Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study
Abstract
Irine Normalina, Setyarina Indrasari, Reviany V. Nidom, Muhammad K. J. Kusala, M. Yusuf Alamudi, Kuncoro P. Santoso, Kadek Rachmawati, Chairul A. Nidom.
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.
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| Pubmed Style Normalina I, Indrasari S, Nidom RV, Kusala MKJ, Alamudi MY, Santoso KP, Rachmawati K, Nidom CA. Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study. SRP. 2020; 11(7): 404-413. doi:10.31838/srp.2020.7.60 Web Style Normalina I, Indrasari S, Nidom RV, Kusala MKJ, Alamudi MY, Santoso KP, Rachmawati K, Nidom CA. Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study. http://www.sysrevpharm.org/?mno=128401 [Access: March 29, 2021]. doi:10.31838/srp.2020.7.60 AMA (American Medical Association) Style Normalina I, Indrasari S, Nidom RV, Kusala MKJ, Alamudi MY, Santoso KP, Rachmawati K, Nidom CA. Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study. SRP. 2020; 11(7): 404-413. doi:10.31838/srp.2020.7.60 Vancouver/ICMJE Style Normalina I, Indrasari S, Nidom RV, Kusala MKJ, Alamudi MY, Santoso KP, Rachmawati K, Nidom CA. Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study. SRP. (2020), [cited March 29, 2021]; 11(7): 404-413. doi:10.31838/srp.2020.7.60 Harvard Style Normalina, I., Indrasari, . S., Nidom, . R. V., Kusala, . M. K. J., Alamudi, . M. Y., Santoso, . K. P., Rachmawati, . K. & Nidom, . C. A. (2020) Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study. SRP, 11 (7), 404-413. doi:10.31838/srp.2020.7.60 Turabian Style Normalina, Irine, Setyarina Indrasari, Reviany V. Nidom, Muhammad K. J. Kusala, M. Yusuf Alamudi, Kuncoro P. Santoso, Kadek Rachmawati, and Chairul A. Nidom. 2020. Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study. Systematic Reviews in Pharmacy, 11 (7), 404-413. doi:10.31838/srp.2020.7.60 Chicago Style Normalina, Irine, Setyarina Indrasari, Reviany V. Nidom, Muhammad K. J. Kusala, M. Yusuf Alamudi, Kuncoro P. Santoso, Kadek Rachmawati, and Chairul A. Nidom. "Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study." Systematic Reviews in Pharmacy 11 (2020), 404-413. doi:10.31838/srp.2020.7.60 MLA (The Modern Language Association) Style Normalina, Irine, Setyarina Indrasari, Reviany V. Nidom, Muhammad K. J. Kusala, M. Yusuf Alamudi, Kuncoro P. Santoso, Kadek Rachmawati, and Chairul A. Nidom. "Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study." Systematic Reviews in Pharmacy 11.7 (2020), 404-413. Print. doi:10.31838/srp.2020.7.60 APA (American Psychological Association) Style Normalina, I., Indrasari, . S., Nidom, . R. V., Kusala, . M. K. J., Alamudi, . M. Y., Santoso, . K. P., Rachmawati, . K. & Nidom, . C. A. (2020) Characterization of the Spike Glycoprotein and Construction of an Epitope-Based Vaccine Candidate against Indonesian SARS-CoV-2: In Silico Study. Systematic Reviews in Pharmacy, 11 (7), 404-413. doi:10.31838/srp.2020.7.60 |
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