Outbreak-related porcine epidemic diarrhea virus strains similar to US strains, South Korea, 2013

Abstract

In late 2013, outbreaks of porcine epidemic diarrhea virus (PEDV) infection recurred in South Korea. Genetic and phylogenetic analyses showed that isolates from the outbreaks were most closely related to emergent US strains of PEDV. These US strain-like PEDV variants are prevalent in South Korea and responsible for recent outbreaks in the country.

Keywords: PED; PEDV; South Korea; US strain–like strains; economic loss; family Coronaviridae; genus Alphacoronavirus genus; order Nidovirales; outbreaks; pigs; porcine epidemic diarrhea; porcine epidemic diarrhea virus; pork industry; viruses.

Figure 1

Phylogenetic analyses based on the nucleotide sequences of the spike gene (A) and S1 portion (B) of porcine epidemic diarrhea virus (PEDV) strains. A putative similar region of the spike protein of transmissible gastroenteritis virus (TGEV) was included as an outgroup in this study. Multiple-sequencing alignments were performed by using ClustalX (http://www.clustal.org/), and the phylogenetic tree was constructed from the aligned nucleotide sequences by using the neighbor-joining method. Numbers at each branch represent bootstrap values >50% of 1,000 replicates. Names of the strains, countries and years of isolation, GenBank accession numbers, and genogroups and subgroups proposed in this study are shown. Solid circles indicate the strains from South Korea from this study that are similar to US PEDV strains; solid triangle indicates the early 2013 strain that is similar to the US PEDV strains; solid diamonds indicate the early 2013 strains that are similar to the previous PEDV strains from South Korea. Scale bars indicate nucleotide substitutions per site.

Figure 2

Phylogenetic analysis based on the nucleotide sequences of the full-length genomes of porcine epidemic diarrhea virus (PEDV) strains (GenBank numbers are shown in Figure 1, panel A). The complete genome sequence of transmissible gastroenteritis virus (TGEV) was included as an outgroup in this study. Numbers at each branch represent bootstrap values >50% of 1,000 replicates. Names of the strains, countries and years of isolation, and genogroups and subgroups proposed in this study are shown. Solid circle indicates the strain from South Korea, KNU-1305, that is similar to the US PEDV strains. The scale bar indicates nucleotide substitutions per site.