Ongoing influenza A surveillance critical for U.S. swine herd health

Part of Swine Health Information Center's mission to protect and enhance the health of the U.S. swine herd includes identifying emerging disease threats through surveillance and monitoring. The recent detection and confirmation by USDA of highly pathogenic avian influenza H5N1 in domestic livestock raises concerns regarding the emerging threat and potential risks to swine herds.

In collaboration with AASV, SHIC recently hosted a webinar on HPAI in livestock which highlighted the ongoing surveillance of influenza A viruses in swine. IAV monitoring is important for early detection of newly emerging strains, to track changes in known viruses over time, and for informing response to an emerging threat. Current influenza monitoring in U.S. swine populations include the SHIC Domestic Disease Monitoring Reports and the USDA Influenza A Swine Surveillance Program.

Supported by funding from SHIC, the Swine Disease Reporting System monitors and provides monthly Domestic Disease Monitoring Reports on the detection of IAV from swine samples submitted to participating veterinary diagnostic laboratories. Samples submitted to the six participating VDLs represent >96% of swine samples being tested in the U.S. The report highlights the detection of IAV by PCR, including the number of IAV submissions tested over time, the percent of positive submissions by age, a comparison of expected versus actual percent of positive submissions for seasonal trends, and the IAV subtype detected by PCR. Further, the IAV subtype distribution and location is now available through the new IAV state-level monitoring dashboard. Additionally, confirmed disease diagnosis for influenza A from porcine tissue cases received at ISU VDL is also available in the report.

These combined reports provide tools to aid veterinarians and producers in timely identification of IAV in their herds and to determine if the influenza A positive cases are above expected in their region. Information from surveillance is necessary to guide prevention and control efforts including evaluation of the use of vaccines within the herd. The SDRS report is included in the monthly SHIC newsletters and can be found online here.

In conjunction with IAV monitoring by VDLs, USDA monitors IAV from multiple surveillance streams and provides additional information regarding these viruses. The USDA Influenza A Swine Surveillance Program was initiated after the 2009 H1N1influenza pandemic. A visual showing the diagnostic criteria for inclusion on the program is available here. Goals of the surveillance program include monitoring the genetic evolution of endemic IAV in swine to better understand endemic and emerging influenza virus ecology, making influenza isolates from swine available for research, and establishing a data management system to facilitate genetic analysis of these isolates and related information. Additional goals include selecting the proper isolates for the development of relevant diagnostic reagents, updated diagnostic assays, and vaccine seed stock products. Samples submitted for influenza detection through this program can originate from sick pig cases submitted to a VDL, samples from pigs at the pig/human interface, such as fairs and exhibitions, and from IAV strains collected from pigs with a link to confirmed isolation of IAV in a human case.

Influenza viruses that have been identified through specific IAV case criteria at the VDLs can be included in the USDA IAV Swine Surveillance Program. Producer data is anonymized with information such as age/production stage of animals sampled, sample type, subtype, and region of origin within the US. Samples that are PCR positive can be further evaluated by virus isolation, subtype sequencing, and whole genome sequencing. Information generated by the Surveillance Program is publicly reported here and a tool for the visualization of aggregate IAV data developed by the USDA ARS National Animal Disease Center is available here.

The American Association of Swine Veterinarians updated their position statement on influenza A viruses on April 25, 2024, and it includes this statement, “It is the position of the AASV that we…recommend pork producers, swine veterinarians and diagnostic laboratories actively participate in IAV surveillance programs that provide information regarding IAV evolution and epidemiology.”