Genomics Inform.  2021 Jun;19(2):e15. 10.5808/gi.20058.

Comparative study: nonsynonymous and synonymous substitution of SARS-CoV-2, SARS-CoV, and MERS-CoV genome

• Sohpal VK

• KMID: 2517576
• DOI: http://doi.org/10.5808/gi.20058

Abstract

The direction of evolution can estimate based on the variation among nonsynonymous to synonymous substitution. The simulative study investigated the nucleotide sequence of closely related strains of respiratory syndrome viruses, codon-by-codon with maximum likelihood analysis, z selection, and the divergence time. The simulated results, dN/dS > 1 signify that an entire substitution model tends towards the hypothesis’s positive evolution. The effect of transition/transversion proportion, Z-test of selection, and the evolution associated with these respiratory syndromes, are also analyzed. Z-test of selection for neutral and positive evolution indicates lower to positive values of dN-dS (0.012, 0.019) due to multiple substitutions in a short span. Modified Nei-Gojobori (P) statistical technique results also favor multiple substitutions with the transition/transversion rate from 1 to 7. The divergence time analysis also supports the result of dN/dS and imparts substantiating proof of evolution. Results conclude that a positive evolution model, higher dN-dS, and transition/transversion ratio significantly analyzes the evolution trend of severe acute respiratory syndrome coronavirus 2, severe acute respiratory syndrome coronavirus, and Middle East respiratory syndrome coronavirus.

Keyword

divergence time; respiratory syndrome; synonymous and nonsynonymous change; transition/transversion ratio