Macroepidemiological aspects of porcine reproductive and respiratory syndrome virus detection by major United States veterinary diagnostic laboratories over time, age group, and specimen

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.

Fig 1. Swine Disease Reporting System schematic flow chart for data processing.

Fig 2. Schematic organization of raw data and final processed and anonymized information.

Bullets with letters on the right represent a case.

Fig 3. Results of PRRSV cases tested by RT-qPCR over time.

Fig 4. Percentage of RT-qPCR-positive results for PRRSV cases over the total number of cases per season.

Each point represents a season within a year. Season are represented as follows: 1-Wi = Winter; 2-Sp = Spring; 3-Su = Summer, and 4-Fa = Fall.

Fig 5. Geographical distribution of PRRSV RNA detection by RT-qPCR.

A: overall distribution of all cases tested for PRRSV RNA. B: only cases with positive results for type 2 (North American)-PRRSV. C: only cases with for positive results type 1 (European)-PRRSV. D: only cases with a positive result for PRRS NA and positive result for PRRS EU. For VDL client confidentiality purposes, only states with hog inventory above 2 million heads [16] have numbers in the maps. Gray color shows the states with no cases.

Fig 6. Proportion of specimens according to number of cases submitted for PRRSV RNA testing by RT-qPCR over time.

Each bar represents a year season, and each color represents a specimen type.

Fig 7. Proportion of age categories according to number of cases submitted for PRRSV RNA testing by RT-qPCR over time.

Each bar represents a year season, and each color represents an age category.