Swine Health

Real-time risk Assessment Platform for Evaluating the Risk of African Swine Fever (ASF) Introduction into the United States
The aim of this project is to develop a user-friendly digital platform for the real-time risk assessment of ASF introduction into the US. This platform would be scalable and could be easily adapted to evaluate other Foreign Animal Diseases (FADS). This platform will allow the gathering, update and integration of different epidemiological data for the near real-time risk assessment of ASF introduction into US through different routes. Specifically, it will provide: i) an updated risk profile (where and when) of ASF risk of introduction into the US, ii) the possibility to set up and send notifications when the risk significantly changed and iii) sensitivity analysis and scenario evaluation tools to quantify the impact of specific scenarios (e.g. the impact of change in policies or trade patterns) on the risk estimates.
AoC – Development and Maintenance of the ASF News Web-Service
The aim is to develop an intelligence technology system refer to as “ASF News”. We will develop the infrastructure and interface to capture, validate, store and provide in near real-time official and unofficial information, news and notifications about African Swine Fever reported in more than 10 languages. During the time of this collaboration we will complete the ASF News infrastructure design, implementation and beta-testing. Following, we will provide real-time information as well as daily reports with qualitative and quantitative details contained in ASF News such as source, type and number of news, space-time evolution of notifications, etc. This information will be stored in a ad hoc database and will be accessible anytime.
Linking veterinary diagnostic laboratory submissions to spatiotemporal mapping tools: the future of disease management, control and elimination
The objectives of this project are to integrate, further develop, and use a number of existing diagnostic and epidemiologic information management technologies to create a functional, scalable, and universally applicable swine diagnostic information network and disease management tool that links participating veterinary diagnostic laboratory (VDL) submissions and corresponding Porcine Epidemic Diarrhea Virus (PEDV) test results and interpreted PEDV health status of the site to a spatiotemporal disease management tool (Disease BioPortal) for use in national, area-regional, veterinary clinic, or production system specific PEDV monitoring and control initiatives. Initially, while the more complex programming work is being completed to adapt the existing software for use in the proposed network and to establish the necessary connectivity amongst its parts; we will use PEDV diagnostic data derived via conventional VDL information management system query algorithms of participating VDL submissions to demonstrate the utility of the tool to monitor and further study the emergence of PEDV in the US swine industry. Participating VDL submissions must i) indicate their willingness to share and release their case (farm site) specific PEDV diagnostic results for use in further epidemiologic study and monitoring of the spread of PEDV throughout the US over the course of the project period and ii) provide the premise identification number, sample type, and type of farm site (Breeding Herd or Growing Pig) on the VDL submission form. These data will be used to map site-specific PEDV positive test results and PEDV phylogenetic summaries over the course of the 12-month project. This PEDV diagnostic information will be uploaded into the Secure Animal Health Diagnostic Database (SAHDD) for case-level interpretation, and subsequently downloaded into Disease Bioportal for further bioinformatic analyses and viewing by permissioned users. Collaborative efforts will be made to ensure the animal health information management network being assembled in this project are synergistic and fully capable of delivering information into a program disease management tool (i.e., AgConnect) being developed by The Center for Foreign Animal and Zoonotic Disease Defense (FAZD). Permissioned users from Centers for Epidemiology and Animal Health (CEAH) and FAZD will be given full access to the PEDV diagnostic results and Disease BioPortal output from participating VDL submissions for further epidemiologic study. Participating veterinary diagnostic laboratories will be given permissioned access to the Disease Bioportal output to share with their stakeholders contributing to the data. The network and area regional disease management tools being created in this project will be betatested and used to support the complete diagnostic information management and reporting needs of the PEDV area-regional control project underway in Southeast Iowa (i.e., including maintaining the current PEDV status of all premises participating in the project). Once fully developed and beta-tested, the network and disease management tool created will be available for use across any number of regions, states, diagnostic laboratories, veterinary practices, and/or production systems. Although PEDV is focus of this project; the network and technologies being developed are being strategically designed to be broadly applicable, scalable, and readily adaptable for use in managing other domestic diseases of high consequence. Similarly, the core elements of this project are well-aligned to help advance US foreign animal disease preparedness and risk-based continuity of business programs being developed for the US Pork Industry. The Secure Pork Supply Plan is being established to maintain the safe movement of pigs that have been determined to be free of infection during the face of a reportable or program disease outbreak in the US.
Evaluation of the Interface between Feral Pigs and Pasture-Raised Pigs, a Multi-Agency Epidemiological Approach: Implications for Infectious Disease Transmission and Surveillance
The growing niche of pasture-raised pigs in the last two decades reflects consumer demand for local, sustainable, humanely-raised meat. One of the challenges of raising pigs outdoors is the increasing probability of domestic pigs interfacing with feral pigs and a corresponding increasing risk of emerging diseases. California has one of the largest and widest distributions of feral pigs.These two parallel trends of an expanding feral pig population and a growing interest in pastureraised pork creates a possible disease transmission link for existing pathogens harbored in feral pigs. The overall research goal is to fill a critical information gap regarding the epidemiology of diseases of interest by building a predictive map of high-risk areas for interaction and disease transmission among feral pig populations that interface with pasture-raised pigs in California. The specific objectives are: 1) Geo-spatial characterization of feral pig populations and building a predictive distribution map using Maxent modeling; 2) Geo-spatial characterization of pastureraised pig operations; 3) Identification of high-risk areas for pasture-raised pigs to feral pig interface and disease transmission; 4) Estimation of Salmonella and STEC prevalence in pasture-raised pigs and feral pigs and identification of its risk factors. This project will provide valuable information to all stakeholders, from farmers to consumers, regarding the potential disease risks associated in the interface between pasture and feral pigs. Furthermore, a multiagency- university approach will synergize individual agency efforts on feral swine issues and should prove invaluable as a model for similar efforts nationwide in the near future. The outcomes of this project and team collaborations and the emerging industry of pasture-raised pig producers, will be useful for all related agencies, institutions, and stakeholders that may be called upon to respond to future disease outbreaks and natural disasters. We expect to expand this project to other states by applying to the combined call on swine health and foreign animal diseases (including ‘feral swine reservoir risks and mitigations’) funded by the Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD) and the National Pork Board (NPB). Other potential funding agency is the USDA AFRI, Foundational Program, Critical Agriculture Research and Extension (CARE).
Evaluating the role of direct (i.e., animal contacts) and indirect (i.e., airborne) transmission of different PRRSV genotypes within and between different swine production systems in the US
Porcine reproductive and respiratory syndrome virus (PRRS) is still one of the swine diseases responsible for large economic losses in the US, despite of preventive and control measures implemented to reduce transmission within and between production systems. However, few studies have investigated how the different PRRSV genotypes are spreading among swine systems in the US and which are the most likely transmission pathways contributing to it.

The aim of this study is to estimate the specific role of direct (i.e., animal movements) and indirect (e.g., airborne or local spread) transmission of PRRSV genotypes within and between different swine production systems in the US.

A mixed Bayesian model will be used to quantify the association between:
1.the pairwise genetic distance of two isolates belonging to the most frequent RFLP types (1-18-4, 1-18-2, 1-26-2, 1-4-4, etc),
2. the spatial and temporal proximity (i.e., pairwise spatial distance and pairwise absolute difference in time between isolates),and frequency
3. and characteristics of swine movements (i.e., social network structure: bidirectional number of incoming and outgoing shipments and number of animals moved).

Social network analysis (SNA) methods will also be used to specifically characterize the structure and characteristics of the network of animal movements. The use of SNA will allow to:

1. identify “communities” (i.e. “groups of sites”) highly connected, with high likelihood to share PRRSV genotypes and where, for example, a “shared” or “common” PRRS control program is recommended to be implemented,

2. characterize sites, areas and time periods at highest risk of PRRSV introduction (i.e. incoming shipments) or spread (i.e. outgoing shipments) thought animal movement and

3. provide recommendations about the most cost-effective way to implement risk-based interventions (e.g. increase of biosecurity, vaccination, air filtering, etc.) in those sites that play a “key role” for PRRSV introduction and/or spread in order to maximize business continuity and improve PRRSV prevention and control at the local and regional level.
Moreover, we will develop a herd score index that will summarize the genetic diversity of PRRSV on site and its association with the direct (i.e. animal movement) and indirect transmission (i.e. airborne spread) potential for each site, which will provide the baseline framework for benchmarking and prioritizing interventions at an individual (i.e., high risk herds) or system level. Methods will be also integrated in Disease BioPortal© (http://bioportal.ucdavis.edu), allowing: the near real-time update of new isolates and of trade networks into the analysis, the secure access and user-friendly visualization of the results while keeping always confidentiality (i.e. no display of sensitive/confidential information).

Methods and results are intended to provide a better understanding of how PRRSV genotypes are spreading among farms as well as to identify “critical points” (i.e. sites, areas, time periods or contacts) where
attention should be focused. Specifically we will quantify the specific role that animal movements and local spread may have in disease transmission in the US swine industry and to identify high-risk herds, areas and time periods where surveillance and control strategies should be prioritized.
Collaborative Research Agreement between Iowa State University and University of California, Davis
The Center for Animal Disease Modeling and Surveillance (CADMS) at the University of California Davis (Principal Investigator, Dr. Beatriz-Martinez Lopez) proposes to work collaboratively with and provide epidemiological and information management development and support services to the Iowa State University Veterinary Diagnostic Laboratory (Principal Investigator, Dr. Rodger Main) in effort to further develop and expand the capabilities and use of Disease BioPortal® across a broad-array of applied epidemiologically focused veterinary diagnostic and production animal medicine applications.

Objectives of Work:
1. Continue to advance the functionality and capabilities of a suite of complementary web-based tools (collectively referred to as the Animal Health Information Management Network, see Figure 1.) that links veterinary diagnostic laboratory submissions, corresponding test results, attending veterinarian insight, and an interpreted health status of farm sites via the Animal Health Monitoring and Evaluation System (AHMES, Iowa State University) to a spatiotemporal disease management tool (Disease BioPortal®, University of California - Davis) for use in area-regional, veterinary clinic, or production system animal health monitoring and control initiatives.

2. Complete the development and provide the technical support and database administrative access necessary for the Iowa State University Veterinary Diagnostic Laboratory to use Disease BioPortal® (University of California-Davis) for creating web-based aggregate summary analysis of the national, state, or regional trends being observed in the diagnostic case submissions being processed at the Iowa State University Veterinary Diagnostic Laboratory as well for client-specific spatiotemporal bioinformatic analysis and study.
3. Continue to advance the functionality and connectivity involving other ISU VDL associated data aggregation tools (or efforts) and Disease BioPortal®.

4. Maintain and protect the confidentiality, security, and integrity of the ISU VDL associated data under this agreement on an isolated database server that contains only information pertaining to ISU VDL associated data (and backed-up) at the University of California-Davis.