor binding motif grafted on a protein scaffold: An epitope-focused vaccine approach. Int J Biol Macromol 2022; 209:1359-1367. [PMID: 35469951 PMCID: PMC9033297 DOI: 10.1016/j.ijbiomac.2022.04.148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has a significant burden on the economy and healthcare around the world. Vaccines are the most effective tools to fight infectious diseases by containing the spread of the disease. The current vaccines against SARS-CoV-2 are mostly based on the spike protein of SARS-CoV-2, which is large and has many immune-dominant non-neutralizing epitopes that may effectively skew the antibody response towards non-neutralizing antibodies. Here, we have explored the possibility of immune-focusing the receptor binding motif (RBM) of the spike protein of SARS-CoV-2 that induces mostly neutralizing antibodies in natural infection or in vacinees. The result shows that the scaffolded RBM can bind to Angiotensin Converting Enzyme 2 (ACE2) although with low affinity and induces a strong antibody response in mice. The immunized sera can bind both, the receptor binding domain (RBD) and the spike protein, which holds the RBM in its natural context. Sera from the immunized mice showed robust interferon γ response but poor neutralization of SARS-CoV-2 suggesting presence of a predominant T cell epitope on scaffolded RBM. Together, we provide a strategy for inducing strong antigenic T cell response which could be exploited further for future vaccine designing and development against SARS-CoV-2 infection.
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14
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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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15
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Andries J, Viranaicken W, Cordonin C, Herrscher C, Planesse C, Roquebert B, Lagrange-Xelot M, El-Kalamouni C, Meilhac O, Mavingui P, Couret D, Gadea G, Despres P. The SARS-CoV-2 spike residues 616/644 and 1138/1169 delineate two antibody epitopes in COVID-19 mRNA COMINARTY vaccine (Pfizer/BioNTech). Sci Rep 2022; 12:5999. [PMID: 35397679 PMCID: PMC8994064 DOI: 10.1038/s41598-022-10057-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/16/2022] [Indexed: 01/07/2023] Open
Abstract
The newly identified coronavirus SARS-CoV-2 is responsible for the worldwide pandemic COVID-19. Considerable efforts have been devoted for the development of effective vaccine strategies against COVID-19. The SARS-CoV-2 spike protein has been identified as the major antigen candidate for the development of COVID-19 vaccines. The Pfizer-BioNTech COVID-19 vaccine comirnaty is a lipid nanoparticle-encapsulated mRNA encoding a full-length and prefusion-stabilized SARS-CoV-2 spike protein. In the present study, synthetic peptide-based ELISA assays were performed to identify linear B-cell epitopes into the spike protein that contribute to elicitation of antibody response in comirnaty-vaccinated individuals. The synthetic S2P6 peptide containing the spike residues 1138/1169 and to a lesser extent, the synthetic S1P4 peptide containing the spike residues 616/644 were recognized by the immune sera from comirnaty vaccine recipients but not COVID-19 recovered patients. We assume that the synthetic S2P6 peptide and to a lesser extent the synthetic S1P4 peptide, could be of interest to measure the dynamic of antibody response to COVID-19 mRNA vaccines. The S2P6 peptide has been identified as immunogenic in adult BALB/c mice that received protein-peptide conjugates in a prime-boost schedule. This raises the question on the role of the B-cell epitope peptide containing the SARS-CoV-2 spike residues 1138/1169 in protective efficacy of the Pfizer-BioNTech COVID-19 vaccine comirnaty.
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Affiliation(s)
- Jessica Andries
- Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Wildriss Viranaicken
- Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Colette Cordonin
- Plate-Forme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Charline Herrscher
- Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Cynthia Planesse
- Université de La Réunion, INSERM U1188, Unité Mixte Diabète Athérothrombose Thérapies Réunion Océan Indien (DeTROI), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Bénédicte Roquebert
- Laboratoire CERBA, Parc d'activités « Les Béthunes », 95310, Saint-Ouen-l'Aumône, France
| | - Marie Lagrange-Xelot
- Centre Hospitalier Felix Guyon, Centre Hospitalier Universitaire-La Réunion, 97000, Saint-Denis, La Réunion, France
| | - Chaker El-Kalamouni
- Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Olivier Meilhac
- Université de La Réunion, INSERM U1188, Unité Mixte Diabète Athérothrombose Thérapies Réunion Océan Indien (DeTROI), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Patrick Mavingui
- Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - David Couret
- Université de La Réunion, INSERM U1188, Unité Mixte Diabète Athérothrombose Thérapies Réunion Océan Indien (DeTROI), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France.,Groupe Hospitalier Sud Réunion, Centre Hospitalier Universitaire-La Réunion, 97410, Saint-Pierre, La Réunion, France
| | - Gilles Gadea
- Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France.,IRCM, U1194, MetaSarc Team, 34298, Montpellier, France
| | - Philippe Despres
- Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Unité Mixte Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France.
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16
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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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Sofia F. Oliveira A, Shoemark DK, Avila Ibarra A, Davidson AD, Berger I, Schaffitzel C, Mulholland AJ. The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Comput Struct Biotechnol J 2021; 20:139-147. [PMID: 34934478 PMCID: PMC8670790 DOI: 10.1016/j.csbj.2021.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
The SARS-CoV-2 spike protein is the first contact point between the SARS-CoV-2 virus and host cells and mediates membrane fusion. Recently, a fatty acid binding site was identified in the spike (Toelzer et al. Science 2020). The presence of linoleic acid at this site modulates binding of the spike to the human ACE2 receptor, stabilizing a locked conformation of the protein. Here, dynamical-nonequilibrium molecular dynamics simulations reveal that this fatty acid site is coupled to functionally relevant regions of the spike, some of them far from the fatty acid binding pocket. Removal of a ligand from the fatty acid binding site significantly affects the dynamics of distant, functionally important regions of the spike, including the receptor-binding motif, furin cleavage site and fusion-peptide-adjacent regions. Simulations of the D614G mutant show differences in behaviour between these clinical variants of the spike: the D614G mutant shows a significantly different conformational response for some structural motifs relevant for binding and fusion. The simulations identify structural networks through which changes at the fatty acid binding site are transmitted within the protein. These communication networks significantly involve positions that are prone to mutation, indicating that observed genetic variation in the spike may alter its response to linoleate binding and associated allosteric communication.
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Key Words
- ACE2, angiotensin-converting 2 enzyme
- CD, connector domain
- CH, central helix
- FA, fatty acid
- FP, fusion peptide
- FPPR, fusion-peptide proximal region
- HR1, heptad repeat 1
- LA, Linoleic acid
- MD, Molecular dynamics
- MERS, middle east respiratory syndrome
- NTD, N-terminal domain
- RBD, receptor binding domain
- RBM, receptor-binding motif
- RMB, receptor binding motif
- SARS, severe acute respiratory syndrome
- SARS-CoV-2, severe acute respiratory syndrome 2
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Affiliation(s)
- A. Sofia F. Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Deborah K. Shoemark
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Amaurys Avila Ibarra
- Research Software Engineering, Advanced Computing Research Centre, University of Bristol, Bristol BS1 5QD, UK
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Imre Berger
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
| | - Christiane Schaffitzel
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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Gorshkov K, Susumu K, Wolak M, Oh E. Fluorescent quantum dots enable SARS-CoV-2 antiviral drug discovery and development. Expert Opin Drug Discov 2021; 17:225-230. [PMID: 34817309 DOI: 10.1080/17460441.2022.2005025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION SARS-CoV-2 is a highly infectious and deadly coronavirus whose study requires the use of a biosafety level 3 (BSL-3) containment facility to investigate viral biology and pathogenesis, which limits the study of live virus and slows progress toward finding suitable treatments for infection. While vaccines from several companies have proven very effective in combating the virus, few treatments exist for those who do succumb to the viral-induced systemic disease called COVID-19. AREAS COVERED This short review focuses on fluorescent quantum dot-based modeling of SARS-CoV-2. New BSL-2 viral models are essential for finding small molecules and biologics that may be effective in stopping viral infection, as well as treating already infected individuals. Nanoparticles are invaluable tools for biological research as they can be used to both model pathogens and serve as a platform for developing vaccines. EXPERT OPINION Visualizing viral activity with fluorescent quantum dots enables both biochemical and cell-based assays to detect virus-host receptor interactions, cellular activity after binding to the cell plasma membrane, screening for interventions using small-molecule drug repurposing, and testing of novel biologics. Quantum dots can also be used for diagnostic assays, vaccine development, and importantly, pan-antiviral drugs to address variants that may escape the immune response.
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Affiliation(s)
- Kirill Gorshkov
- National Center for Advancing Translational Sciences, Rockville, MD, USA.,Bristol-Myers Squibb, Lead Development and Optimization, High Content Screening, Princeton, NJ, USA
| | - Kimihiro Susumu
- Jacobs Corporation, Hanover, MD, USA.,Optical Sciences Division, Naval Research Laboratory, Washington, DC, USA
| | - Mason Wolak
- Optical Sciences Division, Naval Research Laboratory, Washington, DC, USA
| | - Eunkeu Oh
- Optical Sciences Division, Naval Research Laboratory, Washington, DC, USA
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