3.2 Phylogenetic analysis of PCV2
In this study, fifty-one PCV2 isolates were selected from 49 farms
during 2019-2020 for genetic characterization based on the previously
described criteria. The nucleotide sequences of PCV2 were deposited in
the NCBI GenBank database under accession no. OL677572-OL677622 (Table
2).
Genetic analysis using complete genome sequences showed that all 51 PCV2
isolates during 2019-2020 were 1,767 nt in length containing 945 nt of
ORF1 and 702-705 nt of ORF2. Phylogenetic analysis based on ORF2 and
genome sequences revealed that 86.27% (44 out 51) of the strains belong
to PCV2d and the remaining 13.73% (7 out 51) were PCV2b (Figure 1).
Notably, PCV2b and PCV2d could be found from the same farms for two
farms (farm A003 and A036, Table 2).
Phylogenetic trees based on the genome, ORF1 and ORF2 showed consistent
topology except for one isolate, 19NPT29. Based on the genome and ORF2
sequences, 19NPT29 was in the PCV2d cluster; however, it was in the
PCV2b cluster based on the ORF1 sequences (Figure 1).
Further investigation of deduced amino acid sequences of ORF2 was
performed by pairwise alignment with reference strains from various
genotypes. The ORF2 amino acid variations were analyzed focused on
antibody recognition sites from four regions at positions 51-84,
113-139, 161-207, and 228-233 (Lekcharoensuk et al., 2004; Mahe et al.,
2000). All the seven PCV2b isolates in this study had typical SNPRSV and
A/TGIE motifs without unique amino acid substitution. Likewise, 43 of 44
PCV2d isolates have typical SNPLTV and TGID motifs corresponding to
PCV2d strains. Notably, 19NPT29 isolate presented the SNPRSV and TGID
motifs, belonging to the PCV2b and PCV2d, respectively, suggesting the
recombination event. In this study, 31of 44 PCV2d isolates exhibited
unique amino acids at four positions: H133, D134, M136, and K232 (Figure
S2). Some of these variable regions correspond to antibody recognition
sites at positions 51-84, 113-139, 161-207, and 228-233 (Lekcharoensuk
et al., 2004; Mahe et al., 2000).