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Studies that have simultaneously assessed the impact of vaccination on the emergence of IAV reassortment and genetic variation in pigs are limited. Here, we directly sequenced 28 bronchoalveolar lavage fluid (BALF) samples collected from vaccinated and unvaccinated pigs co-infected with H1N1 and H3N2 IAV strains, and characterized 202 individual viral plaques recovered from 13 BALF samples. We identified 54 reassortant viruses that were grouped in 17 single and 16 mixed genotypes. Notably, we found that prime-boost vaccinated pigs had less reassortant viruses than nonvaccinated pigs, likely due to a reduction in the number of days pigs were co-infected with both challenge viruses. However, direct sequencing from BALF samples revealed limited impact of vaccination on viral variant frequency, evolutionary rates, and nucleotide diversity in any IAV coding regions. Overall, our results highlight the value of IAV vaccination not only at limiting virus replication in pigs but also at protecting public health by restricting the generation of novel reassortants with zoonotic and\/or pandemic potential.<\/jats:p>","DOI":"10.7554\/elife.78618","type":"journal-article","created":{"date-parts":[[2022,8,11]],"date-time":"2022-08-11T05:15:12Z","timestamp":1660194912000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.78618","source":"Crossref","is-referenced-by-count":12,"title":["Vaccination decreases the risk of influenza A virus reassortment but not genetic variation in pigs"],"prefix":"10.7554","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6375-0181","authenticated-orcid":true,"given":"Chong","family":"Li","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/017zqws13","id-type":"ROR","asserted-by":"publisher"}],"name":"College of Veterinary Medicine, University of Minnesota","place":["Saint Paul, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie R","family":"Culhane","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/017zqws13","id-type":"ROR","asserted-by":"publisher"}],"name":"College of Veterinary Medicine, University of Minnesota","place":["Saint Paul, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Declan C","family":"Schroeder","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/017zqws13","id-type":"ROR","asserted-by":"publisher"}],"name":"College of Veterinary Medicine, University of Minnesota","place":["Saint Paul, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxim C-J","family":"Cheeran","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/017zqws13","id-type":"ROR","asserted-by":"publisher"}],"name":"College of Veterinary Medicine, University of Minnesota","place":["Saint Paul, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucina","family":"Galina Pantoja","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03k2dnh74","id-type":"ROR","asserted-by":"publisher"}],"name":"Zoetis","place":["Parsippany, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Micah L","family":"Jansen","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03k2dnh74","id-type":"ROR","asserted-by":"publisher"}],"name":"Zoetis","place":["Parsippany, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9626-6537","authenticated-orcid":true,"given":"Montserrat","family":"Torremorell","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/017zqws13","id-type":"ROR","asserted-by":"publisher"}],"name":"College of Veterinary Medicine, University of Minnesota","place":["Saint Paul, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4374","published-online":{"date-parts":[[2022,9,2]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1111\/irv.12193","article-title":"Population dynamics of cocirculating swine influenza A viruses in the united states from 2009 to 2012","volume":"7 Suppl 4","author":"Anderson","year":"2013","journal-title":"Influenza and Other Respiratory Viruses"},{"key":"bib2","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a038737","article-title":"Swine influenza A viruses and the tangled relationship with humans","volume":"11","author":"Anderson","year":"2021","journal-title":"Cold Spring Harbor Perspectives in Medicine"},{"key":"bib3","article-title":"Fast QC: A quality control tool for high throughput sequence data","author":"Andrew","year":"2010","unstructured":"Andrew S. 2010. 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