Investigation of envelope gene sequence of SARS coronavirus 2 (SARS-CoV-2) in patients with COVID-19, Tabriz, 2020

Abstract

Since December 2019, COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) has spread rapidly in the world and had devastating consequences for many countries in various fields such as health and economy. The dramatic increase in the number of COVID-19 cases worldwide leads to the emergence of various mutations which acts as the main obstacle to the control and treatment of the disease. The Envelope (E) protein which is a structural protein of the virus is less studied than other viral structural proteins. This study aimed to determine the prevalence of E protein mutations in Tabriz and how it influences the structure, stability, antigenicity, and it s binding afinity to PALS1 protein.

Materials and Methods A total of 120 SARS-CoV-2 positve samples were selected from the central laboratory of Tabriz province. After genome extraction and confirmation of positivity by Real-Time PCR using a special kit for variant detection, variant of the samples was determined. cDNA was synthesized from the RNA extracted from the samples. Using a special software, specific primer for the envelope (E) protein was designed. Afterward, the standard PCR was performed, followed by visualization of bands by gel electrophoresis. Finally, the PCR products were sent to the Virology Center of the University of Tehran for sequencing. The results were analyzed using bioinformatics softwares. Results After matching the sequence of patient samples with the reference sequence, a total of 10 mutations were found (Same sense and Missense mutations). Of these, only two mutations caused amino acid substitutions and the rest caused silent mutations. The Non-synonymous mutation in E protein was at amino acids 68 and 73, with phenylalanine substituting serine at position 68 (S68F) and phenylalanine substituting leucine at position 73 (L73F). The L73F and S68F mutants belonged to the alpha and delta variants, respectively. The amino acid position of 73 in E protein is in a motif called DLLV. These mutations alter the structure of E protein and are important for its interaction with the PALS-1 cell protein.