PREVALENCE OF PRRS AND PEDV IN BARN PITS DURING MANURE PUMPING AND LAND APPLICATION IN MINNESOTA

• Sponsoring Institution: State Agricultural Experiment Station
• Project Status: COMPLETE
• Funding Source: STATE
• Reporting Frequency: Annual
• Accession No.: 1019513
• Project Start Date: Jun 1, 2019
• Project End Date: Jun 30, 2021
• Program Code: [(N/A)]- (N/A)

Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108

Performing Department
Veterinary Population Medicine

Non Technical Summary
The US swine industry continues to battle with infectious diseases year after year. Data from the Morrison Swine Health Monitoring Project (MSHMP) which accounts for approximately 50% of the breeding herd of the country has shown that viruses such as PRRS, PEDv and PDCoV continue to be a concern for producers. For instance, PRRSv and PEDv have been infecting on average 30% and 10%, of the herds, respectively. These viruses have changed the industry as producers are more aware of the importance of on-farm biosecurity; however, the industry has reached a point in which there have been no more improvements from a disease control and prevention standpoint for these diseases as the incidence has not decreased. Despite efforts in biosecurity and the fact that there are no improvements in disease incidence, the industry continues to wonder how these viruses continue to be introduced into breeding herds. Due to the fact that there are more questions than answers regarding the occurrence of these diseases, our MSHMP group has continued to explore different potential transmission pathways for viral dissemination after analyzing PRRS and PED incidence data in different manners. Interestingly, PRRSv and PEDv tend to behave in a similar manner in that the somewhat these viruses have a predictable incidence (Tousignant et al., 2015). For instance, PRRSv cases begin to spike between October and November without any clear explanation. Coincidently at the same time, producers are both harvesting their crops and performing manure management practices. Modern pig farms collect manure and urine in pits under the barn floor slats and it is either sent to a lagoon or stored until is transported to the field. Once these solids and liquids have been stored for a certain amount of time, they are then transported off-site to crop lands for fertilizing properties. However, this benefit for farmers may pose a risk from a swine infectious disease standpoint as these effluents may contain microorganisms which can be readily transmissible to pig populations in the neighborhood either directly or indirectly. Therefore, manure management protocols such as dedicated manure pumping equipment together with washing and disinfection of equipment between sites are being implemented. Despite the adoption of these measures, the industry continues to see outbreaks of PRRSv, PEDv and PDCoV. Our group through data analysis has identified areas of high pig density as those with high risk of infection (Sanhueza et al., 2018). It is not clear whether these outbreaks may or may not be related to this practice making the understanding of the presence and viability of these pathogens a priority as the industry requires answers to the questions mentioned above. Even though there are anecdotal reports in which the pathogens have been detected, there is no data on the prevalence of these pathogens in manure pits which makes this pilot project unique. Therefore, the objective of this study is to determine how often PRRSv and PEDv are present in manure pits at the time when producers are applicating manure in the crop field. We propose to estimate the prevalence of these pathogens in manure pits by testing pit manure samples for both PRRSv and PEDv together with assessing their viability and genetic conformation. This information will allow us to understand the frequency of this event and thus explore relationships between these viruses and outbreaks reported in that region.

Animal Health Component

100%

Research Effort Categories

Basic

(N/A)

Applied

100%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
311	4030	1170	100%

Knowledge Area
311 - Animal Diseases;

Subject Of Investigation
4030 - Viruses;

Field Of Science
1170 - Epidemiology;

Keywords

prrsv

pedv

manure

transmission

biosecurity

swine

Goals / Objectives
The swine industry is currently facing infectious disease challenges on a yearly basis. In the last two decades, two viral pathogens 1) Porcine reproductive and respiratory syndrome virus (PRRSv) and 2) Porcine epidemic diarrhea virus (PEDv) have been causing important enconomic losses to the industry. Outbreaks of these diseases in sow herd farms represent an important production concern from every standpoint. As per our national voluntary monitoring project (e.g. Morrison Swine Health Monitoring Project - MSHMP), indicence of disease tends to significantly increase in the midwest during the fall season. Unfortunatelly, producers and practitioners have been tackling these pathogens through biosecuirty investmentswith no clear improvementgenerating frustration. Through our MSHMP network, there have been different observations made, one of them being processes related to manure management during the fall season, the same season where there is a spike on incidence of disease. However, up to date there has not been a clear investigation of what are the implications of manure management (e.g. manure pumping and spreading) on disease incidence. Therefore, the over-arching goal of this project is to determine what the risk of manure management practices are for disease ocurrence in the swine population. More specifically, the objectives of this project are: 1) Estimate the prevalence of PRRSv in manure pits in Minnesota pig farms during the manure pumping and spreading season; 2) Estimate the prevalence of PEDv in manure pits in Minnesota pig farms during the manure pumping and spreading season; 3) Determine whether pathogens are viableand 4) Explore whether there are spatial and temporal relationships on the detection of these pathogens.

Project Methods
Study design: This pilot project will be conducted as a cross-sectional study as samples and farm information will be collected at the same time and during one sampling event. Samples will be obtained from Minnesota environmental agencies who receive manure samples on a yearly basis from pig producers in the state. These samples were shipped to these laboratories during the manure application season. Samples will be accompanied by date of collection and county where these were collected.Sample size - Number of barns: Since the prevalence of these viruses in manure samples is unknown, a default barn level prevalence of 50% with an allowable absolute error of 5% and a 95% level of confidence was used for sample size calculation. Based on this calculation, a total of 385 pig barns are needed to estimate herd level prevalence for both PRRS and PEDv.Testing: Samples will be submitted to the University of Minnesota Veterinary Diagnostic Laboratory for testing by RT-PCR for both PRRSv and PEDv. A subset of samples with a cycle threshold of <30 will proceed for further testing by sequencing and virus isolation.Data analysis: Descriptive statistics and spatial analysis will be used to understand patterns of pathogen occurrence. Date of collection and county will be used for geographical visualization of results through Tableau and sequences obtained will be used for comparison with concurrent sequences obtained from the MSHMP.

Progress 06/01/19 to 06/30/21

Outputs
Target Audience:The target audience for this study remains the same, basically swine practitioners and pig producers. Both of these populations are interested in ways to minimize risk of PRRS transmission and are keen on supporting us find other potential routes of virus transmission that generates a breeding herd epidemic on a yearly basis generating important losses. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?Results have been shared through different outlets, 1) Scientific meetings (e.g. American Association of Swine Veterinarians)and 2) Popular press. (e.g. National Hog Farmer). What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Objective 1 and 2. Out of a total of 300 manure pit samples, 27 (7.75%) and 48 (13.79%) tested postive for PRRS and PEDV, respectively. In the case of PRRS, the median cycle threshold (ct) was 37.56 with most of the positve farm corresponding to growing pig farms. As for PEDV, the median ct value was 33.11 and 43 out of the 48 positive samples corresponded to growing pig farms. Objective 3. We tested PCR positive samples through virus isolation and none of them yielded positive results. Objective 4. Due to the low prevalence and clustering within company, our data analysis was hampered due to low prevalence; therefore, we couldn't assess these relationships. A fifth and complementary objective was developed based on the preliminary results. The objective focused on assessing the relationship between PRRS infected pigs shedding and the probability of virus detection in the manure pits. Two wean-to-finish farms housing prrs infected pigs were longitudinally sampled by collected orla fluids and manure pits samples. These samples were PRRS-PCR tested for PRRS and a poor relationship between shedding and manure pit presence was found.

Publications

• Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Montoya J. et al. 2021. Herd prevalence of PRRSV, PEDV, PDCoV and TGEV in pig farm manure pits. American Association of Swine Veterinarians.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:U.S. swine practitioners, producers and researchers have been exposed to preliminary resuls of this study. Changes/Problems:Besides the delayed due to COVID-19 that forced us to change our sampling dates there have been no other changes/problems. What opportunities for training and professional development has the project provided?A master's student has been leading the project since the beginning. The student has been able to work on study design, sample size calculation and approaches to developed a sampling methodology for manure pits. How have the results been disseminated to communities of interest?Results have been disseminated through different communication channels including: the 2020 Leman swine conference, 2020 Conference of research workers in animal diseases and to the select group of practitioners participating in the Morrison Swine health Monitoring Project. What do you plan to do during the next reporting period to accomplish the goals?The plan during the next reporting period is to finish the second phase of the project as farms are being enrolled, sampled and tested. The scond phase of the project should end once the last sample of the third farm is collected, data summarized and analyzed.

Impacts
What was accomplished under these goals? A total of 300 manure pit samples have been tested for the four pathogens. Evidence onthe presence of PRRSv, PEDv, and PDCoVin pig barn manure pits has been geenrated. Furthermore, evidence of the lack of detection of transmissible gastroenteritis has also been generated. In addition, 2 out of the three farms have been enrolled in the second phase of this project. The second phase of this project comprised a longitudinal study in which manure pits of farms housing PRRS positive pigs will be tested over time. Samples before pig arrival have been collected. The first sample after arrival has been collected in one of these farms yielding negative results.

Publications

• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: 2020 Leman Swine Conference 2020 CRWAD

Progress 06/01/19 to 09/30/19

Outputs
Target Audience:Pig production companies and swine veterinarians in the state of Minnesota were contacted to invite them to participate in this project. Invitations were made either through a quick meeting, email or phone call. The project objective, methods and data analysis were explained to each potential participant. Changes/Problems:Fortunately the porject has progressed without major problems. There have been 2 unexpected outcomes. 1) Sample Origin -The project was supposed to test samples from manure pits located in Minnesota, however, we learned that samples tested had also originated from other states such as Iowa and Illinois. While this is not concerning since the objective is the same, we would like to report it as this is a slight deviation of the protocol. 2) Prevalence - Our project was designed to estimate a prevalence of 50% since there are no data published reporting the presence of these viruses in manure pits, in other words, we opted for the worst case scenario. However, we are surprised with the low prevalence found so far. At this point we are considering a change in the protocol in order to better use the remaining funds. What opportunities for training and professional development has the project provided?Both graduate student and post-doctoral associate that are currentlyconducting the project have been able to collect the samples for one of the companies. The process not only forced us to develop a sampling protocol which it is currently non-existant but also lead us to learn about the manure pumping practices carried in the swine industry which has sparked many questions around the biosecurity of this processes that could likely be related to disease occurrence. How have the results been disseminated to communities of interest?The preliinary results have only been shared with participating companies through an excel spreadhseet followed by phone calls. What do you plan to do during the next reporting period to accomplish the goals?As we continue to gather the metadata related to the samples, analysis of the data will be begin. We are currently seeking information on the pigs that were housed in the barns from where samples were collected to begin assessing whether the presence of the virus could be related to pig status. In addition, we are gathering data on the vaccination history for PRRS as there are live vaccine viruses used that can be used in every stage of pig production. Altogether will lead us to run an analysis assessing the probability of testing positive while accounting for farm type, pig type, vaccination history and location.

Impacts
What was accomplished under these goals? The project has been progressing at a fast pace. Five different pig production companies / swine veterinary practices were contacted in order to formally invite them to participate in this project. All of the invitations were well recevied and all agreed to participate. Participants allowed us to contact the manure testing laboratory where they currently send their manure samples to and retreive those for testing at the UMN VDL. One company allowed our team to come to their pig farms and collect the samples. In addition, all invited participants agreed to provide metadata related to these samples once test results were shared. So far, a total of 300 manure pit samples have been tested as described in the original protocol. Out of these 300 samples, 27 (9%) tested positive for Porcine reproductive and respiratory syndrome virus with an average cycle threshold value of 37.20 and ranging between 35.53 to 39.57. As for Porcine epidemic diarrhea virus, 48 (16%) yielded a positive RT-PCR results with an average cycle threshold value of 31.49 and ranging between 24.13 and 36.87. Since the PEDv RT-PCR is a triplex assay, Porcine Delta Coronavirus and Transmissible Gastro Enteritis were also tested. The former yielded 19 (6.3%) positive samples with a mean cycle threshold value of 33.87 and raging between 28.65 and 39.75 whereas the latter had no positive results. At the moment of writting, all PRRSV RT-PCR positive samples submitted for virus isolation had yielded negative results. As for the PEDv RT-PCR positive samples, the results are pending.

Publications