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

Abstract

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.

Keywords: Epidemiology; Oral fluids; PCV3; Phylogenetic analysis.

Fig. 1

Phylogenetic analysis based on the complete genome and the cap gene. a Phylogenetic tree of the complete genome of different porcine circoviruses. All PCV3 strains cluster together independently with PCV1 and PCV2 species. b Phylogenetic tree and amino acids alignment based on the cap gene of 89 viruses. All the PCV3 strains clustered three subgroups, subgroup 1, subgroup 2 and subgroup 3. The special amino acid patterns for each subgroup were also showed. The black solid circles (●) represent the PCV3 viruses investigated in this study. The phylogenetic tree was constructed using the neighbour-joining method in MEGA 6.0 software with a bootstrap test of 1000 replicates. Scale bar indicates nucleotide substitutions per site

Fig. 2

The sequence alignment based on amino acids of capsid protein. 34 PCV3 strains isolated in this study and 3 reference strains were aligned by clustal W method in MEGA6.0 software. All the isolates were cluster into three subgroups, subgroup 1 (green), subgroup 2 (blue), subgroup 3 (yellow). The potential genetic marker were showed in the black rectangles