Genomic and epidemiological characteristics provide new insights into the phylogeographical and spatiotemporal spread of porcine epidemic diarrhea virus in Asia

Abstract

Porcine epidemic diarrhea has become pandemic in the Asian pig-breeding industry, causing significant economic loss. In the present study, 11 complete genomes of porcine epidemic diarrhea virus (PEDV) field isolates from China were determined and analyzed. Frequently occurring mutations were observed, which suggested that full understanding of the genomic and epidemiological characteristics is critical in the fight against PEDV epidemics. Comparative analysis of 49 available genomes clustered the PEDV strains into pandemic (PX) and classical (CX) groups and identified four hypervariable regions (V1 to V4). Further study indicated key roles for the spike (S) gene and the V2 region in distinguishing between the PX and CX groups and for studying genetic evolution. Genotyping and phylogeny-based geographical dissection based on 219 S genes revealed the complexity and severity of PEDV epidemics in Asia. Many subgroups have formed, with a wide array of mutations in different countries, leading to the outbreak of PEDV in Asia. Spatiotemporal reconstruction based on the analysis suggested that the pandemic group strains originated from South Korea and then extended into Japan, Thailand, and China. However, the novel pandemic strains in South Korea that appeared after 2013 may have originated from a Chinese variant. Thus, the serious PED epidemics in China and South Korea in recent years were caused by the complex subgroups of PEDV. The data in this study have important implications for understanding the ongoing PEDV outbreaks in Asia and will guide future efforts to effectively prevent and control PEDV.

FIG 1

(A) Variation analysis of 49 whole PEDV genomes from NCBI. The graph shows the variation coefficient (window size = 100 bp, step = 20 bp) in the alignment of 49 whole PEDV genomes. The detailed calculation method of the variation coefficient is shown in Fig. S1A in the supplemental material. Dashed and thick red lines, positions of four high mutation regions (V1, V2, V3, and V4) containing more nucleic acid deletions/insertions/mutations. (B) Organization of the PEDV genome. The approximate positions and sizes of genes in the PEDV genome correspond to the scale bar. The putative S1-S2 boundary (amino acid positions) of the S protein is also shown. (C) Analysis of nucleotide positions distinguishing classical and pandemic pathotypes (DCP). Graph showing the DCP position content (window size = 100 bp, step = 20 bp) in the alignment of 49 whole PEDV genomes. The detailed calculation method of DCP position is shown in Fig. S1B in the supplemental material. Dashed and green thick line, the major regions containing abundant DCP positions.

FIG 2

Phylogenetic trees of whole PEDV genomes (A), complete S genes encoded in the 49 whole PEDV genomes (B), and the corresponding N-terminal domain (NTD) sequences (C). The three neighbor-joining trees (bootstrap n = 1,000; p-distance) were constructed based on ClustalW alignments of their respective nucleic acid sequences. The sequences in red and branches were revealed for the first time in this study. All three phylogenetic trees were divided into two deep branches, a pandemic branch and a classical branch. The only exception was PEDV isolate OH851, which is linked by blue lines among the three phylogenetic trees.

FIG 3

Comparison of the antigenic index (A) and hydrophilicity plot (B) of the NTD of S protein fragments between classical and pandemic pathotypes. Dashed and green thick lines, the positions of several regions containing significant differences between classical and pandemic pathotypes. Red shading, mismatched amino acids. PEDV isolates CHZ and 7C belong to the pandemic group, whereas LZC and SD-M isolates are from the classical group.

FIG 4

Map and phylogenetic tree of 219 PEDV S gene sequences. (Left) Phylogeny-based genotyping of 219 PEDV strains with available complete S gene sequences from Asia. The neighbor-joining tree (bootstrap n = 1,000; p-distance) was constructed based on a ClustalW alignment of full-length nucleotide sequences of the S gene. The names of the strains, years, places of isolation, and GenBank accession numbers are shown in Table S3 in the supplemental material. The genogroups and subgroups were proposed according to the above phylogenetic analysis. The pandemic pathotype was divided into six subgroups (PX1a, PX1b, PX1c, PX2a, PX2b, and PX2c) and the classical pathotype into three groups (CX1a, CX1b, and CX1c). (Right) Phylogeny-based geographical dissection of PEDV strains from Asia. A map of Asia shows the districts where PEDV strains with available complete S gene sequences were isolated. The numbers in order and the colors for PEDV strains correspond to those labeled in the left panel.

FIG 5

The reconstructed spatiotemporal diffusion of PEDV at different time points in east Asia. Note that strains in China were located accurately for every province, but the other data only provided the country of origin. Some PEDV strains had no basic information, had no available whole-genome or complete S gene sequence, and were not included in this count (such as some strains from Taiwan and Vietnam). Red and pink plots, newly added strains relative to the previous period.