Complete genome sequence of a novel S-insertion variant of porcine epidemic diarrhea virus from South Korea

Abstract

Porcine epidemic diarrhea virus (PEDV) is an emerging and re-emerging viral pathogen of pigs that is causing significant economic concerns in the global pork industry. The virulent G2b PEDV subgroup, which was responsible for the 2013-2014 pandemics on the American and Asian continents, hit Jeju Island in 2014, which had been PEDV-free since 2004. This study presents molecular characterization of a novel PEDV variant with a 5-amino acid (aa) insertion (DTHPE) in the spike (S) gene (an S-insertion) that was identified in diarrheic piglets from Jeju Island. The genome of the PEDV strain KOR/KNU-1601/2016 was sequenced and analyzed to characterize the S-insertion variant circulating on Jeju Island. The full-length genome sequence of KNU-1601 is 28,053 nucleotides (nt) in length, which is 24 nt and 15 nt longer than the genome sequences of G1 classical and G2 epidemic field strains, respectively. KNU-1601 shares 99.5-99.6% nucleotide sequence identity at the genome level and 98.0-98.6% amino acid sequence identity at the S gene level with other global G2b PEDV strains. Genetic and phylogenetic analyses indicated that the KNU-1601 variant is most closely related to the G2b field isolates but appears to undergo continuous evolution in the field. These data advance our understanding of the genetic diversity and evolutionary characteristics of the PEDV field strains circulating in South Korea.

Fig. 1

Alignment of the amino acid sequences of the S proteins of various PEDV strains, including classical G1a, pandemic G2b, and KNU-1601 strains. Potential N-glycosylation sites predicted by the NetNGlyc 1.0 Server (http://www.cbs.dtu.dk/services/NetNGlyc/) are shown in boldface type. Genetic signatures, consisting of insertions and deletions (INDELs), in the PEDV epidemic G2b strains are shaded. Amino acids representing potential hypervariable domains (solid boxes) and a unique 5-aa (DTHPE) insertion (red color) are also indicated (color figure online)

Fig. 2

Phylogenetic analysis based on the nucleotide sequences of the spike genes (A) and full-length genomes (B) of PEDV strains. A region of the spike gene and the complete genome sequence of TGEV were included as the outgroups in A and B, respectively. Multiple sequence alignments were generated with ClustalX, and a phylogenetic tree was constructed from the aligned nucleotide sequences using the neighbor-joining method. Numbers at each branch are bootstrap values greater than 50% based on 1000 replicates. The names of the strains, countries and dates (year) of isolation, GenBank accession numbers, and genogroups and subgroups proposed in this study are shown. A solid circle indicates the KNU-1601 strain identified in this study; solid diamonds indicate the re-emergent Jeju strains detected in 2014. Scale bars indicate nucleotide substitutions per site