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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.<\/jats:p>","DOI":"10.7554\/elife.60940","type":"journal-article","created":{"date-parts":[[2021,7,27]],"date-time":"2021-07-27T08:00:19Z","timestamp":1627372819000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.60940","source":"Crossref","is-referenced-by-count":35,"title":["Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses"],"prefix":"10.7554","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4819-6869","authenticated-orcid":true,"given":"Pia","family":"Ryt-Hansen","sequence":"first","affiliation":[{"name":"Technical University of Denmark, National Veterinary Institute, Lyngby, Denmark"},{"name":"University of Copenhagen, Department of Health Sciences, Institute for Animal and Veterinary Sciences, Frederiksberg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesper Schak","family":"Krog","sequence":"additional","affiliation":[{"name":"Statens Serum Institut, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Solvej \u00d8stergaard","family":"Breum","sequence":"additional","affiliation":[{"name":"Statens Serum Institut, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7557-8876","authenticated-orcid":true,"given":"Charlotte Kristiane","family":"Hjulsager","sequence":"additional","affiliation":[{"name":"Statens Serum Institut, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anders Gorm","family":"Pedersen","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramona","family":"Trebbien","sequence":"additional","affiliation":[{"name":"Statens Serum Institut, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars Erik","family":"Larsen","sequence":"additional","affiliation":[{"name":"Technical University of Denmark, National Veterinary Institute, Lyngby, Denmark"},{"name":"University of Copenhagen, Department of Health Sciences, Institute for Animal and Veterinary Sciences, Frederiksberg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4374","published-online":{"date-parts":[[2021,7,27]]},"reference":[{"key":"bib1","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1177\/135965350601100804","article-title":"Impact of neuraminidase mutations conferring influenza resistance to neuraminidase inhibitors in the N1 and N2 genetic backgrounds","volume":"11","author":"Abed","year":"2006","journal-title":"Antiviral Therapy"},{"key":"bib2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00275-16","article-title":"A Phylogeny-Based global nomenclature system and automated annotation tool for H1 hemagglutinin genes from swine influenza A viruses","volume":"1","author":"Anderson","year":"2016","journal-title":"mSphere"},{"key":"bib3","doi-asserted-by":"publisher","DOI":"10.1186\/1743-422X-6-180","article-title":"The first Swedish H1N2 swine influenza virus isolate represents an uncommon reassortant","volume":"6","author":"B\u00e1lint","year":"2009","journal-title":"Virology Journal"},{"key":"bib4","volume-title":"NetNGlyc 1.0 Server","author":"Bioinformatics, D","year":"2017","unstructured":"Bioinformatics, D. 2017a. 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