3.3 Recombination analysis
Previously, recombination has been observed in various PCV2 strains (Cai
et al., 2011; Jang et al., 2021; Kleymann et al., 2020; Neira et al.,
2017; Ramos, Mirazo, Castro, & Arbiza, 2013; Wei et al., 2019). This
study determined genetic recombination analysis using seven methods
(RDP, GeneConv, BootScan, Maxchi, Chimera, SiScan, and 3Seq) implemented
in RDP software. The results showed that 19NPT29 was identified as an
intergenotypic PCV2b/PCV2d recombinant by all seven methods with a high
degree of statistical support (average p -value = 3.84 x
10-9) (Table 3). The recombination analysis also
revealed PCV2b (South Korea/2016/KU-1605) and PCV2d
(Thailand/2019/19RBR10) as the major and minor parents, respectively.
Furthermore, the putative recombination breakpoints were determined inRep and Cap genes at nucleotide positions 508 and 1356.
The recombination was also confirmed using SIMPLOT software (data not
shown). For further analysis, the 19NPT29 genome was divided into two
regions, ’recombinant region 1’ and ’recombinant region 2’, using the
recombination breakpoints (Figure 2).
The recombination events of 19NPT29 were also achieved by using
nucleotide-by-nucleotide comparisons with the major and minor parental
strains, as shown in Figure 2. In recombinant region 1, 19NPT29 showed a
higher nucleotide identity of 99.8% with 19RBR10, while it showed
95.7% nucleotide identity with KU-1605 (Table 4). On the other hand, in
recombinant region 2, 19NPT29 showed a higher nucleotide identity of
99.9% with KU-1605 and showed 95% nucleotide identity with 19RBR10.
Furthermore, the recombination event in 19NPT29 was confirmed by PCR
amplification and analysis of a nucleotide fragment (nt 453-1598)
covering the recombination breakpoint (data not shown).
Taken together, it is the first report in Thailand revealing a novel
emerging PCV2 variant generated by intergenotypic recombination between
PCV2b and PCV2d.