The persistence of influenza A viruses in swine breeding herds

Influenza A viruses (IAVs) are a main cause of respiratory disease in pigs and endemic in North American swine, however the mechanisms that allow IAVs to persist in pig herds are not clearly understood. The objective of this longitudinal study was to characterize the genetic diversity of IAV in pig breeding herds using next generation sequencing technologies.

Five pig breeding herds were selected for this study. In each herd 90 nasal swabs were collected on a monthly basis during a year from new gilts (replacement animals on site for less than 30 days, n=30), gilts (replacement animals on site for more than 30 days, n=30), and piglets (n=30). All samples were tested for IAV by RT-PCR and positive samples were used for IAV isolation using MDCK cells. Positive IAV isolates were used for deep genome sequencing using next generation sequencing technologies (NGS). IAVs were classified based on the HA and NA combination and compared to IAV circulating in North America between 2003 and 2014.

All farms and pig subpopulations tested positive for IAV at least once and 123 IAVs were successfully sequenced. Viruses from the same monophyletic group were found for 183 days within the same herd. Seven different genetic clusters were identified during the study period and represented three different IAV subtypes (H1N1, H1N2 and H3N2). However, several reassortment events were found.

In conclusion our results demonstrate the complexity and plasticity of IAV genetic diversity in pig breeding herds and highlights the advantage of NGS technologies to understand virus diversity and evolution.

Disclosure of Interest: None Declared.