Table 1.
Details of sample information in this study.
Table 2.
List of primers used in this study.
Table 3.
PDEV reference strains described in this study.
Fig 1.
Phylogenetic analysis of full-length S gene of 13 PEDV strains collected in this study.
MAFFT (Multiple Alignment using Fast Fourier Transform) in the UGENE software was used to align 98 PEDV reference strains with 13 PEDV strains (Version 36.0). With IQ-TREE, the phylogenetic tree was built using the maximum likelihood (ML) method with 1,000 bootstrap replicates (Version 1.6.12). PEDV’s S gene PEDV was divided into six categories: GI-a (light grey), GI-b (blue), GII-a (light green), GII-b (light cyan), and GII-c (light cyan) (light yellow). The CV777 reference strains are highlighted in blue, while the 13 strains reported in this study are highlighted in red. Nucleotide substitutions per site are indicated by a 0.007 bar.
Fig 2.
Analysis of animo acid mutations in the S protein of 13 PEDV strains.
MUSCLE was used to align the sequences, and Geneious software (Version 11.0.9) was used to visualize them. (A) The common insertions (red box) and deletions (blue box) of amino acid (aa) mutations compared with the reference strains ZJ08 and CV777. (B). The regions in the S1 protein with a relative high polymorphism of mutations. (C) The predicted N-linked glycosylation sites of reference strain (CV777 and ZJ08), and 13 PEDV strains collected in this study. MUSCLE and the Geneious software were used to align the sequences (Version 11.0.9). The purple arrow represents the predicted N-linked glycosylation site based on the consensus N-X-S/T (X can be any amino acid except proline) glycosylation motif.
Table 4.
Sequence comparison of S gene of 13 PEDV strains and 3 vaccine strains.
Table 5.
Statistics of mutations in the S protein of the 13 PEDV strains in comparison with ZJ08.
Fig 3.
Detection of possible recombination events in the PEDV strains.
The recombination detection software (RDP v5) was used to recognize recombination events in the GDsg12 (A) and GDsg01 (B) genomes using nine detection algorithms (RDP, GENECONV, Bootscan, Maxchi, Chimaera, SiSscan, PhylPro, LARD, 3Seq). The Y-axis represents the pairwise identity between the recombinant and its putative parents. The X-axis represents the position in alignment with a 30-nt sliding window. The comparison of recombinant-major parent, recombinant-minor parent, major-minor parent was indicated as cyan, purple, and yellow lines, respectively.
Fig 4.
Predicted N-linked glycosylation sites of reference strains (CV777 and ZJ08) and 13 PEDV strains collected in this study.
The sequences were aligned using MUSCLE with the Geneious software (Version 11.0.9). The purple arrow represents the predicted N-linked glycosylation site based on the consensus N-X-S/T (X can be any amino acid except proline) glycosylation motif.