A study of genetic variants of SARS-CoV-2 using bioinformatics tools

Abstract

The severe acute respiratory syndrome coronavirus 2, that is commonly known as SARS-CoV-2, appeared for the first time in December 2019 in the City of Wuhan (China) and has since affected most countries around the world, hence becoming a major global threat to all humans. The present study was carried out for the purpose of better understanding the molecular structure of this virus. It is based on the inventory and processing of all DNA sequences that have been published to date on the general biological data storage bank GenBank. In order to carry out this study, it was deemed necessary to use various bioinformatics tools such as MEGA 11 software for building the phylogenetic trees, DnaSP 6 for identifying haplotypes, NetWork 10 for determining phylogenetic networks, and DAMBE 7 to perform statistical analyses which were then supplemented by the new DnBA program that was developed in the present work. These analyses allowed us to classify the 11 SARS-CoV-2 genes under study into 3three categories; first, the most variable genes, such as ORF1ab, ORF3a, N, and S, next, the less variable genes, such as ORF8, ORF10, ORF7a, and ORF7b, and then the unvaried genes, such as ORF6, E, and  M.