3.6 Recombination analysis in PiCV genomes
For 67 identified in this study PiCV strains, 31 recombination events
were detected using RDP4 (Table S3). 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 were found to be located
within both the intergenic region between the rep and capstop 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 indicate little
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.