Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea

Abstract

Porcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae family, is an enveloped, positive-sense, single-stranded RNA virus, which causes severe diarrhea and dehydration in suckling pigs. We detected three PEDV strains from ten small intestine samples from piglets with acute diarrhea and we determined the complete genome sequences of the reemerging Korean PEDV field isolates, except for the noncoding regions from both ends. The complete genome sequences of the strains were identical or almost identical (one synonymous single-nucleotide polymorphism (SNP) in the ORF1a/1b genomic sequence). Interestingly, comparative genome analysis of recent Korean PEDV isolates and other strains revealed that the complete genome sequences of recent Korean strains were almost identical (99.9%) to those of the US PEDV strains isolated in 2013. These results suggest that the three reemerging Korean strains are distinct from previous endemic Korean PEDV strains and has been recently introduced into Korea from oversea with high likelihood.

Keywords: Animal virus; Complete genome; Coronavirus; Phylogenetic analysis; Porcine epidemic diarrhea virus.

Fig. 1

Nucleotide sequence alignment and phylogenetic tree analysis for complete genomes of PEDV strains. (A) Alignment of the complete genome sequences of the reemerging Korean PEDV field strains and other strains was performed using MAFFT. One of the reemerging Korean strain sequences was set as the reference sequence. Vertical lines indicate the SNPs compared to the reference sequence and dashes indicate sequence gaps. Protein-coding regions are indicated with arrows. (B) A maximum likelihood phylogenetic tree was generated using the alignment. One-hundred bootstrap replicates were used to assess the significance of the tree topology. A bar indicates nucleotide substitutions per site.

Fig. 2

Phylogenetic tree showing the relationship between the reemerging Korean strains from previous endemic Korean strains and strains from overseas, based on the analysis of the S gene. A maximum likelihood phylogenetic tree was generated from the alignment of complete S gene sequences. One-hundred bootstrap replicates were used to assess the significance of the tree topology. A bar indicates nucleotide substitutions per site. Korean PEDV strains are denoted using bold characters.