Isolation, genomic characterization, and pathogenicity of an emerging PEDV variant in Korea related to virulent Chinese strains

Introduction: The ongoing evolution of porcine epidemic diarrhea virus (PEDV) continues to significantly threaten the swine industry, necessitating extensive surveillance for the emergence of new PEDV variants in the field. Although genotype 2b (G2b) PEDV strains have been predominant in Korea since 2013, this study reports PEDV strains distinct from Korean G2b strains from two Korean pig farms experiencing severe diarrhea and mortality in sucking piglets. Methods: We report the first isolation and detailed characterization of a PEDV strain, designated KPED2021-1, from clinical specimens collected during outbreaks. Results: At the whole-genome level, KPED2021-1 demonstrated over 99G2c PEDV strains, which exhibit substantial genetic variation in China. In contrast, it shared 96.6%-98.7% homology with PEDV strains from Korea and other countries. Furthermore, KPED2021-1 showed greater nucleotide divergence in the NSP1, ORF3, and N genes from Korean and other global PEDV strains, while remaining more closely related to Chinese G2c strains in these regions. The amino-acid sequence of the spike (S) protein from KPED2021-1 was compared with that of the S protein from the Korean G2b strains, revealing 27 amino- acid substitutions and a unique deletion (11197). In experimental infection of suckling piglets, severe clinical symptoms and histopathological lesions were observed, resulting in a 100% mortality rate, suggesting that the KPED2021-1 strain is virulent. Discussion/Conclusion: This is the first report on the emergence of a G2c-subtype PEDV closely related to Chinese variants in Korea, and the isolate may serve as a useful reference strain for future vaccine development and cross-protection studies.