Distinct codon usage bias evolutionary patterns between weakly and strongly virulent respiratory viruses

Feng Chen; Jian-Rong Yang

doi:10.1016/j.isci.2021.103682

Distinct codon usage bias evolutionary patterns between weakly and strongly virulent respiratory viruses

iScience. 2022 Jan 21;25(1):103682. doi: 10.1016/j.isci.2021.103682. Epub 2021 Dec 24.

Authors

Feng Chen¹, Jian-Rong Yang¹

Affiliation

¹ Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.

Abstract

Human respiratory viruses are of vastly different virulence, giving rise to symptoms ranging from common cold to severe pneumonia or even death. Although this most likely impacts molecular evolution of the corresponding viruses, the specific differences in their evolutionary patterns remain largely unknown. By comparing structural and nonstructural genes within respiratory viruses, greater similarities in codon usage bias (CUB) between nonstructural genes and humans were observed in weakly virulent viruses, whereas in strongly virulent viruses, it was structural genes whose CUBs were more similar to that of humans. Further comparisons between genomes of weakly and strongly virulent coronaviruses revealed greater similarities in CUBs between strongly virulent viruses and humans. Finally, using phylogenetic independent contrasts, dissimilation of viral CUB from that of humans was observed in SARS-CoV-2. Our work revealed distinct CUB evolutionary patterns between weakly and strongly virulent viruses, a previously unrecognized interaction between CUB and virulence in respiratory viruses.

Keywords: Evolutionary biology; Microbial genomics; Phylogenetics; Virology.