Pigs in a pen.

2014-15 Rapid Ag: Development of RT-PCR Diagnostic Tool and Genome Characterization of US Porcine Epidemic Diarrhea Virus

November 15, 2014

Principal Leader

Jim Collins

Department

Veterinary Population Medicine

Funding Awarded

2014 Fiscal Year: $33,000

2015 Fiscal Year: $66,500

The Problem

Porcine epidemic diarrhea virus (PEDV) is a severe threat to the United States swine industry. The US was considered free of PEDV until April 29, 2013. US PEDV cases were first detected in west central and eastern Iowa. Within weeks, PEDV was identified in central Illinois, Minnesota, and Colorado. Due to the introduction of PEDV into the US swine population, the effects of PEDV will be devastating due to the lack of prior PEDV immunity. Mortality rates of 100% have been reported in young pigs. While the University of Minnesota Veterinary Diagnostic Laboratory (UMVDL) has recently detected PEDV by gel based RT-PCR, the swine industry needs a more rapid and high throughput detection method to help diagnose and reduce the spread of PEDV.

Background

Classified into the family Coronaviridae, PEDV's 28 kb genome is composed of single-stranded RNA 7 . In 1971, the United Kingdom reported the first case of PEDV in feeder and finishing pigs, which displayed the same clinical signs of watery diarrhea, resembling a transmissible gastroenteritis coronavirus (TGEV) infection 7 . Unlike TGEV, PEDV's clinical signs were more prevalent in pigs older than 4 weeks. However, in 1976, PEDV caused severe watery diarrhea in all swine age groups 5 . PEDV spread into China, where the first confirmed case of PEDV occurred in 1984. Additionally, Belgium, Hungary, Korea, Italy, Thailand and Japan have both reported outbreaks of PEDV 14 ' 6 .

The US was considered free of PEDV until April 29, 2013. PEDV's primary clinical sign is diarrhea, lasting 3-4 days. Pigs of all age groups are affected, but young piglets are the most severely affected and experience a high fatality rate. Mortality rates of 100% have been reported in young pigs. While the University of Minnesota Veterinary Diagnostic Laboratory (UMVDL) has recently detected PEDV by gel based RT-PCR, the swine industry needs a more rapid and high throughput detection method to help diagnose and reduce the spread of PEDV.

Therefore, urgent action is needed to develop a real time PEDV RT-PCR and characterize the complete genome of several outbreak PEDV strains. Locally, reducing the impact of PEDV disease will directly benefit the Minnesota pork industry, ranked second in production in the United States, and valued in excess of 6.9 billion dollars in gross income annually to the state of Minnesota. A real-time PEDV RT-PCR test will allow rapid testing of numerous samples, facilitating swift producer response to the PEDV infection. Additionally, characterizing the new PEDV outbreak will lead to a greater understanding of PEDV's disease ecology, introduction and spread into the US. By using Next Generation Sequencing technology, the complete genome of US PEDV strains can be ascertained to better access molecular diversity and evolution.

Objectives

  1. Develop and validate a rapid, high throughput real-time RT-PCR diagnostic tool to detect PEDV in swine samples.

  2. Characterize the phylogenetic and evolutionary relationships between global PEDV strains by sequencing the complete genome of -25 PEDV positive samples from geographically distinct areas using the Next Generation Sequencing (NGS) platform.

  3. Develop an archive of PEDV isolates and clinical samples that can be utilized by the research community to study PEDV.