ABSTRACT
Context: SARS-CoV-2, a member of family Coronaviridae and the causative agent of COVID-19, is a virus which is transmitted to human and other mammals. Aims: To analyze the B-cell epitope conserved region and viroinformatics-based study of the SARS-CoV-2 lineage from Indonesian B.1.1.7 isolates to invent a vaccine nominee for overcoming COVID-19. Methods: The sequences of seven Indonesian B.1.1.7 isolates, Wuhan-Hu- 1 isolate, and WIV04 isolate were extracted from the GISAID EpiCoV and GenBank, NCBI. MEGA X was employed to understand the transformations of amino acid in the S protein and to develop a molecular phylogenetic tree. The IEDB was implemented to reveal the linear B-cell epitopes. In addition, PEP-FOLD3 web server was utilized to perform peptide modeling, while docking was performed using PatchDock, FireDock, and the PyMOL software. Moreover, in silico cloning was developed by using SnapGene v.3.2.1 software. Results: In this study, the changes of amino acid in all seven Indonesian B.1.1.7 isolates were uncovered. Furthermore, various peptides based on the B-cell epitope prediction, allergenicity prediction, toxicity prediction from S protein to generate a vaccine contrary to SARS-CoV-2 were identified. Furthermore, the development of in silico cloning using pET plasmid was successfully achieved. Conclusions: This study exhibits the transformations of amino acid in Indonesian B.1.1.7 isolates, and proposes four peptides ("LTPGDSSSGWTAG", "VRQIAPGQTGKIAD", "ILPDPSKPSKRS", and "KNHTSPDVDLG") from S protein as the candidate for a peptide-based vaccine. However, further advance trials such as in vitro and in vivo testing are involved for validation.
ABSTRACT
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. © 2020 EManuscript Technologies. All rights reserved.
ABSTRACT
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 RRGPEQTQGNFGDQELIRQGTDYK 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. © 2020 EManuscript Technologies. All rights reserved.