Macroepidemiological trends of Influenza A virus detection through reverse transcription real-time polymerase chain reaction (RT-rtPCR) in porcine samples in the United States over the last 20 years

Influenza A virus (IAV) in swine is a major respiratory pathogen with global significance. This study aimed to characterize the macroepidemiological patterns of IAV detection using reverse transcription real-time polymerase chain reaction (RT-rtPCR) assays, including subtype identification, in samples submitted between January 2004 and December 2024 to veterinary diagnostic laboratories (VDLs) participating in the Swine Disease Reporting System (SDRS). A secondary objective was establishing an IAV monitoring capability to inform stakeholders of weekly changes in IAV detection patterns. Of the 372,659 samples submitted, 31% tested positive for IAV RNA via RT-rtPCR. The most frequent sample types were oral fluids (44.1%) and lung tissue (38.7%). Submissions from the wean-to-market category had a higher positivity rate (34.4%) than those from the adult/sow farm category (26.9%). IAV detection followed a seasonal pattern, with peaks in spring and fall and lower positivity rates in summer. Of the total of 118,490 samples tested for IAV subtyping using RT-rtPCR, the most frequently detected subtypes were H1N1 (33.1%), H3N2 (25.5%), H1N2 (24.3%), H3N1 (0.2%), mixed subtypes (5.4%), and partial subtype detection (11.5%). Mixed IAV subtypes were detected in individual samples-including lung tissue, nasal swabs, and bronchoalveolar lavage-indicating co-infection with two or more IAV strains. For IAV forecasting, a combined model using dynamic regression and a neural network outperformed individual models in 2023, achieving the lowest root mean square error (RMSE) and an improved overall skill score. This study highlights the importance of using laboratory submission data for IAV surveillance and macroepidemiological analysis. The findings provide valuable insights into IAV dynamics and highlight the need for standardized monitoring systems in VDLs to enhance understanding of IAV in swine populations across the United States.

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Publication Details

Journal
Frontiers in Veterinary Science
Published
2025-04-24
DOI
https://doi.org/10.3389/fvets.2025.1572237
Citations
6
Primary Topic
Influenza Virus Research Studies
Type
article
Field-Weighted Citation Impact
8.13
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article

Macroepidemiological trends of Influenza A virus detection through reverse transcription real-time polymerase chain reaction (RT-rtPCR) in porcine samples in the United States over the last 20 years

Sara McReynolds, Megan C. Niederwerder, Klára Werling, Rebecca Robbins et al.
6 citations
Frontiers in Veterinary Science
Influenza Virus Research Studies
8.13
article

Macroepidemiological trends of Influenza A virus detection through reverse transcription real-time polymerase chain reaction (RT-rtPCR) in porcine samples in the United States over the last 20 years

Sara McReynolds, Megan C. Niederwerder, Klára Werling, Rebecca Robbins, Mark Schwartz, Corrine Fruge, Rodger Main, Melanie Prarat, D. C. A. Moraes, Rafael Romero Nicolino, Peter M. Schneider, Rob McGaughey, Travis Clement, Guilherme Cezar, Lauren Glowzenski, James Lyons, Beth E. Thompson, Jon Greseth, Phillip Charles Gauger, Craig W. Bowen, Joseph Boyle, Edison Magalhaes, Bret Crim, Giovani Trevisan, Brooke N. Mason, Jane Christopher‐Hennings, W. AINSLIE HOLLIS, Darren Kersey, Daniel Boykin, Jamie Retallick, Kenitra Hendrix, Eric Ryan Burrough, Hemant Naikare, Angela Pillatzki, Michael Zeller, Andréia G. Arruda, Thomas Petznick, Cesar A. Corzo, Daniel Linhares, Marcelo Nunes de Almeida, Luc Dufresne, Paul Yeske, Samuel Copeland, Gustavo S. Silva, Kinath Rupasinghe, Kurt Kuecker, Srijita Chandra, Deborah Murray, Mary Thurn, Paulo Lages, Franco Matias Ferreyra, Jordan Gebhardt, Darin Madson, Joseph Thomas, Dennis Summers, Mattew Sturos
article en
6 citations

Abstract

Influenza A virus (IAV) in swine is a major respiratory pathogen with global significance. This study aimed to characterize the macroepidemiological patterns of IAV detection using reverse transcription real-time polymerase chain reaction (RT-rtPCR) assays, including subtype identification, in samples submitted between January 2004 and December 2024 to veterinary diagnostic laboratories (VDLs) participating in the Swine Disease Reporting System (SDRS). A secondary objective was establishing an IAV monitoring capability to inform stakeholders of weekly changes in IAV detection patterns. Of the 372,659 samples submitted, 31% tested positive for IAV RNA via RT-rtPCR. The most frequent sample types were oral fluids (44.1%) and lung tissue (38.7%). Submissions from the wean-to-market category had a higher positivity rate (34.4%) than those from the adult/sow farm category (26.9%). IAV detection followed a seasonal pattern, with peaks in spring and fall and lower positivity rates in summer. Of the total of 118,490 samples tested for IAV subtyping using RT-rtPCR, the most frequently detected subtypes were H1N1 (33.1%), H3N2 (25.5%), H1N2 (24.3%), H3N1 (0.2%), mixed subtypes (5.4%), and partial subtype detection (11.5%). Mixed IAV subtypes were detected in individual samples-including lung tissue, nasal swabs, and bronchoalveolar lavage-indicating co-infection with two or more IAV strains. For IAV forecasting, a combined model using dynamic regression and a neural network outperformed individual models in 2023, achieving the lowest root mean square error (RMSE) and an improved overall skill score. This study highlights the importance of using laboratory submission data for IAV surveillance and macroepidemiological analysis. The findings provide valuable insights into IAV dynamics and highlight the need for standardized monitoring systems in VDLs to enhance understanding of IAV in swine populations across the United States.

Frontiers in Veterinary ScienceVol. 12
Wesleyan University (US), University of Minnesota (US), Presbyterian College (US), Iowa State University (US), Carthage College (US), South Dakota State University (US), Kansas State University (US), Purdue University West Lafayette (US), Ohio Department of Agriculture (US), Tyson Foods (United States) (US), Pipestone (United States) (US), National Pork Board (US), Innovative Scientific Solutions (United States) (US), The Ohio State University (US)
Openalex Percentile: Top 2%
Influenza Virus Research Studies
8.13
DOIOpen Access PDFOpenAlex
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