Genetic Diversity of Porcine Epidemic Diarrhea Virus With a Naturally Occurring Truncated ORF3 Gene Found in Guangxi, China

Abstract

Porcine epidemic diarrhea virus (PEDV) is one of the major enteric pathogens, causing severe enteric disease, resulting in enormous economic losses. The ORF3 gene encodes an accessory protein which is related to the infectivity and virulence of PEDV. In this study, 33 PEDV positive field samples were collected from Guangxi, from 2017 to 2019, and the genetic diversity of ORF3 was investigated. Thirty-eight strains of ORF3 were obtained, and these were composed of five strains of ORF3 named Guangxi naturally truncated strains that were 293 bp in length, with continuous deletions from 172 to 554 bp. The Guangxi naturally truncated strains encoded a truncated protein of 89 amino acids, which had clustered into a new group referred to as Group 3, and these might be involved in the variations of virulence. Three genotypes (G1-1 subgroup, G1-3 subgroup, and Group 3) existed simultaneously in Guangxi based on the genetic and evolutionary analysis of the ORF3 gene. The sequence information in the current study will hopefully facilitate the establishment of a diagnostic method that can differentiate the PEDV field stains. Continued surveillance will be useful for monitoring PEDV transmission. Differentiation of the ORF3 genes in PEDV field strains can help us to choose an appropriate PEDV vaccine candidate in the future and prevent outbreaks of PED more effectively.

Comparative Characterization and Pathogenicity of a Novel Porcine Epidemic Diarrhea Virus (PEDV) with a Naturally Occurring Truncated ORF3 Gene Coinfected with PEDVs Possessing an Intact ORF3 Gene in Piglets

“…The ORF3 protein of the HLJBY strain only consists of 91 aa, with 133 aa deletions at the C’ end [ 24 ]. Recently, we discovered a new ORF3 genotype that encoded a truncated protein of 89 aa, with continuous deletions from 172–554 bp [ 25 ]. However, no co-infection of multiple ORF3 genotypes has been reported.…”

“…PEDV ORF3 deletion strains have been reported in China [ 24 ]. In our previous work, we found that two ORF3 genotypes were present in the same piglet, one of which had a naturally truncated ORF3 gene that contained a continuous 382 nucleotides deletion from 172–554 bp, and the other of which had an intact ORF3 gene of 675 nucleotides [ 25 ]. Thus, we suspected that a co-infection with two different PEDV strains occurred in the piglet.…”

Genetic characterization and phylogenetic analysis of porcine epidemic diarrhea virus in Guangdong, China, between 2018 and 2019

“…recombination or accumulation of point mutations, which can result in the virus losing its antigenicity and even the vaccine failing to work [33][34][35]. The molecular characterization of PEDVs is a major focus of swine diarrhea virus research due to the virus's high prevalence.…”

Isolation, Identification, and Evaluation of the Pathogenicity of a Porcine Enterovirus G Isolated From China

“…The primers have been described previously with some of modifications (10) (Table 1). The viral genomic RNA was extracted from the EV-G stock samples using the Axy Prep TM Viral DNA/RNA Miniprep Kit (OMEGA, USA) according to the manufacturer's instructions (31). The cDNA was synthesized in a total volume of 25 µL containing 16 µL of RNA solution, 2 µL of dNTP mixture, 0.5 µL of reverse transcriptase M-MLV, 0.5 µL of RNasin inhibitor, 1 µL of oligo (dT) or the reverse primer, and 5 µL of 5× reverse transcriptase M-MLV buffer.…”