Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China

Abstract

Since late 2010, porcine epidemic diarrhea virus (PEDV) has rapidly disseminated all over the China and caused considerable morbidity and high mortality (up to 100%) in neonatal piglets. 79.66% (141 of 177) pig farms in 29 provinces (excluding Tibet and Hainan, China) and 72.27% (417 of 577) samples were positive for PEDV confirmed by reverse transcription-polymerase chain reaction (RT-PCR). The full-length S genes of representative field strains were sequenced. 33 field strains share 93.5%-99.9% homologies with each other at the nucleotide sequence level and 92.3%-99.8% homologies with each other at the amino acids sequence level. Most field strains have nucleotide deletion and insertion regions, and show lower homologies (93.5%-94.2%) with Chinese classical strain CH/S, however higher homologies (97.1%-99.3%) with recent strain CHGD-1. The phylogenetic analysis showed there are classical strains and variants prevailing in pig herd in China. PEDV has a high detection rate in pig herds in China. Sequence analysis indicated the S genes of recent field strains have heterogeneity and the variants are predominant.

Figure 1

Comparison of the antigen epitopes of S proteins of field strains and reference strains. Dots indicate the amino acids are identical to those of reference strain CV777-attenuated. SS2 is in the yellow region, SS6 is in the green region and the motif against 2C10 is in the pink region.

Figure 2

Phylogenetic analysis based on the nucleotide sequences corresponding to the full-length S gene. Putative similar regions of S gene of other distantly related coronavirus, transmissible gastroenteritis virus (TGEV), was also included in this study. The phylogenetic tree was constructed from the aligned nucleotide sequences by using the maximum likelihood method in MEGA 5.05. The scale bars indicate the number of 0.05 inferred substitutions per site. The GenBank accession numbers of recent field strains and reference strains are in the brackets.