Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes
Neal G Ravindra, Mia Madel Alfajaro, Victor Gasque, Nicholas C Huston, Han Wan, Klara Szigeti-Buck, Yuki Yasumoto, Allison M Greaney, Victoria Habet, Ryan D Chow, Jennifer S Chen, Jin Wei, Renata B Filler, Bao Wang, Guilin Wang, Laura E Niklason, Ruth R Montgomery, Stephanie C Eisenbarth, Sidi Chen, Adam Williams, Akiko Iwasaki, Tamas L Horvath, Ellen F Foxman, Richard W Pierce, Anna Marie Pyle, David Van Dijk, Craig B Wilen
PLOS Biology, doi:10.1371/journal.pbio.3001143
There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 . Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy.
Supporting information S1
References
Augustyn, Borromeo, Wang, Fujimoto, Shao et al., ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers, Proc Natl Acad Sci U S A,
doi:10.1073/pnas.1410419111
Bestle, Heindl, Limburg, Lam Van T, Pilgram et al., TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells, Life Sci Alliance,
doi:10.26508/lsa.202000786
Blanco-Melo, Nilsson-Payant, Liu, Møller, Panis et al., SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems,
doi:10.1101/2020.03.24.004655
Blanco-Melo, Nilsson-Payant, Liu, Uhl, Hoagland et al., Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Cell,
doi:10.1016/j.cell.2020.04.026
Blondel, Guillaume, Lambiotte, Lefebvre, Fast unfolding of communities in large networks, Journal of Statistical Mechanics: Theory and Experiment,
doi:10.1088/1742-5468/2008/10/p10008
Burkhardt, Stanley, Tong, Perdigoto, Gigante et al., Quantifying the effect of experimental perturbations in single-cell RNA-sequencing data using graph signal processing,
doi:10.1101/532846
Chen, Wu, Guo, Cao, Huang et al., Clinical and immunological features of severe and moderate coronavirus disease 2019, J Clin Invest
Chen, Zhou, Dong, Qu, Gong et al., Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study, Lancet,
doi:10.1016/S0140-6736%2820%2930211-7
Coutard, Valle, De Lamballerie, Canard, Seidah 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,
doi:10.1016/j.antiviral.2020.104742
De Wit, Van Doremalen, Falzarano, Munster, SARS and MERS: recent insights into emerging coronaviruses, Nat Rev Microbiol,
doi:10.1038/nrmicro.2016.81
Diao, Wang, Tan, Chen, Liu et al., Reduction and Functional Exhaustion of T Cells in Patients With Coronavirus Disease 2019 (COVID-19), Front Immunol
Firth, Dargitz, Qualls, Menon, Wright et al., Generation of multiciliated cells in functional airway epithelia from human induced pluripotent stem cells, Proc Natl Acad Sci U S A,
doi:10.1073/pnas.1403470111
Garcı ´a, Deprez, Lebrigand, Cavard, Paquet et al., Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures, Development,
doi:10.1242/dev.177428
Glowacka, Bertram, Muller, Allen, Soilleux et al., Evidence that TMPRSS2 Activates the Severe Acute Respiratory Syndrome Coronavirus Spike Protein for Membrane Fusion and Reduces Viral Control by the Humoral Immune Response, J Virol,
doi:10.1128/JVI.02232-10
Go ¨ertz, Fros, Miesen, Vogels, Van Der Bent et al., Noncoding Subgenomic Flavivirus RNA Is Processed by the Mosquito RNA Interference Machinery and Determines West Nile Virus Transmission by Culex pipiens Mosquitoes, J Virol,
doi:10.1128/JVI.00930-16
Griggs, Bochkov, Basnet, Pasic, Brockman-Schneider et al., Rhinovirus C targets ciliated airway epithelial cells, Respir Res,
doi:10.1186/s12931-017-0567-0
Guo, Adams, Wan, Huston, Potapova et al., Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase, J Mol Biol,
doi:10.1016/j.jmb.2020.03.022
Herold, Jurinovic, Arnreich, Lipworth, Hellmuth et al., Elevated levels of IL-6 and CRP predict the need for mechanical ventilation in COVID-19, J Allergy Clin Immunol,
doi:10.1016/j.jaci.2020.05.008
Hikmet, Me ´ar L, Edvinsson, Micke, Uhle ´n, Lindskog, The protein expression profile of ACE2 in human tissues, Mol Syst Biol,
doi:10.15252/msb.20209610
Hoffmann, Kleine-Weber, Po ¨hlmann S, A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells, Mol Cell,
doi:10.1016/j.molcel.2020.04.022
Hoffmann, Kleine-Weber, Schroeder, Kru ¨ger, Herrler et al., SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor, Cell,
doi:10.1016/j.cell.2020.02.052
Hofmann, Pyrc, Van Der Hoek, Geier, Berkhout et al., Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry, Proc Natl Acad Sci,
doi:10.1073/pnas.0409465102
Hou, Okuda, Edwards, Martinez, Asakura et al., SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract, Cell,
doi:10.1016/j.cell.2020.05.042
Huang, Klingbeil, He, Wu, Arun et al., POU2F3 is a master regulator of a tuft celllike variant of small cell lung cancer, Genes Dev,
doi:10.1101/gad.314815.118
Hui, Cheung, Perera, Ng, Bui et al., Tropism, replication competence, and innate immune responses of the coronavirus SARS-CoV-2 in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures, Lancet Respir Med,
doi:10.1016/S2213-2600%2820%2930193-4
Iwata-Yoshikawa, Okamura, Shimizu, Hasegawa, Takeda et al., TMPRSS2 Contributes to Virus Spread and Immunopathology in the Airways of Murine Models after Coronavirus Infection, J Virol,
doi:10.1128/JVI.01815-18
Lauer, Grantz, Bi, Jones, Zheng et al., The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application, Ann Intern Med,
doi:10.7326/M20-0504
Lee, Nakayama, Wu, Goltsev, Jiang et al., ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs, Nat Commun,
doi:10.1038/s41467-020-19145-6
Li, Moore, Vasilieva, Sui, Wong et al., Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus, Nature,
doi:10.1038/nature02145
Liao, Liu, Yuan, Wen, Xu et al., Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19, Nat Med,
doi:10.1038/s41591-020-0901-9
Linton, Kobayashi, Yang, Hayashi, Akhmetzhanov et al., Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data, J Clin Med Res,
doi:10.3390/jcm9020538
Marrazzo, Maccari, Taddei, Bevan, Telford et al., 3D Reconstruction of the Human Airway Mucosa In Vitro as an Experimental Model to Study NTHi Infections, PLoS ONE,
doi:10.1371/journal.pone.0153985
Matsuyama, Nagata, Shirato, Kawase, Takeda et al., Efficient Activation of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein by the Transmembrane Protease TMPRSS2, J Virol,
doi:10.1128/JVI.01542-10
Mcinnes, Healy, Melville, UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
Mi, Muruganujan, Ebert, Huang, Thomas, PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools, Nucleic Acids Res,
doi:10.1093/nar/gky1038
Montoro, Haber, Biton, Vinarsky, Lin et al., A revised airway epithelial hierarchy includes CFTR-expressing ionocytes, Nature,
doi:10.1038/s41586-018-0393-7
Moon, Van Dijk, Wang, Gigante, Burkhardt et al., Visualizing structure and transitions in high-dimensional biological data, Nat Biotechnol,
doi:10.1038/s41587-019-0336-3
Mou, Vinarsky, Tata, Brazauskas, Choi et al., Dual SMAD Signaling Inhibition Enables Long-Term Expansion of Diverse Epithelial Basal Cells, Cell Stem Cell,
doi:10.1016/j.stem.2016.05.012
Nawijn, Timens, Can ACE2 expression explain SARS-CoV-2 infection of the respiratory epithelia in COVID-19?, Mol Syst Biol,
doi:10.15252/msb.20209841
Neuman, Adair, Yoshioka, Quispe, Orca et al., Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy, J Virol,
doi:10.1128/JVI.00645-06
Orlova, Zimmerman, Meehan, Meehan, Waters et al., Earth Mover's Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations, PLoS ONE,
doi:10.1371/journal.pone.0151859
Ou, Liu, Lei, Li, Mi et al., Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its cross-reactivity with SARS-CoV, Nat Commun,
doi:10.1038/s41467-020-15562-9
Pijlman, Funk, Kondratieva, Leung, Torres et al., A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity, Cell Host Microbe,
doi:10.1016/j.chom.2008.10.007
Plasschaert, Choo-Wing, Savova, Knehr, Roma, A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte, Nature,
doi:10.1038/s41586-018-0394-6
Qi, Qian, Zhang, Zhang, Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses, Biochem Biophys Res Commun,
doi:10.1016/j.bbrc.2020.03.044
Satija, Farrell, Gennert, Schier, Regev, Spatial reconstruction of single-cell gene expression data, Nat Biotechnol,
doi:10.1038/nbt.3192
Scudieri, Musante, Venturini, Guidone, Genovese et al., Ionocytes and CFTR Chloride Channel Expression in Normal and Cystic Fibrosis Nasal and Bronchial Epithelial Cells, Cells,
doi:10.3390/cells9092090
Simmons, Gosalia, Rennekamp, Reeves, Diamond et al., Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry, Proc Natl Acad Sci,
doi:10.1073/pnas.0505577102
Smirnova, Schamberger, Nayakanti, Hatz, Behr et al., Detection and quantification of epithelial progenitor cell populations in human healthy and IPF lungs, Respir Res,
doi:10.1186/s12931-016-0404-x
Smith, Sausville, Girish, Yuan, Vasudevan et al., Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract, Dev Cell,
doi:10.1016/j.devcel.2020.05.012
Su, Wong, Shi, Liu, Lai et al., Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses, Trends Microbiol,
doi:10.1016/j.tim.2016.03.003
Tang, Song, Shi, Cheng, Zhang et al., Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition, Sci Rep,
doi:10.1038/srep17155
Travaglini, Nabhan, Penland, Sinha, Gillich et al., A molecular cell atlas of the human lung from single cell RNA sequencing, Nature,
doi:10.1038/s41586-020-2922-4
Tvarogova, Madhugiri, Bylapudi, Ferguson, Karl et al., Identification and Characterization of a Human Coronavirus 229E Nonstructural Protein 8-Associated RNA 3'-Terminal Adenylyltransferase Activity, J Virol,
doi:10.1128/JVI.00291-19
V'kovski, Gultom, Steiner, Kelly, Russeil et al., Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium,
doi:10.1101/2020.04.27.062315
Walls, Park, Tortorici, Wall, Mcguire et al., Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein, Cell,
doi:10.1016/j.cell.2020.02.058
Wang, Lou, Salit, Leopold, Driscoll et al., Characterization of an immortalized human small airway basal stem/progenitor cell line with airway region-specific differentiation capacity, Respir Res,
doi:10.1186/s12931-019-1140-9
Wang, Nabavi, SigEMD: A powerful method for differential gene expression analysis in single-cell RNA sequencing data, Methods,
doi:10.1016/j.ymeth.2018.04.017
Wo ¨lfel, Corman, Guggemos, Seilmaier, Zange et al., Virological assessment of hospitalized patients with COVID-2019, Nature,
doi:10.1038/s41586-020-2196-x
Yonker, Mou, Chu, Pazos, Leung et al., Development of a Primary Human Co-Culture Model of Inflamed Airway Mucosa, Sci Rep,
doi:10.1038/s41598-017-08567-w
You, Huang, Richer, Schmidt, Zabner et al., Role of f-box factor foxj1 in differentiation of ciliated airway epithelial cells, Am J Physiol Lung Cell Mol Physiol,
doi:10.1152/ajplung.00170.2003
Zang, Castro, Mccune, Zeng, Rothlauf et al., TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes, Sci Immunol,
doi:10.1126/sciimmunol.abc3582
Zhou, Yang, Wang, Hu, Zhang et al., A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature,
doi:10.1038/s41586-020-2012-7
Ziegler, Allon, Nyquist, Mbano, Miao 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,
doi:10.1016/j.cell.2020.04.035
Ziegler, Allon, Nyquist, Mbano, Miao et al., SARS-CoV-2 Receptor ACE2 is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Enriched in Specific Cell Subsets Across Tissues, SSRN Elec J,
doi:10.2139/ssrn.3555145
Zou, Chen, Zou, Han, Hao et al., Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to 2019-nCoV infection, Front Med,
doi:10.1007/s11684-020-0754-0
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'DOI': '10.1016/S0140-6736(20)30185-9',
'article-title': 'A novel coronavirus outbreak of global health concern',
'author': 'C Wang',
'year': '2020',
'journal-title': 'The Lancet'},
{ 'key': 'pbio.3001143.ref002',
'doi-asserted-by': 'crossref',
'first-page': '181',
'DOI': '10.1038/s41579-018-0118-9',
'article-title': 'Origin and evolution of pathogenic coronaviruses',
'author': 'J Cui',
'year': '2019',
'journal-title': 'Nat Rev Microbiol'},
{ 'key': 'pbio.3001143.ref003',
'doi-asserted-by': 'crossref',
'first-page': '17155',
'DOI': '10.1038/srep17155',
'article-title': 'Inferring the hosts of coronavirus using dual statistical models based '
'on nucleotide composition',
'volume': '5',
'author': 'Q Tang',
'year': '2015',
'journal-title': 'Sci Rep'},
{ 'key': 'pbio.3001143.ref004',
'unstructured': 'World Health Organization. Novel Coronavirus (2019-nCoV): situation '
'report, 22. 2020 [cited 4 Sep 2020]. Available from: '
'https://apps.who.int/iris/handle/10665/330991'},
{ 'key': 'pbio.3001143.ref005',
'doi-asserted-by': 'crossref',
'first-page': '523',
'DOI': '10.1038/nrmicro.2016.81',
'article-title': 'SARS and MERS: recent insights into emerging coronaviruses',
'volume': '14',
'author': 'E de Wit',
'year': '2016',
'journal-title': 'Nat Rev Microbiol'},
{ 'key': 'pbio.3001143.ref006',
'doi-asserted-by': 'crossref',
'first-page': '270',
'DOI': '10.1038/s41586-020-2012-7',
'article-title': 'A pneumonia outbreak associated with a new coronavirus of probable bat '
'origin',
'volume': '579',
'author': 'P Zhou',
'year': '2020',
'journal-title': 'Nature'},
{ 'key': 'pbio.3001143.ref007',
'doi-asserted-by': 'crossref',
'first-page': '507',
'DOI': '10.1016/S0140-6736(20)30211-7',
'article-title': 'Epidemiological and clinical characteristics of 99 cases of 2019 novel '
'coronavirus pneumonia in Wuhan, China: a descriptive study',
'volume': '395',
'author': 'N Chen',
'year': '2020',
'journal-title': 'Lancet'},
{ 'key': 'pbio.3001143.ref008',
'doi-asserted-by': 'crossref',
'first-page': '465',
'DOI': '10.1038/s41586-020-2196-x',
'article-title': 'Virological assessment of hospitalized patients with COVID-2019',
'volume': '581',
'author': 'R Wölfel',
'year': '2020',
'journal-title': 'Nature'},
{ 'key': 'pbio.3001143.ref009',
'doi-asserted-by': 'crossref',
'first-page': '420',
'DOI': '10.1016/S2213-2600(20)30076-X',
'article-title': 'Pathological findings of COVID-19 associated with acute respiratory '
'distress syndrome',
'volume': '8',
'author': 'Z Xu',
'year': '2020',
'journal-title': 'Lancet Respir Med'},
{ 'key': 'pbio.3001143.ref010',
'doi-asserted-by': 'crossref',
'first-page': '271',
'DOI': '10.1016/j.cell.2020.02.052',
'article-title': 'SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a '
'Clinically Proven Protease Inhibitor',
'volume': '181',
'author': 'M Hoffmann',
'year': '2020',
'journal-title': 'Cell'},
{ 'key': 'pbio.3001143.ref011',
'doi-asserted-by': 'crossref',
'first-page': '450',
'DOI': '10.1038/nature02145',
'article-title': 'Angiotensin-converting enzyme 2 is a functional receptor for the SARS '
'coronavirus',
'author': 'W Li',
'year': '2003',
'journal-title': 'Nature'},
{ 'key': 'pbio.3001143.ref012',
'doi-asserted-by': 'crossref',
'first-page': '7988',
'DOI': '10.1073/pnas.0409465102',
'article-title': 'Human coronavirus NL63 employs the severe acute respiratory syndrome '
'coronavirus receptor for cellular entry',
'author': 'H Hofmann',
'year': '2005',
'journal-title': 'Proc Natl Acad Sci U S A'},
{ 'key': 'pbio.3001143.ref013',
'doi-asserted-by': 'crossref',
'first-page': '4122',
'DOI': '10.1128/JVI.02232-10',
'article-title': 'Evidence that TMPRSS2 Activates the Severe Acute Respiratory Syndrome '
'Coronavirus Spike Protein for Membrane Fusion and Reduces Viral Control '
'by the Humoral Immune Response',
'author': 'I Glowacka',
'year': '2011',
'journal-title': 'J Virol'},
{ 'key': 'pbio.3001143.ref014',
'first-page': '93',
'article-title': 'TMPRSS2 Contributes to Virus Spread and Immunopathology in the Airways '
'of Murine Models after Coronavirus Infection',
'author': 'N Iwata-Yoshikawa',
'year': '2019',
'journal-title': 'J Virol'},
{ 'key': 'pbio.3001143.ref015',
'doi-asserted-by': 'crossref',
'first-page': '281',
'DOI': '10.1016/j.cell.2020.02.058',
'article-title': 'Structure, Function, and Antigenicity of the SARS-CoV-2 Spike '
'Glycoprotein',
'volume': '181',
'author': 'AC Walls',
'year': '2020',
'journal-title': 'Cell'},
{ 'key': 'pbio.3001143.ref016',
'doi-asserted-by': 'crossref',
'first-page': '12658',
'DOI': '10.1128/JVI.01542-10',
'article-title': 'Efficient Activation of the Severe Acute Respiratory Syndrome '
'Coronavirus Spike Protein by the Transmembrane Protease TMPRSS2',
'author': 'S Matsuyama',
'year': '2010',
'journal-title': 'J Virol'},
{ 'key': 'pbio.3001143.ref017',
'doi-asserted-by': 'crossref',
'first-page': '779',
'DOI': '10.1016/j.molcel.2020.04.022',
'article-title': 'A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is '
'Essential for Infection of Human Lung Cells',
'volume': '78',
'author': 'M Hoffmann',
'year': '2020',
'journal-title': 'Mol Cell'},
{ 'key': 'pbio.3001143.ref018',
'doi-asserted-by': 'crossref',
'first-page': '11727',
'DOI': '10.1073/pnas.2003138117',
'article-title': 'Cell entry mechanisms of SARS-CoV-2',
'volume': '117',
'author': 'J Shang',
'year': '2020',
'journal-title': 'Proc Natl Acad Sci U S A'},
{ 'key': 'pbio.3001143.ref019',
'first-page': '3',
'article-title': 'TMPRSS2 and furin are both essential for proteolytic activation of '
'SARS-CoV-2 in human airway cells',
'author': 'D Bestle',
'year': '2020',
'journal-title': 'Life Sci Alliance'},
{ 'key': 'pbio.3001143.ref020',
'doi-asserted-by': 'crossref',
'first-page': '11876',
'DOI': '10.1073/pnas.0505577102',
'article-title': 'Inhibitors of cathepsin L prevent severe acute respiratory syndrome '
'coronavirus entry',
'author': 'G Simmons',
'year': '2005',
'journal-title': 'Proc Natl Acad Sci U S A'},
{ 'key': 'pbio.3001143.ref021',
'doi-asserted-by': 'crossref',
'first-page': '104742',
'DOI': '10.1016/j.antiviral.2020.104742',
'article-title': 'The spike glycoprotein of the new coronavirus 2019-nCoV contains a '
'furin-like cleavage site absent in CoV of the same clade',
'author': 'B Coutard',
'year': '2020',
'journal-title': 'Antiviral Res'},
{ 'key': 'pbio.3001143.ref022',
'doi-asserted-by': 'crossref',
'first-page': '2620',
'DOI': '10.1172/JCI137244',
'article-title': 'Clinical and immunological features of severe and moderate coronavirus '
'disease 2019',
'volume': '130',
'author': 'G Chen',
'year': '2020',
'journal-title': 'J Clin Invest'},
{ 'key': 'pbio.3001143.ref023',
'doi-asserted-by': 'crossref',
'first-page': '827',
'DOI': '10.3389/fimmu.2020.00827',
'article-title': 'Reduction and Functional Exhaustion of T Cells in Patients With '
'Coronavirus Disease 2019 (COVID-19)',
'volume': '11',
'author': 'B Diao',
'journal-title': 'Front Immunol. 2020'},
{ 'key': 'pbio.3001143.ref024',
'doi-asserted-by': 'crossref',
'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': 'M Liao',
'year': '2020',
'journal-title': 'Nat Med'},
{ 'key': 'pbio.3001143.ref025',
'doi-asserted-by': 'crossref',
'first-page': '2202',
'DOI': '10.1172/JCI137647',
'article-title': 'SARS-CoV-2: a storm is raging',
'author': 'SF Pedersen',
'year': '2020',
'journal-title': 'J Clin Invest'},
{ 'key': 'pbio.3001143.ref026',
'unstructured': 'Morbidity and Mortality Weekly Report (MMWR). 2 Sep 2020 [cited 4 Sep '
'2020]. Available from: https://www.cdc.gov/mmwr/index.html'},
{ 'key': 'pbio.3001143.ref027',
'doi-asserted-by': 'crossref',
'first-page': '914',
'DOI': '10.1016/j.cell.2020.04.011',
'article-title': 'The Architecture of SARS-CoV-2 Transcriptome',
'volume': '181',
'author': 'D Kim',
'year': '2020',
'journal-title': 'Cell'},
{ 'key': 'pbio.3001143.ref028',
'doi-asserted-by': 'crossref',
'first-page': '7918',
'DOI': '10.1128/JVI.00645-06',
'article-title': 'Supramolecular architecture of severe acute respiratory syndrome '
'coronavirus revealed by electron cryomicroscopy',
'volume': '80',
'author': 'BW Neuman',
'year': '2006',
'journal-title': 'J Virol'},
{ 'key': 'pbio.3001143.ref029',
'doi-asserted-by': 'crossref',
'first-page': 'L650',
'DOI': '10.1152/ajplung.00170.2003',
'article-title': 'Role of f-box factor foxj1 in differentiation of ciliated airway '
'epithelial cells',
'volume': '286',
'author': 'Y You',
'year': '2004',
'journal-title': 'Am J Physiol Lung Cell Mol Physiol'},
{ 'key': 'pbio.3001143.ref030',
'doi-asserted-by': 'crossref',
'first-page': '84',
'DOI': '10.1186/s12931-017-0567-0',
'article-title': 'Rhinovirus C targets ciliated airway epithelial cells',
'volume': '18',
'author': 'TF Griggs',
'year': '2017',
'journal-title': 'Respir Res'},
{ 'key': 'pbio.3001143.ref031',
'doi-asserted-by': 'crossref',
'first-page': 'E1723',
'DOI': '10.1073/pnas.1403470111',
'article-title': 'Generation of multiciliated cells in functional airway epithelia from '
'human induced pluripotent stem cells',
'volume': '111',
'author': 'AL Firth',
'year': '2014',
'journal-title': 'Proc Natl Acad Sci U S A'},
{ 'key': 'pbio.3001143.ref032',
'article-title': 'SARS-CoV-2 Receptor ACE2 is an Interferon-Stimulated Gene in Human '
'Airway Epithelial Cells and Is Enriched in Specific Cell Subsets Across '
'Tissues',
'author': 'C Ziegler',
'journal-title': 'SSRN Elec J'},
{ 'key': 'pbio.3001143.ref033',
'doi-asserted-by': 'crossref',
'first-page': '1620',
'DOI': '10.1038/s41467-020-15562-9',
'article-title': 'Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and '
'its immune cross-reactivity with SARS-CoV',
'volume': '11',
'author': 'X Ou',
'year': '2020',
'journal-title': 'Nat Commun'},
{ 'key': 'pbio.3001143.ref034',
'first-page': '5',
'article-title': 'TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small '
'intestinal enterocytes',
'author': 'R Zang',
'year': '2020',
'journal-title': 'Sci Immunol'},
{ 'key': 'pbio.3001143.ref035',
'first-page': '363',
'article-title': 'The trinity of COVID-19: immunity, inflammation and intervention',
'author': 'MZ Tay',
'year': '2020',
'journal-title': 'Nat Rev Immunol'},
{ 'key': 'pbio.3001143.ref036',
'doi-asserted-by': 'crossref',
'first-page': '2233',
'DOI': '10.1056/NEJMra0910061',
'article-title': 'Airway mucus function and dysfunction',
'volume': '363',
'author': 'JV Fahy',
'year': '2010',
'journal-title': 'N Engl J Med'},
{ 'key': 'pbio.3001143.ref037',
'doi-asserted-by': 'crossref',
'first-page': '514',
'DOI': '10.1016/j.devcel.2020.05.012',
'article-title': 'Cigarette Smoke Exposure and Inflammatory Signaling Increase the '
'Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract',
'volume': '53',
'author': 'JC Smith',
'year': '2020',
'journal-title': 'Dev Cell'},
{ 'key': 'pbio.3001143.ref038',
'doi-asserted-by': 'crossref',
'first-page': '429',
'DOI': '10.1016/j.cell.2020.05.042',
'article-title': 'SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in '
'the Respiratory Tract',
'volume': '182',
'author': 'YJ Hou',
'year': '2020',
'journal-title': 'Cell'},
{ 'key': 'pbio.3001143.ref039',
'doi-asserted-by': 'crossref',
'first-page': '687',
'DOI': '10.1016/S2213-2600(20)30193-4',
'article-title': 'Tropism, replication competence, and innate immune responses of the '
'coronavirus SARS-CoV-2 in human respiratory tract and conjunctiva: an '
'analysis in ex-vivo and in-vitro cultures',
'volume': '8',
'author': 'KPY Hui',
'year': '2020',
'journal-title': 'Lancet Respir Med'},
{ 'key': 'pbio.3001143.ref040',
'doi-asserted-by': 'crossref',
'first-page': 'e9610',
'DOI': '10.15252/msb.20209610',
'article-title': 'The protein expression profile of ACE2 in human tissues',
'volume': '16',
'author': 'F Hikmet',
'year': '2020',
'journal-title': 'Mol Syst Biol'},
{ 'key': 'pbio.3001143.ref041',
'doi-asserted-by': 'crossref',
'first-page': '185',
'DOI': '10.1007/s11684-020-0754-0',
'article-title': 'Single-cell RNA-seq data analysis on the receptor ACE2 expression '
'reveals the potential risk of different human organs vulnerable to '
'2019-nCoV infection',
'volume': '14',
'author': 'X Zou',
'year': '2020',
'journal-title': 'Front Med'},
{ 'key': 'pbio.3001143.ref042',
'doi-asserted-by': 'crossref',
'first-page': '135',
'DOI': '10.1016/j.bbrc.2020.03.044',
'article-title': 'Single cell RNA sequencing of 13 human tissues identify cell types and '
'receptors of human coronaviruses',
'volume': '526',
'author': 'F Qi',
'year': '2020',
'journal-title': 'Biochem Biophys Res Commun'},
{ 'key': 'pbio.3001143.ref043',
'doi-asserted-by': 'crossref',
'first-page': '5453',
'DOI': '10.1038/s41467-020-19145-6',
'article-title': 'ACE2 localizes to the respiratory cilia and is not increased by ACE '
'inhibitors or ARBs',
'volume': '11',
'author': 'IT Lee',
'year': '2020',
'journal-title': 'Nat Commun'},
{ 'key': 'pbio.3001143.ref044',
'doi-asserted-by': 'crossref',
'first-page': '1016',
'DOI': '10.1016/j.cell.2020.04.035',
'article-title': 'SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human '
'Airway Epithelial Cells and Is Detected in Specific Cell Subsets across '
'Tissues',
'volume': '181',
'author': 'CGK Ziegler',
'year': '2020',
'journal-title': 'Cell'},
{ 'key': 'pbio.3001143.ref045',
'doi-asserted-by': 'crossref',
'first-page': 'e9841',
'DOI': '10.15252/msb.20209841',
'article-title': 'Can ACE2 expression explain SARS-CoV-2 infection of the respiratory '
'epithelia in COVID-19?',
'volume': '16',
'author': 'MC Nawijn',
'year': '2020',
'journal-title': 'Mol Syst Biol.'},
{ 'key': 'pbio.3001143.ref046',
'doi-asserted-by': 'crossref',
'first-page': '490',
'DOI': '10.1016/j.tim.2016.03.003',
'article-title': 'Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses',
'volume': '24',
'author': 'S Su',
'year': '2016',
'journal-title': 'Trends Microbiol'},
{ 'key': 'pbio.3001143.ref047',
'doi-asserted-by': 'crossref',
'first-page': '6117',
'DOI': '10.1128/JVI.66.10.6117-6124.1992',
'article-title': 'RNA recombination in a coronavirus: recombination between viral genomic '
'RNA and transfected RNA fragments',
'author': 'CL Liao',
'year': '1992',
'journal-title': 'J Virol'},
{ 'key': 'pbio.3001143.ref048',
'first-page': '93',
'article-title': 'Identification and Characterization of a Human Coronavirus 229E '
'Nonstructural Protein 8-Associated RNA 3’-',
'author': 'J Tvarogová',
'year': '2019',
'journal-title': 'Terminal Adenylyltransferase Activity. J Virol'},
{ 'key': 'pbio.3001143.ref049',
'doi-asserted-by': 'crossref',
'first-page': '579',
'DOI': '10.1016/j.chom.2008.10.007',
'article-title': 'A highly structured, nuclease-resistant, noncoding RNA produced by '
'flaviviruses is required for pathogenicity',
'volume': '4',
'author': 'GP Pijlman',
'year': '2008',
'journal-title': 'Cell Host Microbe'},
{ 'key': 'pbio.3001143.ref050',
'doi-asserted-by': 'crossref',
'first-page': '10145',
'DOI': '10.1128/JVI.00930-16',
'article-title': 'Noncoding Subgenomic Flavivirus RNA Is Processed by the Mosquito RNA '
'Interference Machinery and Determines West Nile Virus Transmission by '
'Culex pipiens Mosquitoes',
'author': 'GP Göertz',
'year': '2016',
'journal-title': 'J Virol'},
{ 'key': 'pbio.3001143.ref051',
'first-page': '9',
'article-title': 'Incubation Period and Other Epidemiological Characteristics of 2019 '
'Novel Coronavirus Infections with Right Truncation: A Statistical '
'Analysis of Publicly Available Case Data',
'author': 'NM Linton',
'year': '2020',
'journal-title': 'J Clin Med Res'},
{ 'key': 'pbio.3001143.ref052',
'doi-asserted-by': 'crossref',
'first-page': '577',
'DOI': '10.7326/M20-0504',
'article-title': 'The Incubation Period of Coronavirus Disease 2019 (COVID-19) From '
'Publicly Reported Confirmed Cases: Estimation and Application',
'author': 'SA Lauer',
'year': '2020',
'journal-title': 'Ann Intern Med'},
{ 'key': 'pbio.3001143.ref053',
'author': 'D Blanco-Melo',
'journal-title': 'SARS-CoV-2 launches a unique transcriptional signature from in vitro, '
'ex vivo, and in vivo systems'},
{ 'key': 'pbio.3001143.ref054',
'author': 'P V’kovski',
'journal-title': 'Disparate temperature-dependent virus–host dynamics for SARS-CoV-2 and '
'SARS-CoV in the human respiratory epithelium'},
{ 'key': 'pbio.3001143.ref055',
'doi-asserted-by': 'crossref',
'first-page': '128',
'DOI': '10.1016/j.jaci.2020.05.008',
'article-title': 'Elevated levels of IL-6 and CRP predict the need for mechanical '
'ventilation in COVID-19',
'volume': '146',
'author': 'T Herold',
'year': '2020',
'journal-title': 'J Allergy Clin Immunol'},
{ 'key': 'pbio.3001143.ref056',
'doi-asserted-by': 'crossref',
'first-page': '1036',
'DOI': '10.1016/j.cell.2020.04.026',
'article-title': 'Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19',
'volume': '181',
'author': 'D Blanco-Melo',
'year': '2020',
'journal-title': 'Cell'},
{ 'key': 'pbio.3001143.ref057',
'first-page': '223',
'article-title': 'IL-6 Inhibitors in the Treatment of Serious COVID-19: A Promising '
'Therapy?',
'volume': '34',
'author': 'S Atal',
'year': '2020',
'journal-title': 'Pharmaceut Med'},
{ 'key': 'pbio.3001143.ref058',
'doi-asserted-by': 'crossref',
'first-page': '3338',
'DOI': '10.1016/j.jmb.2020.03.022',
'article-title': 'Sequencing and Structure Probing of Long RNAs Using MarathonRT: A '
'Next-Generation Reverse Transcriptase',
'volume': '432',
'author': 'L-T Guo',
'year': '2020',
'journal-title': 'J Mol Biol'},
{ 'key': 'pbio.3001143.ref059',
'doi-asserted-by': 'crossref',
'first-page': '841',
'DOI': '10.1016/j.chom.2020.04.004',
'article-title': 'An Infectious cDNA Clone of SARS-CoV-2',
'volume': '27',
'author': 'X Xie',
'year': '2020',
'journal-title': 'Cell Host Microbe'},
{ 'key': 'pbio.3001143.ref060',
'doi-asserted-by': 'crossref',
'first-page': '495',
'DOI': '10.1038/nbt.3192',
'article-title': 'Spatial reconstruction of single-cell gene expression data',
'author': 'R Satija',
'year': '2015',
'journal-title': 'Nat Biotechnol'},
{ 'key': 'pbio.3001143.ref061',
'article-title': 'SCANPY: large-scale single-cell gene expression data analysis',
'author': 'FA Wolf',
'year': '2018',
'journal-title': 'Genome Biol'},
{ 'key': 'pbio.3001143.ref062',
'article-title': 'BBKNN: fast batch alignment of single cell transcriptomes',
'author': 'K Polański',
'year': '2019',
'journal-title': 'Bioinformatics'},
{ 'key': 'pbio.3001143.ref063',
'author': 'L McInnes',
'year': '2018',
'journal-title': 'UMAP: Uniform Manifold Approximation and Projection for Dimension '
'Reduction'},
{ 'key': 'pbio.3001143.ref064',
'doi-asserted-by': 'crossref',
'first-page': '1482',
'DOI': '10.1038/s41587-019-0336-3',
'article-title': 'Visualizing structure and transitions in high-dimensional biological '
'data',
'author': 'KR Moon',
'year': '2019',
'journal-title': 'Nat Biotechnol'},
{ 'key': 'pbio.3001143.ref065',
'doi-asserted-by': 'crossref',
'first-page': 'P10008',
'DOI': '10.1088/1742-5468/2008/10/P10008',
'article-title': 'Fast unfolding of communities in large networks',
'author': 'VD Blondel',
'year': '2008',
'journal-title': 'Journal of Statistical Mechanics: Theory and Experiment'},
{ 'key': 'pbio.3001143.ref066',
'article-title': 'A molecular cell atlas of the human lung from single cell RNA '
'sequencing',
'author': 'KJ Travaglini',
'journal-title': 'Nature.'},
{ 'key': 'pbio.3001143.ref067',
'doi-asserted-by': 'crossref',
'first-page': '319',
'DOI': '10.1038/s41586-018-0393-7',
'article-title': 'A revised airway epithelial hierarchy includes CFTR-expressing '
'ionocytes',
'author': 'DT Montoro',
'year': '2018',
'journal-title': 'Nature'},
{ 'key': 'pbio.3001143.ref068',
'doi-asserted-by': 'crossref',
'first-page': '196',
'DOI': '10.1186/s12931-019-1140-9',
'article-title': 'Characterization of an immortalized human small airway basal '
'stem/progenitor cell line with airway region-specific differentiation '
'capacity',
'volume': '20',
'author': 'G Wang',
'year': '2019',
'journal-title': 'Respir Res'},
{ 'key': 'pbio.3001143.ref069',
'doi-asserted-by': 'crossref',
'first-page': '217',
'DOI': '10.1016/j.stem.2016.05.012',
'article-title': 'Dual SMAD Signaling Inhibition Enables Long-Term Expansion of Diverse '
'Epithelial Basal Cells',
'volume': '19',
'author': 'H Mou',
'year': '2016',
'journal-title': 'Cell Stem Cell'},
{ 'key': 'pbio.3001143.ref070',
'first-page': '146',
'article-title': 'Novel dynamics of human mucociliary differentiation revealed by '
'single-cell RNA sequencing of nasal epithelial cultures',
'author': 'S Ruiz García',
'year': '2019',
'journal-title': 'Development'},
{ 'key': 'pbio.3001143.ref071',
'doi-asserted-by': 'crossref',
'first-page': '83',
'DOI': '10.1186/s12931-016-0404-x',
'article-title': 'Detection and quantification of epithelial progenitor cell populations '
'in human healthy and IPF lungs',
'volume': '17',
'author': 'NF Smirnova',
'year': '2016',
'journal-title': 'Respir Res'},
{ 'key': 'pbio.3001143.ref072',
'doi-asserted-by': 'crossref',
'first-page': '14788',
'DOI': '10.1073/pnas.1410419111',
'article-title': 'ASCL1 is a lineage oncogene providing therapeutic targets for '
'high-grade neuroendocrine lung cancers',
'volume': '111',
'author': 'A Augustyn',
'year': '2014',
'journal-title': 'Proc Natl Acad Sci U S A'},
{ 'key': 'pbio.3001143.ref073',
'doi-asserted-by': 'crossref',
'first-page': '377',
'DOI': '10.1038/s41586-018-0394-6',
'article-title': 'A single-cell atlas of the airway epithelium reveals the CFTR-rich '
'pulmonary ionocyte',
'volume': '560',
'author': 'LW Plasschaert',
'year': '2018',
'journal-title': 'Nature'},
{ 'key': 'pbio.3001143.ref074',
'first-page': '9',
'article-title': 'Ionocytes and CFTR Chloride Channel Expression in Normal and Cystic '
'Fibrosis Nasal and Bronchial Epithelial Cells',
'author': 'P Scudieri',
'year': '2020',
'journal-title': 'Cells'},
{ 'key': 'pbio.3001143.ref075',
'doi-asserted-by': 'crossref',
'first-page': '915',
'DOI': '10.1101/gad.314815.118',
'article-title': 'POU2F3 is a master regulator of a tuft cell-like variant of small cell '
'lung cancer',
'volume': '32',
'author': 'Y-H Huang',
'year': '2018',
'journal-title': 'Genes Dev'},
{ 'key': 'pbio.3001143.ref076',
'doi-asserted-by': 'crossref',
'first-page': '8182',
'DOI': '10.1038/s41598-017-08567-w',
'article-title': 'Development of a Primary Human Co-Culture Model of Inflamed Airway '
'Mucosa',
'volume': '7',
'author': 'LM Yonker',
'year': '2017',
'journal-title': 'Sci Rep'},
{ 'key': 'pbio.3001143.ref077',
'doi-asserted-by': 'crossref',
'first-page': 'e0153985',
'DOI': '10.1371/journal.pone.0153985',
'article-title': '3D Reconstruction of the Human Airway Mucosa In Vitro as an '
'Experimental Model to Study NTHi Infections',
'volume': '11',
'author': 'P Marrazzo',
'year': '2016',
'journal-title': 'PLoS ONE'},
{ 'key': 'pbio.3001143.ref078',
'doi-asserted-by': 'crossref',
'first-page': '215',
'DOI': '10.1007/978-1-4615-5331-1_26',
'article-title': 'A New Model for Coronavirus Transcription',
'author': 'SG Sawicki',
'year': '1998',
'journal-title': 'Adv Exp Med Biol'},
{ 'key': 'pbio.3001143.ref079',
'author': 'DB Burkhardt',
'journal-title': 'Quantifying the effect of experimental perturbations in single-cell '
'RNA-sequencing data using graph signal processing'},
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