Isolation and characterization of Chinese porcine epidemic diarrhea virus with novel mutations and deletions in the S gene

Abstract

Porcine epidemic diarrhea (PEDV) has raised growing concerns in the pig-breeding industry because it has caused significant economic losses. To better understand the molecular epidemiology and genetic diversity of PEDV field isolates, in this study, the complete spike (S) and ORF3 genes of 17 PEDV variants in Zhejiang, China during 2014 to 2017, were characterized and analyzed. Phylogenetic analysis based on the S gene and ORF3 gene of these 17 novel PEDV strains and PEDV reference strains indicated that all the PEDV strains fell into two groups designated G1 and G2. Notably, the strains identified in 2014-2015 were in G2, while the other five strains identified from 2016 to 2017 were in G1. Sequencing and phylogenetic analyses showed that recently prevalent Chinese PEDV field strains shared higher identities with United States strains than with South Korean strains. Compared with classical vaccine strains, a series of deletions and frequently occurring mutations were observed in the receptor binding domains of our PEDV strains. Besides, we successfully isolated and reported the genetic characterization two novel PEDV strains, PEDV-LA1 and PEDV-LY4-98, found on the Chinese mainland, which had significant variations in the S gene. Meanwhile, the virulence of the new mutants may be changed, the PEDV-LY4-98 strain, which has multiple mutations in the signal peptide-encoding fragment of the S gene showed delayed cytopathic effects and smaller plaque size compared with strain PEDV-LA1, which lacks these mutations. Three unique amino acid substitutions (L7, G8, and V9) were identified in the SP-encoding fragment of the S1 N-terminal domain of the PEDV-LY4-98 S protein compared with the S proteins of all the previous PEDV strains. The animal experiment revealed that these two novel strains were high pathogenic to neonatal pigs. Whether these amino acids substitutions and the N-glycosylation site substitutions influence the antigenicity and pathogenicity of PEDV remains to be investigated. Meanwhile, amino acid substitutions in the neutralizing epitopes may have conferred the capacity for immune evasion in these PEDV field strains. This study improves our understanding of ongoing PEDV outbreaks in China, and it will guide further efforts to develop effective measures to control this virus.

Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia

“…In this article, it was found that the number of PEDV sequences increased significantly after 2010 and most sequences were GII strains. These results are in good agreement with the findings of the PEDV epidemiological investigations in China ( Chen et al, 2019a ; Sun et al, 2018 ). It has been reported that PEDV GII isolates were more virulent than GI isolates ( Vlasova et al, 2014 ).…”

Pathogenicity and immunogenicity of a new strain of porcine epidemic diarrhea virus containing a novel deletion in the N gene

“…After three rounds of plaque isolation the virus was considered clonal and designated PEDV SH (Lee et al, 2017). The virus culture was scaled up over five generations; TCID 50 was then measured and a one-step growth curve was performed (Fan et al, 2017;Sun et al, 2018).…”

Isolation and identification of a variant subtype G 2b porcine epidemic diarrhea virus and S gene sequence characteristic

“…Since the first report in England in the 1970s (Choudhury et al, 2016;Pensaert and Martelli, 2016), PED has been reported in some countries (Pensaert et al, 1981;Takahashi et al, 1983). In the 1980s, PEDV was first identified in China (Sun et al, 2018). Until 2000, PEDV has been widely spread in 26 provinces in China, which made a largescale of economic losses in breeding industry.…”