Detection and subtyping of influenza A virus in porcine clinical samples from Spain in 2020

A total of 1019 samples collected on 726 Spanish swine farms suffering from outbreaks of respiratory disease were screened for influenza A viruses (IAVs) using a RT-qPCR method. A subset of positive samples was further analyzed using a subtype-specific RT-qPCR method (n: 142) and Sanger sequencing (n: 64). A total of 19.4% samples from 23% farms tested positive, with infection being most common in suckling (53.6%) and weaning pigs (30.2%). Viruses belonging to four HA subtypes (H1av, H1hu, H1pdm, H3) were detected, with subtypes H1avN2, H1huN2 and H1avN1 accounting for over half of the specimens. An optimized protocol with newly designed primers allowed the detection of H3 viruses in a significant number of samples (21%). A comparison of antigenic positions revealed that circulating strains exhibited mutations with vaccine strains in a significant percentage of amino acid residues, both in the NA protein (27.8–43.3%) and particularly in the HA protein (51–75.3%). •Detection of influenza A virus in 1019 porcine clinical samples from Spanish farms.•A total of 198 samples (19.4%) from 167 farms (23%) tested positive for IAVs.•Subtypes H1avN2, H1huN2 and H1avN1 accounted for over half of the specimens.•Newly designed primers significantly improved the detection of H3 viruses.•Substitutions of HA/NA amino acid residues between circulating and vaccine strains.