Complete genome characterization of porcine epidemic diarrhea virus in Vietnam

Abstract

Porcine epidemic diarrhea virus (PEDV) first emerged in Vietnam in 2009. In this study, the complete genomes of three Vietnamese PEDV isolates were characterized. These three isolates were isolated from 3-day-old pigs experiencing diarrhea. Two isolates were from swine farms in the south, and the other was from northern Vietnam. The whole genome sequences of these isolates are 28,035 nucleotides in length and have characteristics similar to those of other PEDV isolates. All three Vietnamese PEDV isolates share 99.8 % and 99.6 % sequence identity at the nucleotide and amino acid level, respectively, and have insertions of four amino acids (GENQ) and one amino acid (N) at positions 56-59 and 140, respectively, and one deletion of two amino acids (DG) at positions 160-161. Phylogenetic analysis based on the whole genome revealed that the three Vietnamese PEDV isolates are grouped together with new variants from China from 2011 to 2012 and are genetically distinct from US isolates and the classical PEDV variant. The results suggest that Vietnamese PEDV isolates are new variants, as evidenced by their genetic composition of insertions and a deletion in the spike gene, and they might have originated from the same ancestor as the Chinese PEDV strain. This study provides a better understanding of the molecular characteristics of PEDV in Vietnam.

Porcine epidemic diarrhea virus: current insights

“…41,58 Genotype IIb was another prevalent genotype in the People's Republic of China, and responsible for epidemic outbreaks in Vietnam in 2013. 1,41,64 Compared to the sequencing based on individual genes, whole-genome sequencing can provide more valuable information on the genetic diversity and evolution of the virus. For example, evidences of recombination among the highly virulent variants, and between the highly virulent variant and vaccine strain have been recently reported.…”

“…79 In 2013, three pig herds located in North and South Vietnam experienced PED outbreaks; all the PEDV isolates were identified as the genotype IIb consisted of several Chinese isolates. 64 In addition, from late 2013, PEDV outbreaks were reported in Japan, South Korea, and Taiwan. 55,60,80 The predominant genotypes of PEDV in these regions during 2013-2014 were all phylogenetically related to the highly pathogenic US-like lineage within the genotype IIa.…”

“…97 In addition, the virulence of different PEDV strains or genotypes was shown to be different, as observed in the results of recent studies. 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.…”

Evaluation of two singleplex reverse transcription-Insulated isothermal PCR tests and a duplex real-time RT-PCR test for the detection of porcine epidemic diarrhea virus and porcine deltacoronavirus

“…Since its emergence in the U.S. in April 2013, PEDV has spread rapidly across the country and resulted in the estimated death of 8 million pigs in the first year, causing economic losses of $900 million to $1.8 billion (Paarlberg, 2014). In addition, PEDV has recently also emerged or re-emerged in China, Japan, South Korea, Philippines, Thailand, Vietnam, Canada, Mexico, Germany, Belgium, France and Portugal (Grasland et al, 2015;Mesquita et al, 2015;Pasick et al, 2014;Puranaveja et al, 2009;Song and Park, 2012;Stadler et al, 2015;Theuns et al, 2015;Vlasova et al, 2014;Vui et al, 2015). Currently, PEDV remains a significant threat to the global swine industry.…”

Full-length genome analysis of two genetically distinct variants of porcine epidemic diarrhea virus in Thailand

“…PED was first reported in Belgium and the United Kingdom in 1976(Chasey and Cartwright, 1978Pensaert and De Bouck, 1978;Wood, 1977). The disease was subsequently reported in several Asian countries, including Japan, South Korea, China, Vietnam and Thailand, and became endemic, causing significant welfare and economic problems (Li et al, 2012;Park et al, 2007a;Song and Park, 2012;Temeeyasen et al, 2014;Vui et al, 2015). Since 2013, there has been an emergence of a highly virulent PEDV in the North American continent and its subsequent reports from several countries worldwide.…”