First report and molecular characterization of bovine kobuvirus in beef cattle from eastern Inner Mongolia, China

This study presents the first molecular epidemiological investigation and genomic characterization of bovine kobuvirus (BKoV) in eastern Inner Mongolia, China. A total of 162 clinical samples were collected in July 2023 and tested for BKoV using nested PCR, yielding an overall detection rate of 18.52%. Differences in BKoV detection rates were observed among sample types, with a significantly higher detection rate in faecal samples than in blood samples. Metagenomic sequencing generated a near-complete genome sequence of strain NM21, which has been submitted to the GenBank database under accession number PV797393. Phylogenetic analyses based on the partial 3D gene sequences and the near-complete genome sequence of strain NM21 showed that all BKoV sequences detected in this study clustered within Clade 1. Amino acid sequence alignment revealed 21 clade-associated amino acid differences that were relatively conserved within each clade; among them, position 66 of the VP0 protein showed a consistent difference between the two clades, with the corresponding amino acid absent in Clade 2 sequences. Bioinformatic analysis of the major capsid protein VP1 predicted three candidate linear B-cell epitopes. Selection pressure analysis showed that the VP1 gene was generally under purifying selection. Recombination analysis suggested that strain NM21 may contain a potential recombination signal in the 2B non-structural protein region. These findings provide baseline data for elucidating the epidemiological characteristics, genetic evolution, and potential antigenic features of BKoV in eastern Inner Mongolia. They may serve as a reference for subsequent molecular surveillance and evolutionary studies.