Identifikasi Mutasi dan Variasi Genetik Sars-Cov-2 di Provinsi Sumatera Utara dengan Metode Sanger Sequencing

Abstract

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) is a group of Corona viruses from the genus Betacoronavirus. This zoonotic virus exhibits a high mutation rate, which increases the potential of the pathogen to adapt to efficient human-to-human transmission and potentially makes it more virulent. One of the accelerated strategies in examining mutations of this virus is by molecular detection using Sanger Sequencing. The purpose of this study is to identify the presence of mutations in the genome sequence region as well as genetic variation of SARS-CoV-2 of the three samples using the Sanger Sequencing method. Samples were collected from the Viral Transport Media (VTM) specimen collection of Laboratorium Mikrobiologi Fakultas Kedokteran Universitas Sumatera Utara which have been obtained from various health facilities in North Sumatera on March 2022. The virus was detected using the real-time Reverse Transcription Polymerase Chain Reaction (rRT-PCR) and optimization with qPCR which targets 620 bp of spike glycoprotein gene in the sequence region from 22,202 to 22,821 (NCBI ID: NC_045512.2). Data were analyzed using MEGA11, BioEdit, ExPasy and DNASP6 software. The results showed that two of the samples (NT2 and NT3) had several different mutations, namely; A222V, G339D S371F S373P S375F T376A D405N R408S and K417N. These amino acid changes are involved in antibody susceptibility and antigenic drift.