Genetic characterization of the spike gene of porcine epidemic diarrhea viruses (PEDVs) circulating in Vietnam from 2015 to 2016

Than, Van Thai; Choe, Se Eun; Vu, Thi Thu Hang; Tien, Duy; Nguyễn, Thị Lan; Bui, Thi To Nga; Ngan, Thi; M., Ra; Song, Daesub; An, Dong; Le, Van Phan

doi:10.1002/vms3.256

Cited by 15 publications

(26 citation statements)

References 42 publications

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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that northern Vietnam is an endemic area for PEDV, with a high proportion of PED-positive farms (30.89%) (Mai et al, unpublished).…”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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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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“…PEDV was first reported in the south of Vietnam in 2009 [17]. From 2012 to 2016, PEDV strains belonging to the four classification groups circulated in many regions of Vietnam [33,34]. In this study, eight PEDV strains collected in Vietnam in 2018 were classified into three groups.…”

Section: Discussionmentioning

confidence: 96%

Characteristics and Pathogenicity of the Cell-Adapted Attenuated Porcine Epidemic Diarrhea Virus of the Non-S INDEL Cluster

Yeom

Moon

et al. 2021

Pathogens

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The high antigenic diversity of porcine epidemic diarrhea virus (PEDV) means that porcine epidemic diarrhea (PED) is a challenge for the global pig industry. Understanding the circulation of the virus to determine an optimal vaccine strategy is important in controlling the disease. In this study, we describe the genetic diversity of circulating PEDV based on the full sequences of spike genes of eight positive samples collected in Vietnam since 2018. Additionally, we developed a live attenuated vaccine candidate from the cell-adapted PEDV2 strain, which was continuously passaged until level 103 in VERO-CCL81 cells. PEDV2-p103, which belongs to the emerging non-S INDEL cluster, exhibited low virus shedding, did not induce lesions in the small intestine of challenged piglets, and had a high titer in the VERO-CCL81 cell at 48 h post-infection. These results suggest that the PEDV2-p103 strain could be a potential oral attenuated vaccine, and its immunogenicity and efficacy should be further assessed through in vivo tests.

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“…Vui et al (2015) has sequenced the first complete genome of PEDV from outbreaks in Vietnam in 2013 and suggested that the Vietnamese PEDV isolates were new variants. Other studies mainly focused on the spike gene sequences indicated that there have been remarkable changes in the Vietnamese PEDV strains collected from 2012 to 2016 (Kim et al, 2015;Diep et al, 2018;Than et al, 2020) and these may decrease the vaccine efficiencies. Although PEDV strains remain the main cause of piglet losses in large litters in Vietnam; however, very limited molecular data of their genotypic and genealogy of PEDV are available from Vietnam.…”

Section: Introductionmentioning

confidence: 99%

Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam—a molecular potential for the vaccine development?

Tran¹,

Liên

Thu³

et al. 2021

PeerJ

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Background Porcine epidemic diarrhea virus (PEDV) is a dangerous virus causing large piglet losses. PEDV spread rapidly between pig farms and caused the death of up to 90% of infected piglets. Current vaccines are only partially effective in providing immunity to suckling due to the rapid dissemination and ongoing evolution of PEDV. Methods In this study, the complete genome of a PEDV strain in Vietnam 2018 (IBT/VN/2018 strain) has been sequenced. The nucleotide sequence of each fragment was assembled to build a continuous complete sequence using the DNASTAR program. The complete nucleotide sequences and amino acid sequences of S, N, and ORF3 genes were aligned and analyzed to detect the mutations. Results The full-length genome was determined with 28,031 nucleotides in length which consisted of the 5′UTR, ORF1ab, S protein, ORF3, E protein, M protein, N protein, and 3′UTR region. The phylogenetic analysis showed that the IBT/VN/2018 strain was highly virulent belonged to the G2b subgroup along with the Northern American and Asian S-INDEL strains. Multiple sequence alignment of deduced amino acids revealed numerous mutations in the S, N, and ORF3 regions including one substitution 766P > L766 in the epitope SS6; two in the S0subdomain (135DN136 > 135SI136 and N144> D144); two in subdomain SHR1 at aa 1009L > M1009 and 1089S > L1089; one at aa 1279P > S1279 in subdomain SHR2 of the S protein; two at aa 364N > I364 and 378N > S378 in the N protein; four at aa 25L > S25, 70I > V70, 107C > F107, and 168D > N168 in the ORF3 protein. We identified two insertions (at aa 59NQGV62 and aa 145N) and one deletion (at aa 168DI169) in S protein. Remarkable, eight amino acid substitutions (294I > M294, 318A > S318, 335V > I335, 361A > T361, 497R > T497, 501SH502 > 501IY502, 506I > T506, 682V > I682, and 777P > L777) were found in SA subdomain. Besides, N- and O-glycosylation analysis of S, N, and ORF3 protein reveals three known sites (25G+, 123N+, and 62V+) and three novel sites (144D+, 1009M+, and 1279L+) in the IBT/VN/2018 strain compared with the vaccine strains. Taken together, the results showed that mutations in the S, N, and ORF3 genes can affect receptor specificity, viral pathogenicity, and the ability to evade the host immune system of the IBT/VN/2018 strain. Our results highlight the importance of molecular characterization of field strains of PEDV for the development of an effective vaccine to control PEDV infections in Vietnam.

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Genetic characterization of the spike gene of porcine epidemic diarrhea viruses (PEDVs) circulating in Vietnam from 2015 to 2016

Cited by 15 publications

References 42 publications

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

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

Characteristics and Pathogenicity of the Cell-Adapted Attenuated Porcine Epidemic Diarrhea Virus of the Non-S INDEL Cluster

Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam—a molecular potential for the vaccine development?

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