Fine-Scale Analysis of Influenza A Virus in Swine Reveals Persistent Clade Circulation and Limited Clade Diversity within Owners

Authors: Arruda, Bailey; NEVEAU, MEGAN - Iowa State University; Baker, Amy; Anderson, Tavis; DE-SOUSA-E-SILVA, GUSTAVP - Iowa State University; GAUGER, PHILLIP - Iowa State University

Submitted to: American Association of Swine Veterinarians Annual Meeting
Publication Type: Proceedings
Publication Acceptance Date: 1/15/2023
Publication Date: 3/4/2023
Citation: Arruda, B.L., Neveau, M., Baker, A.L., Anderson, T.K., De-Sousa-E-Silva, G., Gauger, P.C. 2023. Fine-Scale Analysis of Influenza A Virus in Swine Reveals Persistent Clade Circulation and Limited Clade Diversity within Owners. American Association of Swine Veterinarians Annual Meeting. American Association of Swine Veterinarians Annual Meeting, March 4-7, 2023, Aurora, Colorado.

Interpretive Summary: Influenza A virus (IAV) remains a dominant cause of morbidity in swine with continuous expansion of genetic diversity due to incursions of human IAV and evolution in swine. The aggregated national IAV swine surveillance system data documents significant numbers of co-circulating genetic clades; yet, less is known about the diversity present at finer spatial scales or within epidemiologically linked populations of swine within an owner. To identify the amount and duration of diversity shared among sites with the same owner, we conducted a fine-scale analysis of IAV at the owner level using large scale data mining of nearly 8,000 hemagglutinin (HA) sequences collected and submitted between January 2013 and June 2021 to a veterinary diagnostic laboratory. Twenty-five HA clades were detected in the data set, and fourteen of these clades were detected more than 20 times. Of the top contributing owners, clinical clade count ranged from 2/25 (8%) to 9/25 (36%). The average length of time a clade was detected was 3.6 years, most clades were detected for longer than 2 years, and some clades were detected for at least 8 years. A clade was commonly detected within an owner across multiple farm types, including growing, breeding, and isolation stock. Fine-scale analysis demonstrated that the detection of HA genetic clades at the owner level is much less than the national level suggesting control and prevention methods at the owner level may be more achievable. For the owners we evaluated, the duration of circulation of a specific clade detected within a single owner indicated that a vaccine update every 3 to 4 years may be sufficient to facilitate control and preventative measures unless a lateral introduction of a new clade is detected.

Technical Abstract: Influenza A virus (IAV) remains a dominant cause of morbidity in swine with continuous expansion of genetic and antigenic diversity due to incursions of human IAV and evolution in swine. The aggregated national IAV swine surveillance system data documents significant numbers of co-circulating genetic clades; yet, less is known about the diversity present at finer spatial scales or within epidemiologically linked populations of swine within an owner. To identify the amount and duration of diversity shared among sites with the same owner, we conducted a fine-scale analysis of IAV at the owner level using large scale data mining of nearly 8,000 hemagglutinin (HA) sequences collected and submitted between January 2013 and June 2021 to a veterinary diagnostic laboratory. Twenty-five HA clades were detected in the data set, and fourteen of these clades were detected more than 20 times. Of the top contributing owners, clinical clade count ranged from 2/25 (8%) to 9/25 (36%). The average length of time a clade was detected was 3.6 years, most clades were detected for longer than 2 years, and some clades were detected for at least 8 years. A clade was commonly detected within an owner across multiple farm types, including growing, breeding, and isolation stock. Fine-scale analysis demonstrated that the detection of HA genetic clades at the owner level is much less than the national level. For the owners we evaluated, the duration of circulation of a specific clade detected within a single owner indicated that a vaccine update every 3 to 4 years may be sufficient to facilitate control and preventative measures unless a lateral introduction of a new clade is detected.