Progress 03/01/22 to 02/28/25
Outputs
Target Audience:Target audience included wildlife managers, swine industry, animal disease managers (including emergency response officials in foreign animal disease management), livestock and wildlife veterinarians, and researchers in wildlife epidemiology and disese control. Specific audiences included the USDA-APHIS National Feral Swine Damage Management Program, USDA APHIS Veterinary Services and Wildlife Services, and state agency and industry partners. Changes/Problems:Early during implementation of this study, we had the opportunity to leverage collars and personnel from another ongoing study focused on feral swine toxicant development to act as another management technique in our design and provide additional GPS collar data. This added a substantial amount of work and data science challenges that slowed down completion of some of the research products. However, although it was slower, the end products are almost complete and more robust. We experienced some shortcomings with IT systems that slowed productivity with building data pipelines for automating all of our computer code products. This ultimately slowed delivery of our data assets - although they are now complete. Another major challenge was the uncertainty with the change in administration that led our postdoc to leave federal service during the final stages of completion of the research. What opportunities for training and professional development has the project provided?Two field staffwere 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, developing data science skills, presenting scientific results to internal and external stakeholders, and project management.Our biologistgained experience with processing camera images, conducting statistical analysis, and presenting scientific findings to land and wildlife managers, researchers, and academics. How have the results been disseminated to communities of interest?Results have been presented in a wide variety of scientific and operational venues (see presentation titles and venue). Also, PIs Pepin and Miller 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. PI Pepin also organized monthly meetings with the National Feral Swine Damage Management Program, including Coordinator Dana Cole, to provide regular updates on the progress of the objectives and results for ongoing preparedness activities. We provided an update of project progress in the Federal Task Force Feral Swine News - Spring 2023. We have also presented to Wildlife Services personnel during internal seminar series such as 'bite-sized science' - a monthly seminar within APHIS Wildlife Services. Title: Preparedness for emergency management of a foreign animal disease introduction in feral swine Venue: 8thInternational Biosafety & Biocontainment Symposium, Baltimore, MD, Feb. 11th, 2025 Stakeholders present: Industry, government, research, and NGO stakeholders in biosafety Title: In touch with the dead- wild pig contact with conspecific carcasses and its implications for disease management. Venue: Mississippi State University, Wildlife Damage Management Conference, March 26th, 2025. Stakeholders present: Feral swine managers and researchers Title: Preparedness for emergency management of ASF in feral swine Venue: USA-Australian seminar series on feral swine management, virtual, Mar. 5th, 2025 Stakeholders present: Feral swine managers and researchers from USA and Australia Title: Optimizing response to an introduction of ASF in wild pigs: Implications for FMD Venue: FMD symposium, Manhattan, KS, Mar. 12th, 2025 Stakeholders present: Animal disease managers and researchers Title: Modeling for Emergency Management Preparedness of Foreign Animal Diseases in Wildlife: the Case of African Swine Fever in Wild Pigs. Venue: SIAM Conference on Applications of Dynamical Systems (DS25), Denver, CO, May 12th, 2025 Stakeholders present: Mathematical modelers Title: Intensive population control for TAD control influences space-use: case with wild pigs (Sus scrofa) Venue: Conference of Research Workers in Animal Diseases Chicago, IL Jan. 20th, 2025 Stakeholders present: Veterinarians, Wildlife Biologists, Disease managers, Researchers Title: Practice deploying intense control in feral swine: feral swine movement responses, costs, and logistical considerations using different control techniques. Venue: USDA-APHIS-VS-CEAH ASF Symposium, Fort Collins, CO. Sep. 24th, 2024. Stakeholders present: Disease managers, Emergency response personnel, Disease risk analysts Title: Wildlife disease surveillance and management updates. Venue: Food and Agriculture Organization of the United Nations. Rome, Italy. May 6th, 2024. Stakeholders present: International partners planning and implementing wildlife disease surveillance and management. Title: Operational preparedness research for deploying a response to ASF in feral swine. Venue: Q2 National Feral Swine Damage Management Program seminar series, virtual, Mar. 28th, 2024. Stakeholders present: USDA National Feral Swine Damage Management Program, USDA Wildlife Services operations. 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: Bite-Sized Science seminar series, APHIS-Wildlife Services, virtual, Oct. 2nd, 2023 Stakeholders present: USDA National Feral Swine Damage Management Program, USDA Wildlife Services operations, NWRC 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. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Measure wild swine movement and contact in response to intense control and estimate movement in different environments Manuscript "Chalkowski K, Snow NP, Feuka AB, Leland B, VerCauteren KC, Miller RS,Pepin KM.Wildlife movement and contact responses to intensive culling: implications for disease control." has been submitted toJournal of Animal Ecology. All scripts used to process and analyze data for inferring wild pig movement responses to intense control are publicly available on github athttps://github.com/kchalkowski/Removals_Mvmt_Scripts Manuscript "Chalkowski K, Sack AE, Wittemyer G, Miller RS, Boughton RK, Snow NP, Beasley JC, Ditchkoff SS, Evans T, Gray SM, Lewis JS, Parsons MA, VerCauteren KC, Webb SL, Young JK,Pepin KM. Scaling-up predictions of free-ranging animal movements: case study in wild pigs (Sus scrofa) across the United States."has been submitted toJournal of Applied Ecology.All scripts used in pipeline available athttps://github.com/kchalkowski/NatlMvDistandhttps://github.com/kchalkowski/NatlMvmtPref.Entire pipeline, with cleaned data used in analysis and associated outputs, is on aapcoftcfp13 and fully up to date at smb://aapcoftc3fp13/Projects/MUDD/ASF_NIFA/Pipelines/NatlMvmtDist for the step length/displacement pipeline and smb://aapcoftc3fp13/Projects/MUDD/ASF_NIFA/Pipelines/NatlPigPref. Manuscript "Chalkowski K, Miller RS, Chandler J, Campos A, Arruda B, Baker A, Klemm J, Brown VR, VerCauteren KC, Snow NP, Pepin KM. Elevated exposure to influenza A viruses in wild pigs, Texas, USA. Journal of Wildlife Diseases" has been submitted to Journal of Wildlife Diseases. 2 manuscripts describing deployment of intense control in feral swine have been published (DOI: 10.1016/j.prevetmed.2024.106365 and 10.1016/j.prevetmed.2024.106347) Estimate rates of visitation to carcasses and carcass decomposition rates Associated datasets are organized and documented within USDA servers. All photo processing of carcass visitations is complete. Analysis of wild pig contact rates with carcasses is complete. We have completed the analysis evaluating wild pig contact rates and factors influencing interactions with conspecific carcasses during decomposition. We monitored 89 wild pig carcasses over 2999 carcass days and manually processed over 1 million images to evaluate all species interactions with wild pig carcasses throughout decomposition. Wild pigs visited 63 (70.1%) of the carcasses over 239 carcass days (8.0% of total). Of the carcasses visited, 55 (87.3%) experienced direct contact by wild pigs over 175 carcass days (5.8% of total). Scavenging by wild pigs occurred at 21 (23.5%) carcasses; however, 46.2% of the events involved young wild pigs attempting to nurse on carcasses, accounting for 10% of all carcasses scavenged by wild pigs. Our results revealed that wild pig visitation to conspecific carcasses was influenced by the days post-mortem, overall scavenging intensity at the carcass, prior-day scavenging activity, and prior-day pig activity. Given that a carcass was visited, wild pig contact was further influenced by days post-mortem and the carcass origin. Assuming no prior scavenging or pig activity at a local carcass, the probability of at least one wild pig contact with a carcass increased from 0.02 in week 1 to 0.18 in week 8. Manuscript "In touch with the dead: disease implications of conspecific carcass visitation and contact" is under preparation with a target submission date of June 2025. These results are being incorporated into modeling frameworks for optimizing surveillance and response. ?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 Simulations for predicting the spatial area affected by ASF in feral swine are ongoing. CEAH staff are currently generating 10 different realizations of farm locations from the most recent census of agriculture. Once simulations are completed, we will overlay the area affected by ASF in feral swine over the intensity surface for swine farm locations (these analyses are ongoing) Develop a modeling framework for estimating optimal response plans and resource needs in different environments The ASF simulation modeling framework is complete and operational here: https://github.com/kchalkowski/ASF_optimal_radius Movement preference and movement distance prediction pipelines have been integrated into the simulation framework at a weekly scale to allow simulation of ASF spread across real landscapes. A set of landscapes has been selected to model ASF spread across representative landscapes, for determination of the optimal radius for control. The modeling framework includes pipelines for initializing model parameters across multiple landscapes to enable flexible replicate simulation runs. The code is ready for use to estimate optimal response zone sizes for control in feral swine in response to an ASF introduction - considering real landscapes and feral swine movement ecology. 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 Simulations to identify the optimal response plans across the USA are in progress. When complete, results will provide a map of how large the response zone should be in different landscapes across the USA. We have begun development of R Shiny application for stakeholder use, through collaboration with National Feral Swine Program personnel, to integrate optimal radius outputs into useable application with pipeline that incorporates surveillance data.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2025
Citation:
Chalkowski K, Pepin KM, Lavelle M, Miller RS, Fischer J, Brown VR, Glow M, Smith B, Cook S, Kohen K, Sherburne S, Smith H, Leland B, VerCauteren KC, Snow NP. Operational lessons learned from simulating an elimination response to a transboundary animal disease in wild animals. Preventive Veterinary Medicine 234: 106365.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2025
Citation:
Snow NP, Smith B, Lavelle MJ, Glow MP, Chalkowski K, Leland BR, Sherburne S, Fischer JW, Kohen K, Cook SM, Smith H, VerCauteren KC, Miller RS, Pepin KM. Comparing efficiencies of population control methods for responding to foreign animal disease threats in wild pigs. Preventive Veterinary Medicine 233: 106347.
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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
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