GENETIC VARIATIONS OF SPIKE PROTEIN DELTA VARIANT OF SARS- COV-2 FROM INDONESIA COVID-19 PATIENTS

• Main Author: Wilhelmina Soetomo, Kristin
• Format: Final Project
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/62882
• Institution: Institut Teknologi Bandung

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is pathogenic of Coronavirus Disease-2019 (COVID-19) which was first discovered in Wuhan, China. COVID-19 was subsequently declared a global pandemic. SARS-CoV-2 is a beta coronavirus that has four structural proteins, one of which is a spike protein (S). The S protein is divided into two functional subunits, namely the S1 subunit and the S2 subunit which are then divided into protein domains. Protein S is mainly responsible for the entry of viruses into cells. The S1 subunit, especially the Receptor Binding Domain (RBD) plays a role in the recognition and binding of the virus to the host cell. RBD will bind to Angiotensin-Converting Enzyme-2 (ACE2), a human cell receptor. The S2 subunit plays a role in the fusion stage of the virus with human cells. Today, SARS-CoV-2 has evolved through observable changes in its genetic code and is widespread in all regions of the world. The genetic variation of SARS-CoV-2 in the human population makes the degree of transmission and severity of COVID-19 disease change. To date, there are many variants of SARS-CoV-2 that have been grouped, one of which is the delta variant (B.1.617.2) which was first discovered in India. The delta variant is suspected to be the cause of the health crisis in Indonesia. The number of cases in Indonesia increased sharply during June July 2021. Indonesia reported an average death toll of 919 a day with the highest increase in COVID-19 cases on 15 July 2021 as many as 56,757. At that time Indonesia became the epicenter of COVID-19 in Asia. Data collection for the whole genome of the SARS-CoV-2 delta variant from samples of Indonesian COVID-19 patients in the period 1 January 31 August 2021 was carried out through GISAID. The total genome data for SARS-CoV-2 for all variants is 3828 data and 39.76% of them are delta variants with a total of 1522 data. The delta variant first appeared in Indonesia in January 2021 and then in June 2021 the number began to increase significantly. Pulau Jawa became the largest contributor to delta variant cases reaching 48.42% of the total data. In this study, an analysis of the nucleotide and amino acid variations of the SARS-CoV-2 delta variant of the protein S was carried out. Based on the analysis of variation, two types of mutations were obtained, deletion and substitution mutations which were most commonly found in the NTD, one of the S1 subunit domains. Based on the analysis of its phylogenetic tree, the SARS-CoV-2 S protein has evolved rapidly compared to the first isolates of the Wuhan SARS-CoV-2 and the Indian delta variant SARS-CoV-2. Analysis of the protein structure model of the NTD A222V SARS- CoV-2 delta variant from Indonesian COVID-19 patient was also carried out to see the impact of the mutation.