Molecular detection of kobuvirus sequences in stool samples collected from healthy pigs in Japan

This study reports the detection and genetic characterization of porcine kobuvirus, a new member of the genus Kobuvirus in the family Picornaviridae. Among 293 fecal specimens collected from healthy pigs in 2009, in Japan, 133 (45.4%) were positive for kobuvirus using RT-PCR screening method. Of the positive specimens, 124 were obtained from pigs ≤6 months old, while 9 samples were from pigs >6 months old. Fifty-two representative strains of kobuviruses detected in this study were randomly selected and analyzed for their phylogenetic relationships with those other kobuvirus reference strains. The phylogenetic tree confirmed that 51 strains belonged to porcine kobuvirus and formed the exclusive branch with other porcine kobuvirus reference strains. In addition, the nucleotide sequence of H023/2009/JP shared very low levels of sequence identity with those of other porcine kobuvirus strains, but showed the highest level of sequence identity with bovine kobuvirus U-1 prototype strain. Our study demonstrated clearly that, porcine kobuvirus infection was common in healthy pigs and high prevalence of this virus was found in younger age of <6 months old of porcine populations in Tokyo and Hokkaido, Japan.