Analysis of the SARS-COV-2 Molecular Sequences Using Bioinformatics Tools

The aim of the study was to analyze the amino acid sequences of the SARS-CoV-2 coronavirus and homologous sequences with the use of bioinformatics tools. In result, phylogenetic trees were created for all selected sequences that illustrated the changes taking place in coronavirus proteins that could lead to the formation of SARS-CoV-2. Four structural proteins of coronaviruses were selected for analysis: S - forming coronavirus spikes, M - building the membrane, N - occurring in the nucleocapsid and E - being part of the virus envelope. In order to create phylogenetic trees, multiple sequence alignments were created using the progressive method and the PAM210 amino acid substitution matrix. Then, on the basis of the sequences, distance matrices were created and phylogenetic trees were built using two methods: UPGMA and neighbor joining. As a result, eight trees were obtained, two for each protein. The obtained trees were validated using the Bootstrap method for 100 replicates. The analysis of the obtained proteins led to the discovery of a group among the studied viruses that contained the sequences most similar to the SARS-CoV-2 sequence, and thus the closest to it. This group includes the bat viruses RaTG13, Rp3, bat-SL-CoVZXC21 and bat-SL-CoVZC45, the pangolin virus, and the SARS-CoV virus. Regardless of the protein tested or the method used, the closest relationship was found for RaTG13, followed by the pangolin coronavirus.