3.4 Analysis of nucleotide sequence in the rep and amino acid sequence of the rep protein
The rep genes of 68 PiCV strains of the 120 PiCV positive samples were successfully sequenced. Detailed information on the 68 PiCV strains is shown in Table 2 and S1. The rep gene of 68 samples obtained in this study were used to compare with PiCV reference sequences from China and other countries. The results showed that the rep gene of all 68 strains had been detected as two sizes: 948 nt and 954 nt. Forty of the 68 rep nucleotide sequences were 948 nt in length, encoding a rep protein of 315 amino acid residues. Twenty-eight of the 68 rep nucleotide sequences were 954 nt in size, encoding a rep protein of 317 amino acid residues (Table 2 and S1). The sequence comparison of the rep genes revealed nucleotide homologies of 90.3%–100% and deduced amino acid homologies of 92.7%–100% among the 68 PiCV strains. The rep genes of the 68 identified PiCV strains exhibited high sequence similarities with Chinese PiCV reference strains (89.0%–99.2% nucleotide identity, 89.2%–99.6% amino acid identity) and the PiCV reference strains from the other countries (89.5%–98.3% nucleotide identity, 90.5%–99.3% amino acid identity) (Table 3). To investigate variations in the deduced amino acid sequences of rep gene products, the amino acid sequences of 68 PiCV strains including the reference strains were aligned. The results showed that some unique amino acid substitutions at 37 different positions were observed among the 68 identified PiCV strains as shown in Table 5.