Evolutionary characterization of the emerging porcine epidemic diarrhea virus worldwide and 2014 epidemic in Taiwan

Abstract

Since 2010, a new variant of PEDV belonging to Genogroup 2 has been transmitting in China and further spreading to the Unites States and other Asian countries including Taiwan. In order to characterize in detail the temporal and geographic relationships among PEDV strains, the present study systematically evaluated the evolutionary patterns and phylogenetic resolution in each gene of the whole PEDV genome in order to determine which regions provided the maximal interpretative power. The result was further applied to identify the origin of PEDV that caused the 2014 epidemic in Taiwan. Thirty-four full genome sequences were downloaded from GenBank and divided into three non-mutually exclusive groups, namely, worldwide, Genogroup 2 and China, to cover different ranges of secular and spatial trends. Each dataset was then divided into different alignments by different genes for likelihood mapping and phylogenetic analysis. Our study suggested that both nsp3 and S genes contained the highest phylogenetic signal with substitution rate and phylogenetic topology similar to those obtained from the complete genome. Furthermore, the proportion of nodes with high posterior support (posterior probability >0.8) was similar between nsp3 and S genes. The nsp3 gene sequences from three clinical samples of swine with PEDV infections were aligned with other strains available from GenBank and the results suggested that the virus responsible for the 2014 PEDV outbreak in Taiwan clustered together with Clade I from the US within Genogroup 2. In conclusion, the current study identified the nsp3 gene as an alternative marker for a rapid and unequivocal classification of the circulating PEDV strains which provides complementary information to the S gene in identifying the emergence of epidemic strain resulting from recombination.

Keywords: Evolutionary rate; Likelihood mapping; Nsp3; Phylogenetic signal; Porcine epidemic diarrhea virus; Spike; Taiwan.

Fig. 1

Correlation between nucleotide length and phylogenetic noise. Length of each gene tested for phylogenetic noise is plotted on the x-axis, and the phylogenetic noise as measured using TREE-PUZZLE program is plotted on the y-axis. Open circles indicate measurements from the worldwide dataset, filled circles indicate measurements from the Genogroup 2 dataset, and filled triangles indicate measurements from the China dataset. A linear regression line was plotted against each dataset (dashed = worldwide, solid = Genogroup 2, intermittent = China) with statistical significance (worldwide: R² = 0.82, p < 0.001; Genogroup 2: R² = 0.68, p < 0.001; China: R² = 0.82, p < 0.001) by Pearson correlation test. The gray filled region at the bottom of the graph denoted phylogenetic noise < 30%.

Fig. 2

Bayesian maximum clade credibility phylogenetic trees based on the spike (S, left), nsp3 (middle), and E (right) genes for the worldwide dataset according to the indicated substitution models and molecular clock suggested by the ModelTest and Bayes factors. Branch lengths are scaled in years. Branch with posterior support > 0.8 are labeled inside the node. Sequences colored in red clustered within Genogroup 1 and black within Genogroup 2 based on the full-genome phylogenetic analysis (Huang et al., 2013). Each strain is labeled based on the accession number on GeneBank followed by the host, country and year, which could refer to supplementary Table S1 for details.

Fig. 3

Bayesian maximum clade credibility phylogenetic trees with three PEDV strains collected during the 2014 Taiwan epidemic based on the nsp3 for the worldwide dataset (A) and North America dataset (B) according to the substitution model of GTR + I + G and GTR + I suggested by jModeltest, respectively. Branch with posterior support > 0.8 are labeled inside the node. Sequences within each clade are colored consistently across genes. Three local Taiwan PEDV strains are marked with asterisk. North American PEDV strains are labeled based on the accession number on GeneBank (KJ645635–708) followed by the host, country and year.