The antigenic diversity of influenza A viruses during infection of weaned pigs.

Influenza A viruses (IAVs) are endemic in North American swine and cause a respiratory disease. However, the mechanisms that allow IAVs to persist in pigs after weaning are not clearly understood. The objective of this study was to characterize the antigenic diversity of IAV during two contiguous epidemic waves of infection in pigs after weaning.

One hundred and thirty-two pigs were randomly selected at arrival to a wean-to-finish farm. Nasal swabs were collected from all pigs on a weekly basis for 15 weeks and tested for IAV by RT-PCR. Ninety-two positive samples were selected for deep genome sequencing using next-generation sequencing (NGS) technologies. Hemagglutinin (HA) and Neuraminidase (NA) sequences were compared at the nucleotide level to other IAVs circulating in the USA. Amino acid sequences were used to construct median-joining networks and polymorphic amino acid sites were estimated.

Two IAV epidemic waves were identified within 10 weeks after pigs were weaned and two different IAV subtypes (H1N1 and H3N2) were recovered. However, deep genome sequencing allowed us to differentiate three different viral groups (VG). While VG1 contained H1 gamma viruses, VG2 and VG3 contained H1 beta and H3 cluster IV viruses respectively. Although VG1, VG2, and VG3 viruses were identified at several sampling events, VG1 dominated the first epidemic wave of infection and VG3 dominated the second one. Furthermore, the number of polymorphic amino acid sites among the antigenic proteins of viruses from VG1 was higher than the number of polymorphic amino acid sites found in VG2, VG3.

Our results demonstrate that several IAV genotypes can co-circulate in pigs after weaning and that the proportion of genotypes over time can be dynamic.

Disclosure of Interest: None Declared.