Detection and genetic characterization of canine kobuvirus from stray dogs in Shanghai, China.

Abstract In this study, rectal samples from stray dogs (n = 60) collected from dog shelters were screened for the presence of kobuvirus and other enteroviruses by qRT-PCR. Canine kobuvirus were detected in 20 % (15/60) of the samples. Of 15 positive samples, the co-infection rates of canine distemper virus, canine coronavirus, canine astrovirus, canine norovirus and canine rotavirus was 26.67% (4/15), 20% (3/15), 73.33% (11/15), 0% (0/15), 20% (3/15), respectively. By phylogenetic analysis based on partial VP1, we found a novel canine kobuvirus which was recombined by canine and feline kobuvirus. Meanwhile, the result of Bayesian Evolutionary Analysis revealed the evolution rate of VP1 gene of CaKoV was 1.36 × 10−4 substitutions/site/year with 95% HPD interval [6.28× 10−7, 4.30× 10−4 substitutions/site/year] and divergence time of VP1 was aroud 19.44 years ago with 95% HPD interval [12.96, 27.57].