Source: ANIMAL & PLANT HEALTH INSPECTION SERVICE submitted to
OPTIMIZING PREPAREDNESS FOR AN INTRODUCTION OF AFRICAN SWINE FEVER VIRUS IN THE USA
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1028190
Grant No.
2022-67015-36658
Cumulative Award Amt.
$650,000.00
Proposal No.
2021-11285
Multistate No.
(N/A)
Project Start Date
Mar 1, 2022
Project End Date
Feb 28, 2025
Grant Year
2022
Program Code
[A1181]- Tactical Sciences for Agricultural Biosecurity
Project Director
Pepin, K.
Recipient Organization
ANIMAL & PLANT HEALTH INSPECTION SERVICE
4700 RIVER RD UNIT 55
RIVERDALE,MD 207371232
Performing Department
(N/A)
Non Technical Summary
Rationale: African swine fever virus (ASFv) poses an enormous biosecurity threat to the USA swine industry, food security, and economy. The persistence of ASFv in wild boar in Europe and Asia emphasizes that USA's growing feral swine population could challenge elimination and achievement of disease-free status after an introduction. Once ASFv establishes and reaches a state of sustained transmission and persistence in wild boar, it becomes very difficult to eliminate - thus rapid response plans that contain its spread are crucial. Current response plans are tailored to domestic swine and standardized across the Nation. However, rates of ASFv spread and our ability to remove feral swine quickly could vary dramatically across the Nation because these processes depend so much on local ecology (e.g. terrain, thickness of vegetation, how far feral swine move to find food or water). Response plans that consider local ecology would help us to prepare equipment and personnel needs, and to develop optimal strategies for rapid elimination of ASFv in feral swine across regions with different environmental conditions.We know from the European situation that transmission from ASFv-killed carcasses can be an important source of ASFv transmission and persistence, but we do not know how often feral swine make contact with carcasses or how long carcasses remain in different ecologies (i.e., due to weather-related decomposition or local scavenger populations) in the USA. This is important for predicting the rate of spatial spread of ASFv and planning carcass disposal actions during response, so that we can optimize response plans. Secondly, we also have little knowledge about how feral swine respond to intense, consistent removal in an area. In other social species it has been noted that disruption of social groups can alter movement rates, potentially driving higher rates of disease spread.Overarching goal: Our proposed work includes data collection and analysis (Obj. 1-3) that will fill these knowledge gaps (i.e., carcass visitation and decay, and feral swine movement during intense removal). These missing data will provide information to develop and apply a modeling framework (Obj. 4-5) that can be used to plan optimal response strategies across different environments in the USA.Specific objectives: 1) Measure wild swine movement and contact in response to intense control and estimate movement in different environments; 2) Estimate rates of visitation to carcasses and carcass decomposition rates; 3) Map the number of swine farms/farm sizes predicted to be affected by an introduction of ASFv in feral swine in different areas across the USA; 4) Develop a modeling framework for estimating optimal response plans and resource needs in different environments; 5) Determine optimal response plans across the USA, identify the most important uncertainties (information that would improve our confidence about response plans), and deliver results to stakeholders in a user-friendly tool.Expected results: Our work will provide a toolbox for estimating optimal response plans that minimize the duration and spatial spread of ASFv in a variety of environments, provide estimates of optimal control zone size, and present information that will help prepare the resources needed to achieve rapid elimination for different environments across the USA.Anticipated impact: Our work will position us to rapidly eliminate ASFv in feral swine if an introduction is to occur to minimize the chance that ASFv will establish and reach sustained transmission in feral swine. By providing optimal plans across the Nation and understanding how resources needs change due to local ecology, response personnel will have a resource to help guide planning for resource stockpiling for rapid deployment, anticipated personnel needs, and optimal response zone sizes in different areas. This will allow for rapid delineation of response zones to optimize containment rates and elimination of ASFv in the event of an introduction.?
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3110830117040%
3110830107020%
3110830310040%
Knowledge Area
311 - Animal Diseases;

Subject Of Investigation
0830 - Wild animals;

Field Of Science
1070 - Ecology; 1170 - Epidemiology; 3100 - Management;
Goals / Objectives
Rationale: African swine fever virus (ASFv) poses an enormous biosecurity threat to the USA swine industry, food security, and economy. The persistence of ASFv in wild boar in Europe and Asia emphasizes that USA's growing feral swine population could challenge elimination and achievement of disease-free status after an introduction. Once ASFv establishes and reaches a state of sustained transmission and persistence in wild boar, it becomes very difficult to eliminate - thus rapid response plans that contain its spread are crucial. Current response plans are tailored to domestic swine and standardized across the Nation. However, rates of ASFv spread and our ability to remove feral swine quickly could vary dramatically across the Nation because these processes depend so much on local ecology (e.g. terrain, thickness of vegetation, how far feral swine move to find food or water). Response plans that consider local ecology would help us to prepare equipment and personnel needs, and to develop optimal strategies for rapid elimination of ASFv in feral swine across regions with different environmental conditions.We know from the European situation that transmission from ASFv-killed carcasses can be an important source of ASFv transmission and persistence, but we do not know how often feral swine make contact with carcasses or how long carcasses remain in different ecologies (i.e., due to weather-related decomposition or local scavenger populations) in the USA. This is important for predicting the rate of spatial spread of ASFv and planning carcass disposal actions during response, so that we can optimize response plans. Secondly, we also have little knowledge about how feral swine respond to intense, consistent removal in an area. In other social species it has been noted that disruption of social groups can alter movement rates, potentially driving higher rates of disease spread.Overarching goal: Our proposed work includes data collection and analysis (Obj. 1-3) that will fill these knowledge gaps (i.e., carcass visitation and decay, and feral swine movement during intense removal). These missing data will provide information to develop and apply a modeling framework (Obj. 4-5) that can be used to plan optimal response strategies across different environments in the USA.Specific objectives: 1) Measure wild swine movement and contact in response to intense control and estimate movement in different environments; 2) Estimate rates of visitation to carcasses and carcass decomposition rates; 3) Map the number of swine farms/farm sizes predicted to be affected by an introduction of ASFv in feral swine in different areas across the USA; 4) Develop a modeling framework for estimating optimal response plans and resource needs in different environments; 5) Determine optimal response plans across the USA, identify the most important uncertainties (information that would improve our confidence about response plans), and deliver results to stakeholders in a user-friendly tool.
Project Methods
Methods: We will conduct field studies in a region that is predicted to be high risk for an ASFv introduction. Studies will include monitoring movement of feral swine by GPS during an intense, consistent removal targeted at eliminating feral swine within an area. We will also monitor vistation rates of tagged feral swine to carcasses and how long the flesh on carcasses remains. We will incorporate this information into a computer model of disease transmission across a landscape, incorporating environmental details that alter rates of spatial spread. The computer simulation model will incorporate the best available information habitat-specific information on feral swine movement,contact, demographic dynamics, and ASFv transmission, and response capabilities in different environments. We will conduct simulations using different environmental conditions from across the USA to identify general rules for how the environmental conditions determine the size of the response zone and resource needs, and sensitivity analyses to determine which parameters present the most important uncertainties. We will create county-level maps for the optimal response strategies and expected number of farms affected in counties across the USA. We will make the information available in maps and a simple Excel application where the user can enter their region and have attributes of the optimal response plan given back.

Progress 03/01/23 to 02/29/24

Outputs
Target Audience:Our target audience is USDA-APHIS WS National Feral Swine Program, USDA-APHIS Veterinary Services,National Preparedness and Incident Coordination, pork industry liaisons, wildlife managers, and wildlife disease ecologists. We have been communicating to all these audiences (see 'How results have been disseminated' section for details). Changes/Problems:Year 1: The start of our field work was slowed by 4 months due to delays in receiving GPS collars and onboarding personnel. We moved our study site to a different site in TX based on more favorable wild pig densities. Year 2: Our technicians left early before photo processing was complete, we have re-filled the positions with a single person that will help with both data organization and analysis. What opportunities for training and professional development has the project provided?Two field staff were trained in field skills related to intense control of feral swine. One field staff gained experience in supervising the other employee. Our postdoc attended a science communication workshop and the Ecology and Evolution of Infectious Disease conference. Our postdoc also gained experience mentoring other project staff on data collection and organization, and presenting scientific results to stakeholders (e.g., NIFA annual meeting project update). How have the results been disseminated to communities of interest?We presented results describing what we learned for deployment of intense control in feral swine in the following venues (see presentation titles and venue). PIs Pepin and Miller also attended bi-weekly meetings hosted by the USDA-APHIS Veterinary Services,National Preparedness and Incident Coordination team and participated in discussions about ASF preparedness in feral swine. Title: Operational preparedness research for planning and deploying a response to ASF in feral swine. Venue: Feral Swine Disease Stakeholder Meeting, Fort Collins, CO, Jan. 30th, 2024. Stakeholders present: USDA National Feral Swine Damage Management Program, USDA Wildlife Services operations, USDA Veterinary Services,Pork industry Liaisons, State Departments of Agriculture, State Departments of Natural Resources, University partners. Title: "ASF preparedness research in feral swine" Venue: North American ASF Forum, Raleigh, North Carolina, Aug. 29th, 2023 Stakeholders present: USDA National Feral Swine Damage Management Program, USDA Wildlife Services operations, USDA Veterinary Services,Pork industry Liaisons - these groups were present for USA, Canada, and Mexico to work on trilateral coordination. Title: "Preparedness for foreign animal disease introductions in wildlife" Venue: Seminar at Mannaki Whenua Landcare Research, Lincoln, New Zealand, June 14th 2023 Stakeholders present: Landcare research scientists that work on developing disease elimination strategies, Some professionals from Ministry for Primary Industries and industry good groups joined virtually. Title: "Optimizing preparedness for an introduction of African swine fever virus (ASFv) in feral swine (FS)" Venue: Virtual NIFA Agricultural Biosecurity Program update, May 4th 2023 Stakeholders present: NIFA-AFRI Agricultural Biosecurity program officers, other PIs funded by the program. Title: "Optimizing preparedness for an introduction of African swine fever virus (ASFv) in feral swine (FS)" Venue: Virtual update to USDA-APHIS Veterinary Services, April 14th 2023. Stakeholders present: USDA-APHIS Veterinary Services,National Preparedness and Incident Coordination, USDA National Feral Swine Damage Management Program, USDA Veterinary Services Centers for Epidemiology and Animal Health. Postdoc Chalkowski presented a poster at Ecology and Evolution of Infectious Diseases conference, State College, PA, May 22nd-25th (academic audience). Poster title: Preparedness against a foreign animal disease introduction in wildlife. We provided an update of project progress in the Federal Task Force Feral Swine News - Spring 2023 What do you plan to do during the next reporting period to accomplish the goals?Complete data analysis for Obj. 1 and 2 (movement response, carcass visitation and decomposition rates). Finish developing maps of pork producer locations and begin running analysis to predict numbers of producers affected by introductions in different areas (Obj. 3). Finish refining code for scenario model on Github (GitHub - kchalkowski/ASF_optimal_radius: ASF optimal radius) to use inputs from Obj 1 and 2 and real landscapes (Obj 4). Identify regions where landscape data will be extracted for scenario modeling. Run the refined scenario model on those regions and analyze results (Obj. 5). Submit threedraft articles for perr-reviewed publication: A draft article describing gaps for deployment of ASF response in feral swine using different methods. Title: Realities of operationalizing an intense elimination response to a foreign-animal disease in wildlife. To be submitted to Preventive Veterinary Medicine. A draft article comparing the time- and cost-efficiencies for multiple methods to remove wild pigs. Title: Comparing efficiencies of population control methods for responding to foreign animal disease threats in wild pigs. To be submitted to Preventive Veterinary Medicine. A draft article reporting the national-scale movement metrics. Title: Use of aggregation at different steps in the modeling process to improve broad-scale movement models. To be submitted to Methods in Ecology and Evolution.

Impacts
What was accomplished under these goals? During Year 2 reporting period (Mar. 1st, 2023 - Feb. 29th 2024) we accomplished the following. Field component Completed field work including: Implemented intense removal of feral swine using aerial operations and trapping. Collared individuals were released. We removed 247 individuals by aerial operations (March 2023) and 296 individuals by trapping (March-May 2023). We placed 69 carcasses in different locations with camera traps to monitor wildlife visitation and decomposition. Data analysis and modeling: Our project generated many different data streams including: GPS data from 115 wild pigs over 8 months, photos from camera traps on carcasses, metadata from each wild pig removed or captured, locations and times of all status changes to bait sites and trap sites, capture dates and locations, personnel number and hours spent on each activity relative to removal. We developed a data management system and have been organizing, cleaning, and linking the different data streams. Obj. 1-2: We have begun analyzing the field data to determine movement responses to intense control and contact rates with carcasses during different stages of decomposition. All GPS collars (except for 3 that malfunctioned) have been collected. Data from these collars have been cleaned and trimmed for future analyses. Camera traps placed on pig carcasses collected 1,503,824 motion activated images during 80 days of monitoring. Initial triaging of camera trap images, using timelapse animations, found that wild pigs were documented to visit 44 (64%) of 69 carcasses. Images (929,792) from these 44 cameras have been prioritized for species classification using CameraTrapDetectoR and manual classification of the type of carcass contact (e.g. direct, indirect, etc). To date 27 (61%) of the cameras accounting for 354,739 images with wild pigs identified at carcasses have been run through CameraTrapDetectoR. Carcass decomposition scoring of photos with pigs is ongoing. Once completed manual classification of contact type will be conducted. We have finished developing a national-scale layer for wild pig movement and have a draft article to be submitted soon for peer-review. We have drafted a manuscript comparing the time- and cost-efficiencies from the removal treatments that will be submitted soon for peer-review. Obj. 3: We have developed a national county-scale layer of domestic swine production that includes the number of farms by production type and size category as well as the average inventory of pigs within each production type and size category. Obj. 4: We continue to refine the scenario modeling framework and have made it open-access on Github (GitHub - kchalkowski/ASF_optimal_radius: ASF optimal radius). We are assimilating management logistic data from the intense control ops to refine the framework. We are developing the movement algorithms to operate on real landscapes with the updated movement layer. Obj. 5: We are refining the analysis approach.

Publications


    Progress 03/01/22 to 02/28/23

    Outputs
    Target Audience:We have met with USDA-APHIS WS National Feral Swine Program to provide updates on progress and results from ongoing analysis to help with ASF response plans. We have met with USDA-APHIS-VS Emergency Response to provide summaries of data and data gaps thus far to help with their response planning. Changes/Problems:The start of our field work was slowed by 4 months due to delays in receiving GPScollars and onboarding personnel. We moved our study site to a different site in TX based on more favorable wild pig densities. What opportunities for training and professional development has the project provided?Two field technicians stationed at the field site have been trained in feral swine capture, immobilization, and monitoring. A postdoctoral researcher has been developing skills in coordinating a large-scale field project and new analytical frameworks (especially inferences about disease dynamics from animal movement data and parameter estimation for practical applications). How have the results been disseminated to communities of interest?Progress is being communicated regularly to USDA-APHIS stakeholders (WS and VS-emergency response). What do you plan to do during the next reporting period to accomplish the goals?Completion of field work including implementation of the intense removal (small-scale mock response to ASF) and carcass monitoring. Analyzing movement data to determine effects of removal on movements. Analyze carcass monitoring data to determine rates of carcass contact and carcass decay. Begin integrating results from the field data analyses into the response optimization framework. Obtain density estimates for integration into the response optimization framework.

    Impacts
    What was accomplished under these goals? Field component: We hired staff and procured supplies for the field work. We built a staging area to conduct the field work and drove equipment and supplies to the field site. We developed applications for field-based data collection. We captured and deployed 80 GPS collars and began monitoring movements. We developed code for automatically summarizing movements. We coordinated with partners for the removal and carcass monitoring phases phase that areschduled for March/April/May 2023. Modeling: We improved our code base for determining optimal control strategies to speed up the code and make it compatible for handling the new data. We developed a code base for analyzing movements from other GPS collar data and predicting movement distances across CONUS.

    Publications