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