Genetic variation analysis of reemerging porcine epidemic diarrhea virus prevailing in central China from 2010 to 2011

Abstract

Porcine epidemic diarrhea has re-emerged with devastating impact in central China since October 2010. To investigate and analyze the reason of this outbreak, the M and ORF3 genes of 15 porcine epidemic diarrhea viruses (PEDV), which were collected from different areas of central China during October 2010 and December 2011, were amplified by reverse transcriptase polymerase chain reaction, cloned, sequenced, and analyzed. Sequence analyses showed that the nucleotides and amino acids were changed at some sites in the M and ORF3 genes of the 15 PEDV strains compared with those genes of CV777 reference strain. Based on the phylogenetic analyses, PEDVs in central China and reference strains could be separated into three groups: G1, G2, and G3. The 15 PEDV strains belonged to G3 group and showed a close relationship with Korean strains (2007), Thai strains (2007–2008), and partial other Chinese strains (2010–2011), but differed genetically from European strains (Br1/87) and the vaccine strain (CV777 vs) being used in China. Furthermore, all 15 PEDV strains from central China and some other isolates in China from 2003 to 2007 (LJB-03, QH, and LZC) belonged to different group. Therefore, PEDV exhibits rapid variation and genetic evolution, and the currently prevailing PEDV strains in central China are a new genotype.

Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation

“…The sequencing results illustrated that the ORF3 gene of the 11 strains in JKa-295 and JMi-277 had the same length of 675 nt, and it did not possess any deletion found in known PEDV vaccine strains [15, 27, 40]. All of the variants with large deletions have the same ORF3 nucleotide sequence excluding JKa-295fSde194Co25.…”

Sequence and phylogenetic analyses of the M and N genes of porcine epidemic diarrhea virus (PEDV) strains in Anhui Province, China

“…Based on the phylogenetic analyses of M and N genes, Anhui strains are linked to Jiangsu strains but not to Shandong strains. The amino acid mutations of the N gene at positions 142, 252, and 255, and of the M gene at positions 13, 62, and 214 were observed in other Chinese strains (Yang et al, 2013).…”

Development of a multiplex TaqMan probe-based real-time PCR for discrimination of variant and classical porcine epidemic diarrhea virus

“…The other field strains, LC and GD-B, share high identity with CH/FJND-3 and have the same characteristics in the S gene (Chen et al, 2012a). All new strains isolated and sequenced after 2010 were clustered together in the same branch and far from the branch of strain CV777, indicating that the current PEDV strains were genetic variants (Li et al, 2012a;Yang et al, 2013). In the present study, the primers and probes were designed based on the conserved and variable region sequences of S gene between the variant and classical PEDV.…”