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.

Prediction of seasonal patterns of porcine reproductive and respiratory syndrome virus RNA detection in the U.S. swine industry

“…The 4 VDLs reporting to the SDRS test > 95% of all porcine submissions submitted for the National Animal Health Laboratory Network (NAHLN) in the United States. 12 Submissions with the following reasons were removed: submission as “research,” reason for testing as “exporting,” specimen as “vaccine,” or specimen as “environmental sample.” After removing these submissions, SDRS recorded 547,873 PRRSV submissions between 2007 and 2018, collected from 49 of 50 states in the United States and submitted for testing by RT-rtPCR. 12…”

Understanding and interpreting a PRRS diagnosis in the context of “disease stages”

“…Поколение современных инструментов диагностики, таких как полимеразная цепная реакция с обратной транскрипцией (РТ-ПЦР) для детекции РНК ВРРСС и твердофазный иммуноферментный анализ (ELISA) для детекции ВРРСС-специфичных антител за последние 30 лет прошли долгий путь технологических усовершенствований. Оба метода обладают достаточной диагностической эффективностью и при правильном применении составляют основу при осуществлении программ по предотвращению, контролю и ликвидации ВРРСС (Trevisan et al, 2019).…”

Data standardization implementation and applications within and among diagnostic laboratories: integrating and monitoring enteric coronaviruses

“…During 2017, we initiated the Swine Disease Reporting System (SDRS), a program to perform aggregation and monitoring of testing data for porcine reproductive and respiratory syndrome virus (PRRSV; Betaarterivirus suid 1 , Betaarterivirus suid 2 ) from 4 U.S. swine-centric VDLs. 29,30 This program aggregated data from multiple VDLs to monitor PRRSV as well as other agents or diseases that are detected on a large scale. Moreover, it also allowed the tabulation, characterization, and visualization of patterns of agent detection or disease diagnosis over time, geographic space, species, age groups, sample type, and other relevant factors.…”

“…Moreover, it also allowed the tabulation, characterization, and visualization of patterns of agent detection or disease diagnosis over time, geographic space, species, age groups, sample type, and other relevant factors. 29 The aggregation of PRRSV test data from 4 VDLs with high swine caseloads allowed us to create a structured platform that can be easily adapted and replicated to report the detection of other agents from other species as well. Thus motivated, the SDRS project was expanded to incorporate and inform stakeholders of rates, trends, and geographic distributions of enteric swine coronaviruses detected by reverse-transcription PCR (RT-PCR).…”