Molecular Characterization of Porcine Epidemic Diarrhea Virus from Field Samples in South Korea

Abstract

Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of swine. PEDV has been a major problem in the pig industry since its first identification in 1992. The aim of this study was to investigate the diversity, molecular characteristics, and phylogenetic relationships of PEDVs in field samples from Korea. Six PEDVs were identified from the field samples, and the full spike (S) glycoprotein gene sequences were analyzed. A phylogenetic analysis of the S gene sequences from the six isolates revealed that they were clustered into the G2b subgroup with genetic distance. The genetic identity of the nucleotide sequences and deduced amino acid sequences of the S genes of those isolates was 97.9-100% and 97.4-100%, respectively. A BLAST search for new PEDVs revealed an identity greater than 99.5% compared to the highest similarity of two different Korean strains. The CO-26K equivalent (COE) epitope had a 521H→Y/Q amino acid substitution compared to the subgroup G2b reference strain (KNU-1305). The CNU-22S11 had 28 amino acid substitutions compared to the KNU-1305 strain, which included two newly identified amino acid substitutions: 562S→F and 763P→L in the COE and SS6 epitopes, respectively. Furthermore, the addition and loss of N-linked glycosylation were observed in the CNU-22S11. The results suggest that various strains of PEDV are prevalent and undergoing evolution at swine farms in South Korea and can affect receptor specificity, virus pathogenicity, and host immune system evasion. Overall, this study provides an increased understanding of the prevalence and control of PEDV in South Korea.

Keywords: molecular characterization; phylogenetic analysis; porcine epidemic diarrhea virus; spike.

Figure 1

Phylogenetic relationships based on the full S (A); S1 (B); and S2 (C) glycoprotein genes of PEDV isolates and PEDV reference strains. Phylogenetic trees were constructed using Molecular Evolutionary Genetics Analysis Version (MEGA) 11.0. The evolutionary distances were computed using the neighbor-joining method, and the statistical values greater than 60% of the measure of reliability from the bootstrap (n = 1000) iterations are shown. The analyzed isolates in this study are labeled with blue triangles.

Figure 2

Schematic representation of specific domains of the PEDV S protein and insertion–deletion–substitution analysis. The S protein consists of two subdomains, the S1 and S2 subunits. The S1 subunit contains a signal peptide (SP) and two receptor-binding domains: the N-terminal domain (S1-NTD) and the C-terminal domain (S1-CTD) covering the CO-26K equivalent (COE) region. The S2 subunit contains three neutralization epitopes (SS2, SS6, and 2C10), two heptad repeat domains (HR1 and HR2), a transmembrane domain (TM), and a cytoplasmic domain (CT). The orange-shadowed boxes are the isolates identified in this study, and the green-shadowed and gray-shadowed boxes are subgroup reference strains (CV777 and KNU-1305). The arrows indicate proteolytic cleavage sites. The dashes (-) indicate regions of insertion or deletion relative to CV777. The red letters indicate amino acid substitutions compared to the KNU-1305 strain.