The VP1 proteins in viruses belonging to the genus Enterovirus are widely known to components that form the receptor binding site (this site is referred to as the “canyon”) together with VP2 and VP3 . Reverse genetic analysis of other enteroviruses revealed that amino acid substitution in the VP1 region was responsible for the virus phenotype, such as pathogenicity and cell tropism [32–34]. Mutations in capsid protein genes may influence the structure of the “canyon” and receptor-binding capacity. BEVs also form a “canyon” on the outer side of the virion, although the cell surface receptor for BEVs is unknown. Therefore, BEVs may also have specific determinants for their phenotypes based on the aa sequences in the capsid protein encoding region. We also tried to investigate the prevalence of BEV-AN12, using VP1 specific primers, (Additional file 1: Table S1) in 38 diarrheal and 28 non-diarrheal feces samples collected from calves in Kagoshima prefecture during 2014–2015; feces from only one calf was positive, as revealed in the results. Therefore, we could not analyze the relationship between BEV-AN12 and its pathogenicity. According to the results of deep sequencing, we identified bovine picornavirus- and bovine kobu-like virus in the Kagoshima sample. There are reports suggesting that bovine picornavirus and bovine kobuvirus are associated with diarrhea [39, 57]. However, the pathogenicity of these viruses is still unknown. There is a possibility that all viruses can cause diarrhea. To clarify the determinants of the pathogenicity of BEVs, experimental infection based on reverse genetic analysis is necessary.