3.6 Recombination analysis in PiCV genomes
For 67 identified PiCV strains, 31 recombination events were detected using RDP4 (Table S4). These recombination events indicated that the strains originally from different types of pigeons or from different geographical locations may have some evidence of recombination. For example, a segment (~1001bp) of three PiCV strains (LT3/SN/2018/MW181940, LT2/SN/2018/MW181939, and WQ6/SN/2018/MW181948) obtained in this study was likely descended from a large number of ancestral PiCV genomes that originated from Chinese meat pigeons, German racing pigeons, British racing pigeons, Polish fancy pigeons, and French meat pigeons (event 2). The possible breakpoints for recombination were determined during the recombination analysis. The results also indicated that the recombination breakpoint hot plots located within both the intergenic region between the rep and cap stop codons and near the virion strand origin of replication. Furthermore, the recombination breakpoint cold spots were detected within the central region of cap gene, which indicated few evidence for recombination within cap gene (Figure 5). Additionally, four PiCV genomes (TF1/SN/2016/MW181925, DA1/XJ/2018/MW181982, QD7/SN/2019/MW181990, and LH2/HE/2019/MW181988) had no evidence for recombination.