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

Abstract

Porcine epidemic diarrhea virus (PEDV) is a deadly epizootic swine coronavirus that is of importance to the world pork industry. Since the re-emergence of the virulent genotype 2b (G2b) in 2014, Jeju Island in South Korea has faced periodic outbreaks, leading to the occurrence of endemics in provincial herds. In this study, we examined the complete genome sequences and molecular characteristics of novel G2b PEDV variants with a two-amino-acid deletion in the neutralizing epitope of the spike (S) gene, which were concurrently identified on a re-infected farm and its neighboring farm on Jeju Island. Whole-genome sequencing of the Jeju S-DEL isolates KNU-1829 and KNU-1830 revealed the presence of a continuous 9-nucleotide deletion within the nonstructural protein coding region. Their genomes were 28,023 nucleotides in length, 15 nucleotides shorter than those of the classical G2b PEDV strains. The two S-DEL isolates had 96.4-99.2% and 98.3-99.7% identity at the S-gene and full-genome level, respectively, to other global G2b PEDV strains. Genetic and antigenic analyses indicated that the S-DEL isolates are most closely related to the primary strain identified from the initial exposure at the same farm, but the virus appears to undergo continuous evolution, possibly leading to antigenic drift under recurrent or endemic pressure. This study provides important information about the antigenic diversity of PEDV circulating in the endemic areas, which arises from continuous non-lethal mutations to ensure viral fitness in the host environment.

Immune response does not prevent homologous Porcine epidemic diarrhoea virus reinfection five months after the initial challenge

“…This pattern is related to the development of immunity in sows that transfer colostral/lactogenic immunity that protects suckling piglets (Clement et al., 2016). Some evidence suggests that recurrent epidemics, in the whole farm, may also happen up to two years after the original introduction of the virus (Diep et al., 2017 and Diep et al., 2018; Jang et al., 2019). Those new outbreaks can be caused by variants of the strain detected in the first case.…”

Systemic and Oral Immunogenicity of Porcine Epidemic Diarrhea Virus Antigen Fused to Poly-Fc of Immunoglobulin G and Expressed in ΔXT/FT Nicotiana benthamiana Plants

“…The first recorded case was in the United Kingdom in 1971 (Antas and Wozniakowski, 2019) and it subsequently spread to many European countries, followed by the current epidemic in Asian countries. Increasing problem is due to an appearance of new variants of PEDV with deletions/insertion, and several mutations in S (spike) 1 region (Lee et al, 2010;Lee, 2015;Jang et al, 2019). The reason for partial protection against PEDV with the current vaccine based on the CV777 strain could be explained by several sequence analyses.…”

Porcine epidemic diarrhea virus: an update overview of virus epidemiology, vaccines, and control strategies in South Korea

“…Genetic mutations, including insertions (IN) and deletions (DEL), and recombination in the S gene can drive alterations in viral pathogenicity and tissue or species tropism [ 33 34 35 36 37 38 39 40 ]. Considering the phenotypic and genotypic traits, the S gene is a suitable locus for sequencing to investigate the genetic relatedness (i.e., genotyping) and molecular epidemiology of PEDV [ 23 27 41 42 43 44 45 46 47 ]. Thus, using S gene-based phylogeny, PEDV can be genetically separated into two main genotypes with two sub-genotypes: low pathogenic (LP)-G1 (classical G1a and recombinant G1b) and HP-G2 (local epidemic G2a and global epidemic or pandemic G2b) [ 5 6 ].…”

“…G2b has continued to independently evolve and undergo genetic diversity with specific geographic clustering, ranging from 96.3% to 99.4% amino acid (aa) identity with an HP-G2b South Korean prototype strain (KNU-141112). In particular, some domestic HP-G2b strains (except for one isolate with a 200-aa DEL in the S1/S2 junction region [ 79 ]) possessed small IN or/and DEL in the N-terminal domain (NTD) of S1 [ 13 44 45 47 ], which differed from G2b variants with large 194–216-aa DELs within the S1 NTD reported in Japan, Taiwan, and the US [ 25 37 80 81 82 83 84 ]. The domestic isolates are phylogenetically clustered into six disjunct clades according to the geographic origin, that includes nationwide (NW clade with 1.3%–1.9% aa variation), Kyeongnam and Jeonnam Provinces (KJ clade with 2.2%–2.9% aa variation), Chungcheong and Kyeongbuk Provinces (CK clade with 0.6%–1.7% aa variation), Jeju Hallim (JH clade with 1.8%–2.6% aa variation), Jeju Daejeong (JD clade with 1.6%–2.7% aa variation), and not geographically classified (NC clade with 0.9%–3.7% aa variation) ( Fig.…”