Although virus isolation using supernatants of the Kagoshima feces was repeated three times, no cytopathic effect could be detected. Therefore, RNA extracted from the Kagoshima sample collected in 2014 and virus stocks of BEV-IS1, BEV-IS2 and BEV-Ho12 were subjected to deep sequencing. The Kagoshima sample was sequenced twice, and all reads obtained from the two runs were used to generate contigs (the first and second deep sequencing yielded 1,304,032 and 929,976 reads, respectively). The results of BlastN analysis revealed that bovine enterovirus F, group A rotavirus (RVA), bovine kobu-like virus and bovine picornavirus were identified with E value = 0. However, RVA was not detected in feces by Dembo-PCR.