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.