First detection and genetic characterization of donkey-like kirkovirus in diarrhoeal piglets in Xinjiang, China

Kirkovirus (kirV), a seemingly novel virus family, has been found in horses and donkey. The objectives of the study intend to investigate the presence of the virus in swine. In this study, donkey-like kirkovirus (kirV) was detected in anal swabs of piglets with diarrhoea and the positive rate was found to be 100% (149/149), but this virus was detected in only one of 261 clinically healthy piglets, which suggested a strong relationship between the kirV and the diarrhoeal disease. We obtained the whole-genome sequences of three kirVs (named Cj-D5, Cj-D32 and Cj-D43), with length of 3750 nt and sharing 99.9% nucleotide (nt)-identity with donkey kirVs. Furthermore, three viruses shared 88.5%–100%, and 23%–51% of the Rep protein sequence identity with available reference strains of the families Kirkoviridae, Circoviridae, respectively. Moreover, like horse and donkey kirVs, RCR domain and P-loop NTPase domains of Rep protein and nonanucleotide motif (CAATATTAC), of the three viruses, were similar to those of Circovirusesand Cycloviruses. Phylogenetic analysis showed that these viruses could be potentially grouped together with members in the proposed family Kirkoviridae. This is the first report to describe that kirV can circulate in piglets with diarrhoea and future studies are needed to determine the pathogenesis of this virus.