Phylogenomics Analysis of SARS-CoV2 Genomes Reveals Distinct Selection Pressure on Different Viral Strains

Abstract

We are witnessing a tremendous outbreak of a novel coronavirus (SARS-CoV2) across the globe. Upon exposure to different population and changing environment, the viral strain might experience different mutational bias that leads to genetic diversity among the viral population. Also, the diversification can be influenced by distinct selection pressure on different viral genomes. We have carried out a comparative genomic analysis of 82 SARS-CoV2 genomes. We have evaluated their evolutionary divergence, substitution pattern, and rates. Viral genomes under distinct selection pressure have been identified. Sites that experience strong selection pressure also have been identified. Our result shows that the translational preference of a few codons is strongly correlated with the mutational bias imposed by genome compositional constraint and influenced by natural selection. Few genomes are evolving with a higher mutational rate with a distinct signature of nucleotide substitution in comparison to others. Four viral strains are under the effect of purifying selection, while nine SARS-CoV2 genomes are under strong positive selection bias. Site analysis indicates a strong positive selection pressure on two codon positions at 3606th and 8439th positions. Our study elucidates adaptation of few SARS-CoV2 viral strain during the outbreak shaping by natural selection and genomic compositional constraints.