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Genetic characterization of porcine kobuvirus variants identified from healthy piglets in China

Jin, Wen-Jie, Yang, Zhen, Zhao, Zhen-Peng, Wang, Wan-Yi, Yang, Juan, Qin, Ai-Jian, Yang, Han-Chun
Infection, genetics, and evolution 2015 v.35 pp. 89-95
Kobuvirus, amino acid deletion, bioinformatics, computer software, diarrhea, feces, genes, geography, nucleotides, phylogeny, piglets, reverse transcriptase polymerase chain reaction, viruses, China
In this study, two porcine kobuvirus strains, JS-01-CHN and JS-02a-CHN were detected from piglets with diarrhea and asymptomatic, respectively. The sequences of the two strains were analyzed using a bioinformatics software package. The full-length genome of JS-02a-CHN, was detected in healthy piglets was 8121 nucleotides (nt) long excluding the poly(A) tail. There was a 30 amino acid deletion in the 2B-coding region of JS-02a-CHN. We are the first to report a 30 amino acid deletion in porcine kobuvirus from asymptomatic piglets, indicating that porcine kobuvirus may have evolved differently based on geography and host differences. Fecal samples were obtained from pigs with diarrhea (n=91) and healthy (n=126) pigs and analyzed using RT-PCR. Of these, 64.8% (59/91) of diarrheic piglets and 19.8% (25/126) of healthy piglets were positive for PKV using VP1 specific primers. Twenty-eight (28) virus positive samples were randomly selected and the VP1 gene was analyzed. Phylogenetic analysis indicated that the 15 strains isolated from pigs with diarrhea clustered into different branches, while the VP1 sequences from clinically healthy pigs clustered into a single large group. These results indicate that the VP1 gene is diverse in pigs with diarrhea but conserved in healthy pigs in the Jiangsu Province.