Since the 2013-2014 incursion of the virulent G2b porcine epidemic diarrhoea virus (PEDV) pandemic strains in South Korea, frequent moderate-scale regional outbreaks have recurred. In particular, areas of Jeju Island with extensive swine production have faced repeated epidemics since the re-emergence in 2014. The current study reports the complete genome sequences and molecular characterization of the representative PEDV strains responsible for the 2018 endemic outbreaks on Jeju Island. All isolates were determined to belong genetically to the highly pathogenic pandemic G2b group. Full-length genome sizes of four isolates differed from that of the G2b epidemic field strain due to insertion or deletion (DEL) mutations in the non-structural protein (nsp)-or spike (S) protein-coding regions. The 2018 Jeju isolates shared 96.7%-98.7% and 98.5%-99.4% identity at the S gene and whole-genome levels, respectively, compared to global G2b PEDV strains. Genetic and phylogenetic analyses indicated that the 2018 isolates were closest to the 2014 G2b re-emergent Jeju strains, but appeared to have undergone substantial rapid independent evolution.Among the isolates, a notable nsp3 DEL variant strain, KOR/KNU-1807/2018, was isolated and propagated by continuous passages in Vero cells, and displayed typical PEDV-induced syncytia formation. Genomic sequencing identified a unique 8-nt DEL in the extreme C-terminal region of the S gene at the 4th passage (KNU-1807-P4) compared to its original sample. This DEL resulted in the premature termination of S by nine amino acid residues (EVFEKVHVQ), which contained a KxHxx motif that is a potential endoplasmic reticulum retrieval signal. In vivo animal studies showed that variant strain KNU-1807 had decreased virulence in suckling piglets. These results advance our knowledge regarding the genetic variation and pathogenicity of the G2b PEDV endemic strains prevalent in Jeju swine herds in South Korea. K E Y W O R D S endemic outbreaks, genome analysis, pathogenicity, PEDV, virus isolation | 1895 LEE Et aL.

Summary After the unintentional vaccination of the LOM vaccine strain in 2014, classical swine fever virus (CSFV) reemerged in naïve pig herds on Jeju Island, South Korea, which had been a CSF‐free region with a non‐vaccination policy for a decade. Since the re‐emergence, endemic outbreaks of CSFV have occurred in the island, causing enormous damage to provincial pig farms. The present study reports the complete genome sequences and molecular characterization of the LOM‐derived field CSFV strains responsible for the current outbreaks on Jeju Island. The emergent Jeju LOM‐derived isolates shared 98.9%–99.7% and 98.7%–99.0% nucleotide sequence identity at the E‐gene and whole‐genome levels compared to the LOM vaccine strain respectively. Genetic and phylogenetic analyses indicated that the CSFV field isolates were closest to the LOM strains, but appeared to have undergone substantial evolution. The total number of nucleotide and amino acid differences between the LOM vaccine strain and LOM‐derived field isolates ranged from 111 and 28 to 148 and 42. These variations were found to be widely distributed throughout the genome and particularly accumulated in non‐structural proteins, which might be associated with the potential for LOM to revert to its original low pathogenic form and subsequent horizontal transmission in Jeju swine herds. These data improve our knowledge regarding safety of the LOM vaccine and inherent risk of reversion to natural virulence in host animals.

Background Reemergent local outbreaks of classical swine fever (CSF) occurred simultaneously in multiple pig farms on CSF‐free Jeju Island, South Korea, in 2014 because of inadvertent injection of a commercial CSF (LOM) vaccine into pregnant sows. The LOM virus has since spread across the island and has become endemic in Jeju herds, raising concern about possible reversion to the virulence of the LOM vaccine. We previously isolated LOM‐derived field CSF virus (CSFV) strains with unique insertion‐deletion (INDEL) mutations in the 3′‐untranslated region (UTR), designated LOM‐derived Jeju 3′‐UTR INDEL variants, from CSF‐recurrent swine farms on Jeju Island in 2019. Methods The present study conducted animal experiments to investigate whether a 2019 emergent LOM 3′‐UTR INDEL variant, KNU‐1905, has reverted to a pathogenic form in conventional pigs (n = 10). Results Experimental animal infection showed that pigs inoculated with the commercial LOM vaccine strain developed no adverse effects compared to the sham‐infected pigs. However, KNU‐1905 displayed pathogenic characteristics in pigs, including clinical symptoms (e.g., lethargy, conjunctivitis, nasal discharge, and diarrhoea), weight loss, and gross lesions. Moreover, viremia, virus shedding in faeces and nasal fluids, and viral loads in various tissues of all the KNU‐1905‐infected pigs were highly significant, in contrast to those of the LOM‐infected group in which CSFV RNA was detected only in the serum, nasal, and tonsil samples of one identical pig. Conclusions Overall, the LOM‐derived field isolate with molecular variations induced clinical adverse events in pigs, which commonly shed considerable amounts of CSFV. This study provides evidence that the genetic evolution of the LOM‐derived CSFV circulating on Jeju Island might have allowed the LOM vaccine to recover its primary prototype and that these variants might have induced chronic or persistent infection in pigs that can shed CSFV in field farms leading to a risk of transmission among pigs or farms in this former CSF‐free region.

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