{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T02:25:03Z","timestamp":1793931903109,"version":"4.8.0"},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"8","license":[{"start":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T00:00:00Z","timestamp":1593129600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T00:00:00Z","timestamp":1593129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["874710"],"award-info":[{"award-number":["874710"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B"],"award-info":[{"award-number":["031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["01ZX1304B"],"award-info":[{"award-number":["01ZX1304B"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["FKZ 01KI20160A"],"award-info":[{"award-number":["FKZ 01KI20160A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["FKZ 01KI20160A"],"award-info":[{"award-number":["FKZ 01KI20160A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["114933180"],"award-info":[{"award-number":["114933180"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Biotechnol"],"published-print":{"date-parts":[[2020,8]]},"DOI":"10.1038\/s41587-020-0602-4","type":"journal-article","created":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T06:19:43Z","timestamp":1593152383000},"page":"970-979","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1064,"title":["COVID-19 severity correlates with airway epithelium\u2013immune cell interactions identified by single-cell analysis"],"prefix":"10.1038","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5945-9957","authenticated-orcid":false,"given":"Robert Lorenz","family":"Chua","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7045-6327","authenticated-orcid":false,"given":"Soeren","family":"Lukassen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9894-1807","authenticated-orcid":false,"given":"Saskia","family":"Trump","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7733-8160","authenticated-orcid":false,"given":"Bianca P.","family":"Hennig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1968-5751","authenticated-orcid":false,"given":"Daniel","family":"Wendisch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3700-1691","authenticated-orcid":false,"given":"Fabian","family":"Pott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivia","family":"Debnath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1109-1924","authenticated-orcid":false,"given":"Loreen","family":"Th\u00fcrmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3807-473X","authenticated-orcid":false,"given":"Florian","family":"Kurth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Theresa","family":"V\u00f6lker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7962-2165","authenticated-orcid":false,"given":"Julia","family":"Kazmierski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernd","family":"Timmermann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sven","family":"Twardziok","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6108-5269","authenticated-orcid":false,"given":"Felix","family":"Machleidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Holger","family":"M\u00fcller-Redetzky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie","family":"Maier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Krannich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sein","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felix","family":"Balzer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9188-036X","authenticated-orcid":false,"given":"Johannes","family":"Liebig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3222-9777","authenticated-orcid":false,"given":"Jennifer","family":"Loske","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norbert","family":"Suttorp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00fcrgen","family":"Eils","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8426-901X","authenticated-orcid":false,"given":"Naveed","family":"Ishaque","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5129-0875","authenticated-orcid":false,"given":"Uwe Gerd","family":"Liebert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christof","family":"von Kalle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Hocke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Witzenrath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3959-004X","authenticated-orcid":false,"given":"Christine","family":"Goffinet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7923-0519","authenticated-orcid":false,"given":"Christian","family":"Drosten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2117-0944","authenticated-orcid":false,"given":"Sven","family":"Laudi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8875-5587","authenticated-orcid":false,"given":"Irina","family":"Lehmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7036-342X","authenticated-orcid":false,"given":"Christian","family":"Conrad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0476-9947","authenticated-orcid":false,"given":"Leif-Erik","family":"Sander","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0034-4036","authenticated-orcid":false,"given":"Roland","family":"Eils","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,6,26]]},"reference":[{"key":"602_CR1","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1001\/jama.2020.2648","volume":"323","author":"Z Wu","year":"2020","unstructured":"Wu, Z. & McGoogan, J. M. Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China: summary of a report of 72314 cases from the Chinese Center for Disease Control and Prevention. JAMA 323, 1239\u20131242 (2020).","journal-title":"JAMA"},{"key":"602_CR2","doi-asserted-by":"publisher","first-page":"1708","DOI":"10.1056\/NEJMoa2002032","volume":"382","author":"WJ Guan","year":"2020","unstructured":"Guan, W. J. et al. Clinical characteristics of coronavirus disease 2019 in China. N. Engl. J. Med. 382, 1708\u20131720 (2020).","journal-title":"N. Engl. J. Med."},{"key":"602_CR3","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1016\/S0140-6736(20)30183-5","volume":"395","author":"C Huang","year":"2020","unstructured":"Huang, C. et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 395, 497\u2013506 (2020).","journal-title":"Lancet"},{"key":"602_CR4","doi-asserted-by":"publisher","first-page":"1033","DOI":"10.1016\/S0140-6736(20)30628-0","volume":"395","author":"P Mehta","year":"2020","unstructured":"Mehta, P. et al. COVID-19: consider cytokine storm syndromes and immunosuppression. Lancet 395, 1033\u20131034 (2020).","journal-title":"Lancet"},{"key":"602_CR5","doi-asserted-by":"publisher","unstructured":"Bost, P. et al. Host-viral infection maps reveal signatures of severe COVID-19 patients. Cell https:\/\/doi.org\/10.1016\/j.cell.2020.05.006 (2020).","DOI":"10.1016\/j.cell.2020.05.006"},{"key":"602_CR6","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1038\/s41591-020-0901-9","volume":"26","author":"M Liao","year":"2020","unstructured":"Liao, M. et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat. Med. 26, 842\u2013844 (2020).","journal-title":"Nat. Med."},{"key":"602_CR7","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1038\/s41385-019-0158-0","volume":"12","author":"WJ Branchett","year":"2019","unstructured":"Branchett, W. J. & Lloyd, C. M. Regulatory cytokine function in the respiratory tract. Mucosal Immunol. 12, 589\u2013600 (2019).","journal-title":"Mucosal Immunol."},{"key":"602_CR8","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1128\/MMBR.05015-11","volume":"76","author":"JR Tisoncik","year":"2012","unstructured":"Tisoncik, J. R. et al. Into the eye of the cytokine storm. Microbiol. Mol. Biol. Rev. 76, 16\u201332 (2012).","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"602_CR9","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/s41421-020-0168-9","volume":"6","author":"W Wen","year":"2020","unstructured":"Wen, W. et al. Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing. Cell Discov. 6, 31 (2020).","journal-title":"Cell Discov."},{"key":"602_CR10","unstructured":"Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) https:\/\/www.who.int\/docs\/default-source\/coronaviruse\/who-china-joint-mission-on-covid-19-final-report.pdf (2020)."},{"key":"602_CR11","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/s41586-018-0393-7","volume":"560","author":"DT Montoro","year":"2018","unstructured":"Montoro, D. T. et al. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 560, 319\u2013324 (2018).","journal-title":"Nature"},{"key":"602_CR12","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/s41586-018-0394-6","volume":"560","author":"LW Plasschaert","year":"2018","unstructured":"Plasschaert, L. W. et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377\u2013381 (2018).","journal-title":"Nature"},{"key":"602_CR13","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1038\/s41591-019-0468-5","volume":"25","author":"FA Vieira Braga","year":"2019","unstructured":"Vieira Braga, F. A. et al. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153\u20131163 (2019).","journal-title":"Nat. Med."},{"key":"602_CR14","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1146\/annurev-immunol-032713-120231","volume":"32","author":"WM Schneider","year":"2014","unstructured":"Schneider, W. M., Chevillotte, M. D. & Rice, C. M. Interferon-stimulated genes: a complex web of host defenses. Annu. Rev. Immunol. 32, 513\u2013545 (2014).","journal-title":"Annu. Rev. Immunol."},{"key":"602_CR15","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1007\/s00281-016-0558-0","volume":"38","author":"AH Newton","year":"2016","unstructured":"Newton, A. H., Cardani, A. & Braciale, T. J. The host immune response in respiratory virus infection: balancing virus clearance and immunopathology. Semin. Immunopathol. 38, 471\u2013482 (2016).","journal-title":"Semin. Immunopathol."},{"key":"602_CR16","doi-asserted-by":"publisher","first-page":"7469","DOI":"10.1128\/JVI.02677-05","volume":"80","author":"A Ibricevic","year":"2006","unstructured":"Ibricevic, A. et al. Influenza virus receptor specificity and cell tropism in mouse and human airway epithelial cells. J. Virol. 80, 7469\u20137480 (2006).","journal-title":"J. Virol."},{"key":"602_CR17","doi-asserted-by":"publisher","first-page":"2741","DOI":"10.1128\/JVI.01712-07","volume":"82","author":"WY Lam","year":"2008","unstructured":"Lam, W. Y. et al. Avian influenza virus A\/HK\/483\/97(H5N1) NS1 protein induces apoptosis in human airway epithelial cells. J. Virol. 82, 2741\u20132751 (2008).","journal-title":"J. Virol."},{"key":"602_CR18","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1016\/j.cels.2018.05.008","volume":"6","author":"Y Steuerman","year":"2018","unstructured":"Steuerman, Y. et al. Dissection of influenza infection in vivo by single-cell RNA sequencing. Cell Syst. 6, 679\u2013691 (2018).","journal-title":"Cell Syst."},{"key":"602_CR19","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1016\/j.stem.2015.01.002","volume":"16","author":"A Pardo-Saganta","year":"2015","unstructured":"Pardo-Saganta, A. et al. Injury induces direct lineage segregation of functionally distinct airway basal stem\/progenitor cell subpopulations. Cell Stem Cell 16, 184\u2013197 (2015).","journal-title":"Cell Stem Cell"},{"key":"602_CR20","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nature14112","volume":"517","author":"AE Vaughan","year":"2015","unstructured":"Vaughan, A. E. et al. Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury. Nature 517, 621\u2013625 (2015).","journal-title":"Nature"},{"key":"602_CR21","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1038\/nature13903","volume":"517","author":"W Zuo","year":"2015","unstructured":"Zuo, W. et al. p63(+)Krt5(+) distal airway stem cells are essential for lung regeneration. Nature 517, 616\u2013620 (2015).","journal-title":"Nature"},{"key":"602_CR22","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1038\/nmeth.4402","volume":"14","author":"X Qiu","year":"2017","unstructured":"Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979\u2013982 (2017).","journal-title":"Nat. Methods"},{"key":"602_CR23","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1038\/ng.263","volume":"40","author":"X Yu","year":"2008","unstructured":"Yu, X., Ng, C. P., Habacher, H. & Roy, S. Foxj1 transcription factors are master regulators of the motile ciliogenic program. Nat. Genet. 40, 1445\u20131453 (2008).","journal-title":"Nat. Genet."},{"key":"602_CR24","doi-asserted-by":"publisher","first-page":"4271","DOI":"10.1242\/dev.051714","volume":"137","author":"C Cruz","year":"2010","unstructured":"Cruz, C. et al. Foxj1 regulates floor plate cilia architecture and modifies the response of cells to sonic hedgehog signalling. Development 137, 4271\u20134282 (2010).","journal-title":"Development"},{"key":"602_CR25","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1091\/mbc.e16-11-0813","volume":"28","author":"T Hirano","year":"2017","unstructured":"Hirano, T., Katoh, Y. & Nakayama, K. Intraflagellar transport-A complex mediates ciliary entry and retrograde trafficking of ciliary G protein-coupled receptors. Mol. Biol. Cell 28, 429\u2013439 (2017).","journal-title":"Mol. Biol. Cell"},{"key":"602_CR26","doi-asserted-by":"crossref","unstructured":"Ruiz Garcia, S. et al. Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures. Development 146, dev177428 (2019).","DOI":"10.1242\/dev.177428"},{"key":"602_CR27","doi-asserted-by":"publisher","first-page":"D1040","DOI":"10.1093\/nar\/gks1215","volume":"41","author":"I Rusinova","year":"2013","unstructured":"Rusinova, I. et al. Interferome v2.0: an updated database of annotated interferon-regulated genes. Nucleic Acids Res. 41, D1040\u2013D1046 (2013).","journal-title":"Nucleic Acids Res."},{"key":"602_CR28","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1016\/j.cell.2020.02.052","volume":"181","author":"M Hoffmann","year":"2020","unstructured":"Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271\u2013280 (2020).","journal-title":"Cell"},{"key":"602_CR29","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.cell.2020.02.058","volume":"181","author":"AC Walls","year":"2020","unstructured":"Walls, A. C. et al. Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181, 281\u2013292 (2020).","journal-title":"Cell"},{"key":"602_CR30","doi-asserted-by":"publisher","first-page":"1444","DOI":"10.1126\/science.abb2762","volume":"367","author":"R Yan","year":"2020","unstructured":"Yan, R. et al. Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2. Science 367, 1444\u20131448 (2020).","journal-title":"Science"},{"key":"602_CR31","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","volume":"579","author":"P Zhou","year":"2020","unstructured":"Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270\u2013273 (2020).","journal-title":"Nature"},{"key":"602_CR32","doi-asserted-by":"crossref","unstructured":"Coutard, B. et al. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Res. 176, 104742 (2020).","DOI":"10.1016\/j.antiviral.2020.104742"},{"key":"602_CR33","unstructured":"Ravindra, N. G. et al. Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/2020.05.06.081695v1 (2020)."},{"key":"602_CR34","doi-asserted-by":"crossref","unstructured":"Lee, I. T. et al. Robust ACE2 protein expression localizes to the motile cilia of the respiratory tract epithelia and is not increased by ACE inhibitors or angiotensin receptor blockers. Preprint at https:\/\/www.medrxiv.org\/content\/10.1101\/2020.05.08.20092866v1 (2020).","DOI":"10.1101\/2020.05.08.20092866"},{"key":"602_CR35","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1038\/s41586-020-2196-x","volume":"581","author":"R Wolfel","year":"2020","unstructured":"Wolfel, R. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465\u2013469 (2020).","journal-title":"Nature"},{"key":"602_CR36","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1080\/22221751.2020.1747363","volume":"9","author":"Y Xiong","year":"2020","unstructured":"Xiong, Y. et al. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Emerg. Microbes Infect. 9, 761\u2013770 (2020).","journal-title":"Emerg. Microbes Infect."},{"key":"602_CR37","doi-asserted-by":"publisher","first-page":"e105114","DOI":"10.15252\/embj.2020105114","volume":"39","author":"S Lukassen","year":"2020","unstructured":"Lukassen, S. et al. SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells. EMBO J. 39, e105114 (2020).","journal-title":"EMBO J."},{"key":"602_CR38","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1038\/s41591-020-0868-6","volume":"26","author":"W Sungnak","year":"2020","unstructured":"Sungnak, W. et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat. Med. 26, 681\u2013687 (2020).","journal-title":"Nat. Med."},{"key":"602_CR39","doi-asserted-by":"publisher","first-page":"1016","DOI":"10.1016\/j.cell.2020.04.035","volume":"181","author":"CGK Ziegler","year":"2020","unstructured":"Ziegler, C. G. K. et al. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues. Cell 181, 1016\u20131035 (2020).","journal-title":"Cell"},{"key":"602_CR40","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/sj.cr.7310015","volume":"16","author":"CD Krause","year":"2006","unstructured":"Krause, C. D., He, W., Kotenko, S. & Pestka, S. Modulation of the activation of Stat1 by the interferon-gamma receptor complex. Cell Res. 16, 113\u2013123 (2006).","journal-title":"Cell Res."},{"key":"602_CR41","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","volume":"15","author":"M Efremova","year":"2020","unstructured":"Efremova, M., Vento-Tormo, M., Teichmann, S. A. & Vento-Tormo, R. CellPhoneDB: inferring cell\u2013cell communication from combined expression of multi-subunit ligand\u2013receptor complexes. Nat. Protoc. 15, 1484\u20131506 (2020).","journal-title":"Nat. Protoc."},{"key":"602_CR42","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1016\/0092-8674(93)90118-A","volume":"72","author":"K Neote","year":"1993","unstructured":"Neote, K., DiGregorio, D., Mak, J. Y., Horuk, R. & Schall, T. J. Molecular cloning, functional expression, and signaling characteristics of a C-C chemokine receptor. Cell 72, 415\u2013425 (1993).","journal-title":"Cell"},{"key":"602_CR43","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1093\/cvr\/cvv147","volume":"107","author":"T Gerhardt","year":"2015","unstructured":"Gerhardt, T. & Ley, K. Monocyte trafficking across the vessel wall. Cardiovasc. Res. 107, 321\u2013330 (2015).","journal-title":"Cardiovasc. Res."},{"key":"602_CR44","doi-asserted-by":"crossref","first-page":"4099","DOI":"10.4049\/jimmunol.154.8.4099","volume":"154","author":"J Meerschaert","year":"1995","unstructured":"Meerschaert, J. & Furie, M. B. The adhesion molecules used by monocytes for migration across endothelium include CD11a\/CD18, CD11b\/CD18, and VLA-4 on monocytes and ICAM-1, VCAM-1, and other ligands on endothelium. J. Immunol. 154, 4099\u20134112 (1995).","journal-title":"J. Immunol."},{"key":"602_CR45","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1089\/aid.1995.11.541","volume":"11","author":"ED Rivadeneira","year":"1995","unstructured":"Rivadeneira, E. D., Sauls, D. L., Yu, Y., Haynes, B. F. & Weinberg, J. B. Inhibition of HIV type 1 infection of mononuclear phagocytes by anti-CD44 antibodies. AIDS Res. Hum. Retroviruses 11, 541\u2013546 (1995).","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"602_CR46","doi-asserted-by":"publisher","first-page":"4492","DOI":"10.1182\/blood-2007-02-076539","volume":"110","author":"E Vachon","year":"2007","unstructured":"Vachon, E. et al. CD44-mediated phagocytosis induces inside-out activation of complement receptor-3 in murine macrophages. Blood 110, 4492\u20134502 (2007).","journal-title":"Blood"},{"key":"602_CR47","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1182\/blood-2007-06-098327","volume":"112","author":"H Xu","year":"2008","unstructured":"Xu, H., Manivannan, A., Crane, I., Dawson, R. & Liversidge, J. Critical but divergent roles for CD62L and CD44 in directing blood monocyte trafficking in vivo during inflammation. Blood 112, 1166\u20131174 (2008).","journal-title":"Blood"},{"key":"602_CR48","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/s12929-016-0247-2","volume":"23","author":"X He","year":"2016","unstructured":"He, X. et al. CD44-mediated monocyte transmigration across Cryptococcus neoformans-infected brain microvascular endothelial cells is enhanced by HIV-1 gp41-I90 ectodomain. J. Biomed. Sci. 23, 28 (2016).","journal-title":"J. Biomed. Sci."},{"key":"602_CR49","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.2174\/1389450117666160727142401","volume":"18","author":"TR Rodrigues Prestes","year":"2017","unstructured":"Rodrigues Prestes, T. R., Rocha, N. P., Miranda, A. S., Teixeira, A. L. & Simoes, E. S. A. C. The anti-inflammatory potential of ACE2\/angiotensin-(1-7)\/Mas receptor axis: evidence from basic and clinical research. Curr. Drug Targets 18, 1301\u20131313 (2017).","journal-title":"Curr. Drug Targets"},{"key":"602_CR50","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.ejim.2020.04.037","volume":"76","author":"P Verdecchia","year":"2020","unstructured":"Verdecchia, P., Cavallini, C., Spanevello, A. & Angeli, F. The pivotal link between ACE2 deficiency and SARS-CoV-2 infection. Eur. J. Intern. Med. 76, 14\u201320 (2020).","journal-title":"Eur. J. Intern. Med."},{"key":"602_CR51","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1038\/nature03712","volume":"436","author":"Y Imai","year":"2005","unstructured":"Imai, Y. et al. Angiotensin-converting enzyme 2 protects from severe acute lung failure. Nature 436, 112\u2013116 (2005).","journal-title":"Nature"},{"key":"602_CR52","doi-asserted-by":"crossref","unstructured":"Coomes, E. A., & Haghbayan, H. Interleukin-6 in COVID-19: a systematic review and meta-analysis. Preprint at https:\/\/www.medrxiv.org\/content\/10.1101\/2020.03.30.20048058v1 (2020).","DOI":"10.1101\/2020.03.30.20048058"},{"key":"602_CR53","doi-asserted-by":"publisher","first-page":"76","DOI":"10.2174\/138945011701151217110917","volume":"17","author":"DA Covino","year":"2016","unstructured":"Covino, D. A., Sabbatucci, M. & Fantuzzi, L. The CCL2\/CCR2 axis in the pathogenesis of HIV-1 infection: a new cellular target for therapy? Curr. Drug Targets 17, 76\u2013110 (2016).","journal-title":"Curr. Drug Targets"},{"key":"602_CR54","doi-asserted-by":"crossref","unstructured":"Kurth, F. et al. Studying the pathophysiology of coronavirus disease 2019 - a protocol for the Berlin prospective COVID-19 patient cohort (Pa- COVID-19). Preprint at https:\/\/www.medrxiv.org\/content\/10.1101\/2020.05.06.20092833v1 (2020).","DOI":"10.1101\/2020.05.06.20092833"},{"key":"602_CR55","doi-asserted-by":"crossref","unstructured":"Corman, V. M. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT\u2013PCR. Euro. Surveill. 25, 2000045 (2020).","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045"},{"key":"602_CR56","doi-asserted-by":"crossref","unstructured":"Young, M. & Behjati, S. SoupX removes ambient RNA contamination from droplet based single-cell RNA sequencing data. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/303727v1 (2020).","DOI":"10.1093\/gigascience\/giaa151"},{"key":"602_CR57","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888\u20131902 (2019).","journal-title":"Cell"},{"key":"602_CR58","doi-asserted-by":"publisher","first-page":"2159","DOI":"10.1093\/bioinformatics\/bty916","volume":"35","author":"T Moerman","year":"2019","unstructured":"Moerman, T. et al. GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks. Bioinformatics 35, 2159\u20132161 (2019).","journal-title":"Bioinformatics"},{"key":"602_CR59","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1038\/nmeth.4463","volume":"14","author":"S Aibar","year":"2017","unstructured":"Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083\u20131086 (2017).","journal-title":"Nat. Methods"},{"key":"602_CR60","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","volume":"566","author":"J Cao","year":"2019","unstructured":"Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496\u2013502 (2019).","journal-title":"Nature"},{"key":"602_CR61","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1006\/jsbi.1998.3957","volume":"122","author":"PM Steinert","year":"1998","unstructured":"Steinert, P. M., Candi, E., Kartasova, T. & Marekov, L. Small proline-rich proteins are cross-bridging proteins in the cornified cell envelopes of stratified squamous epithelia. J. Struct. Biol. 122, 76\u201385 (1998).","journal-title":"J. Struct. Biol."},{"key":"602_CR62","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1002\/bies.10144","volume":"24","author":"AE Kalinin","year":"2002","unstructured":"Kalinin, A. E., Kajava, A. V. & Steinert, P. M. Epithelial barrier function: assembly and structural features of the cornified cell envelope. Bioessays 24, 789\u2013800 (2002).","journal-title":"Bioessays"},{"key":"602_CR63","doi-asserted-by":"publisher","first-page":"7303","DOI":"10.4049\/jimmunol.177.10.7303","volume":"177","author":"FO Martinez","year":"2006","unstructured":"Martinez, F. O., Gordon, S., Locati, M. & Mantovani, A. Transcriptional profiling of the human monocyte-to-macrophage differentiation and polarization: new molecules and patterns of gene expression. J. Immunol. 177, 7303\u20137311 (2006).","journal-title":"J. Immunol."},{"key":"602_CR64","doi-asserted-by":"publisher","first-page":"e0144351","DOI":"10.1371\/journal.pone.0144351","volume":"10","author":"ST Gren","year":"2015","unstructured":"Gren, S. T. et al. A single-cell gene-expression profile reveals inter-cellular heterogeneity within human monocyte subsets. PLoS ONE 10, e0144351 (2015).","journal-title":"PLoS ONE"},{"key":"602_CR65","doi-asserted-by":"crossref","unstructured":"Travaglini, K. J. et al. A molecular cell atlas of the human lung from single cell RNA sequencing. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/742320v1 (2019).","DOI":"10.1101\/742320"}],"container-title":["Nature Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41587-020-0602-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41587-020-0602-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41587-020-0602-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T19:49:11Z","timestamp":1696276151000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41587-020-0602-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,26]]},"references-count":65,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2020,8]]}},"alternative-id":["602"],"URL":"https:\/\/doi.org\/10.1038\/s41587-020-0602-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.04.29.20084327","asserted-by":"object"}]},"ISSN":["1087-0156","1546-1696"],"issn-type":[{"value":"1087-0156","type":"print"},{"value":"1546-1696","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,26]]},"assertion":[{"value":"3 June 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 June 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 June 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}]}}