1
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Hwang JH, You YS, Yeom SW, Lee MG, Lee JH, Kim MG, Kim JS. Influenza viral infection is a risk factor for severe illness in COVID-19 patients: a nationwide population-based cohort study. Emerg Microbes Infect 2023; 12:2164215. [PMID: 36580041 PMCID: PMC9858545 DOI: 10.1080/22221751.2022.2164215] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In order to prepare for the twindemic of influenza and SARS-CoV-2 infection, we investigated the association between influenza infection and subsequent severity of SARS-CoV-2 infection. A population-based nationwide cohort study was performed using data from the National Health Insurance Service (NHIS) in the Republic of Korea. This study included 274,126 individuals who underwent SARS-CoV-2 PCR testing between 20 January 2020 and 1 October 2020. Among these patients, 28,338 tested positive for SARS-CoV-2, and 4,003 of these individuals had a history of influenza. The control group was selected through 1:1 propensity score matching. In the group of 4,003 COVID-19-positive individuals with no history of influenza, 192 (4.8%) experienced severe illness from COVID-19 infection. In the group of 4,003 COVID-19-positive individuals with a history of influenza, 260 (6.5%) had severe illness from COVID-19, and the overall adjusted odds ratio (aOR) was 1.29 (95% confidence interval 1.04-1.59). Among the 4,003 COVID-19-positive individuals with a history of influenza, severe COVID-19 infection was experienced by 143 of 1,760 (8.1%) with an influenza history within 1 year before the onset of COVID-19, 48 of 1,129 (4.3%) between 1 and 2 years, and 69 of 1,114 (6.2%) between 2 and 3 years before COVID-19 onset, and the aORs were 1.54 (1.20-1.98), 1.19 (0.84-1.70), and 1.00 (0.73-1.37), respectively. In conclusion, individuals who had an influenza infection less than 1 year before COVID-19 infection were at an increased risk of experiencing severe illness from the SARS-CoV-2 infection. To control the public health burden, it is essential that effective public health control measures, which include influenza vaccination, hand washing, cough etiquette, and mask use are in place.
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Affiliation(s)
- Jeong-Hwan Hwang
- Department of Internal Medicine, Division of Infectious Diseases, Jeonbuk National University Medical School, Jeonju, South Korea,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
| | - Yeon Seok You
- Department of Medical Informatics, Jeonbuk National University, Jeonju, South Korea,Department of Otorhinolaryngology, Jeonbuk National University Medical School, Jeonju, South Korea
| | - Sang Woo Yeom
- Department of Medical Informatics, Jeonbuk National University, Jeonju, South Korea
| | - Min Gyu Lee
- Department of Medical Informatics, Jeonbuk National University, Jeonju, South Korea
| | - Jong-hwan Lee
- Department of Otorhinolaryngology, Jeonbuk National University Medical School, Jeonju, South Korea
| | - Min Gul Kim
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea,Department of Pharmacology, Jeonbuk National University Medical School, Jeonju, South Korea, Min Gul Kim Department of Pharmacology, Jeonbuk National University Medical School, Jeonju54907, South Korea
| | - Jong Seung Kim
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea,Department of Medical Informatics, Jeonbuk National University, Jeonju, South Korea,Department of Otorhinolaryngology, Jeonbuk National University Medical School, Jeonju, South Korea,Jong Seung Kim Department of Medical Informatics, Jeonbuk National University, Jeonju54907, South Korea; Department of Otorhinolaryngology, Jeonbuk National University Medical School, Jeonju54907, South Korea
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2
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Castro ÍA, Yang Y, Gnazzo V, Kim DH, Van Dyken SJ, López CB. Murine Parainfluenza Virus Persists in Lung Innate Immune Cells Sustaining Chronic Lung Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566103. [PMID: 37986974 PMCID: PMC10659393 DOI: 10.1101/2023.11.07.566103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Respiratory viruses including the human parainfluenza viruses (hPIVs) are a constant burden to human health, with morbidity and mortality frequently increased after the acute phase of the infection. Although is proven that respiratory viruses can persist in vitro, the mechanisms of virus or viral products persistence, their sources, and their impact on chronic respiratory diseases in vivo are unknown. Here, we used Sendai virus (SeV) to model hPIV infection in mice and test whether virus persistence associates with the development of chronic lung disease. Following SeV infection, virus products were detected in lung macrophages, type 2 innate lymphoid cells (ILC2s) and dendritic cells for several weeks after the infectious virus was cleared. Cells containing viral protein showed strong upregulation of antiviral and type 2 inflammation-related genes that associate with the development of chronic post-viral lung diseases, including asthma. Lineage tracing of infected cells or cells derived from infected cells suggests that distinct functional groups of cells contribute to the chronic pathology. Importantly, targeted ablation of infected cells or those derived from infected cells significantly ameliorated chronic lung disease. Overall, we identified persistent infection of innate immune cells as a critical factor in the progression from acute to chronic post viral respiratory disease.
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Affiliation(s)
- Ítalo Araujo Castro
- Department of Molecular Microbiology and Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Yanling Yang
- Department of Molecular Microbiology and Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Victoria Gnazzo
- Department of Molecular Microbiology and Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Do-Hyun Kim
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Steven J Van Dyken
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Carolina B López
- Department of Molecular Microbiology and Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
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3
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Hamele CE, Spurrier MA, Leonard RA, Heaton NS. Segmented, Negative-Sense RNA Viruses of Humans: Genetic Systems and Experimental Uses of Reporter Strains. Annu Rev Virol 2023; 10:261-282. [PMID: 37774125 DOI: 10.1146/annurev-virology-111821-120445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Negative-stranded RNA viruses are a large group of viruses that encode their genomes in RNA across multiple segments in an orientation antisense to messenger RNA. Their members infect broad ranges of hosts, and there are a number of notable human pathogens. Here, we examine the development of reverse genetic systems as applied to these virus families, emphasizing conserved approaches illustrated by some of the prominent members that cause significant human disease. We also describe the utility of their genetic systems in the development of reporter strains of the viruses and some biological insights made possible by their use. To conclude the review, we highlight some possible future uses of reporter viruses that not only will increase our basic understanding of how these viruses replicate and cause disease but also could inform the development of new approaches to therapeutically intervene.
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Affiliation(s)
- Cait E Hamele
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA;
| | - M Ariel Spurrier
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca A Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA;
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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4
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Raach B, Bundgaard N, Haase MJ, Starruß J, Sotillo R, Stanifer ML, Graw F. Influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics within human airway epithelium. PLoS Comput Biol 2023; 19:e1011356. [PMID: 37566610 PMCID: PMC10446191 DOI: 10.1371/journal.pcbi.1011356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/23/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023] Open
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.
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Affiliation(s)
- Benjamin Raach
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Nils Bundgaard
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Marika J. Haase
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Jörn Starruß
- Center for Information Services and High Performance Computing, TU Dresden, Dresden, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Megan L. Stanifer
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- University of Florida, College of Medicine, Dept. of Molecular Genetics and Microbiology, Gainesville, Florida, United States of America
| | - Frederik Graw
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Medicine 5, Erlangen, Germany
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5
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Wellford SA, Moseman AP, Dao K, Wright KE, Chen A, Plevin JE, Liao TC, Mehta N, Moseman EA. Mucosal plasma cells are required to protect the upper airway and brain from infection. Immunity 2022; 55:2118-2134.e6. [PMID: 36137543 PMCID: PMC9649878 DOI: 10.1016/j.immuni.2022.08.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/25/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022]
Abstract
While blood antibodies mediate protective immunity in most organs, whether they protect nasal surfaces in the upper airway is unclear. Using multiple viral infection models in mice, we found that blood-borne antibodies could not defend the olfactory epithelium. Despite high serum antibody titers, pathogens infected nasal turbinates, and neurotropic microbes invaded the brain. Using passive antibody transfers and parabiosis, we identified a restrictive blood-endothelial barrier that excluded circulating antibodies from the olfactory mucosa. Plasma cell depletions demonstrated that plasma cells must reside within olfactory tissue to achieve sterilizing immunity. Antibody blockade and genetically deficient models revealed that this local immunity required CD4+ T cells and CXCR3. Many vaccine adjuvants failed to generate olfactory plasma cells, but mucosal immunizations established humoral protection of the olfactory surface. Our identification of a blood-olfactory barrier and the requirement for tissue-derived antibody has implications for vaccinology, respiratory and CNS pathogen transmission, and B cell fate decisions.
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Affiliation(s)
| | - Annie Park Moseman
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Kianna Dao
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Katherine E Wright
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Allison Chen
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Jona E Plevin
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Tzu-Chieh Liao
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Naren Mehta
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - E Ashley Moseman
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA.
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6
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Hamele CE, Russell AB, Heaton NS. In Vivo Profiling of Individual Multiciliated Cells during Acute Influenza A Virus Infection. J Virol 2022; 96:e0050522. [PMID: 35867557 PMCID: PMC9327675 DOI: 10.1128/jvi.00505-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/03/2022] [Indexed: 01/09/2023] Open
Abstract
Influenza virus infections are thought to be initiated in a small number of cells; however, the heterogeneity across the cellular responses of the epithelial cells during establishment of disease is incompletely understood. Here, we used an H1N1 influenza virus encoding a fluorescent reporter gene, a cell lineage-labeling transgenic mouse line, and single-cell RNA sequencing to explore the range of responses in a susceptible epithelial cell population during an acute influenza A virus (IAV) infection. Focusing on multiciliated cells, we identified a subpopulation that basally expresses interferon-stimulated genes (ISGs), which we hypothesize may be important for the early response to infection. We subsequently found that a population of infected ciliated cells produce most of the ciliated cell-derived inflammatory cytokines, and nearly all bystander ciliated cells induce a broadly antiviral state. From these data together, we propose that variable preexisting gene expression patterns in the initial cells targeted by the virus may ultimately affect the establishment of viral disease. IMPORTANCE Influenza A virus poses a significant threat to public health, and each year, millions of people in the United States alone are exposed to the virus. We do not currently, however, fully understand why some individuals clear the infection asymptomatically and others become severely ill. Understanding how these divergent phenotypes arise could eventually be leveraged to design therapeutics that prevent severe disease. As a first step toward understanding these different infection states, we used a technology that allowed us to determine how thousands of individual murine lung epithelial cells behaved before and during IAV infection. We found that small subsets of epithelial cells exhibited an antiviral state prior to infection, and similarly, some cells made high levels of inflammatory cytokines during infection. We propose that different ratios of these individual cellular responses may contribute to the broader antiviral state of the lung and may ultimately affect disease severity.
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Affiliation(s)
- Cait E. Hamele
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alistair B. Russell
- Division of Biological Sciences, University of California, San Diego, San Diego, California, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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7
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A Virion-Based Combination Vaccine Protects against Influenza and SARS-CoV-2 Disease in Mice. J Virol 2022; 96:e0068922. [PMID: 35862698 PMCID: PMC9364787 DOI: 10.1128/jvi.00689-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vaccines targeting SARS-CoV-2 have been shown to be highly effective; however, the breadth against emerging variants and the longevity of protection remains unclear. Postimmunization boosting has been shown to be beneficial for disease protection, and as new variants continue to emerge, periodic (and perhaps annual) vaccination will likely be recommended. New seasonal influenza virus vaccines currently need to be developed every year due to continual antigenic drift, an undertaking made possible by a robust global vaccine production and distribution infrastructure. To create a seasonal combination vaccine targeting both influenza viruses and SARS-CoV-2 that is also amenable to frequent reformulation, we have developed an influenza A virus (IAV) genetic platform that allows the incorporation of an immunogenic domain of the SARS-CoV-2 spike (S) protein onto IAV particles. Vaccination with this combination vaccine elicited neutralizing antibodies and provided protection from lethal challenge with both pathogens in mice. This approach may allow the leveraging of established influenza vaccine infrastructure to generate a cost-effective and scalable seasonal vaccine solution for both influenza and coronaviruses. IMPORTANCE The rapid emergence of SARS-CoV-2 variants since the onset of the pandemic has highlighted the need for both periodic vaccination “boosts” and a platform that can be rapidly reformulated to manufacture new vaccines. In this work, we report an approach that can utilize current influenza vaccine manufacturing infrastructure to generate combination vaccines capable of protecting from both influenza virus- and SARS-CoV-2-induced disease. The production of a combined influenza/SARS-CoV-2 vaccine may represent a practical solution to boost immunity to these important respiratory viruses without the increased cost and administration burden of multiple independent vaccines.
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8
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SARS-CoV-2 Infection Dysregulates Cilia and Basal Cell Homeostasis in the Respiratory Epithelium of Hamsters. Int J Mol Sci 2022; 23:ijms23095124. [PMID: 35563514 PMCID: PMC9102945 DOI: 10.3390/ijms23095124] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023] Open
Abstract
Similar to many other respiratory viruses, SARS-CoV-2 targets the ciliated cells of the respiratory epithelium and compromises mucociliary clearance, thereby facilitating spread to the lungs and paving the way for secondary infections. A detailed understanding of mechanism involved in ciliary loss and subsequent regeneration is crucial to assess the possible long-term consequences of COVID-19. The aim of this study was to characterize the sequence of histological and ultrastructural changes observed in the ciliated epithelium during and after SARS-CoV-2 infection in the golden Syrian hamster model. We show that acute infection induces a severe, transient loss of cilia, which is, at least in part, caused by cilia internalization. Internalized cilia colocalize with membrane invaginations, facilitating virus entry into the cell. Infection also results in a progressive decline in cells expressing the regulator of ciliogenesis FOXJ1, which persists beyond virus clearance and the termination of inflammatory changes. Ciliary loss triggers the mobilization of p73+ and CK14+ basal cells, which ceases after regeneration of the cilia. Although ciliation is restored after two weeks despite the lack of FOXJ1, an increased frequency of cilia with ultrastructural alterations indicative of secondary ciliary dyskinesia is observed. In summary, the work provides new insights into SARS-CoV-2 pathogenesis and expands our understanding of virally induced damage to defense mechanisms in the conducting airways.
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9
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Reuther P, Martin K, Kreutzfeldt M, Ciancaglini M, Geier F, Calabrese D, Merkler D, Pinschewer DD. Persistent RNA virus infection is short-lived at the single-cell level but leaves transcriptomic footprints. J Exp Med 2021; 218:212556. [PMID: 34398180 PMCID: PMC8493862 DOI: 10.1084/jem.20210408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/14/2021] [Accepted: 07/28/2021] [Indexed: 12/14/2022] Open
Abstract
Several RNA viruses can establish life-long persistent infection in mammalian hosts, but the fate of individual virus-infected cells remains undefined. Here we used Cre recombinase-encoding lymphocytic choriomeningitis virus to establish persistent infection in fluorescent cell fate reporter mice. Virus-infected hepatocytes underwent spontaneous noncytolytic viral clearance independently of type I or type II interferon signaling or adaptive immunity. Viral clearance was accompanied by persistent transcriptomic footprints related to proliferation and extracellular matrix remodeling, immune responses, and metabolism. Substantial overlap with persistent epigenetic alterations in HCV-cured patients suggested a universal RNA virus-induced transcriptomic footprint. Cell-intrinsic clearance occurred in cell culture, too, with sequential infection, reinfection cycles separated by a period of relative refractoriness to infection. Our study reveals that systemic persistence of a prototypic noncytolytic RNA virus depends on continuous spread and reinfection. Yet undefined cell-intrinsic mechanisms prevent viral persistence at the single-cell level but give way to profound transcriptomic alterations in virus-cleared cells.
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Affiliation(s)
- Peter Reuther
- Department of Biomedicine, Division of Experimental Virology, University of Basel, Basel, Switzerland
| | - Katrin Martin
- Department of Biomedicine, Division of Experimental Virology, University of Basel, Basel, Switzerland
| | - Mario Kreutzfeldt
- Department of Pathology and Immunology, Division of Clinical Pathology, Geneva Faculty of Medicine, Geneva University and University Hospital, Geneva, Switzerland
| | - Matias Ciancaglini
- Department of Biomedicine, Division of Experimental Virology, University of Basel, Basel, Switzerland
| | - Florian Geier
- Department of Biomedicine, Bioinformatics Core Facility, University Hospital Basel, Basel, Switzerland
| | - Diego Calabrese
- Department of Biomedicine, Histology Core Facility, University Hospital Basel, Basel, Switzerland
| | - Doron Merkler
- Department of Pathology and Immunology, Division of Clinical Pathology, Geneva Faculty of Medicine, Geneva University and University Hospital, Geneva, Switzerland
| | - Daniel D Pinschewer
- Department of Biomedicine, Division of Experimental Virology, University of Basel, Basel, Switzerland
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10
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Robinot R, Hubert M, de Melo GD, Lazarini F, Bruel T, Smith N, Levallois S, Larrous F, Fernandes J, Gellenoncourt S, Rigaud S, Gorgette O, Thouvenot C, Trébeau C, Mallet A, Duménil G, Gobaa S, Etournay R, Lledo PM, Lecuit M, Bourhy H, Duffy D, Michel V, Schwartz O, Chakrabarti LA. SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance. Nat Commun 2021; 12:4354. [PMID: 34272374 PMCID: PMC8285531 DOI: 10.1038/s41467-021-24521-x] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/21/2021] [Indexed: 01/08/2023] Open
Abstract
Understanding how SARS-CoV-2 spreads within the respiratory tract is important to define the parameters controlling the severity of COVID-19. Here we examine the functional and structural consequences of SARS-CoV-2 infection in a reconstructed human bronchial epithelium model. SARS-CoV-2 replication causes a transient decrease in epithelial barrier function and disruption of tight junctions, though viral particle crossing remains limited. Rather, SARS-CoV-2 replication leads to a rapid loss of the ciliary layer, characterized at the ultrastructural level by axoneme loss and misorientation of remaining basal bodies. Downregulation of the master regulator of ciliogenesis Foxj1 occurs prior to extensive cilia loss, implicating this transcription factor in the dedifferentiation of ciliated cells. Motile cilia function is compromised by SARS-CoV-2 infection, as measured in a mucociliary clearance assay. Epithelial defense mechanisms, including basal cell mobilization and interferon-lambda induction, ramp up only after the initiation of cilia damage. Analysis of SARS-CoV-2 infection in Syrian hamsters further demonstrates the loss of motile cilia in vivo. This study identifies cilia damage as a pathogenic mechanism that could facilitate SARS-CoV-2 spread to the deeper lung parenchyma.
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Grants
- Institut Pasteur
- This work was supported by : Institut Pasteur TASK FORCE SARS COV2 (TROPICORO and COROCHIP projects), DIM ELICIT Region Ile-de-France, and Agence Nationale de Recherche sur le SIDA et les Maladies Infectieuses Emergentes (ANRS; project 19052) (L.A.C.); the Vaccine Research Institute (ANR-10-LABX-77), ANRS, Labex IBEID (ANR-10-LABX-62-IBEID), the French National Research Agency (ANR; projects “TIMTAMDEN” ANR-14-CE14-0029, “CHIKV-Viro-Immuno” ANR-14-CE14-0015-01), the Gilead HIV cure program, ANR/Fondation pour la Recherche Médicale (FRM) Flash Covid PROTEO-SARS-CoV-2 and IDISCOVR (O.S.); Institut Pasteur TASK FORCE SARS COV2 and ANR Flash Covid CoVarImm (D.D.); Institut Pasteur TASK FORCE SARS COV2 (Neuro-Covid project) (H.B.). The Lledo lab is supported by the life insurance company "AG2R-La-Mondiale". The UtechS Photonic BioImaging (Imagopole) and the UtechS Ultrastructural BioImaging (UBI) are supported by the ANR (France BioImaging; ANR-10–INSB–04; Investments for the Future). R.R. is the recipient of a Sidaction fellowship, N.S. of a Pasteur-Roux-Cantarini fellowship, and St.G. of a MESR/Ecole Doctorale B3MI, Université de Paris fellowship. S.L. is supported by FRM (fellowship ECO201906009119) and by “Ecole Doctorale FIRE – Programme Bettencourt”.
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Affiliation(s)
- Rémy Robinot
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569 CNRS, Paris, France
| | - Mathieu Hubert
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569 CNRS, Paris, France
| | | | - Françoise Lazarini
- Perception and Memory Unit, Institut Pasteur, Paris, France
- UMR 3571 CNRS, Paris, France
| | - Timothée Bruel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569 CNRS, Paris, France
| | - Nikaïa Smith
- Translational Immunology Lab, Department of Immunology, Institut Pasteur, Paris, France
| | - Sylvain Levallois
- Biology of Infection Unit, Institut Pasteur, Paris, France
- INSERM U1117, Paris, France
| | - Florence Larrous
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Paris, France
| | - Julien Fernandes
- UtechS Photonics BioImaging, C2RT, Institut Pasteur, Paris, France
| | - Stacy Gellenoncourt
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569 CNRS, Paris, France
| | | | - Olivier Gorgette
- UtechS Ultrastructural BioImaging UBI, C2RT, Institut Pasteur, Paris, France
| | - Catherine Thouvenot
- UtechS Ultrastructural BioImaging UBI, C2RT, Institut Pasteur, Paris, France
| | - Céline Trébeau
- Institut de l'Audition, Institut Pasteur, INSERM, Paris, France
| | - Adeline Mallet
- UtechS Ultrastructural BioImaging UBI, C2RT, Institut Pasteur, Paris, France
| | - Guillaume Duménil
- UtechS Ultrastructural BioImaging UBI, C2RT, Institut Pasteur, Paris, France
| | - Samy Gobaa
- Biomaterials and Microfluidics Core Facility, Institut Pasteur, Paris, France
| | | | - Pierre-Marie Lledo
- Perception and Memory Unit, Institut Pasteur, Paris, France
- UMR 3571 CNRS, Paris, France
| | - Marc Lecuit
- Biology of Infection Unit, Institut Pasteur, Paris, France
- INSERM U1117, Paris, France
- Université de Paris, Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris, France
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Translational Immunology Lab, Department of Immunology, Institut Pasteur, Paris, France
| | - Vincent Michel
- Institut de l'Audition, Institut Pasteur, INSERM, Paris, France.
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.
- UMR 3569 CNRS, Paris, France.
- Vaccine Research Institute, Créteil, France.
| | - Lisa A Chakrabarti
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.
- UMR 3569 CNRS, Paris, France.
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11
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Froggatt HM, Harding AT, Chaparian RR, Heaton NS. ETV7 limits antiviral gene expression and control of influenza viruses. Sci Signal 2021; 14:14/691/eabe1194. [PMID: 34257104 DOI: 10.1126/scisignal.abe1194] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The type I interferon (IFN) response is an important component of the innate immune response to viral infection. Precise control of IFN responses is critical because insufficient expression of IFN-stimulated genes (ISGs) can lead to a failure to restrict viral spread, whereas excessive ISG activation can result in IFN-related pathologies. Although both positive and negative regulatory factors control the magnitude and duration of IFN signaling, it is also appreciated that several ISGs regulate aspects of the IFN response themselves. In this study, we performed a CRISPR activation screen to identify previously unknown regulators of the type I IFN response. We identified the strongly induced ISG encoding ETS variant transcription factor 7 (ETV7) as a negative regulator of the type I IFN response. However, ETV7 did not uniformly suppress ISG transcription. Instead, ETV7 preferentially targeted a subset of antiviral ISGs that were particularly important for IFN-mediated control of influenza viruses. Together, our data assign a function for ETV7 as an IFN response regulator and also identify ETV7 as a potential therapeutic target to increase innate antiviral responses and enhance IFN-based antiviral therapies.
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Affiliation(s)
- Heather M Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ryan R Chaparian
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
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12
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Anomalous influenza seasonality in the United States and the emergence of novel influenza B viruses. Proc Natl Acad Sci U S A 2021; 118:2012327118. [PMID: 33495348 DOI: 10.1073/pnas.2012327118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 2019/2020 influenza season in the United States began earlier than any season since the 2009 H1N1 pandemic, with an increase in influenza-like illnesses observed as early as August. Also noteworthy was the numerical domination of influenza B cases early in this influenza season, in contrast to their typically later peak in the past. Here, we dissect the 2019/2020 influenza season not only with regard to its unusually early activity, but also with regard to the relative dynamics of type A and type B cases. We propose that the recent expansion of a novel influenza B/Victoria clade may be associated with this shift in the composition and kinetics of the influenza season in the United States. We use epidemiological transmission models to explore whether changes in the effective reproduction number or short-term cross-immunity between these viruses can explain the dynamics of influenza A and B seasonality. We find support for an increase in the effective reproduction number of influenza B, rather than support for cross-type immunity-driven dynamics. Our findings have clear implications for optimal vaccination strategies.
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13
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Fiege JK, Thiede JM, Nanda HA, Matchett WE, Moore PJ, Montanari NR, Thielen BK, Daniel J, Stanley E, Hunter RC, Menachery VD, Shen SS, Bold TD, Langlois RA. Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium. PLoS Pathog 2021; 17:e1009292. [PMID: 33507952 PMCID: PMC7872261 DOI: 10.1371/journal.ppat.1009292] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/09/2021] [Accepted: 01/07/2021] [Indexed: 12/27/2022] Open
Abstract
The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNA-sequencing to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of epithelial cell types are susceptible to infection, ciliated cells are the predominant cell target of SARS-CoV-2. The host protease TMPRSS2 was required for infection of these cells. Importantly, remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. Induction of interferon responses within infected cells was rare and there was significant heterogeneity in the antiviral gene signatures, varying with the burden of infection in each cell. We also found that heavily infected secretory cells expressed abundant IL-6, a potential mediator of COVID-19 pathogenesis.
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Affiliation(s)
- Jessica K. Fiege
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Joshua M. Thiede
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Hezkiel Arya Nanda
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William E. Matchett
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Patrick J. Moore
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Noe Rico Montanari
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Beth K. Thielen
- Department of Pediatrics, Division of Infectious Diseases, University of Minnesota, United States of America
| | - Jerry Daniel
- University of Minnesota Genomics Center, Minneapolis, Minnesota, United States of America
| | - Emma Stanley
- University of Minnesota Genomics Center, Minneapolis, Minnesota, United States of America
| | - Ryan C. Hunter
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Steven S. Shen
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Tyler D. Bold
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ryan A. Langlois
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
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14
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Fiege JK, Thiede JM, Nanda H, Matchett WE, Moore PJ, Montanari NR, Thielen BK, Daniel J, Stanley E, Hunter RC, Menachery VD, Shen SS, Bold TD, Langlois RA. Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33106802 PMCID: PMC7587775 DOI: 10.1101/2020.10.19.343954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNA-sequencing to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of epithelial cell types are susceptible to infection, ciliated cells are the predominant cell target of SARS-CoV-2. The host protease TMPRSS2 was required for infection of these cells. Importantly, remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. Induction of interferon responses within infected cells was rare and there was significant heterogeneity in the antiviral gene signatures, varying with the burden of infection in each cell. We also found that heavily infected secretory cells expressed abundant IL-6, a potential mediator of COVID-19 pathogenesis.
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Affiliation(s)
- Jessica K Fiege
- Center for Immunology, University of Minnesota.,Department of Microbiology and Immunology, University of Minnesota
| | - Joshua M Thiede
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota
| | - Hezkiel Nanda
- Institute for Health Informatics, University of Minnesota
| | - William E Matchett
- Center for Immunology, University of Minnesota.,Department of Microbiology and Immunology, University of Minnesota
| | - Patrick J Moore
- Department of Microbiology and Immunology, University of Minnesota
| | | | - Beth K Thielen
- Department of Pediatrics, Division of Infectious Diseases, University of Minnesota
| | | | | | - Ryan C Hunter
- Center for Immunology, University of Minnesota.,Department of Microbiology and Immunology, University of Minnesota
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch
| | - Steven S Shen
- Institute for Health Informatics, University of Minnesota
| | - Tyler D Bold
- Center for Immunology, University of Minnesota.,Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota
| | - Ryan A Langlois
- Center for Immunology, University of Minnesota.,Department of Microbiology and Immunology, University of Minnesota
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15
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Cardenas-Garcia S, Caceres CJ, Rajao D, Perez DR. Reverse genetics for influenza B viruses and recent advances in vaccine development. Curr Opin Virol 2020; 44:191-202. [PMID: 33254031 PMCID: PMC8693393 DOI: 10.1016/j.coviro.2020.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 02/06/2023]
Abstract
Influenza B virus is a respiratory pathogen that affects more severely the pediatric and elderly populations. There are two lineages of influenza B virus that seem to have differential predilection for age groups. Both lineages can co-circulate during the influenza season however one is usually more prominent than the other depending on the season. There are no defined indicators to predict which lineage will dominate in any given season. In recent years, the addition of viruses from both lineages to the seasonal influenza vaccine formulation has improved vaccine protection, although quadrivalent vaccines are not available worldwide. Reverse genetics has facilitated advancements in the field of vaccine development against influenza B virus. Different strategies have been explored showing promising results that could potentially lead to the development broadly protective influenza B virus vaccines.
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Affiliation(s)
- Stivalis Cardenas-Garcia
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA, 30602, USA.
| | - C Joaquin Caceres
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA, 30602, USA
| | - Daniela Rajao
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA, 30602, USA
| | - Daniel R Perez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA, 30602, USA.
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16
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Dumm RE, Wellford SA, Moseman EA, Heaton NS. Heterogeneity of Antiviral Responses in the Upper Respiratory Tract Mediates Differential Non-lytic Clearance of Influenza Viruses. Cell Rep 2020; 32:108103. [PMID: 32877682 PMCID: PMC7462569 DOI: 10.1016/j.celrep.2020.108103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/01/2020] [Accepted: 08/11/2020] [Indexed: 01/06/2023] Open
Abstract
Influenza viruses initiate infection in the upper respiratory tract (URT), but early viral tropism and the importance of cell-type-specific antiviral responses in this tissue remain incompletely understood. By infecting transgenic lox-stop-lox reporter mice with a Cre-recombinase-expressing influenza B virus, we identify olfactory sensory neurons (OSNs) as a major viral cell target in the URT. These cells become infected, then eliminate the virus and survive in the host post-resolution of infection. OSN responses to infection are characterized by a strong induction of interferon-stimulated genes and more rapid clearance of viral protein relative to other cells in the epithelium. We speculate that this cell-type-specific response likely serves to protect the central nervous system from infection. More broadly, these results highlight the importance of evaluating antiviral responses across different cell types, even those within the same tissue, to more fully understand the mechanisms of viral disease.
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Affiliation(s)
- Rebekah E Dumm
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sebastian A Wellford
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - E Ashley Moseman
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
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17
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Moseman EA, Blanchard AC, Nayak D, McGavern DB. T cell engagement of cross-presenting microglia protects the brain from a nasal virus infection. Sci Immunol 2020; 5:eabb1817. [PMID: 32503876 PMCID: PMC7416530 DOI: 10.1126/sciimmunol.abb1817] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022]
Abstract
The neuroepithelium is a nasal barrier surface populated by olfactory sensory neurons that detect odorants in the airway and convey this information directly to the brain via axon fibers. This barrier surface is especially vulnerable to infection, yet respiratory infections rarely cause fatal encephalitis, suggesting a highly evolved immunological defense. Here, using a mouse model, we sought to understand the mechanism by which innate and adaptive immune cells thwart neuroinvasion by vesicular stomatitis virus (VSV), a potentially lethal virus that uses olfactory sensory neurons to enter the brain after nasal infection. Fate-mapping studies demonstrated that infected central nervous system (CNS) neurons were cleared noncytolytically, yet specific deletion of major histocompatibility complex class I (MHC I) from these neurons unexpectedly had no effect on viral control. Intravital imaging studies of calcium signaling in virus-specific CD8+ T cells revealed instead that brain-resident microglia were the relevant source of viral peptide-MHC I complexes. Microglia were not infected by the virus but were found to cross-present antigen after acquisition from adjacent neurons. Microglia depletion interfered with T cell calcium signaling and antiviral control in the brain after nasal infection. Collectively, these data demonstrate that microglia provide a front-line defense against a neuroinvasive nasal infection by cross-presenting antigen to antiviral T cells that noncytolytically cleanse neurons. Disruptions in this innate defense likely render the brain susceptible to neurotropic viruses like VSV that attempt to enter the CNS via the nose.
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Affiliation(s)
- E Ashley Moseman
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Alexa C Blanchard
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Debasis Nayak
- Discipline of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, MP, India
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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18
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Lukassen S, Chua RL, Trefzer T, Kahn NC, Schneider MA, Muley T, Winter H, Meister M, Veith C, Boots AW, Hennig BP, Kreuter M, Conrad C, Eils R. SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells. EMBO J 2020; 39:e105114. [PMID: 32246845 PMCID: PMC7232010 DOI: 10.15252/embj.20105114] [Citation(s) in RCA: 627] [Impact Index Per Article: 156.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. While TMPRSS2 is strongly expressed in both tissues, in the subsegmental bronchial branches ACE2 is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.
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Affiliation(s)
- Soeren Lukassen
- Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Center for Digital HealthBerlin Institute of Health (BIH)BerlinGermany
| | - Robert Lorenz Chua
- Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Center for Digital HealthBerlin Institute of Health (BIH)BerlinGermany
| | - Timo Trefzer
- Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Center for Digital HealthBerlin Institute of Health (BIH)BerlinGermany
| | - Nicolas C Kahn
- Department of Pneumology and Respiratory Critical Care MedicineCenter for interstitial and rare lung diseasesThoraxklinik, Heidelberg University HospitalHeidelbergGermany
- Translational Lung Research Center Heidelberg (TLRC)Member of the German Center for Lung Research (DZL)HeidelbergGermany
| | - Marc A Schneider
- Translational Lung Research Center Heidelberg (TLRC)Member of the German Center for Lung Research (DZL)HeidelbergGermany
- Translational Research UnitThoraxklinik, Heidelberg University HospitalHeidelbergGermany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC)Member of the German Center for Lung Research (DZL)HeidelbergGermany
- Translational Research UnitThoraxklinik, Heidelberg University HospitalHeidelbergGermany
| | - Hauke Winter
- Translational Lung Research Center Heidelberg (TLRC)Member of the German Center for Lung Research (DZL)HeidelbergGermany
- Department of Thoracic SurgeryThoraxklinik, Heidelberg University HospitalHeidelbergGermany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC)Member of the German Center for Lung Research (DZL)HeidelbergGermany
- Translational Research UnitThoraxklinik, Heidelberg University HospitalHeidelbergGermany
| | - Carmen Veith
- Division of Redox RegulationGerman Cancer Research Center (DKFZ) HeidelbergGermany
| | - Agnes W Boots
- Faculty of Health, Medicine and Life SciencesDepartment of Pharmacology and ToxicologyNUTRIM School of NutritionTranslational Research and MetabolismMaastricht UniversityMaastrichtthe Netherlands
| | - Bianca P Hennig
- Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Center for Digital HealthBerlin Institute of Health (BIH)BerlinGermany
| | - Michael Kreuter
- Department of Pneumology and Respiratory Critical Care MedicineCenter for interstitial and rare lung diseasesThoraxklinik, Heidelberg University HospitalHeidelbergGermany
| | - Christian Conrad
- Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Roland Eils
- Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Center for Digital HealthBerlin Institute of Health (BIH)BerlinGermany
- Health Data Science UnitHeidelberg University Hospital and BioQuantHeidelbergGermany
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19
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Lukassen S, Chua RL, Trefzer T, Kahn NC, Schneider MA, Muley T, Winter H, Meister M, Veith C, Boots AW, Hennig BP, Kreuter M, Conrad C, Eils R. SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells. EMBO J 2020. [PMID: 32246845 DOI: 10.1525/embj.20105114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. While TMPRSS2 is strongly expressed in both tissues, in the subsegmental bronchial branches ACE2 is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.
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Affiliation(s)
- Soeren Lukassen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Center for Digital Health, Berlin Institute of Health (BIH), Berlin, Germany
| | - Robert Lorenz Chua
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Center for Digital Health, Berlin Institute of Health (BIH), Berlin, Germany
| | - Timo Trefzer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Center for Digital Health, Berlin Institute of Health (BIH), Berlin, Germany
| | - Nicolas C Kahn
- Department of Pneumology and Respiratory Critical Care Medicine, Center for interstitial and rare lung diseases, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Marc A Schneider
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Thoracic Surgery, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany
| | - Carmen Veith
- Division of Redox Regulation, German Cancer Research Center (DKFZ) , Heidelberg, Germany
| | - Agnes W Boots
- Faculty of Health, Medicine and Life Sciences, Department of Pharmacology and Toxicology, NUTRIM School of Nutrition, Translational Research and Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Bianca P Hennig
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Center for Digital Health, Berlin Institute of Health (BIH), Berlin, Germany
| | - Michael Kreuter
- Department of Pneumology and Respiratory Critical Care Medicine, Center for interstitial and rare lung diseases, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Conrad
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Roland Eils
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Center for Digital Health, Berlin Institute of Health (BIH), Berlin, Germany.,Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany
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20
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Liu W, He H, Zheng SY. Microfluidics in Single-Cell Virology: Technologies and Applications. Trends Biotechnol 2020; 38:1360-1372. [PMID: 32430227 DOI: 10.1016/j.tibtech.2020.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]
Abstract
Microfluidics has proven to be a powerful tool for probing biology at the single-cell level. However, it is only in the past 5 years that single-cell microfluidics has been used in the field of virology. An array of strategies based on microwells, microvalves, and droplets is now available for tracking viral infection dynamics, identifying cell subpopulations with particular phenotypes, as well as high-throughput screening. The insights into the virus-host interactions gained at the single-cell level are unprecedented and usually inaccessible by population-based experiments. Therefore, single-cell microfluidics, which opens new avenues for mechanism elucidation and development of antiviral therapeutics, would be a valuable tool for the study of viral pathogenesis.
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Affiliation(s)
- Wu Liu
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Hongzhang He
- Captis Diagnostics Inc., Pittsburgh, PA 15213, USA
| | - Si-Yang Zheng
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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21
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Lukassen S, Chua RL, Trefzer T, Kahn NC, Schneider MA, Muley T, Winter H, Meister M, Veith C, Boots AW, Hennig BP, Kreuter M, Conrad C, Eils R. SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells. EMBO J 2020. [DOI: 10.15252/embj.2020105114] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Soeren Lukassen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Berlin Germany
- Center for Digital Health; Berlin Institute of Health (BIH); Berlin Germany
| | - Robert Lorenz Chua
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Berlin Germany
- Center for Digital Health; Berlin Institute of Health (BIH); Berlin Germany
| | - Timo Trefzer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Berlin Germany
- Center for Digital Health; Berlin Institute of Health (BIH); Berlin Germany
| | - Nicolas C Kahn
- Department of Pneumology and Respiratory Critical Care Medicine; Center for interstitial and rare lung diseases; Thoraxklinik, Heidelberg University Hospital; Heidelberg Germany
- Translational Lung Research Center Heidelberg (TLRC); Member of the German Center for Lung Research (DZL); Heidelberg Germany
| | - Marc A Schneider
- Translational Lung Research Center Heidelberg (TLRC); Member of the German Center for Lung Research (DZL); Heidelberg Germany
- Translational Research Unit; Thoraxklinik, Heidelberg University Hospital; Heidelberg Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC); Member of the German Center for Lung Research (DZL); Heidelberg Germany
- Translational Research Unit; Thoraxklinik, Heidelberg University Hospital; Heidelberg Germany
| | - Hauke Winter
- Translational Lung Research Center Heidelberg (TLRC); Member of the German Center for Lung Research (DZL); Heidelberg Germany
- Department of Thoracic Surgery; Thoraxklinik, Heidelberg University Hospital; Heidelberg Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC); Member of the German Center for Lung Research (DZL); Heidelberg Germany
- Translational Research Unit; Thoraxklinik, Heidelberg University Hospital; Heidelberg Germany
| | - Carmen Veith
- Division of Redox Regulation; German Cancer Research Center (DKFZ) ; Heidelberg Germany
| | - Agnes W Boots
- Faculty of Health, Medicine and Life Sciences; Department of Pharmacology and Toxicology; NUTRIM School of Nutrition; Translational Research and Metabolism; Maastricht University; Maastricht the Netherlands
| | - Bianca P Hennig
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Berlin Germany
- Center for Digital Health; Berlin Institute of Health (BIH); Berlin Germany
| | - Michael Kreuter
- Department of Pneumology and Respiratory Critical Care Medicine; Center for interstitial and rare lung diseases; Thoraxklinik, Heidelberg University Hospital; Heidelberg Germany
- Translational Lung Research Center Heidelberg (TLRC); Member of the German Center for Lung Research (DZL); Heidelberg Germany
| | - Christian Conrad
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Berlin Germany
- Center for Digital Health; Berlin Institute of Health (BIH); Berlin Germany
| | - Roland Eils
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Berlin Germany
- Center for Digital Health; Berlin Institute of Health (BIH); Berlin Germany
- Health Data Science Unit; Heidelberg University Hospital and BioQuant; Heidelberg Germany
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22
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Garcia GL, Valenzuela A, Manzoni T, Vaughan AE, López CB. Distinct Chronic Post-Viral Lung Diseases upon Infection with Influenza or Parainfluenza Viruses Differentially Impact Superinfection Outcome. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 190:543-553. [PMID: 31866346 DOI: 10.1016/j.ajpath.2019.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 10/07/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) and asthma remain prevalent human lung diseases. Variability in epithelial and inflammatory components that results in pathologic heterogeneity complicates the development of treatments for these diseases. Early childhood infection with parainfluenza virus or respiratory syncytial virus is strongly associated with the development of asthma and COPD later in life, and exacerbations of these diseases correlate with the presence of viral RNA in the lung. Well-characterized animal models of postviral chronic lung diseases are necessary to study the underlying mechanisms of viral-related COPD and asthma and to develop appropriate therapies. In this study, we cross-analyzed chronic lung disease caused by infection with Sendai virus (SeV) or influenza A virus in mice. Differences were observed in lesion composition and inflammatory profiles between SeV- and influenza A virus-induced long-term lung disease. In addition, a primary SeV infection led to worsened pathologic findings on secondary heterologous viral challenge, whereas the reversed infection scheme protected against disease in response to a secondary viral challenge >1 month after the primary infection. These data demonstrate the differential effect of primary viral infections in the susceptibility to disease exacerbation in response to a different secondary viral infection and highlight the usefulness of these viral models as tools to understand the underlying mechanisms that mediate distinct chronic postviral lung diseases.
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Affiliation(s)
- Geyon L Garcia
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Alex Valenzuela
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tomaz Manzoni
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew E Vaughan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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23
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Dumm RE, Heaton NS. The Development and Use of Reporter Influenza B Viruses. Viruses 2019; 11:E736. [PMID: 31404985 PMCID: PMC6723853 DOI: 10.3390/v11080736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022] Open
Abstract
Influenza B viruses (IBVs) are major contributors to total human influenza disease, responsible for ~1/3 of all infections. These viruses, however, are relatively less studied than the related influenza A viruses (IAVs). While it has historically been assumed that the viral biology and mechanisms of pathogenesis for all influenza viruses were highly similar, studies have shown that IBVs possess unique characteristics. Relative to IAV, IBV encodes distinct viral proteins, displays a different mutational rate, has unique patterns of tropism, and elicits different immune responses. More work is therefore required to define the mechanisms of IBV pathogenesis. One valuable approach to characterize mechanisms of microbial disease is the use of genetically modified pathogens that harbor exogenous reporter genes. Over the last few years, IBV reporter viruses have been developed and used to provide new insights into the host response to infection, viral spread, and the testing of antiviral therapeutics. In this review, we will highlight the history and study of IBVs with particular emphasis on the use of genetically modified viruses and discuss some remaining gaps in knowledge that can be addressed using reporter expressing IBVs.
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Affiliation(s)
- Rebekah E Dumm
- Department of Molecular Genetics and Microbiology, University School of Medicine Durham, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology (MGM), Duke University Medical Center, 213 Research Drive, 426 CARL Building, Box 3054, Durham, NC 27710, USA.
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