Technical University of Denmark, National Veterinary Institute, Lyngby, Denmark; University of Copenhagen, Department of Health Sciences, Institute for Animal and Veterinary Sciences, Frederiksberg, Denmark
Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
Ramona Trebbien
Statens Serum Institut, Copenhagen, Denmark
Lars Erik Larsen
Technical University of Denmark, National Veterinary Institute, Lyngby, Denmark; University of Copenhagen, Department of Health Sciences, Institute for Animal and Veterinary Sciences, Frederiksberg, Denmark
Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV-positive submissions, reaching 56% in 2018. Full-genome sequences were obtained from 129 swIAV-positive samples. Altogether, 17 different circulating genotypes were identified including six novel reassortants harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx (clade 1A.3.3.2) viruses. The results provide essential data for the control of swIAV in pigs and emphasize the importance of contemporary surveillance for discovering novel swIAV strains posing a potential threat to the human population.
