MUTATIONAL ANALYSIS ON THE SARS-COV-2 ORF8 PROTEIN FROM COVID-19 PATIENTS IN INDONESIA

• Main Author: Nur Annisa, Novia
• Format: Final Project
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/54787
• Institution: Institut Teknologi Bandung

COVID-19 is a new pneumonia disease caused by the SARS-CoV-2 virus and has spread to more than 200 regions in the world including Indonesia. SARS-CoV-2 has several variants that are believed to be very important because of their potential to increase transmissibility, virulence, and reduce vaccine effectiveness. ORF8 accessory protein is one of the SARS- CoV-2 proteins that evolved the fastest with a tendency to develop deletions. The mutations experienced by the ORF8 protein were deletion of one nucleotide (?1), deletion of 6 nucleotides (?6), deletion of 382 nucleotides (?382), and single amino acid substitution. Deletions of ?382 were associated with less severe symptoms and a reduced incidence of hypoxia. The ORF8 protein can also interact with the MHC-I molecule and significantly decrease the surface expression of the MHC-I molecule in various cell types. Another function is that this protein can be used in serological tests for early detection of COVID-19. It is not yet known whether the ORF8 protein variation occurs in Indonesia, so an analysis of the ORF8 protein mutation and its relation to the functions of the ORF8 protein is carried out through the genome analysis approach of Indonesian COVID-19 patients. Complete genome data of Indonesian patients were obtained from the GISAID database. For all mutations obtained, homology modeling was carried out using SWISS-MODEL. The identification results of 400 ORF8 protein genomes from Indonesian patients showed that 16% of the ORF8 protein had mutations. The types of mutations are ?1 deletion mutation (3%), ?6 deletion (0.5%), and several substitution mutations which are dominated by V62L (3.5%) and A65S (1.5%) substitution mutations. Analysis of the 1 deletion ORF8 structural model showed identical structures, while in the ?6 deletion model structure there was a change in amino acid residues from Gly-Ser-Lys to Glu. The ORF8 protein structure model with the V62L mutation undergoes secondary structural changes in the area around V62L. Meanwhile, the structure of the substitution model A65S shows a different structure from the wild type structure. Changes in the ORF8 structural model may be related to changes in function.