The Swine Health Information Center (SHIC) collaborated with the Morrison Swine Health Information Project to enable a study applying machine-learning to predict porcine epidemic diarrhea virus (PED) outbreaks on sow farms. The researchers were able determine it is possible to predict the probability of an outbreak when considering animal movements and environmental conditions. Another goal was to see if shared producer data could be used to develop critical tools for the prevention of disease spread and implementation of risk mitigation. Further, this work serves as a model for near real-time disease forecasting. The authors hope it will advance disease surveillance and control for endemic swine pathogens in the United States.
Many mechanisms play an apparent role in the spread of viruses: movement of infectious animals, airborne spread of aerosols, wildlife, contaminated fomites, feed, and personnel. Understanding the complexity of animal movements as a whole – routes, volumes, and frequency – is essential. The broader view used in the study, rather than focusing solely on a specific farm, helps to better understand PED epidemiology and spread by analyzing the cumulative effect of animal movement and environment on infection risk.
Analyzing data from PED outbreaks during 2015 as well as a large, retrospective dataset, the study was able to correctly predict when an outbreak occurred during one-week periods with greater than 80 percent accuracy. Because they used a neighborhood-based approach, researchers were able to simultaneously capture disease risks associated with long-distance animal movement as well as local neighborhood effects. They defined a neighborhood as the area 10 kilometers around a farm. They evaluated the relative importance of neighborhood effects in determining infection risk. This included animal movements to farms nearby, hog density in the area, environmental factors, and the landscape.
The team used a machine-learning technique to analyze the data and found their model accuracy ranged from 78.2 to 83.3 percent. In the process, researchers learned the most important predictor for PED outbreaks was the overall number of pigs moved into the neighborhood followed by season of the year. Hog density was also confirmed as a significant factor.
The next steps will be using the model to apply to real-time data so PED outbreak risk can be predicted and interventions can be put into place to prevent the outbreak. The study was done in one region of the country and needs to be repeated in other regions, with different movement, neighborhood and environmental factors. And testing the model to be able to predict outbreaks of other diseases, for example PRRS, will be done.
Authors of the study are Gustavo Machado, Carles Vilalta, Mariana Recamonde-Mendoza, Cesar Corzo, Montserrat Torremorell, Andres Perez & Kimberly VanderWaal. Read the entire study with detail here: https://www.nature.com/articles/s41598-018-36934-8
African swine fever (ASF) was first reported in Vietnam in mid-February 2019 and cases continue to be documented. This is a fluid situation with data being updated frequently from a variety of sources. The Swine Health Information Center (SHIC) has been monitoring these reports and offers this chronological review of information on the outbreak.
SHIC’s Global Swine Disease Monitoring Report Special Announcement included the initial information on the presence of ASF in Vietnam. At that time, ASF had been detected in two provinces in northern Vietnam, Hung Yen and Thai Binh, southeast of the capital city of Hanoi and at approximately 100 miles (160 km) from the Chinese border. Eight outbreaks had been reported, and all pigs in the affected farms have been culled. Neighboring farms were tested and local authorities initiated general measures to contain the outbreaks and disinfect the area through quarantine and restrictions of animal movements.
Vietnam’s Ministry of Agriculture said ASF had been detected in 96 households/farms, across 33 villages, 20 communes, 13 districts of six provinces and cities.
SHIC’s Global Swine Disease Monitoring Report stated a total of six provinces reported more than 33 outbreaks: Hung Yen, Thai Binh, Hai Phong, Thanh Hoa, Hanoi and Ha Nam.
The World Organization for Animal Health (OIE) said 22 additional villages have reported ASF.
Vietnam’s prime minister called for drastic measures to fight the spread of ASF.
Observations and Reaction
Most of Vietnam’s pigs are raised on small farms rather than large enterprises. Because larger farms are becoming more common in Vietnam, the risk of ASF affecting them is significant. Vietnam’s Ministry of Agriculture and Rural Development instructed authorities to cull all pigs on affected premises along with general cleansing, plus establishing a quarantine of the outbreak area. The quarantine includes movement restrictions and testing neighboring farms.
Vietnamese Origin Pork Seized in Taiwan
On February 15, Taiwanese authorities communicated that ASF was detected in seized pork products, presumably from Vietnam, at the Tainan airport. According to Taiwanese authorities, since late August 2018 they have been testing samples of pork products from foreign countries. From a total of 928 tested samples, 20 samples have been found to be ASF-contaminated. All positive samples originated from China, until this first case of a confiscated product of a passenger entering Taiwan on an airline coming from Ho Chi Minh City, Vietnam. Also on February 15, FAO updated the ASF Situation, detailing that the gene sequence showed 100 percent similarity with the ASF virus in China, but the exact source of the meat was unknown. It has been speculated that the most likely route of introduction into Vietnam was through smuggling of contaminated pork products from China, based on volumes and price differentials between the two countries, which generated a positive gradient of pork products into Vietnam illegally.
When returning to the United States after visiting a farm or being in contact with animals in a country (or countries) with African swine fever (ASF), or any other foreign animal disease, you should declare this information to US Customs and Border Patrol via written form, airport kiosk, or verbally. Then you should be diverted for an ag secondary screening by an ag specialist. The Swine Health Information Center (SHIC), National Pork Board, National Pork Producers Council, and American Association of Swine Veterinarians are asking you to report your experience if you are not diverted for secondary screening with return to the US following overseas travel.
If you are NOT diverted for secondary screening after declaring you have been on a farm or in contact with animals in an ASF or other foreign animal disease positive nation, please email the following to [email protected]:
Dr. Sundberg will be aggregating this information and the organizations will share with US Customs and Border Patrol to help identify any weaknesses in their protocol and systems.
Thank you for your help as we continue to implement steps designed to reduce the risk of ASF spreading to the US swine herd.
In the March Swine Health Information Center Domestic Swine Disease Monitoring Report, it was stated monthly cases tested for porcine reproductive and respiratory syndrome virus (PRRS) decreased since the peak in November 2018. It was noted this is in agreement with perception this PRRS season is relatively quiet. Detection of porcine epidemic diarrhea virus (PED) by PCR was above expected one week in February though returned to predicted value. Detection of porcine deltacoronavirus (PDCoV) by PCR was above expected at the end of the reporting period. Other diseases were reported at or near previous winter seasons.
In the March Swine Health Information Center Global Swine Disease Monitoring Report, details on the African swine fever (ASF) outbreak in Vietnam as of February 28 are included as well as information on the further spread of the disease in three Chinese provinces. Information on Australia’s detection of both ASF and foot-and-mouth disease in seized pork products at airports is included. The report also contains information on classical swine fever in Japan.