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.