The emergence of porcine epidemic diarrhea virus in United States is associated with its outbreak in China, 2013

Porcine epidemic diarrhea virus (PEDV) belongs to genus alphacoronavirus. The disease, PED, which causes high mortality rates in newborn piglets, is characterized by acute vomiting and watery diarrhea. During late 2010 in China and Southeast Aisa, several PEDV strains were initially isolated. Subsequently, the disease was pandemic in several provinces neighboring Zhejiang and later in United States in 2013. It aroused our great interest to analyze the reasons behind the outbreak.

A total of 169 fecal and intestinal samples were collected from pigs with typical PED symptoms on 26 farms in 4 provinces neighboring Zhejiang during January 2012— July 2013. Reverse transcription PCRs (RT-PCR) specific for spike (S) gene were performed. Based on the PEDV MN strain(GenBank accession No. KF468752), all primers were designed. Then TA cloning were conducted and Vector NTI software was used to assemble and analyze the sequences. Multiple alignments of sequences measured with available sequences from Asia and United States were performed, and then phylogenetic analyses using MEGA 5.2 program. Recombination events were identified by 6 methods (Recombination Detection Program, GENECONV, BOOTSCAN, MaxChi, CHIMAERA and SISCAN) and MN strain was used as a query. The major recombination breakpoints were detected by bootstrap analysis.

The detection rate was 56.8% (96/169). Among 24 representative samples, the sequences of the full length genomic cDNA of the strain CH/ZJCX1/2012, the S gene of ZJQZ-2w/2012 and CH/ZJDX-1/2012, and the region encoding structural protein genes by an order of 5'-S-ORF3-E-M-N-3' (5'-spike protein-open reading frame 3-envelope-membrane-nucleoprotein-3') of the remaining strains were detected. All the strains isolated were in G2 genogroup, unlike late 2010 isolated in G1 genogroup. Among these, the AH2012 strain was clustered closly with the U.S strains in the ORF1ab and the N gene region, unlike the ZMDZY sublineage in the S-ORF3-E-M region. Two regions of putatively major recombination breakpoints were detected: one covered the 3' half of ORF1a, complete ORF1b, and the N terminus of S, the other spanned partial S, ORF3, E, M, and partial N between the AH2012 strain and ZNDZY sublineage.

It is possible that replacement of a region within the partial S-ORF3-E-M-partial N region of the AH2012 strain with the corresponding fragment close to the ZMDZY sublineage resulted in a recombinant strain related to the outbreak of the virus in swine in eastern China and emergence in the U.S, 2013. Other unidentified recombination events and accumulation of adapted mutations within the structural protein genes were also likely involved in this process.

Disclosure of Interest: None Declared.