Molecular characteristics and pathogenic assessment of porcine epidemic diarrhoea virus isolates from the 2018 endemic outbreaks on Jeju Island, South Korea

Abstract

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.

Emergence and evolution of novel G2b-like porcine epidemic diarrhea virus inter-subgroup G1b recombinants

“…The suspensions were vortexed and centrifuged for 10 min at 4,500 × g (Hanil Centrifuge FLETA5, Incheon, South Korea). The clarified supernatants were initially subjected to RT-PCR analysis using a LiliF PED RT-PCR Kit (iNtRON Biotechnology, Seongnam, South Korea) according to the manufacturer's instructions and to quantitative real-time RT-PCR as described previously [9,10]. To determine if any other diarrhea-causing pathogens, besides PEDV, were present in clinical samples, we performed virus-specific RT-PCR analyses for transmissible gastroenteritis virus, porcine deltacoronavirus, and porcine rotaviruses.…”

Establishment of stable Vero cell lines expressing TMPRSS2 and MSPL: A useful tool for propagating porcine epidemic diarrhea virus in the absence of exogenous trypsin

“…Notably, vaccination failure and high death rate as observed in the 2010 Chinese outbreak, with the reemergence of a more virulent PEDV [4], resulted in huge economic losses for the pig industry. Subsequently, PED rapidly spread to more than 30 states of the United States, causing its first outbreak in 2013 and significant damage to the US pork industry [5], following which further outbreaks were reported in Canada, Mexico, Korea, Germany, and Belgium [6][7][8][9][10].…”

Complete genome sequences of novel S-deletion variants of porcine epidemic diarrhea virus identified from a recurrent outbreak on Jeju Island, South Korea

“…S1) [6,8]. Genetic analysis indicated that the isolates were most closely related to the KNU-1815 strain (GenBank accession number MK032689), which was identified on farm A in early 2018 [12]. Both the KNU-1829 and -1830 viruses were found to contain a novel two-amino-acid (RG) deletion at positions 1,370 and 1,371 in the C-terminal region of the S protein, named S DEL, which is not present in the genome sequences of the other G1 and G2 strains available from the GenBank database ( Fig.…”

“…In early October 2018, enteric and diarrheal diseases accompanied by low-to-moderate mortality rates (30-50%) in newborn piglets broke out almost simultaneously in two vaccinated farrow-to-finishing herds (farms A and B) in a Hallim-swine-dense region of Jeju Province. In particular, farm A experienced an acute PEDV infection in March 2018 [12]. Small-intestine specimens collected from diarrheic piglets at those farms were submitted to our laboratory for diagnosis.…”

“…The KOR/ KNU-1829/2018 and KOR/KNU-1830/2018 sequence data were deposited in the GenBank database under accession numbers MK482396 and MK482397, respectively. Like the primary KNU-1815 strain, the S-DEL strains also possessed a unique nine-nucleotide deletion at genomic positions 3,408-3,416, located in open reading frame 1a, which encodes nsp3 [12]. No additional INDELs were identified throughout their entire genomes.…”