{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T06:21:33Z","timestamp":1782973293016,"version":"3.54.5"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T00:00:00Z","timestamp":1773619200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"Research Foundation of Capital Institute of Pediatrics","award":["XZDX-2025-002"],"award-info":[{"award-number":["XZDX-2025-002"]}]},{"name":"National Science Foundation for Young Scientists of China","award":["82100096"],"award-info":[{"award-number":["82100096"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Rationale<\/jats:title>\n                    <jats:p>The host immune determinants that distinguish protective from life-threatening responses to influenza are poorly understood. Identifying drivers of immunopathology in the human lung is critical for developing potential therapies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To define the cellular and molecular immune landscape of the lung in mild vs severe influenza and to identify key cellular states and pathways associated with disease severity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We generated a large-scale single-cell atlas by sequencing more than 520\u200a000 cells from the bronchoalveolar lavage fluid of 88 nonimmunocompromised adult individuals with mild or severe influenza A and healthy controls. Key findings were validated by flow cytometry and protein quantification, and machine-learning models were used to identify predictive signatures.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Main Results<\/jats:title>\n                    <jats:p>Severe influenza was characterized by profound pulmonary lymphopenia and a massive influx of functionally dysregulated neutrophils. The infiltrating neutrophils were primed for extracellular trap formation, driving a cytokine storm via the S100A8\/A9\/A12\u2013TLR4 and CXCL8-CXCR1\/2 axes. This pathology coincided with the depletion and functional impairment of resident alveolar macrophages and an expansion of pro-inflammatory, monocyte-derived macrophages that amplified neutrophil recruitment. Lymphopenia in severe disease arose from synergistic cell-death programs, while remaining lymphocytes exhibited a dysfunctional state of concurrent exhaustion and hypercytotoxicity. Mild influenza featured a coordinated adaptive immune response, distinguished by an enrichment of T follicular helper cells and plasma cells. Machine-learning models identified robust cellular and transcriptional signatures predictive of disease severity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our atlas defines the divergent immune trajectories in influenza, revealing specific cellular states and pathways that drive immunopathology and provide novel targets for host-directed therapies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/ajrccm\/aamag122","type":"journal-article","created":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T13:06:48Z","timestamp":1773234408000},"page":"1548-1568","source":"Crossref","is-referenced-by-count":1,"title":["A large-scale single-cell atlas reveals the pulmonary immune panorama in adult patients with influenza"],"prefix":"10.1093","volume":"212","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8039-3283","authenticated-orcid":false,"given":"Kun","family":"Xiao","sequence":"first","affiliation":[{"name":"Chinese People's Liberation Army General Hospital Senior Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Cao","sequence":"additional","affiliation":[{"name":"Chinese People's Liberation Army General Hospital Senior Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhihai","family":"Han","sequence":"additional","affiliation":[{"name":"Chinese People's Liberation Army General Hospital Senior Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Da","sequence":"additional","affiliation":[{"name":"Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Feng","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rong","family":"Tian","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, Beijing Geriatric Hospital , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence Don Wai","family":"Luu","sequence":"additional","affiliation":[{"name":"School of Life Sciences, University of Technology Sydney , Sydney,","place":["Australia"]},{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine , Shanghai, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shanghai Pudong New Area Zhoupu Hospital, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital , Shanghai,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruijuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, Ninth Medical Center of PLA General Hospital , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Intensive Care Medicine, The Sixth Medical Center of PLA General Hospital , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mei","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Critical Care Medicine, Ninth Medical Center of Chinese People\u2019s Liberation, Army General Hospital , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fucheng","family":"An","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Mentougou District Hospital , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangxin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, Beijing Changping Hospital , Beijing, P. R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Emergency, First Medical Center, Chinese PLA General Hospital , Beijing,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shubin","family":"Qiao","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Fengtai Hospital of Integrated Traditional Chinese and Western Medicine , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingrong","family":"Nie","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Liangxiang Hospital, Fangshan District , Beijing,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine , Shanghai, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xia","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shijingshan Teaching Hospital of Capital Medical University, Beijing Shijingshan Hospital , Beijing,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ye","family":"Hu","sequence":"additional","affiliation":[{"name":"Chinese People's Liberation Army General Hospital Senior Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaifei","family":"Wang","sequence":"additional","affiliation":[{"name":"Chinese People's Liberation Army General Hospital Senior Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhimei","family":"Duan","sequence":"additional","affiliation":[{"name":"Chinese People's Liberation Army General Hospital Senior Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine , Shanghai, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Chinese People's Liberation Army General Hospital Senior Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjian","family":"Xu","sequence":"additional","affiliation":[{"name":"Experimental Research Center, Capital Center for Children\u2019s Health, Capital Medical University, Capital Institute of Pediatrics , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, China Aerospace Science and Industry Corporation 731 hospital , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Gao","sequence":"additional","affiliation":[{"name":"Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6991-0350","authenticated-orcid":false,"given":"Bin","family":"Cao","sequence":"additional","affiliation":[{"name":"China-Japan Friendship Hospital Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lixin","family":"Xie","sequence":"additional","affiliation":[{"name":"Chinese People's Liberation Army General Hospital Senior Department of Pulmonary and Critical Care Medicine, , Beijing, P.R.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2031-087X","authenticated-orcid":false,"given":"Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"Experimental Research Center, Capital Center for Children\u2019s Health, Capital Medical University, Capital Institute of Pediatrics , Beijing, P.R.","place":["China"]},{"name":"Molecular Diagnostic Center, Capital Center for Children\u2019s Health, Capital Medical University, Capital Institute of Pediatrics , Beijing,","place":["P.R. China"]},{"name":"Beijing Research Center for Respiratory Infectious Diseases , Beijing,","place":["P.R. China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,3,16]]},"reference":[{"key":"2026070113072537100_aamag122-B1","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1016\/S0140-6736(22)00982-5","article-title":"Influenza","volume":"400","author":"Uyeki","year":"2022","journal-title":"Lancet"},{"key":"2026070113072537100_aamag122-B2","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1164\/rccm.202401-0145OC","article-title":"Profiling bacteria in the lungs of patients with severe influenza versus COVID-19 with or without aspergillosis","volume":"210","author":"Feys","year":"2024","journal-title":"Am J Respir Crit Care Med"},{"key":"2026070113072537100_aamag122-B3","doi-asserted-by":"publisher","first-page":"1285","DOI":"10.1016\/S0140-6736(17)33293-2","article-title":"Estimates of global seasonal influenza-associated respiratory mortality: a modelling study","volume":"391","author":"Iuliano","year":"2018","journal-title":"Lancet"},{"key":"2026070113072537100_aamag122-B4","doi-asserted-by":"publisher","first-page":"eadq3003","DOI":"10.1126\/science.adq3003","article-title":"COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses","volume":"386","author":"Chen","year":"2024","journal-title":"Science"},{"key":"2026070113072537100_aamag122-B5","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1164\/rccm.202310-1771LE","article-title":"One-year survival and hospital-free days in critical illness after viral pneumonia","volume":"209","author":"Atramont","year":"2024","journal-title":"Am J Respir Crit Care Med"},{"key":"2026070113072537100_aamag122-B6","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1038\/s41579-021-00542-7","article-title":"Influenza virus and SARS-CoV-2: pathogenesis and host responses in the respiratory tract","volume":"19","author":"Flerlage","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"2026070113072537100_aamag122-B7","doi-asserted-by":"publisher","first-page":"A4606","DOI":"10.1164\/ajrccm.2025.211.Abstracts.A4606","article-title":"Obesity-induced dysregulation of airway ciliary function during influenza A virus infection","volume":"211","author":"Fujisawa","year":"2025","journal-title":"Am J Respir Crit Care Med"},{"key":"2026070113072537100_aamag122-B8","doi-asserted-by":"publisher","first-page":"A7411","DOI":"10.1164\/ajrccm.2025.211.Abstracts.A7411","article-title":"Development of ARDS in influenza A virus-infected mice is ATII cell mitochondria-dependent","volume":"211","author":"Davis","year":"2025","journal-title":"Am J Respir Crit Care Med"},{"key":"2026070113072537100_aamag122-B9","doi-asserted-by":"publisher","first-page":"100452","DOI":"10.1016\/j.jvacx.2024.100452","article-title":"Outlining recent updates on influenza therapeutics and vaccines: a comprehensive review","volume":"17","author":"Malik","year":"2024","journal-title":"Vaccine X"},{"key":"2026070113072537100_aamag122-B10","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1016\/j.immuni.2017.04.025","article-title":"Interferon-\u03bb mediates non-redundant front-line antiviral protection against influenza virus infection without compromising host fitness","volume":"46","author":"Galani","year":"2017","journal-title":"Immunity"},{"key":"2026070113072537100_aamag122-B11","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.33354","article-title":"IFN-\u03bb prevents influenza virus spread from the upper airways to the lungs and limits virus transmission","author":"Klinkhammer","year":"2018","journal-title":"Elife"},{"key":"2026070113072537100_aamag122-B12","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1038\/s41577-024-01029-1","article-title":"Defining the balance between optimal immunity and immunopathology in influenza virus infection","volume":"24","author":"Nguyen","year":"2024","journal-title":"Nat Rev Immunol"},{"key":"2026070113072537100_aamag122-B13","doi-asserted-by":"publisher","first-page":"e1012449","DOI":"10.1371\/journal.ppat.1012449","article-title":"Deficient neutrophil responses early in influenza infection promote viral replication and pulmonary inflammation","volume":"21","author":"Gong","year":"2025","journal-title":"PLoS Pathog"},{"key":"2026070113072537100_aamag122-B14","doi-asserted-by":"publisher","first-page":"110456","DOI":"10.1016\/j.celrep.2022.110456","article-title":"Interferon-\u03b3 promotes monocyte-mediated lung injury during influenza infection","volume":"38","author":"Schmit","year":"2022","journal-title":"Cell Rep"},{"key":"2026070113072537100_aamag122-B15","doi-asserted-by":"publisher","first-page":"A3497","DOI":"10.1164\/ajrccm.2025.211.Abstracts.A3497","article-title":"Influenza infection drives increased polarization towards M1-like microglial phenotypes with gene expression profiles associated with neurodegenerative diseases","volume":"211","author":"Wu","year":"2025","journal-title":"Am J Respir Crit Care Med"},{"key":"2026070113072537100_aamag122-B16","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/j.immuni.2020.07.009","article-title":"Single-cell sequencing of peripheral mononuclear cells reveals distinct immune response landscapes of COVID-19 and influenza patients","volume":"53","author":"Zhu","year":"2020","journal-title":"Immunity"},{"key":"2026070113072537100_aamag122-B17","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1038\/s41586-020-2877-5","article-title":"Exuberant fibroblast activity compromises lung function via ADAMTS4","volume":"587","author":"Boyd","year":"2020","journal-title":"Nature"},{"key":"2026070113072537100_aamag122-B18","doi-asserted-by":"publisher","first-page":"1895","DOI":"10.1016\/j.cell.2021.01.053","article-title":"COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas","volume":"184","author":"Ren","year":"2021","journal-title":"Cell"},{"key":"2026070113072537100_aamag122-B19","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/j.jinf.2023.03.020","article-title":"Systemic immune dysregulation in severe tuberculosis patients revealed by a single-cell transcriptome atlas","volume":"86","author":"Wang","year":"2023","journal-title":"J Infect"},{"key":"2026070113072537100_aamag122-B20","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1038\/s41392-024-02093-8","article-title":"A pan-immune panorama of bacterial pneumonia revealed by a large-scale single-cell transcriptome atlas","volume":"10","author":"Xiao","year":"2025","journal-title":"Signal Transduction and Targeted Therapy"},{"key":"2026070113072537100_aamag122-B21","doi-asserted-by":"publisher","first-page":"e226","DOI":"10.1002\/imt2.226","article-title":"Single-cell landscape revealed immune characteristics associated with disease phases in brucellosis patients","volume":"3","author":"Wang","year":"2024","journal-title":"iMeta"},{"key":"2026070113072537100_aamag122-B22","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1038\/nri2301","article-title":"TLR4 signalling","volume":"8","author":"Bell","year":"2008","journal-title":"Nat Rev Immunol"},{"key":"2026070113072537100_aamag122-B23","doi-asserted-by":"publisher","first-page":"1543","DOI":"10.7150\/thno.15625","article-title":"Role of the CXCL8-CXCR1\/2 axis in cancer and inflammatory diseases","volume":"7","author":"Ha","year":"2017","journal-title":"Theranostics"},{"key":"2026070113072537100_aamag122-B24","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1016\/j.immuni.2019.01.019","article-title":"Emerging principles in myelopoiesis at homeostasis and during infection and inflammation","volume":"50","author":"Schultze","year":"2019","journal-title":"Immunity"},{"key":"2026070113072537100_aamag122-B25","doi-asserted-by":"publisher","first-page":"L1102","DOI":"10.1152\/ajplung.00380.2014","article-title":"Increased expression of neutrophil-related genes in patients with early sepsis-induced ARDS","volume":"308","author":"Kangelaris","year":"2015","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"key":"2026070113072537100_aamag122-B26","doi-asserted-by":"publisher","first-page":"R163","DOI":"10.1186\/cc14003","article-title":"Neutrophils with myeloid derived suppressor function deplete arginine and constrain T cell function in septic shock patients","volume":"18","author":"Darcy","year":"2014","journal-title":"Crit Care"},{"key":"2026070113072537100_aamag122-B27","doi-asserted-by":"publisher","first-page":"e1003993","DOI":"10.1371\/journal.ppat.1003993","article-title":"Immune suppression by neutrophils in HIV-1 infection: role of PD-L1\/PD-1 pathway","volume":"10","author":"Bowers","year":"2014","journal-title":"PLoS Pathog"},{"key":"2026070113072537100_aamag122-B28","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1038\/s41591-020-0901-9","article-title":"Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19","volume":"26","author":"Liao","year":"2020","journal-title":"Nat Med"},{"key":"2026070113072537100_aamag122-B29","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00670-17","article-title":"Key role of the scavenger receptor MARCO in mediating adenovirus infection and subsequent innate responses of macrophages","volume":"8","author":"Maler Mareike","year":"2017","journal-title":"mBio"},{"key":"2026070113072537100_aamag122-B30","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1007\/s00018-024-05131-4","article-title":"The role of fatty acid metabolism in acute lung injury: a special focus on immunometabolism","volume":"81","author":"Lu","year":"2024","journal-title":"Cell Mol Life Sci"},{"key":"2026070113072537100_aamag122-B31","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1016\/j.immuni.2006.09.010","article-title":"Perforin and granzymes have distinct roles in defensive immunity and immunopathology","volume":"25","author":"van Dommelen","year":"2006","journal-title":"Immunity"},{"key":"2026070113072537100_aamag122-B32","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1038\/s41577-019-0221-9","article-title":"Defining \u201cT cell exhaustion","volume":"19","author":"Blank","year":"2019","journal-title":"Nat Rev Immunol"},{"key":"2026070113072537100_aamag122-B33","doi-asserted-by":"publisher","first-page":"e748","DOI":"10.1002\/mco2.748","article-title":"Single-cell transcriptome atlas revealed bronchoalveolar immune features related to disease severity in pediatric Mycoplasma pneumoniae pneumonia","volume":"5","author":"Shen","year":"2024","journal-title":"MedComm (2020)"},{"key":"2026070113072537100_aamag122-B34","doi-asserted-by":"publisher","first-page":"eabe4782","DOI":"10.1126\/sciimmunol.abe4782","article-title":"Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2\u2013reactive CD8+ T cells","volume":"6","author":"Kusnadi","year":"2021","journal-title":"Sci Immunol"},{"key":"2026070113072537100_aamag122-B35","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1016\/j.cell.2020.08.001","article-title":"Severe COVID-19 is marked by a dysregulated myeloid cell compartment","volume":"182","author":"Schulte-Schrepping","year":"2020","journal-title":"Cell"},{"key":"2026070113072537100_aamag122-B36","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1007\/s10753-022-01726-w","article-title":"The role of macrophages and alveolar epithelial cells in the development of ARDS","volume":"46","author":"Tao","year":"2023","journal-title":"Inflammation"},{"key":"2026070113072537100_aamag122-B37","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1038\/s41577-020-0402-6","article-title":"T cell responses in patients with COVID-19","volume":"20","author":"Chen","year":"2020","journal-title":"Nat Rev Immunol"},{"key":"2026070113072537100_aamag122-B38","doi-asserted-by":"publisher","first-page":"eabd1554","DOI":"10.1126\/sciimmunol.abd1554","article-title":"Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19","volume":"5","author":"Lee","year":"2020","journal-title":"Sci Immunol"},{"key":"2026070113072537100_aamag122-B39","doi-asserted-by":"publisher","first-page":"5304","DOI":"10.1002\/jmv.28012","article-title":"Single-cell transcriptomic atlas reveals distinct immunological responses between COVID-19 vaccine and natural SARS-CoV-2 infection","volume":"94","author":"Wang","year":"2022","journal-title":"J Med Virol"},{"key":"2026070113072537100_aamag122-B40","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1038\/s41392-023-01641-y","article-title":"Single-cell transcriptomic analysis reveals a systemic immune dysregulation in COVID-19-associated pediatric encephalopathy","volume":"8","author":"Wang","year":"2023","journal-title":"Signal Transduct Target Ther"},{"key":"2026070113072537100_aamag122-B41","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"2026070113072537100_aamag122-B42","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2026070113072537100_aamag122-B43","doi-asserted-by":"publisher","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci Rep"},{"key":"2026070113072537100_aamag122-B44","doi-asserted-by":"publisher","first-page":"2363","DOI":"10.1164\/rccm.202501-0217OC","article-title":"A large-scale single-cell atlas reveals the peripheral immune panorama of bacterial pneumonia","volume":"211","author":"Xiao","year":"2025","journal-title":"Am J Respir Crit Care Med"},{"key":"2026070113072537100_aamag122-B45","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1186\/s13059-019-1663-x","article-title":"PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells","volume":"20","author":"Wolf","year":"2019","journal-title":"Genome Biol"},{"key":"2026070113072537100_aamag122-B46","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1136\/gutjnl-2021-325915","article-title":"Single-cell RNA sequencing reveals intrahepatic and peripheral immune characteristics related to disease phases in HBV-infected patients","volume":"72","author":"Zhang","year":"2023","journal-title":"Gut"}],"container-title":["American Journal of Respiratory and Critical Care Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ajrccm\/advance-article-pdf\/doi\/10.1093\/ajrccm\/aamag122\/67373480\/aamag122.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ajrccm\/article-pdf\/212\/7\/1548\/67373480\/aamag122.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ajrccm\/article-pdf\/212\/7\/1548\/67373480\/aamag122.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T17:07:39Z","timestamp":1782925659000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ajrccm\/article\/212\/7\/1548\/8525336"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,16]]},"references-count":46,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,3,16]]},"published-print":{"date-parts":[[2026,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/ajrccm\/aamag122","relation":{},"ISSN":["1073-449X","1535-4970"],"issn-type":[{"value":"1073-449X","type":"print"},{"value":"1535-4970","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,7]]},"published":{"date-parts":[[2026,3,16]]}}}