Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution

Area of Science:

• Virology
• Evolutionary Biology
• Genetics

Background:

• Nucleotide substitution rates vary widely among RNA viruses, influenced by selection and population size.
• Understanding these evolutionary dynamics is crucial for predicting viral evolution and developing interventions.

Purpose of the Study:

• To investigate the roles of negative selection, positive selection, and population size in RNA virus nucleotide substitution rates.
• To compare evolutionary patterns between RNA viruses, DNA viruses, and mammals.

Main Methods:

• Analysis of nonsynonymous-to-synonymous substitution rate ratios (dN/dS) in protein-coding genes.
• Comparative genomics across diverse RNA viruses, DNA viruses, and mammalian species/strains.

Main Results:

• Most RNA viruses exhibit low dN/dS ratios (0.01-0.10), indicating strong negative selection.
• Positive selection and population size significantly contribute to dN/dS variation among genes and species.
• DNA viruses show higher dN/dS ratios compared to most RNA viruses.

Conclusions:

• Negative selection is dominant in RNA viruses, but positive selection and population size are key drivers of evolutionary rate variation.
• Evolutionary dynamics differ between RNA viruses, DNA viruses, and mammals.
• Findings enhance understanding of viral evolution mechanisms.