3.5 Phylogenetic analysis of the cap genes
A phylogenetic analysis using 126 cap gene reported in GenBank, and cap genes of 90 PiCV strains obtained in our study was performed to investigate genetic relationship (Table S1 and S2). The phylogenetic tree indicated that a total of 216 analyzed PiCV strains could be divided into 9 clades, which were defined by the contractual letters A–I (Figure 4). The 90 cap gene sequences reported in the present study were clustered into 7 clades: A (14.1%), B (60.9%), C (62.2%), E (25.0%), G (51.4%), H (28.6%), and I (40.0%). As shown in Figure 4, the PiCV strains from different geographical locations were clustered into the same clades, such as QYQX1/HE/2018/MW181909, TY1/SN/2016/MW181929, DS1/GS/2018/MW181970, and QD3/SN/2018/MW181965. On the other hand, the PiCV strains from the same geographical locations were divided into different clades, such as LH1/HE/2018/MW181918 (clade B), LH2/HE/2019/MW181988 (clade A), and LH3/HE/2019/MW181989 (clade C). Furthermore, the PiCV strains collected in the different years were grouped closely in the same clade. Due to the fact that the racing pigeons were supplied by breeders from different provinces or municipalities of China, the 78 PiCV strains isolated from the pigeons in the racing clubs in Shannxi province, belonged to six separate clades except for clade D, F, and H.