Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study.

Introduction: SARS-CoV-2, a new member of the coronavirus family that originated from Wuhan, China, is the agent of COVID-19 pandemic and has rapidly spread globally. Objective: We characterized the spike (S) glycoprotein gene from the Indonesian SARS-CoV-2 isolates to investigate its genetic composition, predict the B cell epitopes, and construct the molecular phylogenetic among Indonesian SARS-CoV-2 isolates. Methods: We employed Wuhan-Hu-1 isolate available in GenBank, NCBI and fourteen Indonesian SARS-CoV-2 isolates acquired from the database (GISAID EpiCoV). We performed using the MEGA X for genetic and amino acid mutations and construct molecular phylogenetic tree. We used IEDB web server to predict epitopes, evaluated allergenicity by applying AllerTOP v.2.0 web server, and non-toxic antigens applying the ToxinPred web server. Results: Interestingly, we discovered that the Indonesian SARS-CoV-2 isolates genetic composition do not have significant changes compared with the reference sequence based on the S glycoprotein gene. In addition, we proposed NSASFSTFKCYGVSPTKLNDLCFTNV as a candidate for a peptide-based vaccine against COVID-19. Furthermore, we also presented the molecular phylogenetic of Indonesian SARS-CoV-2 isolates and other coronaviruses. Conclusion: In summary, this study supplied data regarding mutations in the S glycoprotein and we proposed a candidate for peptide-based vaccine against COVID-19. However, this research still requires further genetic analysis and we recommend improvement in the molecular epidemiological surveillance on COVID-19 in Indonesia. [ABSTRACT FROM AUTHOR]