Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus Strain from Vietnam, HUA-14PED96, with a Large Genomic Deletion

Choe, SeEun; Park, Kee-Hwan; Lim, Suk-Kyung; Le, Van Phan; Hien, Nguyen Ba; Thach, Pham Ngoc; Phuong, Le Huynh Thanh; An, Byung-Hyun; Han, Song; Cho, In‐Soo; An, Dong-Jun

doi:10.1128/genomea.00002-16

Cited by 6 publications

(6 citation statements)

References 8 publications

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“…Two recent studies reported that five Vietnamese PEDV strains isolated in 2013 and early 2014 including VN/JFP1013_1/2013/Vinh An/Vietnam, VN/VAP1113_1/2013/Vung Tua/Vietnam, VN/KCHY‐310113/2013/KhoaiChau/HungYen/Vietnam (Vui et al., ), HUA‐PED45 and HUA‐PED47 2010 (Kim, Lim et al., ) were related to new Chinese variants that have emerged since 2010. The Vietnamese PEDV strain HUA‐14PED96 (accession number KT941120), which was identified in a Northern province, was reported to have a unique 72‐nucleotide deletion in the ORF1a gene (Choe et al., ). Consistent with the previous results, several Vietnamese PEDV strains in our study were genetically similar to the reported Vietnamese strains and re‐emerging Chinese strains.…”

Section: Discussionmentioning

confidence: 99%

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

Diep

Sueyoshi

Izzati

et al. 2017

Transbound Emerg Dis

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Summary Porcine epidemic diarrhoea virus (PEDV) is the aetiologic agent of porcine epidemic diarrhoea (PED), a highly contagious enteric disease that is threatening the swine industry globally. Since PED was first reported in Southern Vietnam in 2009, the disease has spread throughout the country and caused substantial economic losses. To identify PEDVs responsible for the recent outbreaks, the full‐length spike (S) gene of 25 field PEDV strains collected from seven northern provinces of Vietnam was sequenced and analysed. The sequence analysis revealed that the S genes of Vietnamese PEDVs were heterogeneous and classified into four genotypes, namely North America and Asian non‐S INDEL, Asian non‐S INDEL, new S INDEL and classical S INDEL. This study reported the pre‐existence of US‐like PEDV strains in Vietnam. Thirteen Vietnamese variants had a truncated S protein that was 261 amino acids shorter than the normal protein. We also detected one novel variant with an 8‐amino acid insertion located in the receptor‐binding region for porcine aminopeptidase N. Compared to the commercial vaccine strains, the emerging Vietnamese strains were genetically distant and had various amino acid differences in epitope regions and N‐glycosylation sites in the S protein. The development of novel vaccines based on the emerging Vietnamese strains may be contributive to the control of the current PED outbreaks.

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Section: Discussionmentioning

confidence: 99%

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

Diep

Sueyoshi

Izzati

et al. 2017

Transbound Emerg Dis

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“…It contains a 72 nt-deletion in the open reading frame 1a (ORF1a), corresponding to a 24 aa-DEL in the nsp3 protein, and is grouped with the Chinese highly virulent PEDV cluster ( Fig. 1) (Choe et al, 2016).…”

Section: Pedv Variants That Have Deletions In the Orf1a Regionmentioning

confidence: 99%

Evolution, antigenicity and pathogenicity of global porcine epidemic diarrhea virus strains

et al. 2016

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Emerging and re-emerging coronaviruses cause morbidity and mortality in human and animal populations, resulting in serious public and animal health threats and economic losses. The ongoing outbreak of a highly contagious and deadly porcine epidemic diarrhea virus (PEDV) in Asia, the Americas and Europe is one example. Genomic sequence analyses of PEDV variants have revealed important insights into the evolution of PEDV. However, the antigenic variations among different PEDV strains are less explored, although they may contribute to the failure of PEDV vaccines in Asian countries. In addition, the evolution of PEDV results in variants with distinct genetic features and virulence differences; thus PEDV can serve as a model to explore the molecular mechanisms of coronavirus evolution and pathogenesis. In this article, we review the evolution, antigenic relationships and pathologic features of PEDV strains. This information and review of researches will aid in the development of strategies for control and prevention of PED.

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“…In Vietnam, PEDV was first observed in the southern provinces in 2009 (21). Published studies have demonstrated that PEDV is present in all major swine-producing regions in Vietnam (21)(22)(23)(24)(25)(26). A descriptive survey recently provided evidence that northern Vietnam is an endemic area for PEDV, with a high proportion of PED-positive farms (30.89%) (Mai et al, unpublished).…”

Section: Introductionmentioning

confidence: 99%

Evaluating the Risk Factors for Porcine Epidemic Diarrhea Virus Infection in an Endemic Area of Vietnam

Ngan

Bui²,

Huynh

et al. 2020

Front. Vet. Sci.

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Porcine epidemic diarrhea virus (PEDV) causes enteritis, vomiting, watery diarrhea, and high mortality in suckling pigs, threatening the swine industry. Porcine epidemic diarrhea (PED) re-emerged globally in 2013 in many important swine-producing countries in Asia and the Americas. Several studies have identified the risk factors for the spread of PEDV in acute outbreaks. However, limited information is available on the risk factors for the transmission of PEDV in endemic regions. We hypothesized that poor biosecurity, location, and some social or cultural practices are the main risk factors for PEDV transmission in the Vietnamese pig population. The aim of this study was to evaluate the potential risk factors for the transmission of PEDV in an endemic area in Vietnam. In this case-control study, questionnaires containing 51 questions were completed for 92 PEDV-positive and 95 PEDV-negative farms. A logistic regression analysis was performed to assess the risk factors associated with PEDV infection. Province and the total number of pigs were included as random effects to determine their influence on the risk of PEDV infection. Twenty-nine variables of interest that have been associated with PEDV status were analyzed in a univariate analysis (P < 0.20), with backward stepwise selection. Only three of these 29 variables in four models remained significant PEDV risk factors in the final model: farrow-to-wean production type, distance from the farm to the slaughterhouse (< 1,000 m), and the presence of chickens on site (P < 0.05). This is the first study to identify the main risk factors for PEDV infection in an endemic area. Our findings suggest that hygiene measures should be strictly implemented on farms for the effective control and prevention of PEDV infection.

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Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus Strain from Vietnam, HUA-14PED96, with a Large Genomic Deletion

Cited by 6 publications

References 8 publications

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

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

Evolution, antigenicity and pathogenicity of global porcine epidemic diarrhea virus strains

Evaluating the Risk Factors for Porcine Epidemic Diarrhea Virus Infection in an Endemic Area of Vietnam

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