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Swine have many physiological, anatomical, and immunological similarities to humans, and are an excellent model for human influenza. Here, we employed single cell RNA-sequencing (scRNA-seq) and flow cytometry to characterize the major leukocyte subsets in bronchoalveolar lavage (BAL), twenty-one days after H1N1pdm09 infection or respiratory immunization with an adenoviral vector vaccine expressing hemagglutinin and nucleoprotein with or without IL-1\u03b2. Mapping scRNA-seq clusters from BAL onto those previously described in peripheral blood facilitated annotation and highlighted differences between tissue resident and circulating immune cells. ScRNA-seq data and functional assays revealed lasting impacts of immune challenge on BAL populations. First, mucosal administration of IL-1\u03b2 reduced the number of functionally active Treg cells. Second, influenza infection upregulated IFI6 in BAL cells and decreased their susceptibility to virus replication\n                    <jats:italic>in vitro<\/jats:italic>\n                    . Our data provide a reference map of porcine BAL cells and reveal lasting immunological consequences of influenza infection and respiratory immunization in a highly relevant large animal model for respiratory virus infection.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1011910","type":"journal-article","created":{"date-parts":[[2024,7,18]],"date-time":"2024-07-18T13:22:04Z","timestamp":1721308924000},"page":"e1011910","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Single-cell analysis reveals lasting immunological consequences of influenza infection and respiratory immunization in the pig lung"],"prefix":"10.1371","volume":"20","author":[{"given":"Andrew","family":"Muir","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Basudev","family":"Paudyal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Selma","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ehsan","family":"Sedaghat-Rostami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soumendu","family":"Chakravarti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia","family":"Villanueva-Hern\u00e1ndez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katy","family":"Moffat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noemi","family":"Polo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicos","family":"Angelopoulos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Tenbusch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graham","family":"Freimanis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2431-5889","authenticated-orcid":true,"given":"Wilhelm","family":"Gerner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arianne C.","family":"Richard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elma","family":"Tchilian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,7,18]]},"reference":[{"key":"ppat.1011910.ref001","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1128\/jb.89.1.170-174.1965","article-title":"Induction of Partial Specific Heterotypic Immunity in Mice by a Single Infection with Influenza a Virus","volume":"89","author":"JL Schulman","year":"1965","journal-title":"J Bacteriol"},{"issue":"1","key":"ppat.1011910.ref002","doi-asserted-by":"crossref","first-page":"48","DOI":"10.3201\/eid1201.051237","article-title":"Cell-mediated protection in influenza infection","volume":"12","author":"PG Thomas","year":"2006","journal-title":"Emerg Infect Dis"},{"key":"ppat.1011910.ref003","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1146\/annurev-immunol-032712-095954","article-title":"Memory T cell subsets, migration patterns, and tissue residence","volume":"31","author":"SN Mueller","year":"2013","journal-title":"Annu Rev Immunol"},{"issue":"6","key":"ppat.1011910.ref004","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1016\/j.immuni.2014.12.007","article-title":"Tissue-resident memory T cells","volume":"41","author":"JM Schenkel","year":"2014","journal-title":"Immunity"},{"issue":"2","key":"ppat.1011910.ref005","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1189\/jlb.0313180","article-title":"Lung-resident memory CD8 T cells (TRM) are indispensable for optimal cross-protection against pulmonary virus infection","volume":"95","author":"T Wu","year":"2014","journal-title":"J Leukoc Biol"},{"issue":"18","key":"ppat.1011910.ref006","doi-asserted-by":"crossref","first-page":"9217","DOI":"10.1128\/JVI.01069-10","article-title":"Memory CD4 T cells direct protective responses to influenza virus in the lungs through helper-independent mechanisms","volume":"84","author":"JR Teijaro","year":"2010","journal-title":"J Virol"},{"issue":"6","key":"ppat.1011910.ref007","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/s41577-019-0143-6","article-title":"The human antibody response to influenza A virus infection and vaccination","volume":"19","author":"F. 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