Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2

Abstract

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide. Therefore, this study aimed to build a phylogenetic tree of complete genomes of SARS-CoV-2 and other species of Gamma coronavirus to explore the possibility of finding the evolutionary relationships between them and wished to analyze them in order to forecast the best trees illustrating the sequences' evolutionary relationships and obtain a well-supported phylogenetic tree by using the Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods after performing multiple sequence alignment (MSA). This study utilized 16 isolates of Gamma coronavirus species and SARS-CoV-2 retrieved from the NCBI (National Center for Biotechnology Information) database for this investigation. The experimental outcomes when applying the two methods to the same dataset show that a well-supported and trustworthy phylogenetic tree was obtained with a bootstrapping value of 100% for all branches of the tree when applying the ML method. Additionally, a well-supported and fast-constructing phylogenetic tree was obtained through the NJ method for all branches except one, where the bootstrapping value appeared to be 56%. The research was conducted in 2022 at the College of Science, Diyala University.

Keywords

• SARS-CoV-2, phylogenetic tree construction, Maximum-Likelihood, COVID-19, phylogenetic inference, Neighbor-Joining.