Management Practices Affect Influenza Virus Genetic Diversity in Weaning Piglets

Editor’s note: The following information is based on a presentation by Joaquin Alvarez-Norambuena and colleagues at the University of Minnesota, USA, during the 2025 Leman Swine Conference.

Influenza A virus (IAV) poses a significant economic threat to swine herds, causing substantial losses for producers. The virus’s ability to rapidly evolve, due in part to its segmented genome and the frequent introduction of novel strains – particularly those of human origin – contributes to the emergence of new reassortant viruses. While IAV diversity is well-documented, understanding how farm management practices influence this diversity remains limited.

Study Findings on Management and IAV Diversity

A recent study evaluated the association between herd-level management practices and the genetic diversity of IAV in weaning piglets. Researchers used a whole-genome sequencing approach on IAV-positive nasal swabs collected from 14 Midwestern swine farms (Nirmala et al., 2021). Each gene segment of the virus was classified based on its origin or lineage. A genotype was defined by the unique combination of lineages detected across the entire IAV genome, with “not sequenced (N/S)” used for any segments that could not be sequenced.

To quantify IAV diversity at the herd level, the Shannon diversity index was employed, considering both the number of unique genotypes (richness) and their evenness. Information on production management practices was gathered through a structured survey, including details 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 some exhibiting higher genotype richness and evenness than others. Regression analysis revealed a strong association between genotype diversity and specific management practices.

Key Management Factors Influencing Diversity

• Vaccination Timing: Herds utilizing mass or pre-farrow vaccination demonstrated significantly lower genotype diversity compared to unvaccinated farms.
• Gilt Housing: Farms employing all-in/all-out procedures at the room or barn level showed reduced diversity compared to those with continuous flow gilt housing.
• Ventilation & Gilt Sourcing: Herds with mechanical ventilation and those sourcing gilts from within the same production system had lower diversity than those with mixed ventilation or external gilt sources.
• PRRS & Herd Size: Recent porcine reproductive and respiratory syndrome (PRRS) virus introduction and larger herd size were associated with increased IAV diversity.

Implications for IAV Control

This study provides field-based evidence that herd-level management practices can significantly influence the genetic diversity of IAV in pig populations. Practices like 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 for designing effective IAV control strategies in pigs. Understanding these relationships can support producers optimize their biosecurity and vaccination protocols to minimize the impact of IAV on their herds.