Leman: Influenza genetic diversity in piglets
Management practices affect the genetic diversity of influenza in weaning piglets
16 February 2026
2 minute read
By: Editor's note: Following is from a presentation by Joaquin Alvarez-Norambuena and colleagues at the University of Minnesota, USA, during the 2025 Leman Swine Conference.
Influenza A virus (IAV) is a major pathogen in swine herds causing significant economic losses to producers. Emergence of new influenza viruses is common in part due to the segmented nature of the virus genome, the co-circulation of distinct viral strains and the frequent introductions of novel strains particularly those of human origin which can result in new reassortant viruses.
Although IAV diversity has been well documented, there is limited information on how farm management practices influence the diversity of IAV. A study evaluated the association between herd-level management practices and the genetic diversity of IAV in weaning piglets.
A whole-genome sequence approach was used on IAV-positive nasal swabs collected from weaning piglets obtained from 14 Midwestern swine farms (Nirmala et al., 2021). Each gene segment of the influenza virus was classified based on its origin or lineage. A genotype was defined as the constellation of distinct lineages detected across the whole IAV genome. If a segment could not be sequenced, a genotype included the “not sequenced (N/S)” denomination for that segment.
To quantify diversity of IAV at the herd level the Shannon diversity index was used, taking into consideration the number of unique genotypes (richness) and the evenness of the genotypes. Information on production management practices was obtained for each herd using a structured survey and included information on IAV vaccination, farm ventilation, gilt origin, gilt housing, porcine reproductive and respiratory syndrome (PRRS) status, and herd size.
The Shannon diversity index varied across herds, with herds exhibiting both higher genotype richness (having more genotypes) and higher evenness (genotypes being more evenly distributed). The final regression model showed a strong association between genotype diversity and specific management practices.
Timing of vaccination was the most influential factor with herds using mass or pre-farrow vaccination having significantly lower genotype diversity compared to farms that did not vaccinate.
Gilt housing also affects genotype diversity with gilts using all-in/all-out procedures at the room or barn level also having reduced diversity compared to continuous flow.
Herds with mechanical ventilation and those sourcing gilts from within the same production system had lower diversity than herds with mixed ventilation or external gilt sources.
In contrast, recent porcine reproductive and respiratory syndrome (PRRS) virus introduction and larger herd size were associated with increased IAV diversity.
This study provides field-based evidence that herd-level management practices can influence the genetic diversity of IAV in pig populations. Practices such as vaccination, gilt management and co-infection with other diseases appear to shape the evolutionary landscape of IAV by modulating opportunities for co-infection and reassortment. Integrating IAV surveillance with specific management practices may be essential to design effective IAV control strategies in pigs.
