Whole-genome analysis of porcine epidemic diarrhea virus (PEDV) from eastern China

Abstract

The complete genome sequence of a porcine epidemic diarrhea virus variant, strain SHQP/YM/2013, from China was determined and compared with those of other porcine epidemic diarrhea viruses. The full-length genome was 28,038 nucleotides (nt) in length without the poly (A) tail, and it was similar to that of other reported PEDV strains, with the characteristic gene order 5'-replicase (1a/1b) -S-ORF3-E-M-N-3'. Nucleotide sequence analysis based on individual virus genes indicated a close relationship between the S gene of SHQP/YM/2013 and those of the four Korean field strains from 2008-2009. Its ORF3 gene, however, fell into three groups. Recent prevalent Chinese PEDV field isolates were divided between group 1 and group 3, which suggests that the recent prevalent Chinese PEDV field isolates represent a new genotype that differs from the genotype that includes the vaccine strains. Based on phylogenetic analysis of the M gene, ORF3 gene and S gene, our study demonstrated that prevalent PEDV isolates in China may have originated from Korean strains. This report describes the complete genome sequence of SHQP/YM/2013, and the data will promote a better understanding of the molecular epidemiology and genetic diversity of PEDV field isolates in eastern China.

Porcine epidemic diarrhea in China

“…piglets, jeopardizing the pig farming industry. In October 2010, a highly pathogenic variant PEDV strain was identified in China, and later in 2013, the variant caused a pandemic in the USA, spreading to Canada and Mexico (Chen et al, 2012a;Chen et al, 2012b;Cima, 2013;Jung and Saif, 2015;Ojkic et al, 2015;Pan et al, 2012;Sun et al, 2012;Tian et al, 2014;Yang et al, 2014;Yang et al, 2013). PEDV has spread widely to many countries in Europe, Asia, American, and Australia.…”

Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China

“…The N protein provides a structural basis for the helical nucleocapsid, and is important for the induction of cell-mediated immunity [7]. Two long ORFs (ORF1a and ORF1b) genes, which occupy two thirds of the genome, encode the non-structural replicase polyproteins (replicase 1a and 1b) [8]. These dates increase our insight into PEDV genomic characteristics.…”

Classification of Emergent U.S. Strains of Porcine Epidemic Diarrhea Virus by Phylogenetic Analysis of Nucleocapsid and ORF3 Genes

“…In addition to the N gene, open reading frame 3 (ORF3) is an important virulence gene that can be used as a valuable tool for studying the molecular epidemiology of PEDV (4,5). In recent published studies, phylogenetic analyses of the N and ORF3 genes indicated that Chinese PEDVs circulating between 2010 and 2013 during PED outbreaks have originated mostly from earlier domestic PEDV strains (6,7,8). Based on these results, it is reasonable to reconsider the epidemiological status of U.S. PEDVs in outbreaks of sever acute PED.…”