Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia: spike glycoprotein gene

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Arif Nur Muhammad Ansori Viol Dhea Kharisma Yulanda Antonius Martia Rani Tacharina Fedik Abdul Rantam


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).


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Ansori, A., Kharisma, V., Antonius, Y., Tacharina, M., & Rantam, F. (2020). Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia: spike glycoprotein gene. Jurnal Teknologi Laboratorium, 9(1), 13-20.
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1. Lam TTY, Shum MHH, Zhu HC, et al. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature. 2020. doi:10.1038/s41586-020-2169-0
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

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