A feasibility study of conducting surveillance for swine pathogens in slurry from North Carolina swine farms

Emily S. Bailey, Laura K. Borkenhagen, Jessica Y. Choi, Annette E. Greer, Marie R. Culhane, Gregory C. Gray

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Despite close contact between humans and animals on large scale farms, little to no infectious disease research is conducted at this interface. Our goal in this preliminary study was to explore if we could detect swine pathogens using a non-invasive, indirect approach through the study of swine slurry. From April to November 2018, 105 swine slurry samples were collected by farm personnel from waste pits at two sites on a swine farm in North Carolina. These samples were tested for DNA and RNA viruses using a real-time PCR and RT-PCR. Statistical analyses were performed to measure association between virus positive outcomes and potential predictors such as date of sample collection, weight of pigs, number of pigs in barn, temperature, and weather conditions. Overall, 86% of the samples had evidence of at least one of the targeted viruses. Ultimately, this study demonstrated the utility of conducting noninvasive surveillance for swine pathogens through the study of swine slurry. Such swine slurry surveillance may supplant the need to handle, restrain, and collect specimens directly from pigs thus providing an approach to emerging pathogen detection that appeals to the swine industry.

Original languageEnglish (US)
Article number10059
JournalScientific reports
Issue number1
StatePublished - Jun 22 2020

Bibliographical note

Funding Information:
This study was supported by pilot funds from the North Carolina Agromedicine Institute, an interinstitutional collaboration of East Carolina University, North Carolina State University, and North Carolina A&T State University and by Duke University discretionary funding (Gray PI). We thank Sarah Paust, Calvin Wang, Christine Wang, Julie Zemke, and Anfal Abdelgadir for assisting with sample extraction.

Publisher Copyright:
© 2020, The Author(s).


  • Animals
  • DNA, Viral/genetics
  • Farms
  • Feasibility Studies
  • Manure/virology
  • North Carolina
  • Phylogeny
  • Polymerase Chain Reaction
  • Population Surveillance
  • RNA, Viral/genetics
  • Swine
  • Swine Diseases/virology
  • Viruses/classification

PubMed: MeSH publication types

  • Research Support, Non-U.S. Gov't
  • Journal Article


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