The Epidemic Situation Research And Genome Sequence Analysis Of Porcine Kobuvirus In Guangxi Province

In this study, porcine kobuvirus were detected by RT-PCR,there were159positive samples among the498pig intestinal tissues and fecal samples, which collected from9cities in Guangxi province. The21isolated strains were cloned and sequenced. To analyze the sequences,the results showed that14strains had7467nucleotides and encoded2488aa,7other strains had7377nucleotides which encoded2458aa and had a90-nucleotide deletion in the2B protein. All of their predicted cleavage sites were similar to PKV S-1strain.The nucleotide identity among the reference PKV ORF sequences was86.6%-90.3%and the deduced amino acid was93.0%-97.2%.Comparing with other species of kobuvirus, the highest homology was with Caprine,which the nucleotide homology was73.2%-74.1%and the deduced amino acid was77.0%-78.2%,but the lowest homology was with human,which the homology of nucleotide and the deduced amino acid was57.9%-59.0%,60.6%-61.5%, respectively. To analyze the PKV each gene,the most frequent nucleotide mutations were observed at VPO gene which nucleotide identity was79.8%-89.7%,3D was the most highly conserved gene which nucleotide identity was91%-94%. To the amino acid,the VP1sequences of strains revealed the highest amino acid mutations,its identity was86.6%-94.4%and the2C amino acid identity was97%-100%, which was the highly conserved protein.To observe the key point of21PKV strains,we found that the highly conserved amino acid motifs KDELR, YGDD and FLKR, which was a viral RNA-dependent RNA polymerase,were presented in kobuvirus3D region,there were no mutation of the amino acid of H-box\NC in2A gene. In2C region,there had amino acid motifs GPPGTGKS was similar to the PKV S-l,which in the nucleotide binding domain of the putative picornavirus helicase.The amino acid residues in3C,which was H-D-C formed picornavirus catalytic triad and a histidine participated in the substrate-binding pocket in the trypsine-like protease was no changes.Phylogenetic analysis of VP1gene infered the all porcine kobuvirus strains were divided into4clusters and the21isolates in Guangxi province were distributed in cluster Ⅰ, cluster Ⅱ and cluster Ⅳ, respectively. Analyzing the origin of gene fragments,we found that the VP1,3D and2B gene of GXPKV-7strain had closer genetic relationship with reference strains K-4(cluster I),WB-1strain(cluster Ⅱ) and XX strain(cluster Ⅳ),respectively,this showed GXPKV-7 strain were possible genetic reassortment.