Estimating the time of infection for African swine fever in pig farms in Korea.

African swine fever (ASF) is a highly contagious and lethal disease with characteristics of hemorrhagic fever. ASF outbreaks in pig farms significantly damage the entire pork industry. Understanding the transmission dynamics of ASF is crucial to effectively respond. Notably, it is important to know when the infection started on the outbreak farm. This study aimed at establishing a procedure for estimating the time of infection on pig farms affected by the ASF outbreak in Korea. The protocol for sampling to detect ASF virus infection, the estimation of the time interval between infection and detection, and the estimation of the infection stage parameters for the simulation model were described. After infection, fattening sheds (9.8 days in median) had the longest detection time compared with pregnant (8.6 days) or farrowing sheds (8.0 days). The intervals were 8.8 days for farrow-to-finisher farms, 7.0 days for farrow-to-weaning farms, and 9.5 days for fattening farms. The findings of this study provide valuable insights into ASF outbreaks in pig farms thus, improving the disease control ability.

Big data-based risk assessment of poultry farms during the 2020/2021 highly pathogenic avian influenza epidemic in Korea.

Outbreaks of H5-type highly pathogenic avian influenza (HPAI) in poultry have been reported in various parts of the world. To respond to these continuous threats, numerous surveillance programs have been applied to poultry raising facilities as well as wild birds. In Korea, a surveillance program was developed aimed at providing a preemptive response to possible outbreaks at poultry farms. The purpose of this study is to comprehensively present the risks of HPAI evaluated by this program in relation to actual outbreak farms during the epidemic of 2020/2021. A deep learning-based risk assessment program was trained based on the pattern of livestock vehicles visiting poultry farms and HPAI outbreaks to calculate the risk of HPAI for farms linked by the movement of livestock vehicles (such farms are termed "epidemiologically linked farms"). A total of 7,984 risk assessments were conducted, and the results were categorized into four groups. The proportion of the highest risk level was greater in duck farms (13.6%) than in chicken farms (8.8%). Among the duck farms, the proportion of the highest risk level was much greater in farms where breeder ducks were raised (accounting for 26.4% of the risk) than in farms where ducks were raised to obtain meat (12.8% of the risk). A higher risk level was also found in cases where the species of the outbreak farm and epidemiologically linked farms were the same (proportion of the highest risk level = 13.2%) compared to that when the species between the two farms were different (7.9%). The overall proportion of farms with HPAI outbreaks among epidemiologically linked farms (attack rate, AR) was 1.7% as HPAI was confirmed on 67 of the 3,883 epidemiologically linked farms. The AR was highest for breeder ducks (15.3%) among duck farms and laying hens (4.8%) among chicken farms. The AR of the pairs where livestock vehicles entered the inner farm area was 1.3 times (95% confidence interval: 1.4-2.9) higher than that of all pairs. With the risk information provided, customized preventive measures can be implemented for each epidemiologically linked farm. The use of this risk assessment program would be a good example of information-based surveillance and support decision-making for controlling animal diseases.

Arthropods as potential vectors of African swine fever virus outbreaks in pig farms in the Republic of Korea.

The seasonality of African swine fever (ASF) in the summers and outbreaks in farms with high biosecurity levels suggest that the ASF virus (ASFV) may be transmitted by arthropod vectors. Arthropods were collected in this study from 14 pig farms with ASF outbreaks in Korea in 2019 to explore the role of arthropods as potential ASFV vectors. A total of 28,729 arthropods, including 28,508 (99.2%) Diptera, were collected using blacklight traps, insect nets and yellow sticky strips. All arthropod samples were negative for ASFV genomic DNA according to laboratory tests using real-time polymerase chain reaction. This result may reflect the effects of immediate control measures following the detection of farms with ASF outbreaks in the early phase of infection in Korea.

Risk Assessment Program of Highly Pathogenic Avian Influenza with Deep Learning Algorithm.

OBJECTIVES: This study presents the development and validation of a risk assessment program of highly pathogenic avian influenza (HPAI). This program was developed by the Korean government (Animal and Plant Quarantine Agency) and a private corporation (Korea Telecom, KT), using a national database (Korean animal health integrated system, KAHIS). METHODS: Our risk assessment program was developed using the multilayer perceptron method using R Language. HPAI outbreaks on 544 poultry farms (307 with H5N6, and 237 with H5N8) that had available visit records of livestock-related vehicles amongst the 812 HPAI outbreaks that were confirmed between January 2014 and June 2017 were involved in this study. RESULTS: After 140,000 iterations without drop-out, a model with 3 hidden layers and 10 nodes per layer, were selected. The activation function of the model was hyperbolic tangent. Precision and recall of the test gave F1 measures of 0.41, 0.68 and 0.51, respectively, at validation. The predicted risk values were higher for the "outbreak" (average ± SD, 0.20 ± 0.31) than "non-outbreak" (0.18 ± 0.30) farms (p < 0.001). CONCLUSION: The risk assessment model developed was employed during the epidemics of 2016/2017 (pilot version) and 2017/2018 (complementary version). This risk assessment model enhanced risk management activities by enabling preemptive control measures to prevent the spread of diseases.

Clinical symptoms of African swine fever in domestic pig farms in the Republic of Korea, 2019.

This study describes the clinical characteristics of the African swine fever (ASF) outbreaks in 14 domestic pig farms in the Republic of Korea. ASF outbreak was identified by farmers' notifications in 11 farms and by active surveillance in the remaining three. At the time of notification, farmers reported sudden death, abortion and anorexia in sows. Death was the primary symptom identified by farmers in fattener pigs. The number of animals exhibiting clinical symptoms did not exceed four heads at notification, and the number of asymptomatic virus positives was four heads per farm on average. As ASF virus was detected only in the same pig house (in a pen for fattener pigs) in each of 14 ASF outbreak farms, there has been no evidence of house-to-house viral spread within any of the ASF outbreak farms. This in turn supports our hypothesis that infection was successfully detected during its initial phase.

Fine-scale tracking of wild waterfowl and their impact on highly pathogenic avian influenza outbreaks in the Republic of Korea, 2014-2015.

Wild migratory waterfowl are considered one of the most important reservoirs and long-distance carriers of highly pathogenic avian influenza (HPAI). Our study aimed to explore the spatial and temporal characteristics of wild migratory waterfowl's wintering habitat in the Republic of Korea (ROK) and to evaluate the impact of these habitats on the risk of HPAI outbreaks in commercial poultry farms. The habitat use of 344 wild migratory waterfowl over four migration cycles was estimated based on tracking records. The association of habitat use with HPAI H5N8 outbreaks in poultry farms was evaluated using a multilevel logistic regression model. We found that a poultry farm within a wild waterfowl habitat had a 3-8 times higher risk of HPAI outbreak than poultry farms located outside of the habitat. The range of wild waterfowl habitats increased during autumn migration, and was associated with the epidemic peak of HPAI outbreaks on domestic poultry farms in the ROK. Our findings provide a better understanding of the dynamics of HPAI infection in the wildlife-domestic poultry interface and may help to establish early detection, and cost-effective preventive measures.