Analysis of the spike, ORF3, and nucleocapsid genes of porcine epidemic diarrhea virus circulating on Thai swine farms, 2011-2016.

Supansa Tuanthap,Sompong Vongpunsawad,Alongkorn Amonsin,Apiradee Theamboonlers,Ausanee Duang-In,Yong Poovorawan,Pornchalit Assavacheep,Supol Luengyosluechakul,Cherdpong Phupolphan,Suphot Wattanaphansak

doi:10.7717/peerj.6843

Supansa Tuanthap, Sompong Vongpunsawad + Show 8 more

Open Access

https://doi.org/10.7717/peerj.6843

Copy DOI

Journal: PeerJ	Publication Date: Apr 30, 2019
Citations: 28	License type: CC BY 4.0

Affiliation: Chulalongkorn University

Abstract

Porcine epidemic diarrhea virus (PEDV) outbreaks on pig farms have caused significant economic loss in the swine industry since it was first reported in Thailand a decade ago. Anecdotal evidence suggests that PEDV is now endemic in this region, therefore genome information of circulating PEDV is important for molecular surveillance and evaluation of potential benefits of field vaccination. Here, we characterized PEDV infection on commercial Thai swine farms by screening 769 samples of feces and small intestinal contents from pigs with diarrhea between 2011 and 2016. Using reverse-transcription polymerase chain reaction targeting the spike (S) gene, 153 PEDV-positive samples were further subjected to analysis of the open reading frame 3 and nucleocapsid (N) genes. Comparison of 95 samples in which nucleotide sequencing was successfully obtained for all three genes revealed evolutionary diversity among the Thai PEDV strains. Phylogenetic analyses suggest that although some Thai strains changed little from years past, others resembled more closely to the recent strains reported in China. Interestingly, eight Thai PEDV strains possessed amino acid deletions in the N protein. The PEDV sequence divergence may be responsible for driving periodic outbreaks and continued persistence of PEDV on commercial swine farms. Our findings provide important insight into regional PEDV strains in circulation, which may assist future inclusions of suitable strains for future PEDV vaccines.

Highlights

Porcine epidemic diarrhea virus (PEDV) contributes to enteropathogenic diarrhea, especially among suckling piglets, and causes significant economic loss to the swine industry worldwide (Choudhury et al, 2016; Jung & Saif, 2015)
PEDV was most prevalent in the central part of Thailand where many pig farms are located (Fig. S2; Table S3)
High variation region on the antigenic CO-26K equivalent (COE) domain seen in the Thai PEDV strains identified between 2011 and 2016 showed that PEDV in Thailand continue to evolve

Summary

Introduction

Porcine epidemic diarrhea virus (PEDV) contributes to enteropathogenic diarrhea, especially among suckling piglets, and causes significant economic loss to the swine industry worldwide (Choudhury et al, 2016; Jung & Saif, 2015). PEDV-infected pigs experience watery diarrhea, vomiting and severe dehydration, which leads to 50–90% mortality among susceptible piglets (Madson et al, 2014; Shibata et al, 2000). Porcine epidemic diarrhea virus is a single-stranded positive-sense RNA virus belonging to the family Coronaviridae and the genus Alphacoronavirus (Lin et al, 2016). The most widely-accepted classification of PEDV is based on the S gene sequence, which categorizes PEDV genotypes into two genogroups (G1 and G2). The highly virulent Asian and North American strains are designated G2a and G2b, respectively (Lin et al, 2016). The original PEDV (represented by the prototypic CV777 strain) was first reported in the 1970s in Europe and was associated with high morbidity and mortality among infected pigs (Pensaert & De Bouck, 1978)

Methods

Results

Conclusion