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Background  Porcine circovirus 3 (PCV3) is an emerging etiological agent to the swine industry. However, its circulating status and genetic characteristics were still unclear in Henan, central China. Here, 318 porcine oral fluid specimens were collected from asymptomatic pigs in five farms and tested by PCR .    Results  The results showed that the positive rate of PCV3 was 12.3% (39/318) for the total samples, and 15.06% (25/166) in the stall-based samples, 9.21% (14/152) in the pen-based samples. Of the PCV3-positive samples, 41.0% were also positive for porcine circovirus 2 (PCV2). Nucleotide sequence comparison indicated that the 10 complete genomes and 34 capsid ( cap ) genes in this study shared 98.7–99.9% and 98–100% pairwise identities to each other, respectively. According to phylogenetic analysis and sequence alignment of  cap  gene, all the isolated sequences were clustered into 3 clades, including subgroup 1 (21/39, 61.8%), subgroup 2 (5/39, 14.7%) and subgroup 3 (8/39, 23.5%). Similar to previous reports, four amino acids (V24A, K27R, S77 T and I150L) in cap protein were identified as a conserved subgroup specific molecular marker.    Conclusion  Our research provided new insights into the epidemiology surveillance and genetic characteristics of PCV3 in China.    Electronic supplementary material  The online version of this article (10.1186/s12917-019-1952-3) contains supplementary material, which is available to authorized users.

Detection and genetic characteristics of porcine circovirus 3 based on oral fluids from asymptomatic pigs in central China