乐胖代购免代理版

{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,12,4]],"date-time":"2024-12-04T18:10:00Z","timestamp":1733335800234,"version":"3.30.1"},"update-to":[{"updated":{"date-parts":[[2023,8,23]],"date-time":"2023-08-23T00:00:00Z","timestamp":1692748800000},"DOI":"10.1371\/journal.pcbi.1011356","type":"new_version","label":"New version"}],"reference-count":71,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2023,8,11]],"date-time":"2023-08-11T00:00:00Z","timestamp":1691712000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["01KI20239A"],"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":["01KI20239B"],"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":["01KI20239C"],"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":["031L0293A"],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012284","name":"Chica and Heinz Schaller Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012284","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"Human airway epithelium (HAE) represents the primary site of viral infection for SARS-CoV-2. Comprising different cell populations, a lot of research has been aimed at deciphering the major cell types and infection dynamics that determine disease progression and severity. However, the cell type-specific replication kinetics, as well as the contribution of cellular composition of the respiratory epithelium to infection and pathology are still not fully understood. Although experimental advances, including Air-liquid interface (ALI) cultures of reconstituted pseudostratified HAE, as well as lung organoid systems, allow the observation of infection dynamics under physiological conditions in unprecedented level of detail, disentangling and quantifying the contribution of individual processes and cells to these dynamics remains challenging. Here, we present how a combination of experimental data and mathematical modelling can be used to infer and address the influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics. Using a stepwise approach that integrates various experimental data on HAE culture systems with regard to tissue differentiation and infection dynamics, we develop an individual cell-based model that enables investigation of infection and regeneration dynamics within pseudostratified HAE. In addition, we present a novel method to quantify tissue integrity based on image data related to the standard measures of transepithelial electrical resistance measurements. Our analysis provides a first aim of quantitatively assessing cell type specific infection kinetics and shows how tissue composition and changes in regeneration capacity, as e.g. in smokers, can influence disease progression and pathology. Furthermore, we identified key measurements that still need to be assessed in order to improve inference of cell type specific infection kinetics and disease progression. Our approach provides a method that, in combination with additional experimental data, can be used to disentangle the complex dynamics of viral infection and immunity within human airway epithelial culture systems.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1011356","type":"journal-article","created":{"date-parts":[[2023,8,11]],"date-time":"2023-08-11T17:31:32Z","timestamp":1691775092000},"page":"e1011356","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics within human airway epithelium"],"prefix":"10.1371","volume":"19","author":[{"given":"Benjamin","family":"Raach","sequence":"first","affiliation":[]},{"given":"Nils","family":"Bundgaard","sequence":"additional","affiliation":[]},{"given":"Marika J.","family":"Haase","sequence":"additional","affiliation":[]},{"given":"J\u00f6rn","family":"Starru\u00df","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0855-7917","authenticated-orcid":true,"given":"Rocio","family":"Sotillo","sequence":"additional","affiliation":[]},{"given":"Megan L.","family":"Stanifer","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1198-6632","authenticated-orcid":true,"given":"Frederik","family":"Graw","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2023,8,11]]},"reference":[{"issue":"5","key":"pcbi.1011356.ref001","doi-asserted-by":"crossref","first-page":"109055","DOI":"10.1016\/j.celrep.2021.109055","article-title":"SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery.","volume":"35","author":"A Mulay","year":"2021","journal-title":"Cell Rep."},{"issue":"3","key":"pcbi.1011356.ref002","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: implications for SARS-CoV-2","volume":"19","author":"P V\u2019Kovski","year":"2021","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"pcbi.1011356.ref003","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1038\/s41385-020-00370-7","article-title":"Cellular and functional heterogeneity of the airway epithelium.","volume":"14","author":"JD Davis","year":"2021","journal-title":"Mucosal Immunol."},{"issue":"7","key":"pcbi.1011356.ref004","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1513\/pats.200805-041HR","article-title":"Airway epithelial cells: current concepts and challenges","volume":"5","author":"RG Crystal","year":"2008","journal-title":"Proc Am Thorac Soc"},{"issue":"3","key":"pcbi.1011356.ref005","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1242\/dev.098186","article-title":"Lung development: orchestrating the generation and regeneration of a complex organ","volume":"141","author":"M Herriges","year":"2014","journal-title":"Development"},{"issue":"7","key":"pcbi.1011356.ref006","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/nrm.2017.21","article-title":"The development and functions of multiciliated epithelia","volume":"18","author":"N Spassky","year":"2017","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pcbi.1011356.ref007","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1146\/annurev-physiol-021014-071931","article-title":"Cilia dysfunction in lung disease","volume":"77","author":"AE Tilley","year":"2015","journal-title":"Annu Rev Physiol"},{"issue":"5 Pt 1","key":"pcbi.1011356.ref008","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1164\/ajrccm.159.5.9806044","article-title":"Number and proliferation of clara cells in normal human airway epithelium","volume":"159","author":"JE Boers","year":"1999","journal-title":"Am J Respir Crit Care Med"},{"issue":"6 Pt 1","key":"pcbi.1011356.ref009","doi-asserted-by":"crossref","first-page":"2000","DOI":"10.1164\/ajrccm.157.6.9707011","article-title":"Number and proliferation of basal and parabasal cells in normal human airway epithelium","volume":"157","author":"JE Boers","year":"1998","journal-title":"Am J Respir Crit Care Med"},{"issue":"1","key":"pcbi.1011356.ref010","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S1357-2725(02)00083-3","article-title":"The airway goblet cell","volume":"35","author":"DF Rogers","year":"2003","journal-title":"Int J Biochem Cell Biol"},{"issue":"4","key":"pcbi.1011356.ref011","doi-asserted-by":"crossref","first-page":"100059","DOI":"10.1016\/j.xcrm.2020.100059","article-title":"Characterization and Treatment of SARS-CoV-2 in Nasal and Bronchial Human Airway Epithelia","volume":"1","author":"A Pizzorno","year":"2020","journal-title":"Cell Rep Med"},{"issue":"1","key":"pcbi.1011356.ref012","doi-asserted-by":"crossref","first-page":"4354","DOI":"10.1038\/s41467-021-24521-x","article-title":"SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance.","volume":"12","author":"R Robinot","year":"2021","journal-title":"Nat Commun."},{"issue":"1","key":"pcbi.1011356.ref013","doi-asserted-by":"crossref","first-page":"e1009292","DOI":"10.1371\/journal.ppat.1009292","article-title":"Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium.","volume":"17","author":"JK Fiege","year":"2021","journal-title":"PLoS Pathog."},{"issue":"2","key":"pcbi.1011356.ref014","article-title":"Air-Liquid-Interface Differentiated Human Nose Epithelium: A Robust Primary Tissue Culture Model of SARS-CoV-2 Infection.","volume":"23","author":"BM Tran","year":"2022","journal-title":"Int J Mol Sci."},{"issue":"6","key":"pcbi.1011356.ref015","article-title":"Long-Term Modeling of SARS-CoV-2 Infection of In Vitro Cultured Polarized Human Airway Epithelium.","volume":"11","author":"S Hao","year":"2020","journal-title":"mBio"},{"key":"pcbi.1011356.ref016","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1103\/PhysRevLett.69.2013","article-title":"Simulation of biological cell sorting using a two-dimensional extended Potts model","volume":"69","author":"J. Graner FG","year":"1992","journal-title":"Phys Rev Lett"},{"issue":"12","key":"pcbi.1011356.ref017","doi-asserted-by":"crossref","first-page":"e1009735","DOI":"10.1371\/journal.pcbi.1009735","article-title":"Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection","volume":"17","author":"ME Moses","year":"2021","journal-title":"PLoS Comput Biol"},{"issue":"12","key":"pcbi.1011356.ref018","doi-asserted-by":"crossref","first-page":"e1008451","DOI":"10.1371\/journal.pcbi.1008451","article-title":"A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness.","volume":"16","author":"TJ Sego","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"pcbi.1011356.ref019","doi-asserted-by":"crossref","DOI":"10.3390\/v14030605","article-title":"Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2.","volume":"14","author":"J Ferrari Gianlupi","year":"2022","journal-title":"Viruses"},{"issue":"1","key":"pcbi.1011356.ref020","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.celrep.2015.06.011","article-title":"Clonal Dynamics Reveal Two Distinct Populations of Basal Cells in Slow-Turnover Airway Epithelium","volume":"12","author":"JK Watson","year":"2015","journal-title":"Cell Rep"},{"key":"pcbi.1011356.ref021","doi-asserted-by":"crossref","first-page":"8163","DOI":"10.1038\/srep08163","article-title":"Cigarette smoke alters primary human bronchial epithelial cell differentiation at the air-liquid interface","volume":"5","author":"AC Schamberger","year":"2015","journal-title":"Sci Rep"},{"issue":"9","key":"pcbi.1011356.ref022","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1093\/bioinformatics\/btt772","article-title":"Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology","volume":"30","author":"J Starruss","year":"2014","journal-title":"Bioinformatics"},{"issue":"Suppl_1","key":"pcbi.1011356.ref023","doi-asserted-by":"crossref","first-page":"i551","DOI":"10.1093\/bioinformatics\/btaa397","article-title":"Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation","volume":"36","author":"Y Schalte","year":"2020","journal-title":"Bioinformatics"},{"key":"pcbi.1011356.ref024","article-title":"A review of mathematical models of influenza A infections within a host or cell culture: lessons learned and challenges ahead.","volume":"111","author":"CA Beauchemin","year":"2011","journal-title":"BMC Public Health"},{"issue":"13","key":"pcbi.1011356.ref025","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1002\/1873-3468.12095","article-title":"Multiscale modeling of virus replication and spread","volume":"590","author":"P Kumberger","year":"2016","journal-title":"FEBS Lett"},{"key":"pcbi.1011356.ref026","first-page":"118","article-title":"In vivo kinetics of SARS-CoV-2 infection and its relationship with a person\u2019s infectiousness","author":"R Ke","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"pcbi.1011356.ref027","doi-asserted-by":"crossref","first-page":"e3001143","DOI":"10.1371\/journal.pbio.3001143","article-title":"Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes","volume":"19","author":"NG Ravindra","year":"2021","journal-title":"PLoS Biol"},{"issue":"1","key":"pcbi.1011356.ref028","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2111400119","article-title":"SARS-CoV-2 spreads through cell-to-cell transmission","volume":"119","author":"C Zeng","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"47","key":"pcbi.1011356.ref029","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abc7112","article-title":"Potency and timing of antiviral therapy as determinants of duration of SARS-CoV-2 shedding and intensity of inflammatory response.","volume":"6","author":"A Goyal","year":"2020","journal-title":"Sci Adv."},{"issue":"1","key":"pcbi.1011356.ref030","doi-asserted-by":"crossref","first-page":"107863","DOI":"10.1016\/j.celrep.2020.107863","article-title":"Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells","volume":"32","author":"ML Stanifer","year":"2020","journal-title":"Cell Rep"},{"issue":"5","key":"pcbi.1011356.ref031","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41579-022-00713-0","article-title":"SARS-CoV-2 pathogenesis.","volume":"20","author":"MM Lamers","year":"2022","journal-title":"Nat Rev Microbiol"},{"issue":"2","key":"pcbi.1011356.ref032","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1177\/2211068214561025","article-title":"TEER measurement techniques for in vitro barrier model systems.","volume":"20","author":"B Srinivasan","year":"2015","journal-title":"J Lab Autom"},{"issue":"5","key":"pcbi.1011356.ref033","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1038\/s41591-020-0868-6","article-title":"SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes","volume":"26","author":"W Sungnak","year":"2020","journal-title":"Nat Med"},{"issue":"2","key":"pcbi.1011356.ref034","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"},{"issue":"10","key":"pcbi.1011356.ref035","doi-asserted-by":"crossref","first-page":"100421","DOI":"10.1016\/j.xcrm.2021.100421","article-title":"Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers","volume":"2","author":"T Nakayama","year":"2021","journal-title":"Cell Rep Med"},{"issue":"6","key":"pcbi.1011356.ref036","doi-asserted-by":"crossref","first-page":"e100537","DOI":"10.1371\/journal.pone.0100537","article-title":"Reconstituted human upper airway epithelium as 3-d in vitro model for nasal polyposis.","volume":"9","author":"F de Borja Callejas","year":"2014","journal-title":"PLoS One."},{"key":"pcbi.1011356.ref037","doi-asserted-by":"crossref","first-page":"S252","DOI":"10.1513\/AnnalsATS.201402-049AW","article-title":"Early events in the pathogenesis of chronic obstructive pulmonary disease. Smoking-induced reprogramming of airway epithelial basal progenitor cells.","volume":"115","author":"R Shaykhiev","year":"2014","journal-title":"Ann Am Thorac Soc"},{"issue":"14","key":"pcbi.1011356.ref038","doi-asserted-by":"crossref","DOI":"10.3390\/ijms22147646","article-title":"Cigarette Smoke Specifically Affects Small Airway Epithelial Cell Populations and Triggers the Expansion of Inflammatory and Squamous Differentiation Associated Basal Cells.","volume":"22","author":"CT Wohnhaas","year":"2021","journal-title":"Int J Mol Sci"},{"issue":"5","key":"pcbi.1011356.ref039","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1378\/chest.103.5.1429","article-title":"Squamous metaplasia of the bronchial mucosa and its relationship to smoking.","volume":"103","author":"EJ Peters","year":"1993","journal-title":"Chest"},{"issue":"8","key":"pcbi.1011356.ref040","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1513\/pats.200605-117SF","article-title":"Airway epithelial stem cells and the pathophysiology of chronic obstructive pulmonary disease","volume":"3","author":"SH Randell","year":"2006","journal-title":"Proc Am Thorac Soc"},{"issue":"9\u201310","key":"pcbi.1011356.ref041","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1242\/dmm.006031","article-title":"Airway basal stem cells: a perspective on their roles in epithelial homeostasis and remodeling","volume":"3","author":"JR Rock","year":"2010","journal-title":"Dis Model Mech"},{"issue":"12","key":"pcbi.1011356.ref042","doi-asserted-by":"crossref","DOI":"10.3390\/v12121425","article-title":"Leveraging 3D Model Systems to Understand Viral Interactions with the Respiratory Mucosa.","volume":"12","author":"E Iverson","year":"2020","journal-title":"Viruses"},{"issue":"4","key":"pcbi.1011356.ref043","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1038\/s41592-022-01453-y","article-title":"Human organoid models to study SARS-CoV-2 infection.","volume":"19","author":"Y Han","year":"2022","journal-title":"Nat Methods"},{"issue":"2","key":"pcbi.1011356.ref044","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"},{"issue":"1","key":"pcbi.1011356.ref045","doi-asserted-by":"crossref","first-page":"L231","DOI":"10.1152\/ajplung.90209.2008","article-title":"Ciliated epithelial cell lifespan in the mouse trachea and lung","volume":"295","author":"EL Rawlins","year":"2008","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"issue":"8","key":"pcbi.1011356.ref046","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1038\/nm.3642","article-title":"Lung regeneration: mechanisms, applications and emerging stem cell populations","volume":"20","author":"DN Kotton","year":"2014","journal-title":"Nat Med"},{"issue":"1","key":"pcbi.1011356.ref047","doi-asserted-by":"crossref","first-page":"3910","DOI":"10.1038\/s41467-020-17796-z","article-title":"Morphogenesis and cytopathic effect of SARS-CoV-2 infection in human airway epithelial cells.","volume":"11","author":"N Zhu","year":"2020","journal-title":"Nat Commun."},{"issue":"1","key":"pcbi.1011356.ref048","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."},{"issue":"4","key":"pcbi.1011356.ref049","doi-asserted-by":"crossref","first-page":"e0194422","DOI":"10.1128\/mbio.01944-22","article-title":"Human Nasal Organoids Model SARS-CoV-2 Upper Respiratory Infection and Recapitulate the Differential Infectivity of Emerging Variants.","volume":"13","author":"MC Chiu","year":"2022","journal-title":"mBio"},{"issue":"3","key":"pcbi.1011356.ref050","doi-asserted-by":"crossref","first-page":"e3001128","DOI":"10.1371\/journal.pbio.3001128","article-title":"A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2","volume":"19","author":"KS Kim","year":"2021","journal-title":"PLoS Biol"},{"issue":"6","key":"pcbi.1011356.ref051","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.chom.2020.11.003","article-title":"Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies","volume":"28","author":"M Cortese","year":"2020","journal-title":"Cell Host Microbe"},{"issue":"9","key":"pcbi.1011356.ref052","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1002\/psp4.12543","article-title":"Timing of Antiviral Treatment Initiation is Critical to Reduce SARS-CoV-2 Viral Load.","volume":"9","author":"A Goncalves","year":"2020","journal-title":"CPT Pharmacometrics Syst Pharmacol."},{"issue":"5","key":"pcbi.1011356.ref053","doi-asserted-by":"crossref","first-page":"2219","DOI":"10.1172\/JCI72948","article-title":"RSV-encoded NS2 promotes epithelial cell shedding and distal airway obstruction","volume":"124","author":"RM Liesman","year":"2014","journal-title":"J Clin Invest"},{"issue":"1","key":"pcbi.1011356.ref054","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1038\/s41467-019-08617-z","article-title":"Non-lytic clearance of influenza B virus from infected cells preserves epithelial barrier function.","volume":"10","author":"RE Dumm","year":"2019","journal-title":"Nat Commun."},{"issue":"1","key":"pcbi.1011356.ref055","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/s13567-018-0568-0","article-title":"Ciliostasis of airway epithelial cells facilitates influenza A virus infection","volume":"49","author":"Y Fu","year":"2018","journal-title":"Vet Res"},{"key":"pcbi.1011356.ref056","doi-asserted-by":"crossref","first-page":"39668","DOI":"10.1038\/srep39668","article-title":"The differentiated airway epithelium infected by influenza viruses maintains the barrier function despite a dramatic loss of ciliated cells.","volume":"6","author":"NH Wu","year":"2016","journal-title":"Sci Rep."},{"issue":"6","key":"pcbi.1011356.ref057","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1016\/j.jaci.2017.07.018","article-title":"Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures","volume":"141","author":"M Essaidi-Laziosi","year":"2018","journal-title":"J Allergy Clin Immunol"},{"issue":"1","key":"pcbi.1011356.ref058","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.cell.2022.11.030","article-title":"SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming","volume":"186","author":"CT Wu","year":"2023","journal-title":"Cell"},{"key":"pcbi.1011356.ref059","article-title":"COVID-19 infection in patients with chronic obstructive pulmonary disease: From pathophysiology to therapy.","author":"M Fekete","year":"2022","journal-title":"Mini-review. Physiol Int"},{"issue":"6","key":"pcbi.1011356.ref060","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1136\/bmjebm-2020-111492","article-title":"Is there a smoker\u2019s paradox in COVID-19?","volume":"26","author":"MS Usman","year":"2021","journal-title":"BMJ Evid Based Med"},{"issue":"6","key":"pcbi.1011356.ref061","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1016\/j.chom.2020.04.017","article-title":"Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients.","volume":"27","author":"Z Zhou","year":"2020","journal-title":"Cell Host Microbe"},{"issue":"12","key":"pcbi.1011356.ref062","doi-asserted-by":"crossref","first-page":"108185","DOI":"10.1016\/j.celrep.2020.108185","article-title":"SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant","volume":"32","author":"Y Konno","year":"2020","journal-title":"Cell Rep"},{"key":"pcbi.1011356.ref063","article-title":"Interactions between Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Major Respiratory Viruses in Human nasal Epithelium","author":"P Andres","year":"2022","journal-title":"J Infect Dis"},{"issue":"1","key":"pcbi.1011356.ref064","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1093\/infdis\/jiab147","article-title":"Human Rhinovirus Infection Blocks Severe Acute Respiratory Syndrome Coronavirus 2 Replication Within the Respiratory Epithelium: Implications for COVID-19 Epidemiology","volume":"224","author":"K Dee","year":"2021","journal-title":"J Infect Dis"},{"issue":"2","key":"pcbi.1011356.ref065","doi-asserted-by":"crossref","DOI":"10.3390\/v14020395","article-title":"Influenza A(H1N1)pdm09 Virus but Not Respiratory Syncytial Virus Interferes with SARS-CoV-2 Replication during Sequential Infections in Human Nasal Epithelial Cells.","volume":"14","author":"C Fage","year":"2022","journal-title":"Viruses"},{"issue":"8","key":"pcbi.1011356.ref066","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20210583","article-title":"Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics","volume":"218","author":"NR Cheemarla","year":"2021","journal-title":"J Exp Med"},{"issue":"9","key":"pcbi.1011356.ref067","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1016\/j.bpj.2022.04.003","article-title":"Modeling insights into SARS-CoV-2 respiratory tract infections prior to immune protection","volume":"121","author":"A Chen","year":"2022","journal-title":"Biophys J"},{"issue":"10","key":"pcbi.1011356.ref068","doi-asserted-by":"crossref","first-page":"e1008874","DOI":"10.1371\/journal.pcbi.1008874","article-title":"Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics","volume":"17","author":"JO Aponte-Serrano","year":"2021","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"pcbi.1011356.ref069","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1109\/TNNLS.2020.3042395","article-title":"BayesFlow: Learning Complex Stochastic Models With Invertible Neural Networks","volume":"33","author":"ST Radev","year":"2022","journal-title":"IEEE Trans Neural Netw Learn Syst"},{"issue":"7","key":"pcbi.1011356.ref070","doi-asserted-by":"crossref","DOI":"10.3390\/v13071308","article-title":"HCV Spread Kinetics Reveal Varying Contributions of Transmission Modes to Infection Dynamics.","volume":"13","author":"K Durso-Cain","year":"2021","journal-title":"Viruses"},{"issue":"1","key":"pcbi.1011356.ref071","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1186\/s12915-021-01115-z","article-title":"Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection.","volume":"19","author":"TJ Sego","year":"2021","journal-title":"BMC Biol."}],"updated-by":[{"updated":{"date-parts":[[2023,8,23]],"date-time":"2023-08-23T00:00:00Z","timestamp":1692748800000},"DOI":"10.1371\/journal.pcbi.1011356","type":"new_version","label":"New version"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011356","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,23]],"date-time":"2023-08-23T17:35:58Z","timestamp":1692812158000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011356"}},"subtitle":[],"editor":[{"given":"James R.","family":"Faeder","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,8,11]]},"references-count":71,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2023,8,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1011356","relation":{},"ISSN":["1553-7358"],"issn-type":[{"type":"electronic","value":"1553-7358"}],"subject":[],"published":{"date-parts":[[2023,8,11]]}}}