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.