March 2021 SHIC eNewsletter

As the world deals with the COVID-19 pandemic, SHIC continues to focus efforts on prevention, preparedness, and response to novel and emerging swine disease for the benefit of US swine health. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. SHIC is funded by America’s pork producers to fulfill its mission to protect and enhance the health of the US swine herd. For more information, visit or contact Dr. Sundberg at [email protected].

SHIC Releases Program Review Detailing Return on Producer Investment

Porcine epidemic diarrhea virus (PEDV) caught the US pork industry by surprise. Both its virulence and widespread consequences devastated the US swine herd as well as producers’ livelihoods and damaged related industries. In response to this transboundary, emerging swine disease, the Swine Health Information Center (SHIC) was launched in July 2015 by the National Pork Board (NPB). Funded by a one-time Checkoff investment of $15 million in supplemental funds, SHIC had an original life span of five years, however, was extended by NPB vote to July 2022 using existing SHIC funds.  A review of the Center’s activities since inception through March 2021 captures the Checkoff return on investment for US pork producers with significant deliverables made possible only by SHIC’s nimble structure, unique responsibilities, and independence.

SHIC’s responsibilities include monitoring and analyzing emerging disease issues and research, monitoring non-program swine diseases, working collaboratively with other industry organizations, and filling gaps in swine disease prevention, preparedness, and response. “In the very short time we’ve been in existence, we have come to play such a vital role in helping defend the health of our industry. I recommend people read the 2020 Progress Report and evaluate our performance. After you’ve read it, you’re going to understand that since receiving initial funding from the National Pork Board, we have filled a void and been very successful. We’re committed to protecting the US pig population,” remarked Daryl Olsen, DVM, AMVC, Audubon, Iowa, SHIC board chair.

Following launch in July 2015, SHIC quickly began providing value to the US pork industry, becoming a conduit balancing practicality with targeted response to disease outbreak prevention, preparedness, and response. This SHIC-led balance between a more rigid preparedness and response structure and grassroots preparedness and response fulfills the Center’s mission to safeguard US swine herd health and serves US pork producers well.

“The importance of coordinated global disease monitoring is imperative in the world today; we see diseases spread easily across political borders, and across countries and oceans. Utilizing experts in many areas, SHIC analyzes the monitoring efforts, and directs funding and efforts into research. The thoughtful process that has been implemented has provided US swine farmers, veterinarians and associated industries with up to date and relevant information. This process has also allowed SHIC to quickly pivot to timely issues with producer oversight,” stated Beth S. Thompson, JD, DVM, Minnesota State Veterinarian, Minnesota Board of Animal Health, SHIC working group member.

SHIC maintains an intentionally responsive structure. This enables quick action on emerging issues and clear accountability for results. SHIC collaborates closely with other industry organizations; each has unique priorities yet together the same over-arching mission to advance the pork industry. Collaboration allows for maximizing resources, time, and outcomes without duplication nor territorialism because responsibilities are shared.

“SHIC and Dr. Paul Sundberg stepped up to plug an important gap in our swine health defenses by providing a fast-moving early warning+response system for emerging and transboundary diseases. We need them now more than ever!” explained Dr. Jeff Zimmerman, Iowa State University.

In fulfilling the Center’s responsibilities, maximizing the financial resources available is essential. Stretching the initial investment by partnering with other agencies, keeping overhead as low as possible, and seeking additional resources means SHIC is able to deliver consistent, quality results while maintaining sufficient funds to extend the original five-year span by two additional years.

“SHIC is a wonderful invention. They take a threat and educate us on it, so it becomes a non-threat. SHIC has been on the cutting edge of several situations I would consider a homerun. And it’s a great value. There’s not a lot of huge overhead or ridiculous amount of expenses yet activities on so many fronts, contributing to the health of our swine industry tremendously,” Russ Nugent, PhD, Dogwood Ag Services, LLC, SHIC board and working group member.

SHIC has developed several assets for the US swine industry, funded extensive research, and contributed countless deliverables as it fulfills its mission which is, “…to protect and enhance the health of the United States swine herd through coordinated global disease monitoring, targeted research investments that minimize the impact of future disease threats, and analysis of swine health data.”

Information sharing activities include outreach with producers, veterinarians, academicians, researchers, and industry stakeholders. Tools used for information sharing include SHIC’s website, newsletter, podcast, webinars, media outreach, as well as article preparation for partners.

“The US pork industry has undergone monumental changes in all aspects of producing bacon, if you will, in the last 30 years. The most pronounced, which has created great opportunity, is feeding the world via export markets, with the US going from being a 7% importer in 1990 to now a net exporter north of one in four pigs we raise. With that it creates unprecedented risk for all of us. We have to ship it as we can’t eat it all. Investing our life and all we have into this industry, our family is appreciative of the work of SHIC to help create awareness and bring the best together with science to protect us from FAD entry. A great example is SHIC’s recent work in Vietnam with ASF. Learn and help where the disease is,” said Jim Pillen, Pillen Family Farms/DNA Genetics.

For further information on SHIC and its contributions to the US pork industry, visit

As the world deals with the COVID-19 pandemic, SHIC continues to focus efforts on prevention, preparedness, and response to novel and emerging swine disease for the benefit of US swine health. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. SHIC is funded by America’s pork producers to fulfill its mission to protect and enhance the health of the US swine herd. For more information, visit or contact Dr. Sundberg at [email protected].

SHIC/AASV PRRS 1-4-4 Lineage 1c Webinar Provides Information on Recent Outbreaks

Midwest veterinary diagnostic labs (VDLs) began diagnosing porcine reproductive and respiratory syndrome virus (PRRSV) 1-4-4 in late 2020 with practitioners and producers reporting dramatic PRRS-like clinical signs on farms. Reacting quickly to this new PRRS strain, the Swine Health Information Center, with co-sponsor American Association of Swine Veterinarians, offered a webinar on PRRSV 1-4-4 on February 4, 2021. Expert presenters on the webinar provided context from the practitioner, diagnostician, and monitoring perspectives. While 1-4-4 is not a new strain, on-farm experience with this new lineage 1c variant has shown it results in higher farrow to finish mortality, abortions, mummies, and slower growth in finishing pigs compared to other PRRSV strains.

Webinar presenters included Dr. Paul Yeske of the Swine Vet Center, St. Peter, Minnesota, Dr. Stephanie Rossow, University of Minnesota (UMN) VDL, Drs. Giovani Trevisan and Daniel Linhares, Iowa State University (ISU)/Swine Disease Reporting System (SDRS), and Dr. Mariana Kikuti, UMN/Morrison Swine Health Monitoring Project (MSHMP). MSHMP is a SHIC-funded program focused on monitoring disease occurrence. The webinar was conducted by the Iowa State University Swine Medicine Education Center.

Dr. Yeske said he and his colleagues at the Swine Vet Center have had the opportunity to see the virus more than they would like in sow farms and grow-finish facilities. While the clinical signs of this lineage are consistent with other PRRS outbreaks, this one is more dramatic. Sows go off feed, abortions begin, and other consequences follow, moving quickly through the herd once clinical signs are noticed. Their experience includes upwards of three to five weeks of production lost to abortion, sow mortality up to 20% within a two to three week period of time, and high piglet mortality in the farrowing house. In the nursery, piglet mortality remains high – 50% in some cases and some up to 80%. In finishing pigs, average daily gain dropped from 2.4 pounds per day to 1 pound per day following a drop in water consumption proceeding the outbreak of PRRS 1-4-4.

Dr. Rossow had spoken with several clients of the UMN VDL to get their input on how this PRRS 1-4-4 lineage 1c variant was impacting their businesses. She said the VDL first became aware of the issue in nursery and grow-finish pigs. Client experience showed the strain is moving laterally easily and is occurring on some farms that have been managed as PRRSV-negative for over 20 years. In some groups, mortality as high as 30% was reported.

Clinical signs reported to the UMN VDL include high fever as well as respiratory disease and it was noted secondary diseases – viruses and bacterial infections – are causing additional problems in affected herds. Without exception, Dr. Rossow said response to treatment – both water medication and injectables – has been poor.

Under the microscope, Dr. Rossow said they are finding really severe lung lesions, which are expected, along with a standout amount of necrosis, or tissue death, in the thymus and lymph nodes of affected pigs. Both the thymus and lymph nodes are important for a proper and coordinated immune response by the pig. “So there’s a marked dysfunction in those tissues and certainly going to relate to a poor response to other viral and bacterial challenges that pig is going to encounter, especially in the nursery/grow-finish environment,” she stated. 

Beginning in October 2020, the SDRS began showing increased PRRSV RNA PCR detection from data provided by cooperating VDLs at ISU, UMN, Kansas State University, and South Dakota State University. Then in December 2020, more than 7000 cases were tested by PCR in the cooperating VDLs, gaining attention of SDRS staff and its advisory board. RFLP typing also confirmed the increase in PRRS 1-4-4 occurrence in late 2020.

Dr. Rossow said PRRS 1-4-4 lineage 1c variant is detected by ThermoFisher and the Tetracore PRRSv PCR tests, the more common ones used in diagnostic labs. She noted fairly consistent viral myocarditis in these pigs which was the case with past PRRS pigs. While the UMN VDL has tested submitted spleens for African swine fever and classical swine fever as well, neither has been found, increasing confidence that this is a uniquely severe PRRSV strain causing these problems.

Across states, there is considerable genetic diversity for the PRRSV strains classified as RFLP 1-4-4, per Dr. Trevisan. More frequent detection of RFLP 1-4-4 strains in Iowa and Minnesota was observed after September 2020, in review of ISU and UMN VDL data. A cluster of 106 sequences was detected in Iowa and Minnesota after October 2020.

Dr. Kikuti said MSHMP participating production systems started independently reporting the occurrence of a virulent PRRSV RFLP 1-4-4 strain, particularly in grow-finish sites where high mortality was observed. The systems noted this was a different virus than the one used in gilt acclimation processes as well as different from others in the systems.

As of January 17, 2021, a genetic cluster of 72 sequences from 60 farms was identified by MSHMP. There were nine MSHMP participating production systems involved in their investigation. Of those 60 farms, 45 were growing pig farms with herds ranging in size from 960 to 8000 pigs. In addition, there were 11 affected breeding herds with an average size ranging from 750 to 4000 sows. Of the 72 PRRS sequences obtained, one was from 2018 (classified as RFLP 1-4-3), 67 were from 2020 (all RFLP 1-4-4; most occurred in October to December 2020), and four did not have a date available (all RFLP 1-4-4). 90% of cases within this genetic cluster occurred in a 50-mile radius. In a phylogenetic analysis, Dr. Kikuti said they were all cases were genetically very similar with identical sequences occurring in different production systems, and it appears to represent the emergence of a new clade within lineage 1c. Dr. Kikuti also said sequences from this cluster of PRRS are being submitted to GenBank to aid on-going investigations.

Herd stabilization is the goal. Dr. Yeske recommends producers identify greatest areas of risk on their farms, asking, “How likely is something going to cause the virus to enter your herd?” Then, once that question is answered, follow-up by asking how many times a week that risk activity takes place. “Review herd biosecurity plans,” he recommended. “Make sure things are being done like they are supposed to be. If possible, improve on any weaknesses, doing so sooner than later.”

A lot is known about biosecurity practices to prevent or minimize the probably of PRRSV spread, per Dr. Linhares. He described a recently completed study by ISU veterinary student Broc Mauch, et. al. which included data from 188 sow herds in 13 systems in 15 states of the US. Based on a 20-question survey, the work applied to biosecurity scoring systems. The objective was to see if a consistent 20-question format can be used to screen for PRRSV introduction into breeding herds, and if they can be good predictors. Dr. Linhares said the 20 questions relate to obvious things, mentioning the number of risky events on farms, annual employee turnover and number of employees which compounded with herd size, distance to main roads, density of sites around the premises, transport biosecurity, and more.

In a summary of work done by Dr. Derald Holtkamp of ISU on 19 investigations of PRRS outbreaks from 2015 to 2017, Dr. Linhares pointed out entry of employees, removal of culls, and repairs were risk events rated high most frequently on those farms. Dr. Linhares shared a reminder on SHIC’s Rapid Response Program designed for situations where outbreak investigations are needed to determine the pathways of entry onto the farm.

Area spread was also facilitated by favorable weather conditions in southern Minnesota and northern Iowa where many overcast days, fog, and warmer than usual winter temperatures were the norm, per Dr. Yeske. Dr. Kikuti also noted winter is the high transmission season for PRRSV. And she concurred with Dr. Linhares who shared the need for further epidemiological investigations, also suggesting molecular studies are needed as well.

Do you have a recommendation for a topic to be addressed in a webinar? SHIC and AASV would like your input! Reach out to SHIC Executive Director Dr. Paul Sundberg at [email protected] or AASV Director of Public Health and Communications Dr. Abbey Canon at [email protected] with your webinar recommendations.

SHIC Talk Podcast Addresses PRRS 1-4-4 lineage 1c Outbreaks

Porcine reproductive and respiratory syndrome virus (PRRSV) 1-4-4 lineage 1c outbreaks in upper Midwest swine barns began in late 2020. SHIC developed an episode of SHIC Talk, posted on February 15, 2021, to share additional information on the PRRSv strain. While it’s typical for PRRS outbreaks to be more common in the colder weather months, occurrence of this new, more aggressive strain, appear to be regional, an important point to remember.

Drs. Paul Yeske, Swine Vet Center of St. Peter, Minnesota, and Daniel Linhares of Iowa State University, were guests on the SHIC Talk podcast.

Dr. Linhares shared information on his recently completed study addressing the industry’s need for the ability to better predict risk of a PRRS outbreak as well as to evaluate the level of biosecurity on their farms. The objective of this SHIC-funded study conducted at Iowa State University was to measure and benchmark the relationship between key biosecurity aspects and PRRS outbreaks in breeding herds, while validating a short biosecurity screening survey (44 questions). The analysis offers a flexible, shortened approach to screen breeding herd’s PRRS biosecurity vulnerability. Plus, this study highlights the value of using data to build upon the understanding of biosecurity risk in an operation.

Dr. Yeske provided a practitioner’s perspective on the strain, sharing first hand experience with PRRS 1-4-4 1c. “So it does look like it’s a different, evolving variant that’s come out here that’s been a more aggressive strain, should we say, as far as it gives us all the clinical signs PRRS does, they’re just a little bit more dramatic,” observed Dr. Yeske.  He also cautioned producers to be aware of efficacy and consistency with existing biosecurity practices, encouraging regular review to be sure what is supposed to be done is actually being done.

SHIC-Funded Study Evaluates TADD to Inactivate ASF Virus in Transport Trailers

Swine transportation plays a major role in spreading infectious pathogens, including African swine fever virus (ASFV). Researchers from the University of Nebraska investigated if it is possible to effectively inactivate ASFV in the presence of organic materials (feces, bedding) through the use of thermal-assisted drying and decontamination (TADD) which commonly operates at the temperature between 63°C and 71°C. Results showed power washing surfaces with room temperature water followed by baking efficiently removed contaminated material.

Conducted in Vietnam, the study was made possible by funding from the Swine Health Information Center via a USDA Foreign Agricultural Service grant. Dr. Hiep Vu, Nebraska Center for Virology and Department of Animal Science, University of Nebraska-Lincoln, designed the study to determine the optimal baking time and temperature required to completely inactivate ASFV on aluminum surfaces contaminated swine feces. Testing for the inactivation efficiency of contaminated trays took place under three conditions:

Two different methods were used to evaluate the efficiency of the treatments – PCR to detect viral genomic DNA and virus isolation to detect infectious virus.

In condition A, swabs collected from contaminated trays at all time-points post incubation at 54oC and 63oC were positive by PCR, indicating that heat treatment could not eliminate viral genomic DNA. However, swabs collected from contaminated tray at five minutes post incubation at either 54oC or 63oC were negative by virus isolation, indicating that holding ASFV in the presence of feces at 54oC for five minutes is sufficient to inactivate the virus.

In conditions B AND C, only two swabs collected after washing and baking were positive by PCR at high Ct value (e.g. 37.03). These swabs were negative for virus isolation. Thus, under the conditions of this study, power washing of the trays with water at room temperature, with or without the use of disinfectant, and then followed by baking efficiently removed contaminated material from the trays.

Collectively, results obtained from this research provide valuable information for the development of effective sanitation protocols to disinfect animal trailers to reduce the spread of ASFV.

SHIC Diagnostic Fee Assistance Fills a Gap When an Answer Is Needed

SHIC’s diagnostic fee assistance program was developed after porcine circovirus 2 (PCV2), porcine circovirus associated disease (PCVAD), porcine deltacoronavirus (PDCoV), porcine epidemic diarrhea virus (PEDV), and Senecavirus A (SVA) outbreaks surprised the US pork industry. Controlling surprises requires diligent diagnostic effort; early recognition and characterization of emerging swine disease increases the chance for containment, elimination, or control. Dr. Kent Schwartz, Iowa State University College of Veterinary Medicine, shares two examples of how Swine Health Information Center-funded (SHIC-funded) diagnostic fee assistance led to unexpected diagnoses.

In one case, diarrhea in five- to seven-day old pigs where atrophic enteritis was detected, but no etiology was identified, led to a further investigation which revealed the possible role for “a newly discovered virus in swine” called porcine sapovirus (PSaV), which is now being further investigated. In another case, an outbreak of tremors and rapid deaths in grow-finish pigs in which no etiology was identified, upon further investigation, ruled out infectious processes and implicated myopathy, which is now being further investigated. There is risk of missing an emerging disease if a definitive diagnosis is not pursued robustly.

By definition, diagnostic fee assistance is appropriate in cases of high morbidity/high mortality, where an etiology is either not identified or there is a strong supposition the identified pathogen is not the likely cause of the outbreak, and there may be a need for further diagnostic work. SHIC recognizes limitations on resources may be a barrier and developed this program to assist at the production level for the benefit of the national herd – to ensure that something isn’t overlooked.

SHIC diagnostic fee assistance is approved by a panel of swine diagnosticians who have reviewed the case history, along with diagnostic investigation, and judge the outbreak to warrant further investigation. “The process will assure only animals representing the specific case definition are sampled, proper selection and preservation of samples to investigate are collected with confidence in their quality, along with assuring the ability to pursue diagnosis using all appropriate, available technologies,” commented Dr. Schwartz. This can include next-generation sequencing, rapid development of probes, in situ hybridization, RNA scope, EM, etc.

Further diagnostic work can determine if the unknown etiology is a new, emerging, or transboundary disease. Equally as important, further diagnostic work can rule out what it is not, meaning, ruling out known foreign animal disease (FAD) or other agents, according to Dr. Schwartz.

Diagnostic fee assistance is available when the disease appears to be clinically unique in presentation as well as infectious and transmissible. Dr. Schwartz also said it is available in approved cases when routine testing (based on clinical signs, gross lesions, microscopic lesions) has ruled out the differential diagnoses and does not implicate a primary cause.

Details on SHIC’s diagnostic fee assistance program are available here, including a description of the process:

SHIC-Funded Study Finds Better Approach for Disease Surveillance

Transboundary diseases, including African swine fever (ASF), pose a significant threat to US pork producers. “We know early detection is the key to their control and elimination. But we also know that the approach that served the industry 30 years ago cannot keep pace with today’s big, fast industry, and the 5.2 million pigs that cross state lines each month,” remarked Dr. Jeffrey Zimmerman, Iowa State University. “We need a new surveillance plan – something effective, yet practical and affordable.” Dr. Zimmerman and colleagues at Iowa State University conducted research funded by the Swine Health Information Center (SHIC) and the National Pork Board and found that “spatially balanced sampling” could achieve a higher probability of detection and at lower cost than previous methods. 

Dr. Zimmerman says spatially balanced surveillance uses a few samples from many farms across a defined region to determine the region’s status.  In contrast, past methods tried to prove that each site was negative to prove a region as negative. “The results have been very promising in terms of developing a better approach for disease surveillance,” he commented. “Work currently in progress by our research team will continue to explore the strength of the approach and its potential to serve the swine industry.”

In their work, five spatially balanced sampling methods were compared to simple random sampling (SRS) in terms of the probability of detection by sample size. Using a livestock disease transmission model in a hypothetical region roughly the size of Iowa and populated with 6000 farms, four of the five spatially balanced sampling methods provided better performance than random sampling. That is, for any given probability of detection, spatially balanced methods required testing fewer farms than SRS.

In an era of pandemics, active regional surveillance for early detection of emerging swine pathogens becomes urgent, yet shrinking budgets impose constraints. To prepare for the introduction of ASF into the US, the USDA Center for Epidemiology and Animal Health in Fort Collins, Colorado, is developing surveillance methods for control areas, for example, determining how best to sample the farm or the population in a barn to verify the farm’s or barn’s disease status.  Outside of control areas, spatially balanced surveillance will be critical in verifying freedom from disease and supporting business continuity.

Surveillance efficiency – achieving highest probability of detection at the lowest cost – is central to the public good. This project represents the first step in the investigation of the use of spatially balanced sampling methods in regional livestock disease surveillance programs. The better performance and higher efficiency of spatially balanced sampling methods suggests a real improvement in regional livestock disease surveillance and the challenge of affordable surveillance. Future work will examine the impact of the rate of disease spread and the threshold distance for farm-to-farm transmission on the performance of spatially balanced sampling methods. 

March Swine Disease Monitoring Reports

As the world deals with the COVID-19 pandemic, SHIC continues to focus efforts on prevention, preparedness, and response to novel
and emerging swine disease for the benefit of US swine health.

Domestic Disease Monitoring Report

This month’s Domestic Swine Disease Monitoring Report shows that porcine reproductive and respiratory syndrome (PRRS) virus detection was similar to January 2021, with a small decrease in positivity in sow herds, but increase in wean-to-market animals. PRRSV RFLP 1-4-4 Lineage 1C variant continues to be associated with severe clinical signs, especially in grow-finish sites. There was a moderate increase in detection for porcine deltacoronavirus (PDCoV) in wean-to-market animals. That increase was regional. There was a moderate decrease in Mycoplasma hyopneumoniae. At a state level, PRRS virus detection was three standard deviations above expected in Nebraska, Ohio, and Indiana; and PDCoV was three standard deviations above expected in Kansas, Oklahoma, and North Carolina. The SDRS hosts talk with Dr. Cesar Corzo (Morrison Swine Health Monitoring Project) about his observations on recent pathogen activity in the US swine herd.

Global Swine Disease Monitoring Report

In this month’s report, read about the first report of African swine fever (ASF) in Malaysia where five outbreaks were identified in the island of Borneo. In Hong Kong, the first report of ASF on a farm is revealed. The rise in smuggling of prohibited meat products into the US is discussed, including details on seized meat shipments smuggled from China into the US doubling in 2020. The US Department of Homeland Security released a new ASF resource for emergency response preparedeness. The report includes information on an increase of ASF cases in South Africa where the virus was found in small-holding farms in Western Cape Province. Lastly, information on ASF natural mutations in China is included. Chinese scientists reported results of surveillance efforts on the evolution of the virus recently.