Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020-2023

Abstract

Porcine epidemic diarrhea virus (PEDV) is a major causative pathogen of a highly contagious, acute enteric viral disease. This study evaluated the emergence of nine variants in Jiangsu and Anhui provinces of China from 2020 to 2023. S gene-based phylogenetic analysis indicated that three variants belong to the G1c subgroup, while the other six strains are clustered within the G2c subgroup. Recombination analyses supported that three variants of the G1c subgroup were likely derived from recombination of parental variants FR0012014 and a donor variant AJ1102. In addition, there are novel mutations on amino acid 141-148 and these likely resulted in changes in antigenicity in the three variants. These results illustrated that the study provides novel insights into the epidemiology, evolution, and transmission of PEDV in China.

Keywords: PEDV; Spike gene; antigenic analysis; phylogenetic analysis; recombination analysis.

Figure 1

The electrophoresis results in amplified fragments of the S gene. Lane M, 2000 bp DNA ladder; Lane 1–4: S1, S2, S3, S4 gene sequence, constituting S gene full-length sequence.

Figure 2

Phylogenetic analysis of PEDV based on nucleotide sequences of the S gene. The phylogenetic tree was constructed with MEGA-X v.10.1.8 software using the neighbor-joining method. Bootstrap analysis was set in 1000 replicates, with a value > 70%, to assess the significance of the tree topology. The information on reference strains is provided in Table 2. “●” indicates the strains detected in this study.

Figure 3

Recombination analysis of S gene of AHbz2023-1, AHbz2023-2, and JSnt2020. The RDP plot clearly illustrates the recombination events detected in AHbz2023-1 (A), AHbz2023-2 (C), and JSnt2020 (E). The similarity of the S gene of AHbz2023-1 (B), AHbz2023-2 (D), and JSnt2020 (F) compared with FR0012014 and AJ1102 is shown.

Figure 4

Alignment of amino acid sequences of S proteins of PEDV detected strains and reference strains. The vaccine strain CV777 (GenBank accession no. AF353511) was set as a reference. The amino acid insertions are colored on a yellow background. The amino acid deletions are marked in a green background. The amino acid mutations in the acquired region (710–1190 bp) are shown in pink. The amino acid mutations in the COE (499–638 aa) region are shown in blue. The amino acid mutations and detected strains are highlighted in red.

Figure 5

Different antigenic indices of PEDV S protein. (A) Antigenic index plots of the amino acid sequences of S protein. The antigenic index plots were calculated using the Protean of DNASTAR Lasergene v.7.1 software under the Jameson–Wolf algorithm. The graphic above zero represents the predictive antigenic sites, and the antigenic discrepancy in the detected strains was labeled with a rectangle. (B) The predicted three-dimensional (3-D) modeling of the S protein of JSnt2020, AHbz2023-1, and AHbz2023-2 strains.