Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains

Abstract

Porcine epidemic diarrhea virus (PEDV), which re-emerged in China in October 2010, has spread rapidly worldwide. Detailed analyses of the complete genomes of different PEDV strains are essential to understand the relationships among re-emerging and historic strains worldwide. Here, we analysed the complete genomes of 409 strains from different countries, which were classified into five subgroup strains (i.e., GI-a, GI-b, GII-a, GII-b, and GII-c). Phylogenetic study of different genes in the PEDV strains revealed that the newly discovered subgroup GII-c exhibited inconsistent topologies between the spike gene and other genes. Furthermore, recombination analysis indicated that GII-c viruses evolved from a recombinant virus that acquired the 5' part of the spike gene from the GI-a subgroup and the remaining genomic regions from the GII-a subgroup. Molecular clock analysis showed that divergence of the GII-c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re-emergence outbreaks. Interestingly, Ascaris suum, a large roundworm occurring in pigs, was found to be an unusual PEDV host, providing potential support for cross-host transmission. This study has significant implications for understanding ongoing global PEDV outbreaks and will guide future efforts to develop effective preventative measures against PEDV.

Keywords: genotyping; molecular epidemiology; porcine epidemic diarrhoea virus; recombination; spike gene.

Figure 1

Genotyping and origin of the 409 PEDV strains based on full‐length genomic sequence analyses. (a) Phylogram was tested by 1,000 bootstrap replicates, branch lengths were measured by the number of substitutions per site (see scale bars). Names of strains, years, places of isolation, GenBank accession numbers, genogroups, and subgroups are shown. (b) Line chart shows the number of PEDV sequences obtained by gene subgroup and year of sampling. Yearly percentages of samples positive for PEDV are indicated by different coloured lines respectively. Data are indicated below sampling years. (c) Subgroup distribution of all available complete or partial PEDV genome sequences from countries reporting PEDV infections (n.a., sequence not available). In the bar charts, counts are shown by country or region. Data are indicated below bar charts [Colour figure can be viewed at http://wileyonlinelibrary.com]

Figure 2

Recombination and origin of the PEDV GII‐c subgroup. (a) SimPlot analysis for possible recombination events of the GII‐c subgroup genome compared to the other four subgroups. (b) Time‐scaled phylogeny of the PEDV S gene from the GII‐c subgroup. Time‐scaled Maximum Clade Credibility (MCC) trees were estimated from the complete S protein from the GII‐c subgroup, as indicated in Figure 2c, with tip times reflecting time of sampling (x‐axis). Node age estimates are shown, and the time line is indicated under the tree [Colour figure can be viewed at http://wileyonlinelibrary.com]

Figure 3

Genotyping and origin of the 409 PEDV strains based on different genes. (a–c) Phylogenetic trees were constructed by the maximum‐likelihood (ML) method based on (a) ORF1ab, (b) ORF3‐E‐M‐N, and (c) S gene sequences, with 1,000 bootstrap replicates. Names of strains, years, places of isolation, GenBank accession numbers, genogroups, and subgroups are shown. (d) Model for the recombination and origin of the S gene in the five different PEDV subgroups [Colour figure can be viewed at http://wileyonlinelibrary.com]

Figure 4

Amino acid variants of S proteins in different PEDV subgroups. (Upper) Amino acid changes in S proteins of the two gene groups, with 11 amino acid changes found to distinguish the two gene groups. (Lower) Amino acid substitutions in the S protein neutralization epitope regions of the five subgroups [Colour figure can be viewed at http://wileyonlinelibrary.com]