Phylogenetic Analysis of the Spike (S) Gene of the New Variants of Porcine Epidemic Diarrhoea Virus in Taiwan

Abstract

New variants of porcine epidemic diarrhoea virus (PEDV), which emerged in Taiwan in late 2013, have caused a high morbidity and mortality in neonatal piglets. To investigate the molecular characteristics of the spike (S) gene of the emerging Taiwan PEDV strains for a better understanding of the genetic diversity and relationship among the Taiwan new variants and the global PEDVs, full-length S genes of PEDVs from nine 1-7 day-old piglets from three pig farms in the central and southern Taiwan were sequenced and analysed. The result of phylogenetic analysis of the S gene showed that all the Taiwan PEDV strains were closely related to the non-S INDEL strains from US, Canada and China, suggesting a common ancestor for these strains. As compared with the historic PEDVs and CV777-based vaccine strains, the nine Taiwan PEDV variants shared almost the same genetic signatures as the global non-S INDEL strains, including a series of insertions, deletions and mutations in the amino terminal as well as identical mutations in the neutralizing epitopes of the S gene. The high similarity of the S protein among the Taiwan and the globally emerged non-S INDEL PEDV strains suggests that the Taiwan new variants may share similar pathogenesis and immunogenicity as the global outbreak variants. The development of a novel vaccine based on the Taiwan or the global non-S INDEL strains may be contributive to the control of the current global porcine epidemic diarrhoea outbreaks.

Evaluation and Comparison of the Pathogenicity and Host Immune Responses Induced by a G2b Taiwan Porcine Epidemic Diarrhea Virus (Strain Pintung 52) and Its Highly Cell-Culture Passaged Strain in Conventional 5-Week-Old Pigs

“…Viral RNA extraction and subsequent reverse transcription of both PEDVPT-P5 and PEDVPT-P96 were performed as previously described [5] using sequence-specific reverse primers (see Supplementary Table S1). The complete genomes of both viruses were obtained by using seven pairs of oligonucleotide primers that flank different regions of the novel strains of PEDV genome with at least 200-base pair overhangs (see Supplementary Table S1).…”

“…Phylogenetic analysis of these field strains indicate that their S gene sequences are highly identical to each other and are closely related to those of G2b PEDV strains [5,13]. In the present study, a Taiwan PEDV Pingtung 52 (PEDVPT) strain was successfully isolated from a suckling pig during a farm outbreak in 2014 and serially passaged in Vero cells.…”

“…Compared to traditional and CV777-based vaccine strains, the high genetic diversity of the genogroup 2b (G2b) PEDV suggests that PEDV CV777- or DR13-based attenuated vaccines may not completely protect pigs against the infection or control the disease progression [2,5]. Therefore, a new generation of PEDV vaccine against G2b PEDV is urgently required.…”

Porcine epidemic diarrhea virus: current insights

“…16,[19][20][21]56,57 Genotype II contains historical isolates in South Korea, and currently prevalent global field isolates. Genotype IIa was a recently prevalent genotype in the People's Republic of China, 58,59 Taiwan, [60][61][62] South Korea, 55,63 and the United States. 41,58 Genotype IIb was another prevalent genotype in the People's Republic of China, and responsible for epidemic outbreaks in Vietnam in 2013.…”

“…The new PEDV variants belonging to genotype II, which included genotype IIb strains emerged in the People's Republic of China from late 2010 (eg, LC, AJ1102) and Vietnam in 2013, 64,68,98 and the genotype IIa PEDV strains currently prevalent in the People's Republic of China and US-like strains in the United States, Taiwan, South Korea, Japan, and Ukraine were shown to be highly virulent. 23,41,55,[58][59][60][61][62]74,81,84,99,100 Those OH851-like variants, which belong to genotype Ib and are distributed in the People's Republic of China, the United States, South Korea, Japan, and Europe, have generally been associated with mildto-moderate clinical outbreaks. 15,20,21,56,57,81 However, severe cases associated with OH851-like strains were reported in Germany, where mortality in suckling piglets reached almost 70% in one of two sow farms, and in Portugal (mortality rate was not given).…”