Funded by the Swine Health Information Center, in collaboration with the Foundation for Food & Agriculture Research, a study entitled, “Epidemiology of JEV in Australian Intensive Piggeries,” has recently revealed important lessons learned from the 2021-2022 Australian experience with Japanese encephalitis virus. Led by Dr. Brendan Cowled of Ausvet Pty Ltd, the study sought to understand how and why JEV spread in Australian pigs and make recommendations to assist the US industry in preparedness should JEV ever arrive in the US, a highly relevant effort due to similarity in production methods and environmental conditions for mosquito vectors in the two countries. Among outcomes were key lessons identified to help the US swine industry respond and adapt to a potential JEV outbreak. The research focused on understanding the transmission and epidemiology of JEV within farms and assessed farm-level risk factors for JEV in the Australian outbreak using quantitative and qualitative approaches for data collection and analysis.
Find a summary of project #25-053 here.
JEV is a mosquito-transmitted virus that impacts domestic swine industries and human health. It can lead to severe production impacts in commercial swine, including reproductive failure, reduced conception, abortion, mummified and stillborn piglets, shaker piglets, deformed and weak piglets, prolonged gestation and boar infertility. The virus is present in the western Pacific and Asia but has not been identified in the US, where it poses an emerging risk to pork production.
Recommendations for US industry preparedness and response to JEV
The investigators have proposed a comprehensive suite of recommendations in their full report. These are divided into preparation for a possible outbreak, response to a confirmed outbreak and what to do if JEV becomes established in the US. However, they detail important recommendations that could be considered by swine farmers and industry largely in advance of any JEV outbreaks to enhance preparedness:
In the event of JEV becoming established in the US, it may be possible to develop machine learning or other AI approaches to predict the occurrence of seasonal JEV outbreaks. These should be developed if JEV is established to provide early warnings, allowing proactive application of surveillance and control activities such as mosquito mitigation (e.g., insecticidal use) or vaccination of breeding stock (if/when a vaccine becomes available).
Quantitative Assessment
For the quantitative approach, industry, environmental, and meteorological data were used to quantify measurable disease outcomes, identify patterns, correlations and risk factors. Further, artificial intelligence (machine learning) was used to provide real time predictive models for early identification of future JEV outbreaks. The study period included in the risk factor analysis was from July 3, 2021, to March 25, 2023, well before and after the outbreak occurred in Australian piggeries.
Researchers analyzed data from six JEV-affected sow units at both the individual sow- and site-levels. Sow-level information included the site at which they were housed (sow unit), parity, farrowing and service dates, outcomes of service (i.e., farrowed, repeat mating, etc.) and details on litters produced by successful matings. The outcome variable for the site level analysis included the weekly rate of services that resulted in four or more mummies at farrowing.
Initial outbreak investigations highlighted that heterogeneity of reproductive outcomes over time could be indicative of JEV infection. Clinical prevalence rates varied from 13.4% to 43.0% in affected sows. Notably, mummified fetuses were the most common clinical sign observed. Mummified fetuses were used as the case definition for the site-level risk factor analysis as it appeared to be an accurate indicator of JEV infection. Using mummies within the analysis was also supported by the qualitative study in which the only clinical sign reported by 100% of pig veterinarians as being present was excessive mummified fetuses in a litter. The lack of consistency for other clinical signs may be due to management or reporting.
In addition, land cover types (inland wetlands, grasslands, farmlands), elevation, and hydrological accumulation using count-based models were evaluated to investigate incidence rate ratios. Implementing machine learning, the researchers developed a model to predict high-risk periods for JEV using a broad range of real-time climatic and environmental variables.
Results showed climatological factors relevant to bird ecology were associated with an increased JEV risk. Statistically significant risk factors included long-term cumulative rainfall, mean proportion of inland wetlands, and the service month, including their interactions. For example, inland wetlands became a risk factor when interacting with increased rainfall. Conversely, more temperate grasslands offered protection, even with heavier rain.
The study demonstrated the predictive power of the machine learning model as an early warning system, accurately forecasting the timing of JEV outbreaks in severely affected sites. In the process, the team identified key influential predictors for the model, such as minimum temperature and cumulative rainfall. Further research on the machine learning model could include a composite outcome (i.e., not just mummified fetuses), and incorporation of later data from the 2025 JEV outbreak, which would increase the generalizability of the model.
Qualitative Assessment
For the qualitative approach, interviews were conducted with experts from the Australian swine industry involved in the 2022 outbreak to capture unrecorded data observations and understandings. Qualitative methods are considered particularly valuable for understanding how individuals interpret and respond to emerging situations. In the context of the Australian JEV outbreak, this approach provides a nuanced view of how veterinarians and others navigated the challenges and made decisions in rapidly evolving circumstances.
The interview participants included 11 veterinarians, two industry professionals, and two medical entomologists who were all involved in the response to the Australian outbreak. Veterinary participants represented a broad range of swine production systems within Australia. This included the two largest swine farming integrator companies collectively managing over 90,000 sows and veterinarians serving various smaller swine operations. Participants located in different areas experienced the outbreak in varied ways.
Key findings included the significant role of environmental and farm management factors influencing transmission, variability in clinical presentations and prevalence across farms, and barriers to timely detection, diagnosis and control. Early detection and effective mosquito control on farms were identified as critical components for mitigating future outbreaks and minimizing economic impacts. The Australian experience demonstrates that JEV introduction can occur without clear warning, with the virus silently circulating among birds and mosquitoes and infecting people for months before being detected in domestic swine.
One of the key challenges observed during the Australian outbreak was the variability in clinical presentation across infected farms. Participants noted that the clinical signs, severity, and timing of disease onset did not consistently align with literature descriptions or with other farms. While classic signs such as reproductive failure in sows and boars and neurological signs and deformities in piglets were observed on many farms, other farms displayed only mild or subclinical cases, which went undetected until antibody assays were conducted.
Further, the extent of disease was not uniform within or between herds – some animals were severely affected (50 – 60% of litters affected) while others were subclinical or exhibited very mild signs. Infected gestating sows showed no clinical signs until they farrowed. While initial surges in cases often declined rapidly after four to six weeks, some herds saw impacts for 10 to 12 weeks. These variable clinical presentations, combined with their subclinical nature until sows farrowed, highlight the challenge of detecting JEV infections early based solely on clinical signs. This is particularly true in completely naïve populations, where sows show no outwards signs of illness, and the first indication may be the sudden appearance of congenital abnormalities at birth.
Once JEV was detected, farm management practices focused on minimizing the impact of the outbreak through supportive animal care and vector control. Animal management strategies were primarily aimed at supporting affected animals and mitigating long-term reproductive impacts. A key management strategy employed by many of the participants was to rest affected sows for at least one estrus cycle before re-mating. Participants observed that rested sows showed significantly better reproductive outcomes compared to those that were mated immediately post-farrowing. In contrast, boars affected by infertility were often culled without time to recover, primarily due to the immediate need to increase breeding capacity. However, farms that chose to retain affected boars reported mixed outcomes; while some boars regained fertility after at least 70 days, others remained infertile.
Without a vaccine approved for swine, mosquito control emerged as the central pillar of the swine farm response in Australia. Producers relied on emergency permits and off label use while facing supply shortages as demand from the swine industry and public health programs exceeded availability. While chemical control is essential, it should not be the sole focus, and an integrated pest management approach is required. For example, environmental measures such as removing standing water, managing vegetation, and using biological larvicidal agents (e.g., Bacillus spp.), chemical larvicides (e.g., aquatain) or insect growth regulators (e.g., methoprene) proved highly effective in controlling mosquito populations on swine farms. Mechanically ventilated systems were more effective at excluding mosquitoes. In the US, integrating routine mosquito control into farm biosecurity standards should be a key activity in preparedness and prevention.
Once JEV is introduced into a new country, endemicity is likely to occur given local mosquito and bird populations can maintain virus circulation. Therefore, rather than aiming for eradication or containment, it may be more practical for the swine industry to implement sustainable management practices from the outset. Australia experiences point to a focus on maintaining vigilance through ongoing surveillance for early detection of JEV emergence in mosquito, bird, or feral swine populations, integrating mosquito control into routine farm operations, ensuring access to veterinary insecticides, repellents and vaccines, and using accurate and reliable diagnostic tools. Human vaccination and bite avoidance measures to reduce the risk of infection in people should also be prioritized.
As JEV’s global range expands due to changing weather and migratory patterns, Australia’s experience offers critical lessons for commercial swine industries like the US. This study offers invaluable insights to help the US swine industry prepare for, respond to, and adapt to a potential JEV outbreak, ultimately reducing economic impacts and safeguarding herd health.
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 the U.S. Department 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.
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 http://www.swinehealth.org or contact Dr. Megan Niederwerder at [email protected] or Dr. Lisa Becton at [email protected].