Leveraging Codon Usage Dynamics to Unravel Host Adaptation Mechanisms in Human Sapovirus

Abstract

Acute gastroenteritis (AGE) is a major public health concern contributing to over 2.5 million annual deaths globally. Sapovirus infection cases have gained prominence in recent outbreaks of gastroenteritis. Given the absence of targeted therapies or vaccines against this virus, understanding its molecular evolution and host adaptation is crucial. In this study, we analyzed 98 complete Sapovirus genomes to investigate nucleotide composition, codon usage bias, and adaptation to the human host. Our results revealed notable codon preferences and a codon bias moderated by both host selection pressure and compositional constraint. Dinucleotide analysis showed over-representation of UpG and CpA, and under-representation of immunogenic motifs like CpG and UpA. The findings of this study underscore the evolutionary pressures shaping Sapovirus genomes and provide a basis for codon profiling for future studies to use in the development of synthetic attenuated vaccines using SAVE technology.