SHIC-Funded Swine Disease Reporting System Expands Near Real-Time Disease Information

The Swine Health Information Center (SHIC)-funded Swine Disease Reporting System (SDRS) initiative has completed another successful year. An aggregated database with diagnostic data from the Iowa State, Kansas State, University of Minnesota, South Dakota State, and Ohio State (beginning in October 2021) veterinary diagnostic labs (VDLs) is regularly updated, with monthly reports and podcasts to SHIC, as well as online interactive dashboards. The database now includes more than 950,000 distinct VDL submissions tested by PCR for the five US porcine endemic agents: porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea (PEDV), porcine deltacoronavirus (PDCoV), transmissible gastroenteritis (TGEV), and Mycoplasma hyopneumoniae. Monthly etiologic summaries of digestive, respiratory, and neurologic diagnostics from the Iowa State VDL are also reported. Interactive online dashboards with filtering capabilities for age category, specimen, geographic region, are kept updated and are available on the project website (https://www.fieldepi.org/sdrs).

The SDRS is the only publicly available source of swine health information from US VDLs. It is also the only source of information on pathogen activity in all age groups (from boar studs to grow-finish pigs). More than 110 monitoring algorithms are currently implemented in the SDRS background to detect changes early in the pattern of agent detection. In addition to SHIC’s website and newsletter, SDRS reports are sent by email to more than 270 registered receivers from 129 organizations/institutions from seven countries (US, Canada, Mexico, Brazil, Chile, Germany, and Spain) and monthly audio and video reports are distributed on the project website, YouTube channel, Swine Cast platform, and LinkedIn.

In July 2020 (SDRS report # 29), monthly PDF reports began to be produced using R Markdown technology in a standard and consistent format. The R Markdown script automates as much as possible the process of generating and updating images, formatting, and description for the monthly detection changes under each agent page. As an ongoing real-time project, there is still the need for staff to interpret the finding, debugging, communicate results with the advisory group, gather feedback, and compile the final report, including the input and feedback from the Advisory group. The usage of an R Markdown script has enhanced SDRS sustainability by reducing the time needed and errors in compiling the final monthly PDF final report.

The SDRS has been built using a building block approach. Initially, SDRS started reporting PRRSV detection from Iowa and Minnesota VDLs and later on added South Dakota, Kansas and Ohio VDLs and additional data for the enteric coronavirus and M. hyopneumoniae. Initially, each agent’s database was kept separate. A restructuring was done to compile, combine, and store all data in a single database. This redesign allowed the database interconnection with the R Markdown to generate monthly reports, analytical tools like R and SAS, and business intelligence tools, like Power BI and Tableau, for data visualization.

SHIC, launched by the National Pork Board in 2015 solely with Pork Checkoff funding, continues to focus efforts on prevention, preparedness, and response to novel and emerging swine disease for the benefit of US swine health. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. SHIC is funded by America’s pork producers to fulfill its mission to protect and enhance the health of the US swine herd. For more information, visit http://www.swinehealth.org or contact Dr. Sundberg at psundberg@swinehealth.org.