SHIC Wean-to-Harvest Biosecurity: Effects of Manure Pumping on Disease Spread in Growing Pigs (Final Report)

A study funded by the Swine Health Information Center Wean-to-Harvest Biosecurity Research Program, in partnership with the Foundation for Food & Agriculture Research and Pork Checkoff, investigated the risks of manure pumping to introduction and spread of pathogens across wean-to-finish sites. Led by Drs. Ana Paula Poeta Silva and Daniel Moraes, working with the principal investigators Drs. Daniel Linhares and Gustavo de Sousa e Silva of Iowa State University, the study provided evidence that the processes associated with manure pumping and land application pose a risk for the introduction of PRRSV into pig sites.  

Also, there was plenty of PEDV RNA detected in pit samples from most herds visited despite the absence of clinical disease or PEDV in oral fluids. Further, the study characterized the level of risk for specific manure pumping practices or site characteristics, such as nursery compared to grow-finish, storage in deep pits or lagoons, timeline of pumping and spread relative to pig placement, and distance of crops for manure application.     

Read the study’s industry summary here.  

SHIC, along with FFAR, a non-profit organization established in the 2014 Farm Bill, and Pork Checkoff, partnered to develop the Wean-to-Harvest Biosecurity Program to investigate research priorities in three areas – bioexclusion (keeping disease off the farm), biocontainment (after a break, keeping disease on the farm to lessen risk to neighbors), and transportation biosecurity (live haul, culls, markets, deadstock, and feed haul along with innovative ways to stop pathogens from moving from markets and concentration points back to the farm). The goal of the program is to leverage funds to develop new tools and technologies that can enhance biosecurity in the wean-to-harvest phases of swine production.  

Manure removal is a common practice typically performed twice yearly at nursery and grow-finish pig sites. Manure is then spread on fields surrounding those sites for its nutritional and fertilizing value to grain and forage crops. Disease introduction can occur through manure agitation and pathogen spread during the pit pump out process or during the application of contaminated manure on nearby fields. To define the risk of manure pumping on disease introduction to pigs, the objectives of this study included 1) identifying the risk factors for disease onset in wean-to-finish sites following manure pumping and spread in nearby fields, 2) determining the frequency of PRRSV and PEDV detection in pit samples from wean-to-finish sites and the likelihood of increasing PCR-positivity of oral fluids after manure pumping. 

For objective one, a retrospective study investigated pig lot- and site-level risk factors related to manure pumping and spread for PRRSV or PEDV onset in wean-to-finish sites. Specifically, the study estimated the odds of a PRRSV or PEDV outbreak occurring within four weeks after manure pumping out from the site (exposure 1) or being near a field receiving manure at 1-, 3-, and 5-miles from the site (exposure 2). Sites included in the study conducted at least one manure pumping event or received manure spread on neighboring crop fields between July 2020 and December 2022. A satellite remote-sensing system was used to locate and characterize manure pumping activities and procedures, such as sites of manure origin and crop fields of manure spread destination.  

PRRSV or PEDV outbreaks (cases) were defined based on veterinarian assessment, pathogen detection in tissues, and increased mortality rate after the pumping event or receiving manure. The odds of a PRRSV or PEDV outbreak within four weeks after manure pumping out from the site was calculated across all data collected. For the analyses, controls were selected to match spatially (within 6.2 miles of cases) and temporally (placement dates within a 4-week interval from outbreak dates) cases. 

As part of the data set, a total of 2,903 pig lots were placed across 612 wean-to-finish sites. Of those, 1,444 pig lots had at least one manure pumping event with 517 reporting at least one PRRSV onset and 114 reporting at least one PEDV onset. The odds of PRRSV onset within a four-week period following pumping and spreading manure increased 1.7 times as compared to lots that were not pumped. Nurseries had higher odds of reporting PRRSV onset following manure pumping compared to grow-finish. Other characteristics associated with higher PRRSV risk included greater volume of pumped manure, and manure application <16 weeks post-placement. No association between PEDV outbreaks and manure pumping was detected in this dataset.  

For objective two, a total of 77 growing pig barns with no evidence of PRRSV or PEDV before the pumping process were investigated. These barns pumped manure within 10 months of the study onset and were monitored over time to investigate the frequency of PRRSV and PEDV detection before and after manure pumping. Manure pumping occurred between April 2023 and December 2023. Oral fluid samples from pigs and environmental samples from the outside the manure pit were collected. Disease onset was based on at least one positive PCR result for PRRSV or PEDV.  

Results of this prospectives study demonstrated an increased likelihood of testing PRRSV-positive in oral fluids after pumping out manure. The PEDV positivity in manure was significantly higher than that of PRRSV in manure; however, there was no increase in oral fluids PEDV positivity after pumping out manure. 

Overall, both study objectives provided evidence that manure pumping is associated with risk of PRRSV outbreaks. Understanding the risk factors that are associated with manure removal from wean-to-finish pig sites will enable producers and veterinarians to develop biosecurity steps and timing considerations for the pumping processes to improve bio-exclusion and bio-containment for PRRSV.  

Foundation for Food & Agriculture Research 

The Foundation for Food & Agriculture Research (FFAR) builds public-private partnerships to fund bold research addressing big food and agriculture challenges. FFAR was established in the 2014 Farm Bill to increase public agriculture research investments, fill knowledge gaps and complement US Department of Agriculture’s research agenda. FFAR’s model matches federal funding from Congress with private funding, delivering a powerful return on taxpayer investment. Through collaboration and partnerships, FFAR advances actionable science benefiting farmers, consumers and the environment. Connect: @FoundationFAR 

Swine Health Information Center 

The Swine Health Information Center, launched in 2015 with Pork Checkoff funding, protects and enhances the health of the US swine herd by minimizing the impact of emerging disease threats through preparedness, coordinated communications, global disease monitoring, analysis of swine health data, and targeted research investments. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. For more information, visit or contact Dr. Megan Niederwerder at [email protected] or Dr. Lisa Becton at [email protected].