Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide and as a result, the World Health Organization (WHO) declared it a pandemic. At present, there are no approved vaccines against SARS-CoV-2. Therefore, the aim of this study was to predict epitope-based vaccines using bioinformatics approaches and phylogenetic tree construction of SARS-CoV-2 against the backdrop of the COVID-19 pandemic. In this study, we employed 27 isolates of SARS-CoV-2 spike glycoprotein genes retrieved from GenBank® (National Center for Biotechnology Information, USA) and the GISAID EpiCoV™ Database (Germany). We analyzed the candidate epitopes using the Immune Epitope Database and Analysis Resource. Furthermore, we performed a protective antigen prediction with VaxiJen 2.0. Data for B-cell epitope prediction, protective antigen prediction, and the underlying phylogenetic tree of SARS-CoV-2 were obtained in this research. Therefore, these data could be used to design an epitope-based vaccine against SARS-CoV-2. However, the advanced study is recommended for confirmation (in vitro and in vivo).
There is no Figure or data content available for this article
References
2. Gorbalenya AE, Baker SC, Baric RS, et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020;5(4):536-544. doi:10.1038/s41564-020-0695-z
3. Wang C, Horby PW, Hayden FG, Gao GF. A novel coronavirus outbreak of global health concern. Lancet. 2020;395(10223):470-473. doi:10.1016/S0140-6736(20)30185-9
4. Holshue ML, DeBolt C, Lindquist S, et al. First case of 2019 novel coronavirus in the United States. N Engl J Med. 2020;382(10):929-936. doi:10.1056/NEJMoa2001191
5. Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395(10223):507-513. doi:10.1016/S0140-6736(20)30211-7
6. Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. Int J Antimicrob Agents. 2020;55(3):105924. doi:10.1016/j.ijantimicag.2020.105924
7. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell. 2020;181(2):281-292.e6. doi:10.1016/j.cell.2020.02.058
8. Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R. COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses. J Adv Res. 2020;24:91-98. doi:10.1016/j.jare.2020.03.005
9. Phan T. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID- 19. The COVID-19 resource centre is hosted on Elsevier Connect , the company ' s public news and information . 2020;(January).
10. Ansori ANM, Kharisma VD. Characterization of Newcastle Disease Virus in Southeast Asia and East Asia: Fusion Protein Gene. EKSAKTA J Ilmu-ilmu MIPA. 2020;20(1):14-20. doi:10.20885/eksakta.vol1.iss1.art3
11. Callaway E. The race for coronavirus vaccines: a graphical guide. Nature. 2020;580(7805):576-577. doi:10.1038/d41586-020-01221-y
12. Adianingsih OR, Kharisma VD. Study of B cell epitope conserved region of the Zika virus envelope glycoprotein to develop multi-strain vaccine. J Appl Pharm Sci. 2019;9(1):98-103. doi:10.7324/JAPS.2019.90114
13. Guzzi PH, Mercatelli D, Ceraolo C, Giorgi FM. Master Regulator Analysis of the SARS-CoV-2/Human Interactome. J Clin Med. 2020;9(4):982. doi:10.3390/jcm9040982
14. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725-2729. doi:10.1093/molbev/mst197
15. Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020;20(5):533-534. doi:10.1016/S1473-3099(20)30120-1
16. Zhang J, Zeng H, Gu J, Li H, Zheng L, Zou Q. Progress and prospects on vaccine development against sars-cov-2. Vaccines. 2020;8(2):1-12. doi:10.3390/vaccines8020153
17. Muthumani K, Falzarano D, Reuschel EL, et al. Coronavirus in Nonhuman Primates. Sci Transl Med. 2015;7(301):1-29. doi:10.1126/scitranslmed.aac7462.A
18. Pallesen J, Wang N, Corbett KS, et al. Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Proc Natl Acad Sci U S A. 2017;114(35):E7348-E7357. doi:10.1073/pnas.1707304114
19. Zahroh H, Ma’rup A, Tambunan USF, Parikesit AA. Immunoinformatics approach in designing epitopebased vaccine against meningitis-inducing bacteria (Streptococcus pneumoniae,Neisseria meningitidis,and Haemophilus influenzae type b). Drug Target Insights. 2016;10:19-29. doi:10.4137/DTI.S38458
20. Fosgerau K, Hoffmann T. Peptide therapeutics: Current status and future directions. Drug Discov Today. 2015;20(1):122-128. doi:10.1016/j.drudis.2014.10.003
21. Gorbalenya AE. Phylogeny Viruses. In: Reference Module in Biomedical Sciences. Main St, Frisco: Elsevier Inc.; 2017:1-7. doi:10.1016/B978-0-12-801238-3.95723-4 1
22. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med. 2020;26(4):450-452. doi:10.1038/s41591-020-0820-9
23. Zhang T, Wu Q, Zhang Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol. 2020;30(7):1346-1351.e2. doi:10.1016/j.cub.2020.03.022
24. Zhou P, Yang X Lou, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270-273. doi:10.1038/s41586-020-2012-7
How to Cite This
Article Metrics
Download Statistics
Downloads
Other Statistics
Copyright and Permissions
Publishing your paper with Jurnal Teknologi Laboratorium (JTL) means that the author or authors retain the copyright in the paper. JTL granted an exclusive reuse license by the author(s), but the author(s) are able to put the paper onto a website, distribute it to colleagues, give it to students, use it in your thesis etc, even commercially. The author(s) can reuse the figures and tables and other information contained in their paper published by JTL in future papers or work without having to ask anyone for permission, provided that the figures, tables or other information that is included in the new paper or work properly references the published paper as the source of the figures, tables or other information, and the new paper or work is not direct at private monetary gain or commercial advantage.
JTL journal provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge. This journal is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. This license lets others remix, transform, and build upon the material for any purpose, even commercially.
JTL journal Open Access articles are distributed under this Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA). Articles can be read and shared for All purposes under the following conditions:
- BY: You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
- SA: If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.