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.

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 S gene exhibits a high degree of genetic diversity [5, 20, 21], and the S protein plays important roles in interactions with cellular receptors during virus entry, the induction of neutralizing antibodies in natural hosts, growth adaptation in vitro, and attenuation of virulence in vivo [22]. Thus, the PEDV S glycoprotein is utilized for determining genetic relatedness among PEDV isolates and developing diagnostic assays and effective vaccines [23, 24].…”

Appearance of US-like porcine epidemic diarrhoea virus (PEDV) strains before US outbreaks and genetic heterogeneity of PEDVs collected in Northern Vietnam during 2012-2015

“…The PEDV genome is composed of the 5′ untranslated region and at least seven open reading frames (ORFs) that encode four structural proteins, namely spike (S), envelope (E), membrane (M) and nucleocapsid (N), and three major non‐structural proteins (1a, 1ab and ORF3) (Song & Park, ). Of the structural proteins, the S glycoprotein is the most diverse protein (Chen et al., ), and it plays a vital role in the induction of neutralizing antibodies and regulation of interactions with cellular receptors to mediate virus entry (Bosch, van der Zee, de Haan, & Rottier, ). It is also associated with growth adaptation in vitro and attenuation of virulence in vivo (Sato et al., ).…”

Porcine epidemic diarrhea virus: current insights

“…67 The results of many studies based on sequencing and phylogenetic analyses showed that these PEDV isolates with high virulence circulating in the People's Republic of China were new variants and differed genetically from the prototype CV777 strain. 11,59,[67][68][69][70][71][72][73][74][75][76][77][78] Now, PED became endemic; however, it remains the most devastating enteric disease leading to serious losses in the People's Republic of China. PED outbreaks in the People's Republic of China from late 2010 were caused by at least three genotypes, including genotypes IIa, IIb, and Ib.…”