Abstract
This project investigates the macroepidemiological aspects of porcine reproductive and respiratory syndrome virus (PRRSV) RNA detection by veterinary diagnostic laboratories (VDLs) for the period 2007 through 2018. Standardized submission data and PRRSV real-time reverse-transcriptase polymerase chain reaction (RT-qPCR) test results from porcine samples were retrieved from four VDLs representing 95% of all swine samples tested in NAHLN laboratories in the US. Anonymized data were retrieved and organized at the case level using SAS (SAS® Version 9.4, SAS® Institute, Inc., Cary, NC) with the use of PROC DATA, PROC MERGE, and PROC SQL scripts. The final aggregated and anonymized dataset comprised of 547,873 unique cases was uploaded to Power Business Intelligence—Power BI® (Microsoft Corporation, Redmond, Washington) to construct dynamic charts. The number of cases tested for PRRSV doubled from 2010 to 2018, with that increase mainly driven by samples typically used for monitoring purposes rather than diagnosis of disease. Apparent seasonal trends for the frequency of PRRSV detection were consistently observed with a higher percentage of positive cases occurring during fall or winter months and lower during summer months, perhaps due to increased testing associated with well-known seasonal occurrence of swine respiratory disease. PRRSV type 2, also known as North American genotype, accounted for 94.76% of all positive cases and was distributed across the US. PRRSV type 1, also known as European genotype, was geographically restricted and accounted for 2.15% of all positive cases. Co-detection of both strains accounted for 3.09% of the positive cases. Both oral fluid and processing fluid samples, had a rapid increase in the number of submissions soon after they were described in 2008 and 2017, respectively, suggesting rapid adoption of these specimens by the US swine industry for PRRSV monitoring in swine populations. As part of this project, a bio-informatics tool defined as Swine Disease Reporting System (SDRS) was developed. This tool has real-time capability to inform the US swine industry on the macroepidemiological aspects of PRRSV detection, and is easily adaptable for other analytes relevant to the swine industry.
Highlights
The most economically important swine disease in the United States (US) is porcine reproductive and respiratory syndrome (PRRS), causing annually losses of more than 600 million dollars[1]
Results released by ISU-veterinary diagnostic laboratories (VDLs) and UMN-VDL during August to November of 2018 and standardized by snomed CT, and Logical Observation Identifiers Names and Codes (LOINC) codes were messaged to a database server using the Health Level Seven International (HL7) format
Server database was accessed by an Open Database Connectivity (ODBC) interface provided by Microsoft1, and allowed the SAS application to access the data at the server using SQL password protected commands in a near real-time base
Summary
The most economically important swine disease in the United States (US) is porcine reproductive and respiratory syndrome (PRRS), causing annually losses of more than 600 million dollars[1]. The MSHMP project has provided useful information; it reports incidence data based on veterinarian’s judgement and is not necessarily confirmed by appropriate diagnostic testing. It does not include information of more than 3.5 million breeding females from an inventory of 6.33 million breeding females, in the US not participating in the voluntary survey, and does not track pathogen detection in 68.2 million heads of market hogs, which represent 91.5% of the swine population in the US based on the December of 2018 USDA Quarterly Hogs and Pigs report [10]. Characteristics include period of time, geographical region (US state), age group, and specimen
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