SHIC Domestic Disease Report Expands to Include State-by-state Pathogen Trends
June 10, 2020 — Paul Sundberg
The Swine Health Information Center (SHIC) funds the Domestic Swine Disease Monitoring Report (DSDMR), a collaborative project among multiple veterinary diagnostic labs (VDLs), to aggregate swine diagnostic data. Prepared by Drs. Daniel Linhares and Giovani Trevisan at Iowa State University, the DSDMR describes dynamics of pathogen detection by VDL-performed assays over time, specimen, age group, and geographical area. Data included is from the Iowa State University VDL, South Dakota State University ADRDL, University of Minnesota VDL, and Kansas State University VDL. Beginning in June 2020, there is a new element included in the DSDMR - specific state-by-state pathogen trends. With this report, veterinarians and producers will know if porcine epidemic diarrhea virus (PEDV), porcine reproductive and respiratory syndrome virus (PRRSV), Mycoplasma hyopneumoniae (MHP), or potentially other pathogens are moving up or down in states being analyzed. Identifying these trends is just the first step to further analysis of the data to understand the reasons for the trends and, thus, to help manage them.
This project includes states where DSDMR participant VDLs are located and those having a swine inventory equal to or greater than 2 million pigs. Authors are using the percentage of PCR-positive submissions by state then applying smoothing models to forecast results for a 12-month period. This report uses predicted values of percentage-positive results by PCR (by pathogen, month, and state) which were then subtracted from observed values, generating residue values. Then, residues were scanned by an exponential weighted moving average (EWMA) model to monitor and generate the changes from the expected baseline. The baseline and monitoring are constructed based on each state's data with no comparison across states.
EWMA findings are reported as changes in standard deviations (STD) from the expected baseline. Changes from baseline are reported as:
- no change when results were within 2 STD from baseline
- changes between 2-3 STD from baseline
- changes of at least 3 STD above or below the baseline
Information for each state regarding the change from baseline, the number of total, positive submissions, and percent of positive results were recovered from the models and transferred to Microsoft Power BI for geographic visualization. The dashboards for state-by-state pathogen trending can be accessed on the SHIC website at Domestic Swine Disease Monitoring Report or by visiting Iowa State University's site for the Swine Disease Reporting System (SDRS).
As the world deals with the COVID-19 pandemic, SHIC 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 firstname.lastname@example.org.
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