Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates
Abstract
Arif N. M. Ansori, Muhammad K. J. Kusala, Irine Normalina, Setyarina Indrasari, Mohammad Y. Alamudi, Reviany V. Nidom, Kuncoro P. Santoso, Kadek Rachmawati, Chairul A. Nidom.
Introduction: SARS-CoV-2 has crossed the species barrier to infect human. It is a rapidly spreading virus that has poses a significant public threat and is a considerable burden on the global economy and human health. Objective: We characterized the nucleocapsid phosphoprotein (N), membrane protein (M), and envelope protein (E) genes of Indonesian isolates to investigate genetic composition, predict B-cell epitopes, and construct a molecular phylogenetic tree. Methods: In the present work, we retrieved the sequences of 16 Indonesian isolates from the GISAID EpiCoV and the Wuhan-Hu-1 isolate (reference sequence) from GenBank, NCBI. We used MEGA X to identify mutations in the three structural protein genes and to construct a molecular phylogenetic tree. The IEDB was employed to reveal the linear B-cell epitopes and other parameters. Allergenicity prediction was evaluated using AllerTOP and ToxinPred was performed to analyze non-toxic antigen prediction. Results: In this study, we report the genetic composition of three structural protein genes in Indonesian SARS-CoV-2 isolates. Furthermore, we identified the peptide RGPEQTQGNFGDQELIRQGTDYK from nucleocapsid phosphoprotein to generate a peptide-based vaccine contrary to SARS-CoV-2. Conclusion: In summary, we propose a candidate for a peptide-based vaccine contrary to SARS-CoV-2. However, advance trials such as in vitro and in vivo testing are involved for validation.
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| Pubmed Style Ansori ANM, Kusala MKJ, Normalina I, Indrasari S, Alamudi MY, Nidom RV, Santoso KP, Rachmawati K, Nidom CA. Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates. SRP. 2020; 11(7): 422-434. doi:10.31838/srp.2020.7.62 Web Style Ansori ANM, Kusala MKJ, Normalina I, Indrasari S, Alamudi MY, Nidom RV, Santoso KP, Rachmawati K, Nidom CA. Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates. http://www.sysrevpharm.org/?mno=128419 [Access: March 29, 2021]. doi:10.31838/srp.2020.7.62 AMA (American Medical Association) Style Ansori ANM, Kusala MKJ, Normalina I, Indrasari S, Alamudi MY, Nidom RV, Santoso KP, Rachmawati K, Nidom CA. Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates. SRP. 2020; 11(7): 422-434. doi:10.31838/srp.2020.7.62 Vancouver/ICMJE Style Ansori ANM, Kusala MKJ, Normalina I, Indrasari S, Alamudi MY, Nidom RV, Santoso KP, Rachmawati K, Nidom CA. Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates. SRP. (2020), [cited March 29, 2021]; 11(7): 422-434. doi:10.31838/srp.2020.7.62 Harvard Style Ansori, A. N. M., Kusala, . M. K. J., Normalina, . I., Indrasari, . S., Alamudi, . M. Y., Nidom, . R. V., Santoso, . K. P., Rachmawati, . K. & Nidom, . C. A. (2020) Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates. SRP, 11 (7), 422-434. doi:10.31838/srp.2020.7.62 Turabian Style Ansori, Arif N. M., Muhammad K. J. Kusala, Irine Normalina, Setyarina Indrasari, Mohammad Y. Alamudi, Reviany V. Nidom, Kuncoro P. Santoso, Kadek Rachmawati, and Chairul A. Nidom. 2020. Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates. Systematic Reviews in Pharmacy, 11 (7), 422-434. doi:10.31838/srp.2020.7.62 Chicago Style Ansori, Arif N. M., Muhammad K. J. Kusala, Irine Normalina, Setyarina Indrasari, Mohammad Y. Alamudi, Reviany V. Nidom, Kuncoro P. Santoso, Kadek Rachmawati, and Chairul A. Nidom. "Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates." Systematic Reviews in Pharmacy 11 (2020), 422-434. doi:10.31838/srp.2020.7.62 MLA (The Modern Language Association) Style Ansori, Arif N. M., Muhammad K. J. Kusala, Irine Normalina, Setyarina Indrasari, Mohammad Y. Alamudi, Reviany V. Nidom, Kuncoro P. Santoso, Kadek Rachmawati, and Chairul A. Nidom. "Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates." Systematic Reviews in Pharmacy 11.7 (2020), 422-434. Print. doi:10.31838/srp.2020.7.62 APA (American Psychological Association) Style Ansori, A. N. M., Kusala, . M. K. J., Normalina, . I., Indrasari, . S., Alamudi, . M. Y., Nidom, . R. V., Santoso, . K. P., Rachmawati, . K. & Nidom, . C. A. (2020) Immunoinformatic Investigation of Three Structural Protein Genes in Indonesian SARS-CoV-2 Isolates. Systematic Reviews in Pharmacy, 11 (7), 422-434. doi:10.31838/srp.2020.7.62 |
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