3.5 Phylogenetic analysis of the cap gene
Phylogenetic analysis based on the cap gene were performed to investigate genetic relationship of the 90 PiCV strains obtained in our study with all the 126 PiCV strains reported in GenBank (Table 2, S1 and S2). The phylogenetic tree indicated that the total 216 analysed PiCV strains could be divided into 9 clades, which are 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 the different geographical locations clustered on the same groups, 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 the different groups, 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, were belonged to six separate clades except for clade D, F and H.