The Swine Health Information Center (SHIC) Plan of Work for 2018, with projects designed to quickly deliver results to safeguard the health of the US swine herd, was approved by the Board of Directors during their January 26 meeting. Just a few Plan of Work highlights include a focused effort to improve transportation biosecurity, the next steps for investigating feed as a possible vehicle for pathogen transport into the country and between farms, improving communication about international and domestic swine diseases, and continued testing of the ability to respond to emerging disease through the Rapid Response Corp.
Building on 2017 accomplishments, the 2018 Plan of Work follows SHIC’s key priority areas:
The 2018 Plan of Work calls for improved transport biosecurity from points of concentration through better understanding of trucker/facility interactions and transmission pathways. Steps for facilitating improved trailer disinfection will also be investigated.
Following-up on 2017 work, SHIC is investigating the ability of common inputs to act as biologic or mechanical vectors for disease introduction into the country or between farms. This includes work on feed transport of pathogens, studying imported feed components and their risk, along with mitigations – including feed additives – that might reduce or eliminate risk.
SHIC programs for improving surveillance and discovery in 2018 will help investigate newly identified agents associated with disease as well as ensure detection of emerging disease to facilitate rapid response. Agents such as sapelovirus, PCV3, parainfluenza virus, and others will be investigated to help ensure response is appropriate, thorough, and rapid when needed. SHIC continues to offer diagnostic fee support for this purpose.
Being prepared to respond quickly and effectively to emerging disease, a priority for the industry, includes SHIC’s new Rapid Response Program with Corps members already being trained. Refinement of the program through actively practicing disease outbreak investigations will take place in 2018. In the event of an emerging disease, the Corps will help SHIC assist producers and veterinarians to quickly respond to and manage incidents with a focus on communications, quick research of pathogens, and supporting a unified response.
SHIC will continue to identify swine disease risks via domestic and international monitoring, working to enhance processes and reporting. As part of the international program, publications are monitored, international disease databases are watched, and international contacts and allied industry partners are asked to give a ‘boots on the ground’ perspective. Domestic monitoring for new or emerging diseases builds on the availability of SHIC-funded standardized veterinary diagnostic laboratory reporting and messaging.
SHIC will continue to support the Morrison Swine Health Monitoring Project to develop industry capacity for detection of emerging disease, rapid response, and continuity of business. The sharing of information through the project will be the foundation for new and innovative analyses to enable prospective swine health decision making.
The Swine Disease Matrix is constantly being reviewed with updates happening in response to disease activity and awareness. In 2018, SHIC will include bacterial pathogens, to reflect the reality seen on farms. Using the prioritized pathogens in the Swine Disease Matrix, SHIC is working to enhance swine disease diagnostic capabilities. SHIC-funded diagnostic tools will be staged for access by Veterinary Diagnostic Labs, so they can quickly be used for disease diagnostic work ups.
SHIC’s 2018 Plan of Work continues the investment made by US pork producers in the health of the US herd. The SHIC Board of Directors considers this investment while setting priorities for the coming year.
December 18, 2017 – January 14, 2018
Report highlight: The current concern continues to focus on African swine fever (ASF) in Poland and surrounding countries.
Infected wild boars continue to be identified in the vicinity surrounding Warsaw and the possibility of spread of the disease to the pig intensive area of eastern Poland continues to be a concern. Countries in the region are using a combination of increased hunting of wild boar along with boar proof fencing along borders to attempt to control the spread of the disease.
German hog markets upset: German farmers are watching the onward movement of ASF towards their western border and German news outlets are saying that it seems to only be a matter of time before it enters. According to the article, the introduction of the virus into their country would have a devastating effect on the value of their livestock and this risk has induced farmers to significantly reduce their inventories. The article goes on to say the added slaughter numbers has, in turn, caused a collapse of pork prices in Europe, with cold storage filling quickly. (Link: www.pig333.com/articles/whirlwhind-ofslaughterings-uncertainty_13353/).
Porcine Parainfluenza Virus 1 (PPIV1) is widespread in US swine herds. Now better diagnostic capability is available to help understand its potential role in disease. Swine Health Information Center (SHIC) funded research has successfully developed and validated a quantitative test to detect PPIV1 in oral fluid saliva and nasal swabs. This is one of many new diagnostic tests developed over the past few years under SHIC’s research umbrella to increase US readiness for emerging diseases.
SHIC asked Dr. Yanhua Li from Kansas State University’s Veterinary Diagnostic Lab to develop and validate a PPIV1 PCR diagnostic labs could adopt. Using available viral sequences in GenBank, Dr. Li designed a one-step real time assay targeting the HN gene of PPIV1. The assay developed showed very high diagnostic sensitivity and specificity for detecting PPIV1 in nasal swab and oral fluid samples. Offering complete coverage to current PPIV1 strains, the rapid and sensitive diagnostic tool developed will be useful for diagnostic of PPIV1 infection which will aid in epidemiological surveillance.
With this new diagnostic ability in saliva and nasal swabs, comes encouragement from SHIC to figure out if early respiratory cases and other clinical signs may be tied to PPIV1, so we can better understand impact and prevalence of this virus in US herds.
When the SHIC Swine Disease Matrix was researched and developed to prioritize emerging and foreign diseases of focus, PPIV1, a paramyxovirus, made the list and gaps in knowledge were assessed. These gaps included the virus’ host range, transmission modes, and pathogenesis. As some viruses in the paramyxovirus family (like Nipah Virus), cause serious disease in humans; it was determined the potential for zoonotic transmission needed to be examined further. Alongside this, experimental infections in pigs had not been conducted. And important to all the above, we didn’t have a good test to detect the virus. Developing this became step one.
First found in 2013 in Hong Kong, clinical signs associated with PPIV1 in pigs include lethargy, coughing, sneezing, and serous nasal discharge. Young pigs (under 21 days) seem most likely to develop clinical disease. However, the virus has also been detected in asymptomatic pigs. There are no pathognomonic lesions caused by PPIV1, and the likelihood of viral co-infection makes the interpretation of observed signs and lesions difficult. Thought to be transmitted via the respiratory route for a viral shedding period of two to 10 days, it is unclear whether other modes of transmission occur. The PPIV1 Fact Sheet on SHIC’s website recommends that it should be considered as a differential when commercial pigs are showing symptoms of respiratory illness, but test negative for known respiratory pathogens.
For incidents of high or ongoing morbidity or mortality where an etiology is either not identified or there is a strong suspicion that the identified etiology is not the likely cause of the outbreak, SHIC offers support for the need for further diagnostic workup to identify newly introduced or emerging swine diseases.
As the Swine Health Information Center (SHIC) continues its mission to pursue emerging disease, focus was turned to porcine circovirus 3 (PCV3). While PCV3 is being found associated with clinical disease, more needs to be done to define its role in disease.
SHIC asked Dr. Jianfa Bai of Kansas State University’s Veterinary Diagnostic Lab to develop a diagnostic assay to reliably differentiate the proven PCV2 from PCV3. With the assay, the ability to study PCV3 without interference from PCV2 is now possible, providing greater understanding of the virus. As part of the project, Dr. Bai also looked at the genetic sequences of PCV3 for perspective on how quickly this virus is changing to ensure the latest technology continues to be able to find it.
From Dr. Bai’s study summary:
The newly identified porcine circovirus 3 (PCV3) is causing problems in swine similar to that caused by porcine circovirus 2 (PCV2). Yet the PCV3 genome shares little similarity to the PCV2 genome. One objective of this study was to develop a molecular diagnostic assay that can detect and differentiate the majority of the field strains of PCV3 and PCV2. As PCV3 is a new virus, there was limited number of genome sequences available. The other objective was to sequence about 50 PCV3 genomes to study how fast the PCV3 genome is changing, and to use the new sequence information to guide the development, or modification of the detection assay developed in this study.
Polymerase-chain reaction (PCR), the most used detection technology, was used in this study. Analyzing all available genome sequences in the PCR assay design may be the most important first step to ensure the diagnostic coverage of the assay.
In this study we have analyzed 1907 available PCV2 full- or near-full genomes and designed two sets of tests that in combination can detect 98.9 percent of PCV2 strains including PCV2a, 2b, 2c, 2d and 2e genotypes. This is a significant improvement to several current PCV2 detection assays.
The PCV3 assay was designed based on the limited 32 genome sequences available at the time of design. The assay was designed to cover all 32 sequences (100 percent coverage). However, when more sequences become available, both from the public database and from our home-sequenced ones, the original design had mismatches to a few strains. To overcome this potential issue, a second set of tests was designed and in combination with the first design, they covered all 89 sequences.
An internal control is included in the assay to reduce the false-negative rate. Phylogenetic analysis of the 89 PCV3 full genomes indicated the largest genetic mutation rate for PCV3 is currently 3.2 percent. Out of 51 PCV3 genomes we sequenced, 37 were unique genomes, and most of them was grouped into different clusters together with published PCV3 genomes of different locations.
As most of our home-sequenced samples were collected from the state of Kansas, our data indicated that the mutations in PCV3 strains do not show a geographic distribution pattern, and they rather mutated randomly in the genome.
The 3.2 percent mutation in the PCV3 genome in just two years indicated that the virus is changing and continued monitoring the evolution of the virus may be necessary to monitor the emerging strains or genotypes of the virus and to modify molecular detection assays accordingly in order to keep assays up to date.
Oral fluids tested at packing plants
Presently, there is no formal, active surveillance for swine disease on finishing floors. When disease is discovered and documented, it is because practitioners submitted tissues or oral fluids for diagnostic workup, not because of an established, industry-wide protocol. To address this gap in surveillance, SHIC commissioned a study to see if oral fluids samples collected in the slaughter lairage could be used for disease surveillance. This process might offer an efficient way to watch for diseases coming into packing plants.
Conducted by Daniel Linhares, DVM, MBA, PhD, Iowa State University, the pilot project used PRRS and Seneca Valley Virus (SVA) to determine if the proposed process was viable. Finding better ways to monitor and manage PRRS is always an interest. And SVA is a close relative of FMD, and of interest itself, so there might be things to learn that will help when the US experiences its next FMD outbreak. Next steps might be to see if and how the PCR detection system can be improved and if the process can be applied to other pathogens.
From Dr. Linhares’ study summary:
Development of practical, affordable, and effective monitoring and surveillance systems for tracking pathogens in swine populations over time and space is crucial to the future of the industry. Although serum is the traditional surveillance sample, oral fluid specimens are increasingly recognized as a bona fide alternative.
The objective of this study was to determine whether organized surveillance can be done using oral fluid samples collected in an U. S. abattoir. Porcine reproductive and respiratory syndrome virus (PRRSV) and Senecavirus A (SVA) were used to represent endemic and emerging pathogens, respectively.
A total of 36 lots of pigs (300 to 450 pigs per lot) were included in the study. On-farm oral fluid and serum samples collected within two days of shipment to the packing plant were used to establish the reference PRRSV and SVA status of the study groups. At the packing plant, environmental samples were collected immediately before and after the pigs were placed in holding. Three veterinary diagnostic laboratories (VDLs) tested the sera and oral fluids for anti-PRRSV antibody (ELISA), PRRSV RNA (rRT-PCR), and SVA RNA (rRT-PCR). Environmental samples were tested for PRRSV RNA and SVA RNA at one VDL.
Oral fluids were successfully collected from 32 lots (89 percent) in holding at the packing plant. All oral fluids (collected at the farm and packing plant) tested positive for PRRSV antibody at all VDLs. PRRSV positivity frequency on serum samples ranged from 92.4 to 94.6 percent among VDLs, with an overall agreement of 98 percent among the laboratories. PRRSV RNA was detected on 2, 18, and 18 percent of sera, farm oral fluids, and packing plant oral fluids, respectively. Between-VDLs agreement for rRT-PCR on sera, and oral fluids was 98 and 81 percent, respectively. For SVA testing, all oral fluids, all farm samples tested negative at all VDLs. However, 70 percent of oral fluids collected at the packing plant tested positive in at least one VDL. Results demonstrate the need to further investigate the source of SVA RNA.
In summary, anti-PRRSV antibodies, and PRRSV and SVA RNA were successfully detected in packing plant oral fluids from pigs. There was a perfect agreement of PRRSV and SVA ELISA results between locations. There is opportunity to improve the between locations agreement of PRRS and SVA PCR testing. Packing Plant surveillance based on oral fluids is an alternative to current practices with tests available or endemic and exotic diseases (including African Swine fever virus, Erysipelothrix rhusiopathiae, Influenza A virus, PCV2, PEDV, Classical swine fever virus, Foot-and-mouth disease virus, and PDCoV), but further studies are needed to better understand how to further improve agreement between packing plant and farm group results.
When Japanese Encephalitis Virus (JEV) infects a naïve herd, the mortality rate of infected piglets is close to 100 percent; and 50 to 70 percent of sows experience reproductive failure. While JEV is endemic in Asia and the Pacific, many countries like the United States don’t have and don’t want this disease. New research has uncovered the ability of the virus to be spread between pigs by direct contact so the Swine Health Information Center (SHIC) has sponsored a novel and convenient means to monitor for and detect JEV in saliva via rope testing.
When Porcine Epidemic Diarrhea (PED) hit the US in 2013, the US diagnostic lab system did not have a means to diagnose the disease at a high throughput quickly and routinely. The need for reagents and high-throughput tests for new or emerging diseases became apparent. The US pork industry is starting to reap the benefits of this urgent, targeted work.
JEV, a flavivirus related to West Nile and dengue fever, is a zoonotic disease classically thought to be persisting in nature through a cycle of transmission involving Culex mosquitoes, some domestic and wild birds, domestic and feral pigs, and humans. According to the World Health Organization, every year close to 68,000 humans are infected with JEV via mosquito vectors in affected Asian countries. The resulting viral encephalitis causes a 30 percent mortality rate in infected humans; and 30 to 50 percent of those infected have permanent neurologic or psychiatric sequelae. Humans are a dead end for the virus as we do not amplify it enough to infect mosquitoes. Pigs, however, are considered the main amplifying host capable of infecting mosquitoes that vector the virus.
It was originally assumed that JEV needed mosquitoes to transmit the virus from pig to pig. However, in laboratory hogs in 2016 and in domestic hogs in 2017, it was discovered pig oronasal contact could lead to direct pig-to-pig transmission. SHIC monitored this research and sponsored a team at Kansas State University College of Veterinary Medicine to investigate a novel way to diagnose and monitor for JEV. These successful efforts recently demonstrated the feasibility of using oral fluid as a diagnostic sample of JEV infection in swine species.
When SHIC was established in 2015, part of its mission was, and still is, to be ready to diagnose endemic and foreign diseases at high risk of causing problems in the US. This began with identifying unwanted diseases that are at greatest risk to enter or emerge in the US, which are listed on the Swine Disease Matrix. Prioritized diseases, like JEV, have been a focus. With SHIC funding, disease fact sheets have also been created to help inform veterinarians and producers (JEV Fact Sheet).