Genotypic characterization of novel S-DEL variants of porcine epidemic diarrhea virus identified in South Korea

Abstract The highly pathogenic-genotype 2b (HP-G2b) porcine epidemic diarrhea virus (PEDV) that caused the 2013–2014 pandemic has evolved in South Korea and has endemically affected the domestic pig industry. This study describes the genotypic traits of novel HP-G2b PEDV strains identified in affected farms experiencing low disease severity with < 10% neonatal mortality. Nucleotide sequencing revealed common deletion (DEL) patterns of duad residues, termed S-DEL2, at positions 60 and 61, 61 and 62, or 63 and 64 in the N-terminal domain of the spike (S) gene of all isolates. Nevertheless, the S barcode profiles of S-DEL2 variants differed from each other and shared 96.0–99.4% and 98.5–99.6% homology with other South Korean HP-G2b PEDV strains at the S and complete genome levels, respectively. Moreover, genetic and phylogenetic analyses confirmed that the S-DEL2 strains belonged to diverse domestic clades, CK, CK.1, CK.2, or NC. The emergence of novel S-DEL2 strains suggests continuous evolution of PEDV under endemic circumstances, which may result in genetic diversity and distinct clinical presentations. Overall, this study advances our knowledge regarding the genetic and pathogenic heterogeneity of PEDV and emphasizes the significance of active monitoring and surveillance to identify novel variants and further explore their genotypic and phenotypic characteristics.