A CANDIDATE MULTI-EPITOPE VACCINE FROM SARS-COV-2 S PROTEIN USING REVERSE VACCINOLOGY

• Main Author: Rudiyanto, Daniel
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/57944
• Institution: Institut Teknologi Bandung

For almost two years of COVID-19 being declared a pandemic by WHO, several strategies have been done to control the spread of COVID-19. The vaccine is one of the strategies that aim to provide artificial immunity against SARS-CoV-2 infection. However, to date, no subunit vaccine-based are available on the size of the world's population. The spike glycoprotein is suitable for a vaccine target because of its antigenicity and immunogenicity. Therefore, we aim to develop a subunit vaccine candidate from the SARS-CoV-2 spike glycoprotein based on world population data using a reverse vaccinology approach. We collected 111,000 spike glycoprotein sequences from GISAID in the period October-November 2020. We processed the pipeline to eliminate ambiguous sequences, indeterminate regions and sizes and used the 80 thousand sequences to predict HTL and CTL epitope content based on world HLA. The predicted epitope results were then screened with several parameters: binding score, antigenicity, allergenicity, toxicity, the similarity of human and mouse peptides, and epitope conservation in each SARS-CoV-2 clad. Based on all these parameters, 9 CTL epitopes and 8 HTL epitopes were obtained and used to construct vaccine candidates with RpfE adjuvants from Mycobacterium tuberculosis. The 3D vaccine constructs from folding de novo were then validated, yielding a Ramachandran favored value of 90.6%, an ERRAT-score of 69.837 and a Z-score of 7.36. The vaccine candidate and TLR-4 showed a spontaneous interaction, assessed from the ?G value of -16.7 kcal/mol and the presence of critical residues in concordance with docking of epitopes and MHC. We concluded that the vaccine candidate can be used for further research.