Source: NORTH CAROLINA STATE UNIV submitted to NRP
FACT: NEAR-REAL TIME SPATIOTEMPORAL RESOURCE ALLOCATION TO IMPROVE SWINE HEALTH
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1023722
Grant No.
2020-67021-32462
Cumulative Award Amt.
$497,560.00
Proposal No.
2019-07452
Multistate No.
(N/A)
Project Start Date
Aug 1, 2020
Project End Date
Jul 31, 2025
Grant Year
2020
Program Code
[A1541]- Food and Agriculture Cyberinformatics and Tools
Recipient Organization
NORTH CAROLINA STATE UNIV
COLLEGE OF VETERINARY MEDICINE
RALEIGH,NC 27606
Performing Department
Population Health Pathobiology
Non Technical Summary
Porcine reproductive and respiratory syndrome (PRRS) and porcine epidemic diarrhea (PED) cost the US swine industry more than $1 billion/year. The detection of these viruses in the US led to the application of regional disease control and elimination efforts. Despite the great reduction in PED incidence, PRRS still affects a third of the US sow herds yearly. Therefore, there is a critical need to identify: i) why PED and PRRS keep spreading and ii) strategies that improve disease control. Our goals combine data-visualization with spatial and statistical methods to increase the fundamental knowledge about PED and PRRS spatial epidemiology, enhancing our understanding of disease spread to develop novel data-integration tools to optimize disease control.This proposal aligns with the program area "Food and Agriculture Cyberinformatics Tools (FACT: A1541)-Animal Health and Production and Animal Products". Our research activities use existing data of PED and PRRS outbreaks from one of the US major swine regions. We will apply Bayesian and machine-learning methodology to quantify the geographic distribution, local variation of intrinsic and extrinsic risk factors and farm characteristics that predispose swine farms to be infected with PED and/or PRRS. We propose the development of spatiotemporal treatment regimen tool to help the swine industry decide the location and when to allocate their control resources (e.g., vaccination, herd exposure to live virus upon an outbreak).Impacts of this study include the promotion of informed disease management and improved animal health through enabling the swine community to effectively use existing data to manage outbreaks.
Animal Health Component
25%
Research Effort Categories
Basic
(N/A)
Applied
25%
Developmental
75%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
31135101170100%
Knowledge Area
311 - Animal Diseases;

Subject Of Investigation
3510 - Swine, live animal;

Field Of Science
1170 - Epidemiology;
Goals / Objectives
To develop spatiotemporal models for the distribution of PED and PRRS and evaluate their performance in predicting dynamic intrinsic and extrinsic risk factors and disease spread and to develop and disseminate treatment regimen for precision and optimal resource allocation to help the swine industry to efficiently preempt and manage outbreaks of PED and PRRS.
Project Methods
We propose to develop models to quantify the local, regional and seasonal variation of the most important intrinsic and extrinsic risk factors coupled with farm characteristics that predispose swine farms to be affected by PED and PRRS outbreaks. Consequently, we will develop and disseminate a forecast system to improve resource allocation and promote informed and targeted disease management based on the most effective intervention. We also hypothesize that animal movements need to be part of the equation, since this parameter seems to increase the risk of infection due to possible (if not yet explored) interactions with extrinsic environmental variables that either facilitate or hinder local disease spread. Finally, it is imperative that intrinsic factors such as host characteristics and rapid spatiotemporal diffusion characteristics in the evolution of emerging PRRS strains alone or interactively can affect significantly the intensity of transmission, therefore, strain genetic variation will be part of our modeling experiments.

Progress 08/01/23 to 07/31/24

Outputs
Target Audience:Dr. Machado: presented the development of this work at several national swine meetings, including the Agricultural and Food Research Initiative, 2024 Project Director's Meeting (Manhattan, KS); Analyzing the intrastate and interstate swine movement network in the United States (Uppsala, Sweden); How on-farm biosecurity, pig, and vehicle movement explain between-farm disease dissemination? (COST (European Cooperation in Science and Technology) BETTER webinar). PhD student was exposed to new methodologies developed in this project, resulting in one peer-reviewed publication and presentations at the CVM Research Day. NCSU (Raleigh, NC) Changes/Problems:We have requested a no-cost extension to finish the reinforcement learning for the optimal swine vehicle routing tool and manuscript What opportunities for training and professional development has the project provided?A graduate student who majors in statistics received training in swine disease epidemiology. He gained real-life experience and developed a tool that is not only complex but user-friendly, allowing swine producers to understand the results and use it. How have the results been disseminated to communities of interest?Via social media and conferences. Other interactions with stakeholders are described under products. What do you plan to do during the next reporting period to accomplish the goals?We will collect additional disease control interventions applied during PRRSV and PEDV. We plan to utilize the already-in-development Rapid Access Biosecurity (RAB) application (app) prototype to communicate with our stakeholders by making the spatiotemporal treatment regime secure and readily available. We will publish the results of the dynamic treatment regimen and the decision-making tool, which now has a provisory title of "Reinforcement learning for optimal swine vehicle routing".

Impacts
What was accomplished under these goals? Our specific research objectives were: 1) The development and validation of spatiotemporal models of the distribution of PED and PRRS to predict dynamic risk for disease spread; 2) To identify potential PED and PRRS risk factors for targeted surveillance through a statistical analysis of farm and production system-specific control measures and their association with positive infection status; 3) To develop and implement a near real-time spatiotemporal treatment regime for precision interventions, assessing its efficacy and cost per PED and PRRS outbreak averted. Objective 1 has been addressed and made public via peer-reviewed publication. Objective 2: With the information on vehicles, we could account for vehicle cleaning and disinfection. This dynamic treatment is used in the PRRSV and is now underway for PEDV. It will be released with objective 3. We will show that the application of this framework to route feed and live pigs in a large network of commercial pig farms results in more efficient use of resources, lower disease spread, and higher production. Objective 3: The dynamic treatment regime tool has been developed to use PRRSV and PED combined. We are creating a novel approach that will consider reinforcing learning for optimal swine vehicle routing.

Publications


    Progress 08/01/22 to 07/31/23

    Outputs
    Target Audience:Dr. Machado: presented the development of this work at several national swine meetings, including U.S. swine industry preparedness for emerging diseases (GIS Week Lightning Talk (NCSU, Raleigh, NC) Swine Innovation Forum (Goldsboro, NC)-Feb-2023; Major Enhancement of U.S. Swine Industry Biosecurity (Cross-Border Threat Screening and Supply Chain Defense (CBTS). While PhD student was exposed to new methodologies developed in this project that resulted in one peer-reviewed publication and conference presented at the 2022 AASV Annual Meeting. Changes/Problems:Due to COVID-19 and hiring freeze we have delayed objective 2 and 3. We hope to achieve the goals in time, however, we do not discard the need for a no-cost extension. What opportunities for training and professional development has the project provided?A graduate student has received training about swine disease epidemiology and developed his skills in modelling such complex system. Two additional publications have been made available while also results were shared to DVM student at NCSU. How have the results been disseminated to communities of interest?Via social media and conferences. Other interactions with stakeholders are described under products. What do you plan to do during the next reporting period to accomplish the goals?Objective 2, With the transportation vehicles information, we were able to account for cleaning and disinfection of vehicles. This dynamic treatment is used in the PRRSV and now is underway for PED. Objective 3, The dynamic treatment regime tool has been developed for PRRSV and PED combined, and main results are being processed and will be available via peer-review publication next year.

    Impacts
    What was accomplished under these goals? Our specific research objectives were: 1) The development and validation of spatiotemporal models of the distribution of PED and PRRS to predict dynamic risk for disease spread; 2) To identify potential PED and PRRS risk factors for targeted surveillance through a statistical analysis of farm and production system-specific control measures and their association with positive infection status; 3) To develop and implement a near real-time spatiotemporal treatment regime for precision interventions, assessing its efficacy and cost per PED and PRRS outbreak averted. Objective1, have been addressed and made public via peer-review publication. Objective 2, With the transportation vehicles information, we were able to account for cleaning and disinfection of vehicles. This dynamic treatment is used in the PRRSV and now is underway for PED. Objective 3, The dynamic treatment regime tool has been developed for PRRSV and PED combined, and main results are being process and will be available via peer-review publication next year.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2023 Citation: Sanchez, F., Galvis, J.A., Cardenas, N.C., Corzo, C., Jones, C., Machado, G., 2023. Spatiotemporal relative risk distribution of porcine reproductive and respiratory syndrome virus in the United States. Front. Vet. Sci. 10, 1158306. https://doi.org/10.3389/fvets.2023.1158306
    • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Oral Presentation: "Spatiotemporal relative risk distribution of porcine reproductive and respiratory syndrome virus in the southeastern United States". Felipe Sanchez, Jason A. Galvis, Nicolas Cardenas, Cesar A Corzo, Chris Jones, Gustavo Machado. American Association of Swine Veterinarians Annual Meeting. Denver, CO.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Poster presentation: "Spatiotemporal relative risk distribution of porcine reproductive and respiratory syndrome virus in the southeastern United Sates". Felipe Sanchez, Jason A. Galvis, Nicolas Cardenas, Cesar A Corzo, Chris Jones, Gustavo Machado. Graduate Student Research Symposium. NCSU.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Trostle, P., Corzo, C.A., Reich, B.J., Machado, G., 2022. A discrete?time survival model for porcine epidemic diarrhoea virus. Transbounding Emerging Dis 69, 36933703. https://doi.org/10.1111/tbed.14739


    Progress 08/01/21 to 07/31/22

    Outputs
    Target Audience:Dr. Galvis presented at the 2021 AASV Annual Meeting, the title of the presentation was "The impact of vaccination strategieson between-farm PRRSV transmission". Dr. Machado presented at Morrison Forum for Advancing Swine Production Medicine, Mankato, MN, titled "Assessing additional transmission routes for PRRSV: vehicle movements and feed ingredients. Swine Debate Group at Iowa State University. Modelling transmission dynamics of routes for porcine reproductive and respiratory syndrome virus: vehicle movements and feed ingredients. The main results of year two include invited presentations at other U.S. institutions and at national conferences. In addition, a major publication on porcine reproductive and respiratory syndrome virus (PRRSV) dissemination and a preprint (submitted to Transboundary and Emerging Diseases) on the spatiotemporal epidemiology of porcine epidemic diarrhea virus (PEDV) References Galvis, J. A., Corzo, C. A., & Machado, G. (2022). Modelling and assessing additional transmission routes for porcine reproductive and respiratory syndrome virus: Vehicle movements and feed ingredients. Transboundary and Emerging Diseases, 00, 1- 12. https://doi.org/10.1111/tbed.14488 Trostle, P., Corzo, C.A., Reich, B. J., Machado, G*.A discrete-time survival model for porcine epidemic diarrhea virus (https://www.biorxiv.org/content/10.1101/2022.06.03.494708v1.abstract) Changes/Problems:This project like many others was impacted by COVID-19. Given the fluid situation of the pandemic, we cannot rule out the risk of project delays, even though we are on track with our original project timetable. What opportunities for training and professional development has the project provided?A graduate student has received training in swine disease epidemiology and developed his skills in modeling such complex systems. A publication has been submitted by Trostle, P., Corzo, C.A., Reich, B. J., Machado, G*. A discrete-time survival model for porcine epidemic diarrhea virus. Dr. Galvis has attended the national swine conference. How have the results been disseminated to communities of interest?Because we have already published one peer-review publication and one submitted. News about the work has been distributed to the general public via NC State media post https://news.ncsu.edu/2022/03/vehicles-prrsv-transmission/, and on social media. Other interactions with stakeholders are described under products What do you plan to do during the next reporting period to accomplish the goals?We will collect additional disease control interventions applied during PRRSV and PEDV. We plan to utilize the already developed Rapid Access Biosecurity (RAB) application (app) ()https://machado-lab.github.io/rabapp/) prototype to communicate with our stakeholders, by making the spatiotemporal treatment regime secure and readily available. Publish results of the dynamic treatment regimen and the decision-making tool.

    Impacts
    What was accomplished under these goals? Our specific research objectives were: 1) The development and validation of spatiotemporal models of the distribution of PED and PRRS to predict dynamic risk for disease spread; 2) To identify potential PED and PRRS risk factors for targeted surveillance through a statistical analysis of farm and production system-specific control measures and their association with positive infection status; 3) To develop and implement a near real-time spatiotemporal treatment regime for precision interventions, assessing its efficacy and cost per PED and PRRS outbreak averted. To address objective 1, we have further extended the between-farm transmission model "Pigspread" to also accommodate other contact networks. We were able to include transportation vehicles data of four different vehicles, trucks use in the delivery of feed, to transport pigs to market and between farms, and small vehicles used to transport staff between farms. The additional transportation vehicle data is used in both the PRRSV and PEDV publications. Objective 2, With the transportation vehicles information, we were able to account for the cleaning and disinfection of vehicles. This dynamic treatment is used in the PRRSV publication and will be further utilized in the real-time spatiotemporal treatment regime next year. Objective 3, the dynamic treatment tool will be developed next year.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Galvis, J. A., Corzo, C. A., & Machado, G. (2022). Modelling and assessing additional transmission routes for porcine reproductive and respiratory syndrome virus: Vehicle movements and feed ingredients. Transboundary and Emerging Diseases, 00, 1 12. https://doi.org/10.1111/tbed.14488
    • Type: Journal Articles Status: Submitted Year Published: 2022 Citation: Trostle, P., Corzo, C.A., Reich, B. J., Machado, G*. A discrete-time survival model for porcine epidemic diarrhea virus (https://www.biorxiv.org/content/10.1101/2022.06.03.494708v1.abstract)
    • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Galvis, J. A., Corzo, C. A., & Machado, G. The impact of vaccination strategies on between-farm PRRSV transmission at 2021 AASV Annual Meeting


    Progress 08/01/20 to 07/31/21

    Outputs
    Target Audience:Dr. Galvis presented at the 2020 AASV Annual Meeting Program, the title of the presentation "The impact of vaccination strategy on between-farm PRRSV transmission". Dr. Machado was a key-note speaker at a seminar series hosted by stakeholders of the swine feed industry hosted online because of covid-19, title of the presentation was "How technology could help predict future Porcine Epidemic Diarrhea virus (PEDV) outbreaks". Dr. Machado has also presented at the CVM (College of Veterinary Medicine) NCSU series results about the movement of live hogs and disease transmission, the title of the presentation is "Quantifying the dynamics of animal movements for improving targeted disease surveillance and control plans". The main results of year one, include 6 presentations to pharmaceutical companies and pig-producing companies. Talks covered results oftheporcine reproductive and respiratory syndrome virus (PRRSV)transmission model in which we implemented control interventions including vaccination, as described in (Galvis et al., 2021b). Additionally, we have also presented the results of (Galvis et al., 2021a, 2021b) to swine veterinarians and key swine industry stakeholders. References Galvis, J.A., Jones, C.M., Prada, J.M., Corzo, C.A., Machado, G., 2021a. The between-farm transmission dynamics of Porcine Epidemic Diarrhea Virus: A short-term forecast modeling comparison and the effectiveness of control strategies. Transbound Emerg Dis tbed.13997. https://doi.org/10.1111/tbed.13997 Galvis, J.A., Prada, J.M., Corzo, C.A., Machado, G., 2021b. Modeling the transmission and vaccination strategy for porcine reproductive and respiratory syndrome virus. Transboundary and Emerging Diseases tbed.14007. https://doi.org/10.1111/tbed.14007 Changes/Problems:This project as many others was impacted by COVID-19, more specifically because of the hiring freeze and other HR complications, we experienced delays in hiring the postdoctoral fellow and graduate student, even though we were able to make progress and deliver for objectives 1 and 2. Given the fluid situation of the pandemic, we cannot rule out the risk of project delays, even though we are on track with our original project timetable. What opportunities for training and professional development has the project provided?We have presented the main modeling results to swine veterinarians, thus provided them with an introductory class about the broad mechanism of the disease transmission modelling, so that they could better understand our main prediction results. Dr. Machado is the course coordinator of disease epidemiology at NCSU, he has utilized the model the PRRSV model (Galvis et al., 2021) to introduce the student to mathematical modeling. The PD and co-PD are mentoring a graduate student with a major in statistics. The student has received training about swine disease epidemiology and developed his skills in modeling such complex systems. Reference Galvis, J.A., Prada, J.M., Corzo, C.A., Machado, G., 2021. Modeling the transmission and vaccination strategy for porcine reproductive and respiratory syndrome virus. Transboundary and Emerging Diseases tbed.14007. https://doi.org/10.1111/tbed.14007 How have the results been disseminated to communities of interest?Because we have already published two peer-review publications, both are available to the scientific community. In addition, NCSU had written media posts to highlight the studies, please visit the link https://cvm.ncsu.edu/multi-model-approach-could-help-farmers-prepare-for-contain-pedv-outbreaks/. We have also developed a dedicated post-session within the PD lab website in which we have also posted the main finding of this project https://machado-lab.github.io/research/PRRSV/. In addition, any presentation related to this study has also been shared via social media. What do you plan to do during the next reporting period to accomplish the goals?We will collect the necessary information about all disease control interventions applied during PRRSV and PED outbreaks. Thus we will make the appropriate model modification to allow for testing the deployment of optimal treatment regime strategies. We will also work on the development of the communication front-end of the near-real-time spatiotemporal recommendation tool. We plan to utilize the already in development Rapid Access Biosecurity (RAB) application (app) prototype to communicate with our stakeholders, by making spatiotemporal treatment regime secure and readily available. Publish results about the potential spatiotemporal PED and PRRS risk factors in peer-reviewed journals

    Impacts
    What was accomplished under these goals? Our specific research objectives were: 1) The development and validation of spatiotemporal models of the distribution of PED and PRRS to predict dynamic risk for disease spread; 2) To identify potential PED and PRRS risk factors for targeted surveillance through a statistical analysis of farm and production system-specific control measures and their association with positive infection status; 3) To develop and implement a near real-time spatiotemporal treatment regime for precision interventions, assessing its efficacy and cost per PED and PRRS outbreak averted. To address objectives 1, we have collected population and between-farm movement data of nearly all commercial pig-producing farms in North Carolina. Along with the infection status of all farms provided by MSMHP (our collaborator from the UofM), we utilized the weekly outbreak data to develop the first model interaction for both PED and PRRSV spatiotemporal models. Thus far, we have successfully developed both transmission dynamic models(Galvis et al., 2021a, 2021b). Overall we have completed objective 1. Along with the models, we have also developed the "Pigspread" model which will become available freely via an R package. Briefly, "PigSpread" is a stochastic population-based model, with a metapopulation structure at the farm level. With this model structure, we can calibrate spatiotemporal distribution of farm-level outbreaks, accounting for the spread dynamics between farms through the two main transmission routes 1) between-farm pig movementsand 2) local transmission dependent on the distance between susceptible and infected farms. Objective 2: We have started collecting the necessary disease control and intervention data from the participating pig-production companies. Therefore, we were able to use some data to develop the novel treatment recommendation regimen model. Objective 3, we have not yet developed the whole back-end infrastructure for planned reporting systems to communicate with our public. Our plans include utilizing a current project that lies in a user-friendly interface that allows pork producers to have access to their biosecurity data. Because our stakeholders are familiar with such a tool, we plan to provide our results of objective 3, through this channel, which is expected to expedite our near-real-time spatiotemporal recommendation results. References Galvis, J.A., Jones, C.M., Prada, J.M., Corzo, C.A., Machado, G., 2021a. The between-farm transmission dynamics of Porcine Epidemic Diarrhea Virus: A short-term forecast modeling comparison and the effectiveness of control strategies. Transbound Emerg Dis tbed.13997. https://doi.org/10.1111/tbed.13997 Galvis, J.A., Prada, J.M., Corzo, C.A., Machado, G., 2021b. Modeling the transmission and vaccination strategy for porcine reproductive and respiratory syndrome virus. Transboundary and Emerging Diseases tbed.14007. https://doi.org/10.1111/tbed.14007

    Publications

    • Type: Journal Articles Status: Published Year Published: 2021 Citation: Galvis, JA, Corzo, CA, Prada, JM, Machado, G. Modelling the transmission and vaccination strategy for porcine reproductive and respiratory syndrome virus. Transbound Emerg Dis. 2021; 00: 1 16. https://doi-org.prox.lib.ncsu.edu/10.1111/tbed.14007
    • Type: Journal Articles Status: Published Year Published: 2021 Citation: Galvis, JA, Jones, CM, Prada, JM, Corzo, CA, Machado, G. The between-farm transmission dynamics of porcine epidemic diarrhoea virus: A short-term forecast modelling comparison and the effectiveness of control strategies. Transbound Emerg Dis. 2021; 00: 1 17. https://doi-org.prox.lib.ncsu.edu/10.1111/tbed.13997
    • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Jason A. G., Joaquin M. P.; Machado, G. The impact of vaccination strategies on between-farm PRRSV transmission. American Association of Swine Veterinarians (AASV)  2021 oral presentation (online).
    • Type: Conference Papers and Presentations Status: Submitted Year Published: 2021 Citation: Jason A. G., Joaquin M. P., Corzo, C., Machado, G. Modeling truck transit and feed ingredients in the between farm transmission of porcine reproductive and respiratory syndrome virus in the United States. 8th International Conference on Infectious Disease Dynamics (online).