Genetic characterization and structural insights of canine astroviruses circulating in South Korea

Background: Canine astrovirus (CAstV), classified as Mamastrovirus 5, has been detected worldwide in dogs with gastrointestinal. Still, information on the genetic and structural properties of strains circulating in South Korea has remained limited. In this study, the molecular, structural, and antigenic characteristics of Korean CAstVs were investigated using full-length ORF2 sequences from 13 strains detected in dogs between 2022 and 2023. Results: CAstV was detected in 16.5% (13/79) of intestinal or fecal samples submitted to the Animal and Plant Quarantine Agency for diagnostic testing (2022–2023). Phylogenetic analysis based on capsid amino acid sequences assigned all Korean strains to Mamastrovirus 5 and classified them into lineages 1, 2, and 4, with the majority of strains clustering within lineages 1 and 4. A putative recombinant strain, JBN/22D16-1, was identified by phylogenetic discordance between ORF1b and ORF2, as well as by recombination analysis, which revealed a group 2–like polymerase backbone and a lineage one capsid gene with a breakpoint near the ORF1b–ORF2 junction. Capsid structures were predicted with AlphaFold and subjected to all-atom quality assessment, which supported a conserved three-domain organization and stereochemically reliable models across all strains. Spike-domain comparisons revealed a conserved β-barrel core and β-strand topology, with most structural differences confined to peripheral β-elements and loop or turn segments. Shannon entropy analysis of the spike domain showed that high-variability sites were clustered in discrete regions within a broadly conserved scaffold. Predicted linear B-cell epitopes were mapped mainly to these variable, surface-exposed segments. They showed lineage-associated patterns, including a recurrent GQKSNSQY-containing central epitope in lineage four and a conserved C-terminal epitope in lineage 1. Conclusions: Taken together, these findings provide new insight into the genetic, structural, and antigenic characteristics of CAstVs currently circulating in South Korea.