Dissecting the evolutionary forces shaping codon usage bias in SFTSV from eastern China: Insights from a previously underrepresented region.
Natural selection primarily drives codon usage bias in SFTSV, particularly in genes associated with viral replication efficiency.
Where it sits
this study against the rest of the kpv corpusSummary and findings
This study analyzed codon usage patterns in SFTSV strains from Shandong using 152 sequenced samples. The analysis identified seven genotypes, with genotype A being dominant. The findings suggest that natural selection primarily drives codon usage bias.
Abstract
Severe fever with thrombocytopenia syndrome (SFTS), caused by <i>Dabie bandavirus</i> (SFTS virus, SFTSV), poses a growing public health concern in East Asia. Limited genomic data from Shandong Province have restricted understanding of viral evolution, while codon usage bias, a key factor in viral fitness and host adaptation, remains uncharacterized. In this study, we analyzed codon usage patterns in SFTSV strains from Shandong using newly 152 sequenced samples and publicly available genomes. Phylogenetic analysis identified seven genotypes, with genotype A being dominant. Viral genomes showed higher adenine (A) and guanine (G) content and a tendency to use G or cytosine (C) at the third codon position. Relative synonymous codon usage analysis demonstrated gene-specific preferences for codons ending in G/C. Effective number of codons values indicated weak overall codon usage bias. Further analyses suggested that both mutation pressure and natural selection influence codon usage, with natural selection playing the dominant role (52.8-91.4%), particularly in the nucleoprotein (91.4%) and nonstructural genes (89.5%). Codon adaptation index analysis across 12 host species indicated stronger codon adaptation to humans and <i>Gallus gallus</i>, implying higher viral replication efficiency in these hosts. Overall, codon usage bias is primarily driven by natural selection rather than mutation pressure. These findings improve understanding of SFTSV molecular evolution and may inform strategies for surveillance, vaccine design, and host-specific intervention.
Background
This paper addresses the evolutionary forces influencing codon usage bias in SFTSV, a virus that poses a public health concern in East Asia. Prior research has indicated that codon usage bias can affect viral fitness and host adaptation, but limited genomic data from certain regions has hindered a comprehensive understanding. This study aims to fill that gap by analyzing newly sequenced samples from Shandong Province.
Methods
The study utilized phylogenetic analysis of 152 sequenced SFTSV samples along with publicly available genomes. It focused on assessing codon usage patterns and determining the influence of mutation pressure and natural selection on these patterns. The primary outcome measures included effective number of codons and relative synonymous codon usage.
Results
The analysis revealed that natural selection plays a dominant role in codon usage bias, accounting for 52.8-91.4% of the observed patterns. The effective number of codons indicated weak overall codon usage bias. Specific gene analyses showed that the nucleoprotein and nonstructural genes exhibited the highest levels of natural selection influence at 91.4% and 89.5%, respectively.
Interpretation
These findings suggest that natural selection is a more significant factor in shaping codon usage bias than mutation pressure, which aligns with previous literature on viral evolution. However, the effect sizes reported may not translate to clinically meaningful implications without further research. Limitations include the reliance on genomic data from a single region and the potential for confounding factors not addressed in the study.
Key findings
- Dominant genotype A identified among seven genotypes.
- Natural selection accounted for 52.8-91.4% of codon usage bias.
- Codon adaptation index analysis indicated stronger adaptation to humans and Gallus gallus.
Limitations
- Sample limited to 152 strains from a single region.
- No clinical outcomes reported.
- Potential confounding factors not addressed.