GENETIC VARIATION OF SARS-COV-2 SPIKE PROTEIN OF INDONESIAN COVID-19 ISOLATES

• Main Author: Muharrifani, Yefinadya
• Format: Final Project
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/55086
• Institution: Institut Teknologi Bandung

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) is a pathogen that causes Coronavirus Disease-2019 (COVID-19). This disease was first discovered in Wuhan City, Hubei Province, Central China and has spread widely in the world and has become a global pandemic. Until May 9, 2021, this virus has caused 1,713,684 cases in Indonesia with a total death toll reaching 47,012. This is the concern of researchers in Indonesia in overcoming the Covid-19 outbreak in Indonesia. The most popular target of SARS-CoV-2 research is the Protein Spike (S). SARS-CoV-2 protein S is an important key for SARS-CoV-2 to infect human cells. This protein plays a role in the process of binding the virus to human cell receptors. Protein S consists of two functional subunits, one of which is the S1 subunit. In the S1 subunit, there is a Receptor Binding Domain (RBD) that will bind to human cell receptors, namely Angiotensin Converting Enzyme-2 (ACE2) in the early stages of SARS-CoV-2 infection in humans. Therefore, it is necessary to conduct research on SARS-CoV-2 S protein for the benefit of developing viral binding inhibitors, vaccines, and antiviral drugs. In this study, a genetic variation analysis of the SARS-CoV-2 S protein from Indonesian Covid-19 patients was conducted using Molecular Evolutionary Genetics Analysis (MEGA) X software. The nucleotide sequence of Wuhan / Hu-1 was taken from GenBank (National Center for Biotechnology Information, USA) and was used as a reference. Meanwhile, nucleotide sequences of 128 samples of Indonesian Covid- 19 patients were taken from the GISAID (Global Initiative on Sharing All Influenza Data) EpiCoVTM Database (Germany). The results of the analysis of these 128 samples showed that there were variations on 120 nucleotide positions which caused 72 mutations in amino acids. The most types of mutations were D614G (97.66%), N439K (32.03%), P681R (32.03%), T617I (14.06%), and P681H (13.28%) mutations. In addition, 7 amino acid mutations that are currently under international attention have been found, namely D614G (97.66%), N439K (32.03%), N501Y (10.94%), Q677H (3.91%), L452R (3.13%), E484K (2.34%), and K417N (0.78%). The new variant SARS-CoV-2 which includes B.1.1.7, B.1.6.1.7, B.1.3.5.1 and B.1.5.2.5 has been found in 128 samples studied. This study also concluded that the SARS-CoV-2 S protein in Indonesia had evolved after being compared to the first SARS-CoV-2 S protein in Wuhan based on its phylogenetic analysis. This study hopefully can become the basis for the Indonesian government's policy in supporting research to find the best Merah Putih vaccine candidates.