Senecavirus A Enhances Its Adaptive Evolution via Synonymous Codon Bias Evolution

Abstract

Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes to virus evolvability remains elusive. In this paper, we characterize how the Senecavirus A (SVA), a picornavirus, utilizes synonymous codon mutations to influence its evolution, resulting in the adaptive evolution of the virus to adverse environments. The phylogenetic tree and Median-joining (MJ)-Network of these SVA lineages worldwide were constructed to reveal SVA three-stage genetic development clusters. Furthermore, we analyzed the codon bias of the SVA genome of selected strains and found that SVA could increase the GC content of the third base of some amino acid synonymous codons to enhance the viral RNA adaptive evolution. Our results highlight the impact of recessive mutation of virus codon bias on the evolution of the SVA and uncover a previously underappreciated evolutionary strategy for SVA. They also underline the importance of understanding the genetic evolution of SVA and how SVA adapts to the adverse effects of external stress.

RNA recombination: non-negligible factor for preventing emergence or reemergence of Senecavirus A

“…Due to the low-fidelity characteristics of SVA RdRp, SVA displays a relatively high mutation rate during serial passaging in vitro , as demonstrated by our previous study ( 17 ). Therefore, SVA can rapidly enhance its own adaptive ability via synonymous codon bias evolution ( 18 ). Indeed, the codon preference analysis has indicated that natural selection is a primary driving force that affects the codon usage bias in SVA ( 15 ).…”

Analysis of codon usage bias in Ziziphi Spinosae Semen based on transcriptome data

“…Each point in the plot represents the position of the corresponding gene. It was used to analyze the correlation between GC 12 and GC 3 , and to judge the factors affecting the preference for codon usage (Zhao et al 2022). In the regression curve, natural selection dominates when the slope of the regression curve approaches 0, while the mutational pressure plays the main role if the slope approaches 1 (Zhang et al 2022 Parity rule 2 (PR 2 )-plot analysis…”

Analysis for codon usage bias in membrane anchor of nonstructural protein 5A from BVDV

“…One of the insights into RNA viruses' evolution is that synonymous codon usage generally follows a nonrandom and species-specific pattern [15][16][17][18][19][20][21][22]. The relevant investigations indicate that synonymous codon changes without altering the primary amino acid sequence are influenced by multiple selective forces.…”