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Punacha G, Adiga R. Feature selection for effective prediction of SARS-COV-2 using machine learning. Genes Genomics 2024; 46:341-354. [PMID: 37985549 DOI: 10.1007/s13258-023-01467-6] [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: 05/06/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND With rise in variants of SARS-CoV-2, it is necessary to classify the emerging SARS-CoV-2 for early detection and thereby reduce human transmission. Genomic and proteomic information have less frequently been used for classifying in a machine learning (ML) approach for detection of SARS-CoV-2. OBJECTIVE With this aim we used nucleoprotein and viral proteomic evolutionary information of SARS-CoV-2 along with the charge and basicity distribution of amino acids from various strains of SARS-CoV-2 to generate a disease severity model based on ML. METHODS All sequence and clinical data were obtained from GISAID. Proteomic level calculations were added to comprise the dataset. The training set was used for feature selection. Select K- Best feature selection method was employed which was cross validated with testing set and performance evaluated. Delong's test was also done. We also employed BIRCH clustering on SARS-CoV-2 for clustering the strains. RESULTS Out of six ML models four were successful in training and testing. Extra Trees algorithm generated a micro-averaged F1-score of 74.2% and a weighted averaged area under the receiver operating characteristic curve (AUC-ROC) score of 73.7% with multi-class option. The feature selection set to 5, enhanced the ROC AUC from 73.7 to 76.4%. Accuracy of the selected model of 86.9% was achieved. CONCLUSION The unique features identified in the ML approach was able to classify disease severity into classes and had potential for predicting risk in newer variants.
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Affiliation(s)
- Gagan Punacha
- Nitte (Deemed to be University), Department of Molecular Genetics & Cancer, Nitte University Centre for Science Education & Research (NUCSER), Mangalore, Karnataka, India
| | - Rama Adiga
- Nitte (Deemed to be University), Department of Molecular Genetics & Cancer, Nitte University Centre for Science Education & Research (NUCSER), Mangalore, Karnataka, India.
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Sam S, Ofoghi H, Farahmand B. Developing of SARS-CoV-2 fusion protein expressed in E. coli Shuffle T7 for enhanced ELISA detection sensitivity - an integrated experimental and bioinformatic approach. J Biomol Struct Dyn 2024:1-16. [PMID: 38234051 DOI: 10.1080/07391102.2024.2302941] [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: 07/24/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
In the recent COVID-19 pandemic, developing effective diagnostic assays is crucial for controlling the spread of the SARS-CoV-2 virus. Multi-domain fusion proteins are a promising approach to detecting SARS-CoV-2 antibodies. In this study, we designed an antigen named CoV2-Pro, containing two RBD domains from SARS-CoV-2 Omicron and Delta variants and one CTD domain of the nucleoprotein in the order of RBD-RBD-N, linked by a super flexible glycine linker. We evaluated the suitability of E. coli Shuffle T7 and BL21 (DE3) strain for expressing CoV2-Pro. Moreover, Bioinformatic studies were conducted first to analyze the tertiary structure of CoV2-Pro. The CoV2-Pro sequences were cloned into a pET-32b (+) vector for expression in E. coli Shuffle T7 and BL21 (DE3). SDS-PAGE and western blot confirmed the protein expression and folding structure. The CoV2-Pro-TRX was purified by Ni-NTA affinity chromatography. Dot blot analysis was performed to evaluate the antigenic characterization of the CoV2-Pro. A molecular docking simulation was conducted to assess the binding affinity of CoV2-Pro with LY-COV555 (Bamlanivimab) monoclonal antibody. A molecular dynamic was performed to analyze the stability of the structure. Bioinformatic and experimental studies revealed a stable conformational 3D structure of the CoV2-Pro. The CoV2-Pro interacted with SARS-CoV-2 antibodies, confirming the correct antigenic structure. We assert with confidence that CoV2-Pro is ideal for developing an ELISA assay for precise diagnosis and rigorous vaccine evaluation during the COVID-19 prevalence.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sohrab Sam
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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Bonam SR, Hu H. Next-Generation Vaccines Against COVID-19 Variants: Beyond the Spike Protein. ZOONOSES (BURLINGTON, MASS.) 2023; 3:10.15212/zoonoses-2023-0003. [PMID: 38031548 PMCID: PMC10686570 DOI: 10.15212/zoonoses-2023-0003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Vaccines are among the most effective medical countermeasures against infectious diseases. The current Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spurred the scientific strategies to fight against the disease. Since 2020, a great number of vaccines based on different platforms have been in development in response to the pandemic, among which mRNA, adenoviral vector, and subunit vaccines have been clinically approved for use in humans. These first-generation COVID-19 vaccines largely target the viral spike (S) protein and aim for eliciting potent neutralizing antibodies. With the emergence of SARS-CoV-2 variants, especially the highly transmissible Omicron strains, the S-based vaccine strategies have been faced constant challenges due to strong immune escape by the variants. The coronavirus nucleocapsid (N) is one of the viral proteins that induces strong T-cell immunity and is more conserved across different SARS-CoV-2 variants. Inclusion of N in the development of COVID-19 vaccines has been reported. Here, we briefly reviewed and discussed COVID-19 disease, current S-based vaccine strategies, and focused on the immunobiology of N protein in SARS-CoV-2 host immunity, as well as the next-generation vaccine strategies involving N protein, to combat current and emerging SARS-CoV-2 variants.
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Affiliation(s)
- Srinivasa Reddy Bonam
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA 77555
| | - Haitao Hu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA 77555
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA 77555
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA 77555
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4
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Khan WH, Khan N, Mishra A, Gupta S, Bansode V, Mehta D, Bhambure R, Ansari MA, Das S, Rathore AS. Dimerization of SARS-CoV-2 nucleocapsid protein affects sensitivity of ELISA based diagnostics of COVID-19. Int J Biol Macromol 2022; 200:428-437. [PMID: 35051498 PMCID: PMC8762837 DOI: 10.1016/j.ijbiomac.2022.01.094] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/27/2022]
Abstract
Nucleocapsid protein (N protein) is the primary antigen of the virus for development of sensitive diagnostic assays of COVID-19. In this paper, we demonstrate the significant impact of dimerization of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) N-protein on sensitivity of enzyme-linked immunosorbent assay (ELISA) based diagnostics. The expressed purified protein from E. coli is composed of dimeric and monomeric forms, which have been further characterized using biophysical and immunological techniques. Indirect ELISA indicated elevated susceptibility of the dimeric form of the nucleocapsid protein for identification of protein-specific monoclonal antibody as compared to the monomeric form. This finding also confirmed with the modelled structure of monomeric and dimeric nucleocapsid protein via HHPred software and its solvent accessible surface area, which indicates higher stability and antigenicity of the dimeric type as compared to the monomeric form. The sensitivity and specificity of the ELISA at 95% CI are 99.0% (94.5-99.9) and 95.0% (83.0-99.4), respectively, for the highest purified dimeric form of the N protein. As a result, using the highest purified dimeric form will improve the sensitivity of the current nucleocapsid-dependent ELISA for COVID-19 diagnosis, and manufacturers should monitor and maintain the monomer-dimer composition for accurate and robust diagnostics.
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Affiliation(s)
- Wajihul Hasan Khan
- Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Nida Khan
- Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Avinash Mishra
- Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Surbhi Gupta
- Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vikrant Bansode
- Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Deepa Mehta
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Rd, Pune, Maharashtra 411008, India
| | - Rahul Bhambure
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Rd, Pune, Maharashtra 411008, India
| | - M. Ahmad Ansari
- Department of Microbiology, The University College of Medical Sciences (UCMS) and Guru Teg Bahadur Hospital (GTB), Dilshad Garden, Delhi 110095, India
| | - Shukla Das
- Department of Microbiology, The University College of Medical Sciences (UCMS) and Guru Teg Bahadur Hospital (GTB), Dilshad Garden, Delhi 110095, India
| | - Anurag S. Rathore
- Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India,Corresponding author at: DBT Centre of Excellence for Biopharmaceutical Technology, Department of Chemical Engineering, Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016, India
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5
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Salem R, El-Kholy AA, Waly FR, Ayman D, Sakr A, Hussein M. Generation and utility of a single-chain fragment variable monoclonal antibody platform against a baculovirus expressed recombinant receptor binding domain of SARS-CoV-2 spike protein. Mol Immunol 2021; 141:287-296. [PMID: 34915268 PMCID: PMC8660258 DOI: 10.1016/j.molimm.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 02/08/2023]
Abstract
As the second wave of COVID-19 launched, various variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have emerged with a dramatic global spread amongst millions of people causing unprecedented case fatalities and economic shut-downs. That initiated a necessity for developing specific diagnostics and therapeutics along with vaccines to control such a pandemic. This endeavor describes generation of murine derived recombinant single-chain fragment variable (scFv) as a monoclonal antibody (MAb) platform targeting the receptor binding domain (RBD) of Spike protein of SARS-CoV-2. A specific synthesized RBD coding sequence was cloned and expressed in Baculovirus expression system. The recombinant RBD (rRBD) was ascertained to be at the proper encoding size of ∼ 600bp and expressed protein of the molecular weight of ∼ 21KDa. Purified rRBD was proved genuinely antigenic and immunogenic, exhibiting specific reactivity to anti-SARS-CoV-2 antibody in an indirect enzyme-linked immunosorbent assay (ELISA), and inducing strong seroconversion in immunized mice. The scFv phage display library against rRBD was successfully constructed, revealing ∼ 90 % recombination frequency, and great enriching factor reaching 88 % and 25 % in polyclonal Ab-based and MAb-based ELISAs, respectively. Typically, three unique scFvs were generated, selected, purified and molecularly identified. That was manifested by their: accurate structure, close relation to the mouse immunoglobulin (Ig) superfamily, right anchored six complementarily-determining regions (CDRs) as three within variable heavy (vH) and variable light (vL) regions each, and proper configuration of the three-dimensional (3D) structure. Besides, their expression downstream in a non-suppressive amber codon of E. coli strain SS32 created a distinct protein band at an apparent molecular weight of ∼ 27KDa. Moreover, the purified scFvs showed authentic immunoreactivity and specificity to both rRBD and SARS-CoV-2 in western blot and ELISA. Accordingly, these developed scFvs platform might be a functional candidate for research, inexpensive diagnostics and therapeutics, mitigating spread of COVID-19.
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Affiliation(s)
- Reda Salem
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, 12619, Giza, Egypt.
| | - Alaa A El-Kholy
- Veterinary Sera and Vaccines Research Institute (VSVRI), ARC, Abbassia, P.O. Box #131, 11381, Cairo, Egypt
| | - Fatma R Waly
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, 12619, Giza, Egypt
| | - Dalia Ayman
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, 12619, Giza, Egypt
| | - Aya Sakr
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, 12619, Giza, Egypt
| | - Mai Hussein
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, 12619, Giza, Egypt
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Bansal R, Mohagaonkar S, Sen A, Khanam U, Rathi B. In-silico study of peptide-protein interaction of antimicrobial peptides potentially targeting SARS and SARS-CoV-2 nucleocapsid protein. In Silico Pharmacol 2021; 9:46. [PMID: 34336545 PMCID: PMC8315091 DOI: 10.1007/s40203-021-00103-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/12/2021] [Indexed: 12/23/2022] Open
Abstract
This study is an attempt to find a suitable therapy using antimicrobial peptides (AMPs) by identifying peptide-protein interaction of AMPs and nucleocapsid protein of SARS and SARS-CoV- 2. The AMPs were shortlisted from the APD3 database (Antimicrobial peptide database) based on various physicochemical parameters. The binding efficacy of AMPs was measured using the lowest energy score of the docked complexes with 10 selected AMPs. For SARS-CoV, AP00180 showed the best pose with a binding affinity value of - 6.4 kcal/mol. Prominent hydrogen bonding interactions were observed between Lys85 (nucleocapsid receptor) and Arg13 (antimicrobial peptide ligand) having the least intermolecular distance of 1.759 Å. For SARS-CoV-2, AP00549 was docked with a binding affinity value of - 3.4 kcal/mol and Arg119 and Glu14 of receptor nucleocapsid protein and ligand AMP having the least intermolecular distance of 2.104 The dynamic simulation was performed at 50 ns to check the stability of the final docked complexes, one with each protein. The two best AMPs were AP00180 (Human Defensin-5) for SARS and AP00549 (Plectasin) for SARS-CoV-2. From positive results of dynamic simulation and previously known knowledge that some AMPs interact with the nucleocapsid of coronaviruses, these AMPs might be used as a potential therapeutic agent for the treatment regime of SARS-CoV-2 and SARS infection. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00103-z.
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Affiliation(s)
- Ritu Bansal
- National Institute of Technology, Warangal, Telangana India
| | | | | | - Uzma Khanam
- Amity University, Noida, Uttar Pradesh India
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7
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Dobaño C, Santano R, Jiménez A, Vidal M, Chi J, Rodrigo Melero N, Popovic M, López-Aladid R, Fernández-Barat L, Tortajada M, Carmona-Torre F, Reina G, Torres A, Mayor A, Carolis C, García-Basteiro AL, Aguilar R, Moncunill G, Izquierdo L. Immunogenicity and crossreactivity of antibodies to the nucleocapsid protein of SARS-CoV-2: utility and limitations in seroprevalence and immunity studies. Transl Res 2021; 232:60-74. [PMID: 33582244 PMCID: PMC7879156 DOI: 10.1016/j.trsl.2021.02.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/23/2022]
Abstract
COVID-19 patients elicit strong responses to the nucleocapsid (N) protein of SARS-CoV-2 but binding antibodies are also detected in prepandemic individuals, indicating potential crossreactivity with common cold human coronaviruses (HCoV) and questioning its utility in seroprevalence studies. We investigated the immunogenicity of the full-length and shorter fragments of the SARS-CoV-2 N protein, and the crossreactivity of antibodies with HCoV. We identified a C-terminus region in SARS-CoV2 N of minimal sequence homology with HCoV that was more specific for SARS-CoV-2 and highly immunogenic. IgGs to the full-length SARS-CoV-2 N also recognized N229E N, and IgGs to HKU1 N recognized SARS-CoV-2 N. Crossreactivity with SARS-CoV-2 was stronger for alpha- rather than beta-HCoV despite having less sequence identity, revealing the importance of conformational recognition. Higher preexisting IgG to OC43 N correlated with lower IgG to SARS-CoV-2 N in rRT-PCR negative individuals, reflecting less exposure and indicating a potential protective association. Antibodies to SARS-CoV-2 N were higher in patients with more severe and longer duration of symptoms and in females. IgGs remained stable for at least 3 months, while IgAs and IgMs declined faster. In conclusion, N protein is a primary target of SARS-CoV-2-specific and HCoV crossreactive antibodies, both of which may affect the acquisition of immunity to COVID-19.
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Key Words
- ade, antibody-dependent disease enhancement
- covid-19, coronavirus disease 2019
- ct, c-terminus
- fl, full-length
- hcov, common cold human coronavirus
- loess, locally estimated scatterplot smoothing
- m, month
- mfi, median fluorescence intensity
- n, nucleocapsid
- nt, n-terminus
- rbd, receptor-binding domain
- rrt-pcr, real-time reverse-transcriptase polymerase chain reaction
- s, spike
- sars-cov-2, severe acute respiratory syndrome coronavirus 2
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Affiliation(s)
- Carlota Dobaño
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain; Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Spain.
| | - Rebeca Santano
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alfons Jiménez
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain; Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Spain
| | - Marta Vidal
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Jordi Chi
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Natalia Rodrigo Melero
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Matija Popovic
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rubén López-Aladid
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clinic, Barcelona, Spain
| | - Laia Fernández-Barat
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clinic, Barcelona, Spain
| | - Marta Tortajada
- Occupational Health Department, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Francisco Carmona-Torre
- Infectious Diseases Division and Clinical Microbiology, Clínica Universidad de Navarra, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Spain
| | - Gabriel Reina
- Clínica Universidad de Navarra, Navarra Institute for Health Research, Pamplona, Spain
| | - Antoni Torres
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clinic, Barcelona, Spain; Pneumology Service, Hospital Clinic, Barcelona, Spain
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain; Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Carlo Carolis
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Alberto L García-Basteiro
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; International Health Department, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - Ruth Aguilar
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Gemma Moncunill
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Luis Izquierdo
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
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Terry JS, Anderson LB, Scherman MS, McAlister CE, Perera R, Schountz T, Geiss BJ. Development of a SARS-CoV-2 nucleocapsid specific monoclonal antibody. Virology 2021; 558:28-37. [PMID: 33714753 PMCID: PMC7849420 DOI: 10.1016/j.virol.2021.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 12/30/2022]
Abstract
To help fight COVID-19, new molecular tools specifically targeting critical components of the causative agent of COVID-19, SARS-Coronavirus-2 (SARS-CoV-2), are desperately needed. The SARS-CoV-2 nucleocapsid protein is critical for viral replication, integral to viral particle assembly, and a major diagnostic marker for infection and immune protection. Currently the limited available antibody reagents targeting the nucleocapsid protein are not specific to SARS-CoV-2 nucleocapsid protein, and sequences for these antibodies are not publicly available. In this work we developed and characterized a series of new mouse monoclonal antibodies against the SARS-CoV-2 nucleocapsid protein, with a specific clone, mBG86, targeting only SARS-CoV-2 nucleocapsid protein. The monoclonal antibodies were validated in ELISA, Western blot, and immunofluorescence analyses. The variable regions from six select clones were cloned and sequenced, and preliminary epitope mapping of the sequenced clones was performed. Overall, these new antibody reagents will be of significant value in the fight against COVID-19.
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Affiliation(s)
- James S Terry
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Loran Br Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Michael S Scherman
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Carley E McAlister
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Tony Schountz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.
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9
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Rehman Z, Fahim A, Bhatti MF. Scouting the receptor-binding domain of SARS coronavirus 2: a comprehensive immunoinformatics inquisition. Future Virol 2021. [PMCID: PMC7899787 DOI: 10.2217/fvl-2020-0269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aim: December 2019 witnessed the emergence of a worldwide outbreak of a novel strain of coronavirus (CoV) termed SARS-CoV-2. Several preventive strategies are being developed, such as vaccines, to stop the spread of infection. Materials & methods: A comprehensive immunoinformatics approach was used to map conserved peptide sequences on the receptor binding domain of SARS-CoV-2 for their B-cell, T-helper & T-cytotoxic cell epitope profiles. Results & conclusion: The antigenic B-cell epitopes were LFRKSN and SYGFQPT. Among T-cell epitopes, CVADYSVLY and FTNVYADSF exhibited affinity for MHC class I, while YRLFRKSNL and VYAWNRKRI exhibited affinity for of MHC class II alleles. The overlapping epitope between B- and T-cells was YRLFRKSNL. The deployment of these epitopes in potential vaccine development against COVID-19 may help in slowing down the SARS-CoV-2 spread.
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Affiliation(s)
- Zaira Rehman
- Department of Virology, National Institute of Health (NIH), Islamabad, Pakistan
| | - Ammad Fahim
- Department of Multidisciplinary Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB),National University of Sciences & Technology (NUST), Sector H-12, Islamabad, Pakistan
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Soleimanpour S, Yaghoubi A. COVID-19 vaccine: where are we now and where should we go? Expert Rev Vaccines 2021; 20:23-44. [PMID: 33435774 PMCID: PMC7898300 DOI: 10.1080/14760584.2021.1875824] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 01/11/2021] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has currently caused the pandemic with a high progressive speed and has been considered as the global public health crisis in 2020. This new member of the coronavirus family has created a potentially fatal disease, called coronavirus disease-2019 (COVID-19). Despite the continuous efforts of researchers to find effective vaccines and drugs for COVID-19, there is still no success in this matter. AREAS COVERED Here, the literature regarding the COVID-19 vaccine candidates currently in the clinical trials, as well as main candidates in pre-clinical stages for development and research, were reviewed. These candidates have been developed under five different major platforms, including live-attenuated vaccine, mRNA-based vaccine, DNA vaccines, inactivated virus, and viral-vector-based vaccine. EXPERT OPINION There are several limitations in the field of the rapid vaccine development against SARS-CoV-2, and other members of the coronavirus family such as SARS-CoV and MERS-CoV. The key challenges of designing an effective vaccine within a short time include finding the virulence ability of an emerging virus and potential antigen, choosing suitable experimental models and efficient route of administration, the immune-response study, designing the clinical trials, and determining the safety, as well as efficacy.
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Affiliation(s)
- Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Mathew S, Faheem M, Hassain NA, Benslimane FM, Al Thani AA, Zaraket H, Yassine HM. Platforms Exploited for SARS-CoV-2 Vaccine Development. Vaccines (Basel) 2020; 9:11. [PMID: 33375677 PMCID: PMC7824029 DOI: 10.3390/vaccines9010011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only zoonotic-origin coronavirus (CoV) that has reached the pandemic stage. The virus uses its spike (S) glycoprotein to attach to the host cells and initiate a cascade of events that leads to infection. It has sternly affected public health, economy, education, and social behavior around the world. Several scientific and medical communities have mounted concerted efforts to limit this pandemic and the subsequent wave of viral spread by developing preventative and potential vaccines. So far, no medicine or vaccine has been approved to prevent or treat coronavirus disease 2019 (COVID-19). This review describes the latest advances in the development of SARS-CoV-2 vaccines for humans, mainly focusing on the lead candidates in clinical trials. Moreover, we seek to provide both the advantages and the disadvantages of the leading platforms used in current vaccine development, based on past vaccine delivery efforts for non-SARS CoV-2 infections. We also highlight the population groups who should receive a vaccine against COVID-19 in a timely manner to eradicate the pandemic rapidly.
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Affiliation(s)
- Shilu Mathew
- Biomedical Research Center, Qatar University, Doha 2173, Qatar; (S.M.); (F.M.B.); (A.A.A.T.)
| | - Muhammed Faheem
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
| | - Neeraja A. Hassain
- Department of Biotechnology, Jamal Mohamed College, Tamil Nadu 620020, India;
| | - Fatiha M. Benslimane
- Biomedical Research Center, Qatar University, Doha 2173, Qatar; (S.M.); (F.M.B.); (A.A.A.T.)
| | - Asmaa A. Al Thani
- Biomedical Research Center, Qatar University, Doha 2173, Qatar; (S.M.); (F.M.B.); (A.A.A.T.)
- Department of Public Health, College of Health Sciences, Qatar University, Doha 2173, Qatar
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut 11-0236, Lebanon;
- Center for Infectious Diseases Research, American University of Beirut, Beirut 11-0236, Lebanon
| | - Hadi M. Yassine
- Biomedical Research Center, Qatar University, Doha 2173, Qatar; (S.M.); (F.M.B.); (A.A.A.T.)
- Department of Public Health, College of Health Sciences, Qatar University, Doha 2173, Qatar
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Designing of Nucleocapsid Protein Based Novel Multi-epitope Vaccine Against SARS-COV-2 Using Immunoinformatics Approach. Int J Pept Res Ther 2020; 27:941-956. [PMID: 33192207 PMCID: PMC7653218 DOI: 10.1007/s10989-020-10140-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2020] [Indexed: 12/11/2022]
Abstract
The COVID-19 disease is caused by SARS-CoV-2 and spreading rapidly worldwide with extremely high infection rate. Since effective and specific vaccine is not available to combat the deadly COVID-19, the objective of our study was to design a multi-epitope vaccine using immunoinformatics approach with translational implications. Nucleocapsid (N) protein of SARS-CoV-2 is stable, conserved and highly immunogenic along with being less prone to mutations during infection, which makes it a suitable candidate for designing vaccine. In our study, B- and T-cells epitopes were identified from N protein and screened based on crucial parameters to design the multi-epitope vaccine construct. Additionally, human beta-defensin-2 was incorporated into the vaccine construct as an adjuvant along with suitable linkers followed by its further evaluation based on crucial parameters including allergenicity, antigenicity, stability etc. Combined major histocompatibility complexes (MHC-I and MHC-II) binding epitopes presented broader population coverage of the vaccine throughout the world. The three-dimensional structure of vaccine candidate implied strong interaction with toll-like receptor 3 (TLR3) using molecular docking. The vaccine-TLR3 complex was observed to be highly stable during simulation and electrostatic free energy was foremost contributor for stabilization of the structure. Subsequently, in silico cloning of vaccine candidate was carried out to generate the construct into pET-28a(+) expression vector succeeded by its virtual confirmation. Altogether, our results advocate that the designed vaccine candidate could be an effective and promising weapon to fight with COVID-19 infection worldwide.
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Aljabali AAA, Bakshi HA, Satija S, Metha M, Prasher P, Ennab RM, Chellappan DK, Gupta G, Negi P, Goyal R, Sharma A, Mishra V, Dureja H, Dua K, Tambuwala MM. COVID-19: Underpinning Research for Detection, Therapeutics, and Vaccines Development. Pharm Nanotechnol 2020; 8:323-353. [PMID: 32811406 DOI: 10.2174/2211738508999200817163335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/22/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND The newly emerged coronavirus SARS-CoV-2, first reported in December 2019, has infected about five and a half million people globally and resulted in nearly 9063264 deaths until the 24th of June 2020. Nevertheless, the highly contagious virus has instigated an unimaginably rapid response from scientific and medical communities. OBJECTIVES Pioneering research on molecular mechanisms underlying the viral transmission, molecular pathogenicity, and potential treatments will be highlighted in this review. The development of antiviral drugs specific to SARS-CoV-2 is a complicated and tedious process. To accelerate scientific discoveries and advancement, researchers are consolidating available data from associated coronaviruses into a single pipeline, which can be readily made available to vaccine developers. METHODS In order to find studies evaluating the COVID-19 virus epidemiology, repurposed drugs and potential vaccines, web searches and bibliographical bases have been used with keywords that matches the content of this review. RESULTS The published results of SARS-CoV-2 structures and interactomics have been used to identify potential therapeutic candidates. We illustrate recent publications on SARS-CoV-2, concerning its molecular, epidemiological, and clinical characteristics, and focus on innovative diagnostics technologies in the production pipeline. This objective of this review is to enhance the comprehension of the unique characteristics of SARS-CoV-2 and strengthen future control measures. Lay Summary An innovative analysis is evaluating the nature of the COVID-19 pandemic. The aim is to increase knowledge of possible viral detection methods, which highlights several new technology limitations and advantages. We have assessed some drugs currently for patients (Lopinavir, Ritonavir, Anakinra and Interferon beta 1a), as the feasibility of COVID-19 specific antivirals is not presently known. The study explores the race toward vaccine development and highlights some significant trials and candidates in various clinical phases. This research addresses critical knowledge gaps by identifying repurposed drugs currently under clinical trials. Findings will be fed back rapidly to the researchers interested in COVID 19 and support the evidence and potential of possible therapeutics and small molecules with their mode of action.
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Affiliation(s)
- Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Irbid 566, Jordan
| | - Hamid A Bakshi
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, United Kingdom
| | - Saurabh Satija
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Meenu Metha
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Dehradun 248007, India
| | - Raed M Ennab
- Department of Clinical sciences, Faculty of Medicine, Yarmouk University, Irbid 566, Jordan
| | - Dinesh K Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Jaipur 302017, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Rohit Goyal
- Neuropharmacology Laboratory, School of Pharmaceutical Sciences, Shoolini University, Solan 173 212, Himachal Pradesh, India
| | - Ashish Sharma
- Neuropharmacology Laboratory, School of Pharmaceutical Sciences, Shoolini University, Solan 173 212, Himachal Pradesh, India
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak 124001, India
| | - Kamal Dua
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, United Kingdom
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Terry JS, Anderson LBR, Scherman MS, McAlister CE, Perera R, Schountz T, Geiss BJ. Development of SARS-CoV-2 Nucleocapsid Specific Monoclonal Antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.03.280370. [PMID: 32908982 PMCID: PMC7480041 DOI: 10.1101/2020.09.03.280370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The global COVID-19 pandemic has caused massive disruptions in every society around the world. To help fight COVID-19, new molecular tools specifically targeting critical components of the causative agent of COVID-19, SARS-Coronavirus-2 (SARS-CoV-2), are desperately needed. The SARS-CoV-2 nucleocapsid protein is a major component of the viral replication processes, integral to viral particle assembly, and is a major diagnostic marker for infection and immune protection. Currently available antibody reagents targeting the nucleocapsid protein were primarily developed against the related SARS-CoV virus and are not specific to SARS-CoV-2 nucleocapsid protein. Therefore, in this work we developed and characterized a series of new mouse monoclonal antibodies against the SARS-CoV-2 nucleocapsid protein. The anti-nucleocapsid monoclonal antibodies were tested in ELISA, western blot, and immunofluorescence analyses. The variable regions from the heavy and light chains from five select clones were cloned and sequenced, and preliminary epitope mapping of the sequenced clones was performed. Overall, the new antibody reagents described here will be of significant value in the fight against COVID-19.
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Affiliation(s)
- James S. Terry
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Loran BR Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Michael S. Scherman
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Carley E. McAlister
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Tony Schountz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
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15
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Badgujar KC, Badgujar VC, Badgujar SB. Vaccine development against coronavirus (2003 to present): An overview, recent advances, current scenario, opportunities and challenges. Diabetes Metab Syndr 2020; 14:1361-1376. [PMID: 32755836 PMCID: PMC7371592 DOI: 10.1016/j.dsx.2020.07.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIM The pandemic COVID-19 occurring due to novel emerging coronavirus-2019 (SARS-CoV-2) is severely affecting the worldwide public health, culture, economy and human social behaviour. Till date, there is no approved medicine/treatment to cure COVID-19, whereas, vaccine development efforts are going on high priority. This review aimed to provide an overview of prior art, recent advances, vaccine designing strategies, current scenario, opportunities and challenges related to development of coronavirus vaccine. METHOD A literature survey was conducted using Scopus, PubMed and Google Scholar with the search key as: coronavirus vaccine, SARS vaccine, MERS vaccine and COVID-19 vaccine. Articles related to above search query were retrieved, sorted, analyzed and developed into an easy-to-understand review. RESULTS The genome phylogenetic analysis suggested that genomic sequence of SARS-CoV-2 is almost 80% similar to that of SARS-CoV, further both these viruses bind to same host cell receptor ACE-2. Hence it is expected that, previously available literature data about coronavirus vaccine designing may play crucial role in development of rapid vaccine against COVID-19. In view of this, the present review discuss (i) existing information (from 2003 to present) about the type of vaccine, antigen, immunogenic response, animal model, route of administration, adjuvants and current scenario for designing of coronavirus vaccine (ii) potential factors and challenges related to rapid development of COVID-19 vaccine. CONCLUSION In conclusion, we discuss possible clues/ target sites for designing of vaccine against SARS-CoV-2 virus based on prior-art.
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Affiliation(s)
- Kirtikumar C Badgujar
- Assistant Professor, Department of Chemistry, SIES College of Arts, Science and Commerce, Near SION Hospital, Sion, Mumbai, 400022, Maharashtra, India.
| | - Vivek C Badgujar
- Assistant Professor, Department of Chemistry, Pratap College of Arts, Science and Commerce, Amalner, Dist Jalgaon, 425401, Maharashtra, India
| | - Shamkant B Badgujar
- Scientist, Laboratory of Native Antigens, Research and Development Division, Advy Chemical Private Limited, Thane, 400604, Maharashtra, India.
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Abstract
Since the end of 2019, the global COVID-19 outbreak has once again made coronaviruses a hot topic. Vaccines are hoped to be an effective way to stop the spread of the virus. However, there are no clinically approved vaccines available for coronavirus infections. Reverse genetics technology can realize the operation of RNA virus genomes at the DNA level and provide new ideas and strategies for the development of new vaccines. In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. An efficient reverse genetics platform is useful for obtaining the ideal attenuated strain to prepare an attenuated live vaccine.
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18
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Sheikh A, Al-Taher A, Al-Nazawi M, Al-Mubarak AI, Kandeel M. Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design. J Virol Methods 2020; 277:113806. [PMID: 31911390 PMCID: PMC7119019 DOI: 10.1016/j.jviromet.2019.113806] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 02/08/2023]
Abstract
The nucleotide variations among the N genes of 13 different coronaviruses (CoVs) were interpreted. Overall, 18 amino acids observed with varying preferred codons. The effective number of codon values ranged from 40.43 to 53.85, revealing a slight codon bias. A highly significant correlation between GC3s and ENc values was observed in porcine epidemic diarrhea CoV, followed by Middle East respiratory syndrome CoV.
The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus’s genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3rd position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus’s host adaptation, evolution and is thus of value to vaccine design strategies.
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Affiliation(s)
- Abdullah Sheikh
- The Camel Research Center, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Abdulla Al-Taher
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Mohammed Al-Nazawi
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Abdullah I Al-Mubarak
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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19
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Epitope-Based Vaccine Target Screening against Highly Pathogenic MERS-CoV: An In Silico Approach Applied to Emerging Infectious Diseases. PLoS One 2015; 10:e0144475. [PMID: 26641892 PMCID: PMC4671582 DOI: 10.1371/journal.pone.0144475] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/18/2015] [Indexed: 12/12/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) with pandemic potential is a major worldwide threat to public health. However, vaccine development for this pathogen lags behind as immunity associated with protection is currently largely unknown. In this study, an immunoinformatics-driven genome-wide screening strategy of vaccine targets was performed to thoroughly screen the vital and effective dominant immunogens against MERS-CoV. Conservancy and population coverage analysis of the epitopes were done by the Immune Epitope Database. The results showed that the nucleocapsid (N) protein of MERS-CoV might be a better protective immunogen with high conservancy and potential eliciting both neutralizing antibodies and T-cell responses compared with spike (S) protein. Further, the B-cell, helper T-cell and cytotoxic T lymphocyte (CTL) epitopes were screened and mapped to the N protein. A total of 15 linear and 10 conformal B-cell epitopes that may induce protective neutralizing antibodies were obtained. Additionally, a total of 71 peptides with 9-mer core sequence were identified as helper T-cell epitopes, and 34 peptides were identified as CTL epitopes. Based on the maximum HLA binding alleles, top 10 helper T-cell epitopes and CTL epitopes that may elicit protective cellular immune responses against MERS-CoV were selected as MERS vaccine candidates. Population coverage analysis showed that the putative helper T-cell epitopes and CTL epitopes could cover the vast majority of the population in 15 geographic regions considered where vaccine would be employed. The B- and T-cell stimulation potentials of the screened epitopes is to be further validated for their efficient use as vaccines against MERS-CoV. Collectively, this study provides novel vaccine target candidates and may prompt further development of vaccines against MERS-CoV and other emerging infectious diseases.
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Louz D, Bergmans HE, Loos BP, Hoeben RC. Animal models in virus research: their utility and limitations. Crit Rev Microbiol 2012; 39:325-61. [PMID: 22978742 DOI: 10.3109/1040841x.2012.711740] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viral diseases are important threats to public health worldwide. With the number of emerging viral diseases increasing the last decades, there is a growing need for appropriate animal models for virus studies. The relevance of animal models can be limited in terms of mimicking human pathophysiology. In this review, we discuss the utility of animal models for studies of influenza A viruses, HIV and SARS-CoV in light of viral emergence, assessment of infection and transmission risks, and regulatory decision making. We address their relevance and limitations. The susceptibility, immune responses, pathogenesis, and pharmacokinetics may differ between the various animal models. These complexities may thwart translating results from animal experiments to the humans. Within these constraints, animal models are very informative for studying virus immunopathology and transmission modes and for translation of virus research into clinical benefit. Insight in the limitations of the various models may facilitate further improvements of the models.
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Affiliation(s)
- Derrick Louz
- National Institute for Public Health and the Environment (RIVM), GMO Office , Bilthoven , The Netherlands
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21
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Lee NH, Lee JA, Park SY, Song CS, Choi IS, Lee JB. A review of vaccine development and research for industry animals in Korea. Clin Exp Vaccine Res 2012; 1:18-34. [PMID: 23596575 PMCID: PMC3623508 DOI: 10.7774/cevr.2012.1.1.18] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 05/20/2012] [Accepted: 06/15/2012] [Indexed: 12/17/2022] Open
Abstract
Vaccination has proven to be the most cost-effective strategy for controlling a wide variety of infectious diseases in humans and animals. For the last decade, veterinary vaccines have been substantially developed and demonstrated their effectiveness against many diseases. Nevertheless, new vaccines are greatly demanded to effectively control newly- and re-emerging pathogens in livestock. However, development of veterinary vaccines is a challenging task, in part, due to a variety of pathogens, hosts, and the uniqueness of host-susceptibility to each pathogen. Therefore, novel concepts of vaccines should be explored to overcome the limitation of conventional vaccines. There have been greatly advanced in the completion of genomic sequencing of pathogens, the application of comparative genomic and transcriptome analysis. This would facilitate to open opportunities up to investigate a new generation of vaccines; recombinant subunit vaccine, virus-like particle, DNA vaccine, and vector-vehicle vaccine. Currently, such types of vaccines are being actively explored against various livestock diseases, affording numerous advantages over conventional vaccines, including ease of production, immunogenicity, safety, and multivalency in a single shot. In this articles, the authors present the current status of the development of veterinary vaccines at large as well as research activities conducted in Korea.
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Affiliation(s)
- Nak-Hyung Lee
- Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Konkuk University, Seoul, Korea
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Electroporation-Mediated DNA Vaccination. CLINICAL ASPECTS OF ELECTROPORATION 2011. [PMCID: PMC7122510 DOI: 10.1007/978-1-4419-8363-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Lv Y, Ruan Z, Wang L, Ni B, Wu Y. Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV. BMC Immunol 2009; 10:61. [PMID: 19958537 PMCID: PMC2792222 DOI: 10.1186/1471-2172-10-61] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 12/03/2009] [Indexed: 01/10/2023] Open
Abstract
Background The spike (S) protein is a major structural glycoprotein of coronavirus (CoV), the causal agent of severe acute respiratory syndrome (SARS). The S protein is a potent target for SARS-specific cell-mediated immune responses. However, the mechanism CoV pathogenesis in SARS and the role of special CTLs in virus clearance are still largely uncharacterized. Here, we describe a study that leads to the identification of a novel HLA-A*0201-restricted epitope from conserved regions of S protein. Results First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. Four of eight candidate peptides were tested by HLA-A*0201 binding assays. Among the four candidate peptides, Sp8 (S958-966, VLNDILSRL) induced specific CTLs both ex vivo in PBLs of healthy HLA-A2+ donors and in HLA-A2.1/Kb transgenic mice immunized with a plasmid encoding full-length S protein. The immunized mice released IFN-γ and lysed target cells upon stimulation with Sp8 peptide-pulsed autologous dendritic cells in comparison to other candidates. Conclusion These results suggest that Sp8 is a naturally processed epitope. We propose that Sp8 epitope should help in the characterization of mechanisms of virus control and immunopathology in SARS-CoV infection.
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Affiliation(s)
- Yanbo Lv
- Institute of Immunology, PLA, Third Military Medical University, 30 Gaotanyan Street, Chongqing 400038, PR China.
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Du L, He Y, Zhou Y, Liu S, Zheng BJ, Jiang S. The spike protein of SARS-CoV--a target for vaccine and therapeutic development. Nat Rev Microbiol 2009; 7:226-36. [PMID: 19198616 PMCID: PMC2750777 DOI: 10.1038/nrmicro2090] [Citation(s) in RCA: 1145] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This Review provides an overview on the spike (S) protein of severe acute respiratory syndrome-coronavirus (SARS-CoV) as a target for the development of vaccines and therapeutics for the prevention and treatment of SARS. SARS is a newly emerging infectious disease, caused by SARS-CoV, a novel coronavirus that caused a global outbreak of SARS. SARS-CoV S protein mediates binding of the virus with its receptor angiotensin-converting enzyme 2 and promotes the fusion between the viral and host cell membranes and virus entry into the host cell. SARS-CoV S protein induces humoral and cellular immune responses against SARS-CoV. SARS S protein is the target of new SARS vaccines. These vaccines are based on SARS-CoV full-length S protein and its receptor-binding domain, including DNA-, viral vector- and subunit-based vaccines Peptides, antibodies, organic compounds and short interfering RNAs are additional anti-SARS-CoV therapeutics that target the S protein. The work on SARS-CoV S protein-based vaccines and drugs will be useful as a model for the development of prophylactic strategies and therapies against other viruses with class I fusion proteins that can cause emerging infectious diseases.
The outbreaks of severe acute respiratory syndrome (SARS) between 2002 and 2004 killed hundreds of people. Vaccines against the SARS coronavirus (SARS-CoV) could protect the population during future outbreaks. In this Review, Shibo Jiang and colleagues describe such vaccines, as well as other therapeutics, based on the SARS-CoV spike protein. Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease caused by a novel coronavirus, SARS-coronavirus (SARS-CoV). The SARS-CoV spike (S) protein is composed of two subunits; the S1 subunit contains a receptor-binding domain that engages with the host cell receptor angiotensin-converting enzyme 2 and the S2 subunit mediates fusion between the viral and host cell membranes. The S protein plays key parts in the induction of neutralizing-antibody and T-cell responses, as well as protective immunity, during infection with SARS-CoV. In this Review, we highlight recent advances in the development of vaccines and therapeutics based on the S protein.
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Affiliation(s)
- Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY 10065, USA
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