Molecular epidemiology of porcine epidemic diarrhea virus in China

Abstract

Since early 2006, porcine epidemic diarrhea virus (PEDV) has been reemerging in immunized swine herds. Open reading frame 3 (ORF3) is the only accessory gene in the PEDV genome. The entire ORF3 genes of 12 PEDV field strains and one vaccine strain were sequenced. The ORF3 genes of Chinese PEDV field strains (excluding CH/GSJIII/07) contain a single 672- or 675-nucleotide (nt) ORF, which encodes a 223- or 224-aa-long peptide. However, the CV777 vaccine strain and CH/GSJIII/07 contain a 276-nt ORF because of a 49-nt deletion at nt 245-293. The Chinese PEDV field strains and PEDV reference strains are divided into three groups based on the phylogenetic relationship of their ORF3 genes. Chinese PEDV field strains (excluding CH/GSJIII/07) have a close phylogenetic relationship to Korean strains and are genetically different from the PEDV vaccine strains. However, CH/GSJIII/07 has a close phylogenetic relationship to two vaccine strains, suggesting that it might have evolved from a live vaccine strain. Chinese PEDV field strains (excluding CH/GSJIII/07) can be differentiated from PEDV vaccine strains by a nested RT-PCR method.

Fig. 1

Nested RT-PCR on the PEDV strains (including CV777 vaccine strain). a The first PCR products for the 11 field PEDV strains and the CV777 vaccine strain. b The second PCR products for the 11 field PEDV strains and CV777 vaccine strain. From left to right: A CH/HLJH/06, B CH/HNCH/06, C CH/IMT/06, D CH/SHH/06, E CH/HLJM/07, F CH/GSJI/07, G CH/GSJII/07, H CH/HNHJ/08, I CH/JL/08, J CH/JL/09, K CH/GSJIII/07, L CV777 vaccine strain, M negative control, N DNA marker (DL2,000)

Fig. 2

Comparison of partial nucleotide sequences of ORF3 genes of Chinese PEDV strains and PEDV reference strains. The dashes indicate deleted nucleotides. The oligonucleotide in the box is the primer ORF3U2, and the nucleotides (nt 264, 274) are identical in Br1/87, CV777 and LZC, but different from those in other PEDV strains. vs vaccine strain. The region (nt 409–419) is the previously reported variable region II

Fig. 3

Phylogenetic analysis of the nucleotide sequences of ORF3 genes of Chinese PEDV strains and PEDV reference strains. The tree was constructed based on the minimum-evolution method using MEGA 4 software. Numbers above branches indicate bootstrap values calculated from 1,000 bootstrap replicates. The scale bar indicates the branch lengths for 0.5% nucleotide differences. The Chinese PEDV strains are in bold