Molecular evolutionary analysis of ORF3 and M genes of porcine epidemic diarrhea virus in HeiLongJiang province of China

Abstract

In this present study, 11 porcine epidemic diarrhea viruses (PEDVs) were isolated from the fecal samples of piglets
infected with PEDV in HeiLongJiang province of China. In order to analyze the molecular evolution of these reemerging PEDVs, the ORF3 and M genes of 11 PEDVs were amplified by reverse transcriptase polymerase chain
reaction, cloned, sequenced, and analyzed with each other as well as other PEDV reference strains. The complete
nucleotide sequence comparison was performed with Bioedit software, and the results showed that the similarity of 11
ORF3 and M genes ranged from 97% to 100%. Nucleotides and amino acids were changed at some sites in the ORF3
and M genes of the 11 PEDV isolates when compared with CV777 reference strain, indicating that high level of variation
may have occurred in the ORF3 and M genes of PEDV strains. To establish genetic relationships of the fully sequenced
ORF3 and M genes, multiple sequence alignments were carried and phylogenetic analysis was performed. The results
indicated that these PEDV isolates belonged to genotype 3.4 that is dominant subgroup in PEDV Group, showed a close
relationship with some recent reported Chinese PEDV strains, and exhibited comparatively rapid genetic evolution, as
revealed by these viruses responsible for the recent PEDV outbreak in HeiLongJiang province clustered closely together
with other Chinese strains with rapid evolution rate. This study might be not only crucial to understand the currently
prevailing PEDV strains in northeast of China, but also provides valuable data for preventing and controlling PEDV.