Comparative Genomic and Phylogenetic Analysis of Spike and Nucleocapsid Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and 9 Other Taxonomically Related Coronaviruses using in-Silico Tools

Abstract

The world is witnessing a global pandemic due to COVID-19 disease, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2. It is an enveloped ss-RNA virus, in which spike and nucleoprotein genes play an important role in the pathogenesis of Covid-19. Spike protein is required for attachment of virus to the host cell receptor, while nucleoprotein is important for replication of viral genome. Keeping this perspective in mind, we investigated nucleoprotein (N) and spike (S) genes in SARS-CoV-2 and 9 other taxonomically related coronaviruses using in-silico tools. The results obtained from our comparative genomics and phylogenetic analysis provided important evidences about how these organisms are evolutionarily related to each other. We found that N and S genes of these organisms were more adapted to the host (Homo Sapiens) and also found evidences for negative pervasive selection at different sites in the compared protein sequences of these genes. Thus, this study will help in understanding the epidemiology of SARS-CoV-2 in fine details.