Genetic characterization and evolutionary dynamics of non-epidemic sapovirus GII.5 strains

Human sapovirus has emerged as an important cause of acute gastroenteritis in infants and children, as well as foodborne outbreaks across all age groups worldwide. Although the GI.1 genotype is typically the predominant type detected in pediatric cases, earlier epidemiological studies have reported a broader diversity of circulating genotypes. Sapovirus GII.5 is considered an uncommon genotype, and in this study, we detected two sporadic cases in 2024. We determined the near-complete genomes of the two GII.5 strains and conducted comprehensive genetic and evolutionary analyses. Bayesian phylogenetic analysis showed that GII.5 strains separate into two major clusters. Our two strains, together with recently detected strains from Japan and China, formed Cluster 1 alongside a previous Japanese strain (LC190463) detected in 2010. In contrast, strains detected in North and South America between 2014 and 2016 grouped into Cluster 2. Comprehensive analysis of amino acid sequences of major capsid protein, VP1, indicated distinct evolutionary patterns between the two clusters, suggesting that GII.5 strains have evolved independently in different geographical regions. The estimated evolutionary rate of GII.5 was 3.26 × 10 −4 substitutions/site/year, which is lower than 2.092 × 10 −3 substitutions/site/year observed for GI.1 strains. Overall, this study elucidates the evolutionary dynamics of GII.5 sapovirus and also provides detailed information on sapovirus genotype. • Rare SaV genotype, GII.5 strains were detected and analyzed. • GII.5 SaV strains could be separated into two clusters. • Two clusters have evolved independently in different geographical regions. • Amino acid alignment of GII.5 VP1 was specific for the two clusters. • Evolution rate for GII.5 was estimated to be slower than that for GI.1.