Coronaviruses belong to the family Coronaviridae have emerged as a major global threat to animal and human health. Coronaviruses exhibit a pronounced propensity for interspecies transmission as illustrated by important emerging viruses in humans such as SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), as well as the recent SARS-CoV-2 that is causing the ongoing Coronavirus disease -2019 (COVID-19) pandemic.

Over the past 80 years, several novel coronaviruses have caused extensive outbreaks and economic losses in swine. Due to the wide variability in management and husbandry practices, pigs are in frequent contact with both humans and other animals such as pets, livestock and wild animals than other livestock species. Therefore, pigs theoretically possess a greater chance to promote cross-species viral transmission. Currently there are three coronaviruses of concern to pig production globally. These are porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and emerging swine acute diarrhea syndrome coronavirus (SADS-CoV). Novel PEDV strains emerged in China in 2010 spread to United States in 2013 likely through an intercontinental transmission from China. It was estimated that PEDV caused an annual loss of $1.8 billion to the US hog farmers. PDCoV was initially detected in 2009 in fecal samples from pigs in Asia and caused diarrhea in pigs in the United States in 2014.

Between October 2016 and 2019, outbreaks of SADS-CoV were recorded swine herds throughout China. These outbreaks were associated with acute diarrhea and vomiting with 90% mortality rates in piglets less than 5 d of age. Outbreaks of SADS-CoV continue to happen throughout China. While the SADS-CoV has not been identified in the US, emergence of this virus in the USA could cause a devastating impact to the US hog industry. Most of the coronaviruses cause diarrhea, dehydration, and death in pigs. It is not possible to identify an outbreak of novel coronavirus in pigs based on symptoms alone. To further complicate this, many other infections including bacterial diseases also cause similar symptoms in pigs. Therefore, laboratory confirmatory diagnosis is essential to identify the cause of diarrheal disease and death in pigs. Traditional laboratory diagnosis is based on testing for one disease agent at a time and this approach will not allow simultaneous detection or rule out of multiple pathogens.

To develop a multiplex PCR assay for simultaneous detection of PEDV, PDCoV and SADS-CoV which will be subsequently offered through the PADLS system

Updated August 13, 2021:
We have completed analysis of genome sequences and designed the PCR assays. The reagents have been ordered and the next steps are going to be assay standardization followed by validation. the project is progressing as per plan.

Updated May 2, 2022:
We have complete the analytical validation of the PCR assays establishing the analytical sensitivity and specificity. The clinical validation of the PCR assay is currently in progress

Rapid and specific identification tools for emerging swine coronaviruses can help safeguard PA swine. The aim of this project aligns with the board’s priority of “Advance Animal Agriculture in Pennsylvania and the Eastern Region” and has significant economic benefits for PA soybean and swine producers. Hogs and pigs consume 5 to 6 pounds of soybean-based feed per day. PA is in the top 12 swine-producing states in the US, with 1,310,000 head of market of breeding hogs and pigs, consuming an estimated 212 million pounds of soybean in a single production cycle. Coronavirus outbreaks could have a major impact on soybean consumption by swine. Through early detection and control, reduction in mortality by even 10% would translate to 42 million more pounds of soybean being consumed each year (two production cycles) in PA.