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 https://orcid.org/0000-0002-1279-3904 Viol Dhea Kharisma Yulanda Antonius Martia Rani Tacharina Fedik Abdul Rantam

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).

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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. https://doi.org/https://doi.org/10.29238/teknolabjournal.v9i1.221
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