Novel Kobuvirus species identified from black goat with diarrhea

•Novel caprine kobuvirus (KoV) was identified from the diarrheal feces.•The virus had an 8291-nucleotide-long genome excluding the poly(A) tail.•The caprine KoV was most closely related to porcine KoV.•The caprine KoV TMRCA was determined to be 48.8 years.

In this study, a caprine kobuvirus was identified from the diarrheal feces of a Korean black goat. The virus had an 8291-nucleotide-long genome excluding the poly(A) tail, and the genome contained a large open reading frame of 7437 bp, which encoded a putative polyprotein precursor of 2479 amino acids. Full-genome sequence analysis indicated that the caprine kobuvirus was most closely related to porcine kobuvirus, with 75.9% amino acid similarity and 70.1% nucleotide similarity. The predicted secondary structure of the 5′ terminus (110-bp region) of strain 12Q108 consisted of three stem-loop domains. The first loop sequence of 12Q108 differed from that of strain Y-1-CH1 at one nucleotide position. The full genome substitution rates of caprine kobuvirus were assessed and the time to the most recent common ancestor (TMRCA) of caprine kobuivirus was compared with that of kobuvirus strains from other species. The rate of evolutionary substitution was determined to be 6.40 × 10−3 substitutions per site per year, and the TMRCA was determined to be 149.6 years for kobuviruses. Furthermore, the caprine kobuvirus TMRCA was determined to be 48.8 years (95% highest posterior density: 8.3-88.4).