Evolutionary characterization of the emerging porcine epidemic diarrhea virus worldwide and 2014 epidemic in Taiwan

Abstract

Since 2010, a new variant of PEDV belonging to Genogroup 2 has been transmitting in China and further spreading to the Unites States and other Asian countries including Taiwan. In order to characterize in detail the temporal and geographic relationships among PEDV strains, the present study systematically evaluated the evolutionary patterns and phylogenetic resolution in each gene of the whole PEDV genome in order to determine which regions provided the maximal interpretative power. The result was further applied to identify the origin of PEDV that caused the 2014 epidemic in Taiwan. Thirty-four full genome sequences were downloaded from GenBank and divided into three non-mutually exclusive groups, namely, worldwide, Genogroup 2 and China, to cover different ranges of secular and spatial trends. Each dataset was then divided into different alignments by different genes for likelihood mapping and phylogenetic analysis. Our study suggested that both nsp3 and S genes contained the highest phylogenetic signal with substitution rate and phylogenetic topology similar to those obtained from the complete genome. Furthermore, the proportion of nodes with high posterior support (posterior probability >0.8) was similar between nsp3 and S genes. The nsp3 gene sequences from three clinical samples of swine with PEDV infections were aligned with other strains available from GenBank and the results suggested that the virus responsible for the 2014 PEDV outbreak in Taiwan clustered together with Clade I from the US within Genogroup 2. In conclusion, the current study identified the nsp3 gene as an alternative marker for a rapid and unequivocal classification of the circulating PEDV strains which provides complementary information to the S gene in identifying the emergence of epidemic strain resulting from recombination.

Porcine Epidemic Diarrhea Virus Infection Inhibits Interferon Signaling by Targeted Degradation of STAT1

“…PEDV is the causative agent of porcine epidemic diarrhea (PED), an acute, highly contagious, and devastating viral enteric disease with a high mortality rate in suckling piglets. Since PED was first reported in England in 1971 (3), the disease has broken out frequently in many pig-producing countries (4)(5)(6)(7)(8)(9). Despite the availability of vaccines, outbreaks continue to increase and pose problems for the swine industry, as well as public health concerns (10)(11)(12).…”

Antiviral effect of lithium chloride on porcine epidemic diarrhea virus in vitro

“…Currently, vaccination is the primary measure for prevention of PEDV. However, genetic variants have been identifying in Asia, Europe and North America since 2010 (Hanke et al, 2015;Horie et al, 2016;Huang et al, 2013;Lee and Lee, 2014;Li et al, 2012;Sung et al, 2015;Trujillo-Ortega et al, 2016;Vui et al, 2015;Wang et al, 2013;), which makes current traditional inactivated and attenuated PEDV vaccines are less effective against circulating PEDV variants (Choi et al, 2009;Lee, 2015). The lack of effective therapeutic treatment underlines the importance of research for new antivirals.…”

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).…”