1
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Ueno S, Amarbayasgalan S, Sugiura Y, Takahashi T, Shimizu K, Nakagawa K, Kawabata-Iwakawa R, Kamitani W. Eight-amino-acid sequence at the N-terminus of SARS-CoV-2 nsp1 is involved in stabilizing viral genome replication. Virology 2024; 595:110068. [PMID: 38593595 DOI: 10.1016/j.virol.2024.110068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
Coronavirus disease 19 is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) enveloped virus with a single-stranded positive-sense ribonucleic acid (RNA) genome. The CoV non-structural protein (nsp) 1 is a multifunctional protein that undergoes translation shutoff, messenger RNA (mRNA) cleavage, and RNA binding. The C-terminal region is involved in translational shutoff and RNA cleavage. The N-terminal region of SARS-CoV-2 nsp1 is highly conserved among isolated SARS-CoV-2 variants. However, the I-004 variant, isolated during the early SARS-CoV-2 pandemic, lost eight amino acids in the nsp1 region. In this study, we showed that the eight amino acids are important for viral replication in infected interferon-incompetent cells and that the recombinant virus that lost these amino acids had low pathogenicity in the lungs of hamster models. The loss of eight amino acids-induced mutations occurred in the 5' untranslated region (UTR), suggesting that nsp1 contributes to the stability of the viral genome during replication.
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Affiliation(s)
- Shiori Ueno
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan
| | | | - Yoshiro Sugiura
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan
| | - Tatsuki Takahashi
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan
| | - Kenta Shimizu
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan
| | - Keisuke Nakagawa
- Laboratory of Veterinary Microbiology, Joint Department of Veterinary Medicine, Gifu University, Yanagido, Gifu, Japan
| | - Reika Kawabata-Iwakawa
- Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, Gunma University, Gunma, Japan
| | - Wataru Kamitani
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan.
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2
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Ribó-Molina P, van Nieuwkoop S, Mykytyn AZ, van Run P, Lamers MM, Haagmans BL, Fouchier RAM, van den Hoogen BG. Human metapneumovirus infection of organoid-derived human bronchial epithelium represents cell tropism and cytopathology as observed in in vivo models. mSphere 2024; 9:e0074323. [PMID: 38265200 PMCID: PMC10900881 DOI: 10.1128/msphere.00743-23] [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] [Received: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Human metapneumovirus (HMPV), a member of the Pneumoviridae family, causes upper and lower respiratory tract infections in humans. In vitro studies with HMPV have mostly been performed in monolayers of undifferentiated epithelial cells. In vivo studies in cynomolgus macaques and cotton rats have shown that ciliated epithelial cells are the main target of HMPV infection, but these observations cannot be studied in monolayer systems. Here, we established an organoid-derived bronchial culture model that allows physiologically relevant studies on HMPV. Inoculation with multiple prototype HMPV viruses and recent clinical virus isolates led to differences in replication among HMPV isolates. Prolific HMPV replication in this model caused damage to the ciliary layer, including cilia loss at advanced stages post-infection. These cytopathic effects correlated with those observed in previous in vivo studies with cynomolgus macaques. The assessment of the innate immune responses in three donors upon HMPV and RSV inoculation highlighted the importance of incorporating multiple donors to account for donor-dependent variation. In conclusion, these data indicate that the organoid-derived bronchial cell culture model resembles in vivo findings and is therefore a suitable and robust model for future HMPV studies. IMPORTANCE Human metapneumovirus (HMPV) is one of the leading causative agents of respiratory disease in humans, with no treatment or vaccine available yet. The use of primary epithelial cultures that recapitulate the tissue morphology and biochemistry of the human airways could aid in defining more relevant targets to prevent HMPV infection. For this purpose, this study established the first primary organoid-derived bronchial culture model suitable for a broad range of HMPV isolates. These bronchial cultures were assessed for HMPV replication, cellular tropism, cytopathology, and innate immune responses, where the observations were linked to previous in vivo studies with HMPV. This study exposed an important gap in the HMPV field since extensively cell-passaged prototype HMPV B viruses did not replicate in the bronchial cultures, underpinning the need to use recently isolated viruses with a controlled passage history. These results were reproducible in three different donors, supporting this model to be suitable to study HMPV infection.
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Affiliation(s)
- Pau Ribó-Molina
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Anna Z. Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M. Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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3
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Galanti M, Patiño-Galindo JA, Filip I, Morita H, Galianese A, Youssef M, Comito D, Ligon C, Lane B, Matienzo N, Ibrahim S, Tagne E, Shittu A, Elliott O, Perea-Chamblee T, Natesan S, Rosenbloom DS, Shaman J, Rabadan R. Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people. PLoS Biol 2024; 22:e3002089. [PMID: 38236818 PMCID: PMC10796020 DOI: 10.1371/journal.pbio.3002089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/22/2023] [Indexed: 01/22/2024] Open
Abstract
Viral respiratory infections are an important public health concern due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup, and bacterial coinfections. To understand these interactions within natural infections, we designed a longitudinal cohort study actively surveilling respiratory viruses over the course of 19 months (2016 to 2018) in a diverse cohort in New York City. We integrated the molecular characterization of 800+ nasopharyngeal samples with clinical data from 104 participants. Transcriptomic data enabled the identification of respiratory pathogens in nasopharyngeal samples, the characterization of markers of immune response, the identification of signatures associated with symptom severity, individual viruses, and bacterial coinfections. Specific results include a rapid restoration of baseline conditions after infection, significant transcriptomic differences between symptomatic and asymptomatic infections, and qualitatively similar responses across different viruses. We created an interactive computational resource (Virome Data Explorer) to facilitate access to the data and visualization of analytical results.
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Affiliation(s)
- Marta Galanti
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Juan Angel Patiño-Galindo
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Ioan Filip
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Haruka Morita
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Angelica Galianese
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Mariam Youssef
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Devon Comito
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Chanel Ligon
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Benjamin Lane
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Nelsa Matienzo
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sadiat Ibrahim
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Eudosie Tagne
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Atinuke Shittu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Oliver Elliott
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Tomin Perea-Chamblee
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Sanjay Natesan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Daniel Scholes Rosenbloom
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
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4
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Yang X, Liu X, Nie Y, Zhan F, Zhu B. Oxidative stress and ROS-mediated cellular events in RSV infection: potential protective roles of antioxidants. Virol J 2023; 20:224. [PMID: 37798799 PMCID: PMC10557227 DOI: 10.1186/s12985-023-02194-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
Respiratory syncytial virus (RSV), a member of the Pneumoviridae family, can cause severe acute lower respiratory tract infection in infants, young children, immunocompromised individuals and elderly people. RSV is associated with an augmented innate immune response, enhanced secretion of inflammatory cytokines, and necrosis of infected cells. Oxidative stress, which is mainly characterized as an imbalance in the production of reactive oxygen species (ROS) and antioxidant responses, interacts with all the pathophysiologic processes above and is receiving increasing attention in RSV infection. A gradual accumulation of evidence indicates that ROS overproduction plays an important role in the pathogenesis of severe RSV infection and serves as a major factor in pulmonary inflammation and tissue damage. Thus, antioxidants seem to be an effective treatment for severe RSV infection. This article mainly reviews the information on oxidative stress and ROS-mediated cellular events during RSV infection for the first time.
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Affiliation(s)
- Xue Yang
- Department of Pediatrics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, Hubei, China
| | - Xue Liu
- Department of Pediatrics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, Hubei, China
| | - Yujun Nie
- Department of Pediatrics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, Hubei, China
| | - Fei Zhan
- Department of Pediatrics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, Hubei, China
| | - Bin Zhu
- Department of Pediatrics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, Hubei, China.
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5
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Salve BG, Kurian AM, Vijay N. Concurrent loss of ciliary genes WDR93 and CFAP46 in phylogenetically distant birds. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230801. [PMID: 37621660 PMCID: PMC10445033 DOI: 10.1098/rsos.230801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
The respiratory system is the primary route of infection for many contagious pathogens. Mucociliary clearance of inhaled pathogens is an important innate defence mechanism sustained by the rhythmic movement of epithelial cilia. To counter host defences, viral pathogens target epithelial cells and cilia. For instance, the avian influenza virus that targets ciliated cells modulates the expression of WDR93, a central ciliary apparatus C1d projection component. Lineage-specific prevalence of such host defence genes results in differential susceptibility. In this study, the comparative analysis of approximately 500 vertebrate genomes from seven taxonomic classes spanning 73 orders confirms the widespread conservation of WDR93 across these different vertebrate groups. However, we established loss of the WDR93 in landfowl, geese and other phylogenetically independent bird species due to gene-disrupting changes. The lack of WDR93 transcripts in species with gene loss in contrast to its expression in species with an intact gene confirms gene loss. Notably, species with WDR93 loss have concurrently lost another C1d component, CFAP46, through large segmental deletions. Understanding the consequences of such gene loss may provide insight into their role in host-pathogen interactions and benefit global pathogen surveillance efforts by prioritizing species missing host defence genes and identifying putative zoonotic reservoirs.
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Affiliation(s)
- Buddhabhushan Girish Salve
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Amia Miriam Kurian
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
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6
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Chatziparasidis G, Kantar A, Grimwood K. Pathogenesis of nontypeable Haemophilus influenzae infections in chronic suppurative lung disease. Pediatr Pulmonol 2023. [PMID: 37133207 DOI: 10.1002/ppul.26446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/09/2023] [Accepted: 04/23/2023] [Indexed: 05/04/2023]
Abstract
The respiratory tract antimicrobial defense system is a multilayered defense mechanism that relies upon mucociliary clearance and components of both the innate and adaptive immune systems to protect the lungs from inhaled or aspirated microorganisms. One of these potential pathogens, nontypeable Haemophilus influenzae (NTHi), adopts several, multifaceted redundant strategies to successfully colonize the lower airways and establish a persistent infection. NTHi can impair mucociliary clearance, express multiple multifunctional adhesins for various cell types within the respiratory tract and evade host defenses by surviving within and between cells, forming biofilms, increasing antigenic drift, secreting proteases and antioxidants, and by host-pathogen cross-talk, impair macrophage and neutrophil function. NTHi is recognized as an important pathogen in several chronic lower respiratory disorders, such as protracted bacterial bronchitis, bronchiectasis, cystic fibrosis, and primary ciliary dyskinesia. The persistence of NTHi in human airways, including its capacity to form biofilms, results in chronic infection and inflammation, which can ultimately injure airway wall structures. The complex nature of the molecular pathogenetic mechanisms employed by NTHi is incompletely understood but improved understanding of its pathobiology will be important for developing effective therapies and vaccines, especially given the marked genetic heterogeneity of NTHi and its possession of phase-variable genes. Currently, no vaccine candidates are ready for large phase III clinical trials.
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Affiliation(s)
- Grigorios Chatziparasidis
- Paediatric Respiratory Unit, IASO Hospital, Larissa, Thessaly, Greece
- Faculty of Nursing, Thessaly University, Larissa, Greece
| | - Ahmad Kantar
- Pediatric Asthma and Cough Centre, Instituti Ospedalieri Bergamaschi, Bergamo, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Keith Grimwood
- School of Medicine and Dentistry, and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Departments of Infectious Disease and Paediatrics, Gold Coast Health, Southport, Queensland, Australia
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7
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Essaidi-Laziosi M, Alvarez C, Puhach O, Sattonnet-Roche P, Torriani G, Tapparel C, Kaiser L, Eckerle I. Sequential infections with rhinovirus and influenza modulate the replicative capacity of SARS-CoV-2 in the upper respiratory tract. Emerg Microbes Infect 2022; 11:412-423. [PMID: 34931581 PMCID: PMC8803056 DOI: 10.1080/22221751.2021.2021806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/19/2021] [Indexed: 01/07/2023]
Abstract
Although frequently reported since the beginning of the pandemic, questions remain regarding the impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) interaction with circulating respiratory viruses in coinfected patients. We here investigated dual infections involving early-pandemic SARS-CoV-2 and the Alpha variant and three of the most prevalent respiratory viruses, rhinovirus (RV) and Influenza A and B viruses (IAV and IBV), in reconstituted respiratory airway epithelial cells cultured at air-liquid interface. We found that SARS-CoV-2 replication was impaired by primary, but not secondary, rhino- and influenza virus infection. In contrast, SARS-CoV-2 had no effect on the replication of these seasonal respiratory viruses. Inhibition of SARS-CoV-2 correlated better with immune response triggered by RV, IAV and IBV than the virus entry. Using neutralizing antibody against type I and III interferons, SARS-CoV-2 blockade in dual infections could be partly prevented. Altogether, these data suggested that SARS-CoV-2 interaction with seasonal respiratory viruses would be modulated by interferon induction and could impact SARS-CoV-2 epidemiology when circulation of other respiratory viruses is restored.
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Affiliation(s)
- Manel Essaidi-Laziosi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Catia Alvarez
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olha Puhach
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pascale Sattonnet-Roche
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Giulia Torriani
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, University of Geneva, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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8
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Andrés P, Blandine P, Victoria D, William M, Justine O, Laurent E, Cedrine M, Bruno L, Aurelien T, Thomas J, Sophie TA, Manuel RC, Olivier T. Interactions Between Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Major Respiratory Viruses in Human Nasal Epithelium. J Infect Dis 2022; 226:2095-2104. [PMID: 36031537 PMCID: PMC9452145 DOI: 10.1093/infdis/jiac357] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), along with extensive nonpharmacological interventions, have profoundly altered the epidemiology of major respiratory viruses. Some studies have described virus-virus interactions, particularly manifested by viral interference mechanisms at different scales. However, our knowledge of the interactions between SARS-CoV-2 and other respiratory viruses remains incomplete. Here, we studied the interactions between SARS-CoV-2 and several respiratory viruses (influenza, respiratory syncytial virus, human metapneumovirus, and human rhinovirus) in a reconstituted human epithelial airway model, exploring different scenarios affecting the sequence and timing of coinfections. We show that the virus type and sequence of infections are key factors in virus-virus interactions, the primary infection having a determinant role in the immune response to the secondary infection.
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Affiliation(s)
- Pizzorno Andrés
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Padey Blandine
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,Signia Therapeutics SAS, Lyon, France
| | - Dulière Victoria
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Mouton William
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,Laboratoire Commun de Recherche, Hospices Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Oliva Justine
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Emilie Laurent
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Milesi Cedrine
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Lina Bruno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Traversier Aurelien
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Julien Thomas
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Trouillet Assant Sophie
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,Laboratoire Commun de Recherche, Hospices Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | | | - Terrier Olivier
- Correspondence to: Olivier Terrier. CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France, ()
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9
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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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10
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Kircher M, Chludzinski E, Krepel J, Saremi B, Beineke A, Jung K. Augmentation of Transcriptomic Data for Improved Classification of Patients with Respiratory Diseases of Viral Origin. Int J Mol Sci 2022; 23:ijms23052481. [PMID: 35269624 PMCID: PMC8910329 DOI: 10.3390/ijms23052481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
To better understand the molecular basis of respiratory diseases of viral origin, high-throughput gene-expression data are frequently taken by means of DNA microarray or RNA-seq technology. Such data can also be useful to classify infected individuals by molecular signatures in the form of machine-learning models with genes as predictor variables. Early diagnosis of patients by molecular signatures could also contribute to better treatments. An approach that has rarely been considered for machine-learning models in the context of transcriptomics is data augmentation. For other data types it has been shown that augmentation can improve classification accuracy and prevent overfitting. Here, we compare three strategies for data augmentation of DNA microarray and RNA-seq data from two selected studies on respiratory diseases of viral origin. The first study involves samples of patients with either viral or bacterial origin of the respiratory disease, the second study involves patients with either SARS-CoV-2 or another respiratory virus as disease origin. Specifically, we reanalyze these public datasets to study whether patient classification by transcriptomic signatures can be improved when adding artificial data for training of the machine-learning models. Our comparison reveals that augmentation of transcriptomic data can improve the classification accuracy and that fewer genes are necessary as explanatory variables in the final models. We also report genes from our signatures that overlap with signatures presented in the original publications of our example data. Due to strict selection criteria, the molecular role of these genes in the context of respiratory infectious diseases is underlined.
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Affiliation(s)
- Magdalena Kircher
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17p, 30559 Hannover, Germany; (M.K.); (J.K.); (B.S.)
| | - Elisa Chludzinski
- Department of Pathology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hannover, Germany; (E.C.); (A.B.)
| | - Jessica Krepel
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17p, 30559 Hannover, Germany; (M.K.); (J.K.); (B.S.)
| | - Babak Saremi
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17p, 30559 Hannover, Germany; (M.K.); (J.K.); (B.S.)
| | - Andreas Beineke
- Department of Pathology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hannover, Germany; (E.C.); (A.B.)
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17p, 30559 Hannover, Germany; (M.K.); (J.K.); (B.S.)
- Correspondence: ; Tel.: +49-511-953-8878
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11
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Rüger N, Sid H, Meens J, Szostak MP, Baumgärtner W, Bexter F, Rautenschlein S. New Insights into the Host-Pathogen Interaction of Mycoplasma gallisepticum and Avian Metapneumovirus in Tracheal Organ Cultures of Chicken. Microorganisms 2021; 9:microorganisms9112407. [PMID: 34835532 PMCID: PMC8618481 DOI: 10.3390/microorganisms9112407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 01/04/2023] Open
Abstract
Respiratory pathogens are a health threat for poultry. Co-infections lead to the exacerbation of clinical symptoms and lesions. Mycoplasma gallisepticum (M. gallispeticum) and Avian Metapneumovirus (AMPV) are two avian respiratory pathogens that co-circulate worldwide. The knowledge about the host-pathogen interaction of M. gallispeticum and AMPV in the chicken respiratory tract is limited. We aimed to investigate how co-infections affect the pathogenesis of the respiratory disease and whether the order of invading pathogens leads to changes in host-pathogen interaction. We used chicken tracheal organ cultures (TOC) to investigate pathogen invasion and replication, lesion development, and selected innate immune responses, such as interferon (IFN) α, inducible nitric oxide synthase (iNOS) and IFNλ mRNA expression levels. We performed mono-inoculations (AMPV or M. gallispeticum) or dual-inoculations in two orders with a 24-h interval between the first and second pathogen. Dual-inoculations compared to mono-inoculations resulted in more severe host reactions. Pre-infection with AMPV followed by M. gallispeticum resulted in prolonged viral replication, more significant innate immune responses, and lesions (p < 0.05). AMPV as the secondary pathogen impaired the bacterial attachment process. Consequently, the M. gallispeticum replication was delayed, the innate immune response was less pronounced, and lesions appeared later. Our results suggest a competing process in co-infections and offer new insights in disease processes.
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Affiliation(s)
- Nancy Rüger
- Clinic for Poultry, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (N.R.); (F.B.)
| | - Hicham Sid
- Reproductive Biotechnology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Munich, Germany;
| | - Jochen Meens
- Institute for Microbiology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, 30559 Hannover, Germany;
| | - Michael P. Szostak
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria;
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany;
| | - Frederik Bexter
- Clinic for Poultry, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (N.R.); (F.B.)
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (N.R.); (F.B.)
- Correspondence: ; Tel.: +49-511-953-8779
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12
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Surabhi S, Jachmann LH, Lalk M, Hammerschmidt S, Methling K, Siemens N. Bronchial Epithelial Cells Accumulate Citrate Intracellularly in Response to Pneumococcal Hydrogen Peroxide. ACS Infect Dis 2021; 7:2971-2978. [PMID: 34623132 DOI: 10.1021/acsinfecdis.1c00372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Community-acquired pneumonia is an infection of the lower respiratory tract caused by various viral and bacterial pathogens, including influenza A virus (IAV), Streptococcus pneumoniae, and Staphylococcus aureus. To understand the disease pathology, it is important to delineate host metabolic responses to an infection. In this study, metabolome profiling of mono- and coinfected human bronchial epithelial cells was performed. We show that IAV and S. aureus silently survive within the cells with almost negligible effects on the host metabolome. In contrast, S. pneumoniae significantly altered various host pathways such as glycolysis, tricarboxylic acid cycle, and amino acid metabolism. Intracellular citrate accumulation was the most prominent signature of pneumococcal infections and was directly attributed to the action of pneumococci-derived hydrogen peroxide. No coinfection specific metabolome signatures were observed.
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Affiliation(s)
- Surabhi Surabhi
- Department of Molecular Genetics and Infection Biology, University of Greifswald, D-17489 Greifswald, Germany
| | - Lana H. Jachmann
- Department of Molecular Genetics and Infection Biology, University of Greifswald, D-17489 Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, D-17489 Greifswald, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, University of Greifswald, D-17489 Greifswald, Germany
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, D-17489 Greifswald, Germany
| | - Nikolai Siemens
- Department of Molecular Genetics and Infection Biology, University of Greifswald, D-17489 Greifswald, Germany
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13
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Viral and Bacterial Co-Infections in the Lungs: Dangerous Liaisons. Viruses 2021; 13:v13091725. [PMID: 34578306 PMCID: PMC8472850 DOI: 10.3390/v13091725] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022] Open
Abstract
Respiratory tract infections constitute a significant public health problem, with a therapeutic arsenal that remains relatively limited and that is threatened by the emergence of antiviral and/or antibiotic resistance. Viral–bacterial co-infections are very often associated with the severity of these respiratory infections and have been explored mainly in the context of bacterial superinfections following primary influenza infection. This review summarizes our current knowledge of the mechanisms underlying these co-infections between respiratory viruses (influenza viruses, RSV, and SARS-CoV-2) and bacteria, at both the physiological and immunological levels. This review also explores the importance of the microbiome and the pathological context in the evolution of these respiratory tract co-infections and presents the different in vitro and in vivo experimental models available. A better understanding of the complex functional interactions between viruses/bacteria and host cells will allow the development of new, specific, and more effective diagnostic and therapeutic approaches.
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14
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Adivitiya, Kaushik MS, Chakraborty S, Veleri S, Kateriya S. Mucociliary Respiratory Epithelium Integrity in Molecular Defense and Susceptibility to Pulmonary Viral Infections. BIOLOGY 2021; 10:95. [PMID: 33572760 PMCID: PMC7911113 DOI: 10.3390/biology10020095] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/08/2023]
Abstract
Mucociliary defense, mediated by the ciliated and goblet cells, is fundamental to respiratory fitness. The concerted action of ciliary movement on the respiratory epithelial surface and the pathogen entrapment function of mucus help to maintain healthy airways. Consequently, genetic or acquired defects in lung defense elicit respiratory diseases and secondary microbial infections that inflict damage on pulmonary function and may even be fatal. Individuals living with chronic and acute respiratory diseases are more susceptible to develop severe coronavirus disease-19 (COVID-19) illness and hence should be proficiently managed. In light of the prevailing pandemic, we review the current understanding of the respiratory system and its molecular components with a major focus on the pathophysiology arising due to collapsed respiratory epithelium integrity such as abnormal ciliary movement, cilia loss and dysfunction, ciliated cell destruction, and changes in mucus rheology. The review includes protein interaction networks of coronavirus infection-manifested implications on the molecular machinery that regulates mucociliary clearance. We also provide an insight into the alteration of the transcriptional networks of genes in the nasopharynx associated with the mucociliary clearance apparatus in humans upon infection by severe acute respiratory syndrome coronavirus-2.
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Affiliation(s)
- Adivitiya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Manish Singh Kaushik
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Soura Chakraborty
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Shobi Veleri
- Drug Safety Division, ICMR-National Institute of Nutrition, Hyderabad 500007, India;
| | - Suneel Kateriya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
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15
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RSV and HMPV Infections in 3D Tissue Cultures: Mechanisms Involved in Virus-Host and Virus-Virus Interactions. Viruses 2021; 13:v13010139. [PMID: 33478119 PMCID: PMC7835908 DOI: 10.3390/v13010139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections constitute a global public health concern. Among prevalent respiratory viruses, two pneumoviruses can be life-threatening in high-risk populations. In young children, they constitute the first cause of hospitalization due to severe lower respiratory tract diseases. A better understanding of their pathogenesis is still needed as there are no approved efficient anti-viral nor vaccine against pneumoviruses. We studied Respiratory Syncytial virus (RSV) and human Metapneumovirus (HMPV) in single and dual infections in three-dimensional cultures, a highly relevant model to study viral respiratory infections of the airway epithelium. Our investigation showed that HMPV is less pathogenic than RSV in this model. Compared to RSV, HMPV replicated less efficiently, induced a lower immune response, did not block cilia beating, and was more sensitive to IFNs. In dual infections, RSV-infected epithelia were less permissive to HMPV. By neutralizing IFNs in co-infection assays, we partially prevented HMPV inhibition by RSV and significantly increased the number of co-infected cells in the tissue. This suggests that interference in dual infection would be at least partly mediated by the host immune response. In summary, this work provides new insight regarding virus-host and virus-virus interactions of pneumoviruses in the airway epithelium. This could be helpful for the proper handling of at-risk patients.
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16
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[Virological diagnosis of lower respiratory tract infections]. Rev Mal Respir 2021; 38:58-73. [PMID: 33461842 DOI: 10.1016/j.rmr.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 08/06/2020] [Indexed: 11/21/2022]
Abstract
INTRODUCTION The etiological diagnosis of bronchopulmonary infections cannot be assessed with clinical, radiological and epidemiological data alone. Viruses have been demonstrated to cause a large proportion of these infections, both in children and adults. BACKGROUND The diagnosis of viral bronchopulmonary infections is based on the analysis of secretions, collected from the lower respiratory tract when possible, by techniques that detect either influenza and respiratory syncytial viruses, or a large panel of viruses that can be responsible for respiratory disease. The latter, called multiplex PCR assays, allow a syndromic approach to respiratory infection. Their high cost for the laboratory raises the question of their place in the management of patients in terms of antibiotic economy and isolation. In the absence of clear recommendations, the strategy and equipment are very unevenly distributed in France. OUTLOOK Medico-economic analyses need to be performed in France to evaluate the place of these tests in the management of patients. The evaluation of the role of the different viruses often detected in co-infection, especially in children, also deserves the attention of virologists and clinicians. CONCLUSIONS The availability of new diagnostic technologies, the recent emergence of SARS-CoV-2, together with the availability of new antiviral drugs are likely to impact future recommendations for the management of viral bronchopulmonary infections.
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17
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Nicolas de Lamballerie C, Pizzorno A, Fouret J, Szpiro L, Padey B, Dubois J, Julien T, Traversier A, Dulière V, Brun P, Lina B, Rosa-Calatrava M, Terrier O. Transcriptional Profiling of Immune and Inflammatory Responses in the Context of SARS-CoV-2 Fungal Superinfection in a Human Airway Epithelial Model. Microorganisms 2020; 8:microorganisms8121974. [PMID: 33322535 PMCID: PMC7764715 DOI: 10.3390/microorganisms8121974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 01/08/2023] Open
Abstract
An increasing amount of evidence indicates a relatively high prevalence of superinfections associated with coronavirus disease 2019 (COVID-19), including invasive aspergillosis, but the underlying mechanisms remain to be characterized. In the present study, to better understand the biological impact of superinfection, we determine and compare the host transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) versus Aspergillus superinfection, using a model of reconstituted human airway epithelium. Our analyses reveal that both simple infection and superinfection induce strong deregulation of core components of innate immune and inflammatory responses, with a stronger response to superinfection in the bronchial epithelial model compared to its nasal counterpart. Our results also highlight unique transcriptional footprints of SARS-CoV-2 Aspergillus superinfection, such as an imbalanced type I/type III IFN, and an induction of several monocyte and neutrophil associated chemokines, that could be useful for the understanding of Aspergillus-associated COVID-19 and also the management of severe forms of aspergillosis in this specific context.
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Affiliation(s)
- Claire Nicolas de Lamballerie
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | | | - Lea Szpiro
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | - Blandine Padey
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- Signia Therapeutics SAS, F-69008 Lyon, France;
| | - Julia Dubois
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | - Thomas Julien
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, F-69008 Lyon, France
| | - Aurélien Traversier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | - Victoria Dulière
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, F-69008 Lyon, France
| | - Pauline Brun
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, F-69008 Lyon, France
| | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- Laboratoire de Virologie, Centre National de Référence des virus Influenza Sud, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, F-69004 Lyon, France
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, F-69008 Lyon, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- Correspondence:
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18
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Sajuthi SP, DeFord P, Li Y, Jackson ND, Montgomery MT, Everman JL, Rios CL, Pruesse E, Nolin JD, Plender EG, Wechsler ME, Mak ACY, Eng C, Salazar S, Medina V, Wohlford EM, Huntsman S, Nickerson DA, Germer S, Zody MC, Abecasis G, Kang HM, Rice KM, Kumar R, Oh S, Rodriguez-Santana J, Burchard EG, Seibold MA. Type 2 and interferon inflammation regulate SARS-CoV-2 entry factor expression in the airway epithelium. Nat Commun 2020; 11:5139. [PMID: 33046696 PMCID: PMC7550582 DOI: 10.1038/s41467-020-18781-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/08/2020] [Indexed: 11/08/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2, an emerging virus that utilizes host proteins ACE2 and TMPRSS2 as entry factors. Understanding the factors affecting the pattern and levels of expression of these genes is important for deeper understanding of SARS-CoV-2 tropism and pathogenesis. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci for both ACE2 and TMPRSS2, that vary in frequency across world populations. We find TMPRSS2 is part of a mucus secretory network, highly upregulated by type 2 (T2) inflammation through the action of interleukin-13, and that the interferon response to respiratory viruses highly upregulates ACE2 expression. IL-13 and virus infection mediated effects on ACE2 expression were also observed at the protein level in the airway epithelium. Finally, we define airway responses to common coronavirus infections in children, finding that these infections generate host responses similar to other viral species, including upregulation of IL6 and ACE2. Our results reveal possible mechanisms influencing SARS-CoV-2 infectivity and COVID-19 clinical outcomes.
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Grants
- R01 ES015794 NIEHS NIH HHS
- R01 HL120393 NHLBI NIH HHS
- HL128439 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL141992 NHLBI NIH HHS
- UM1 HG008901 NHGRI NIH HHS
- R01 HL141845 NHLBI NIH HHS
- HL107202 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HHSN268201800001C NHLBI NIH HHS
- U01 HG009080 NHGRI NIH HHS
- HL138626 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL117626 NHLBI NIH HHS
- HL135156 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HL132821 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P01 HL107202 NHLBI NIH HHS
- K01 HL140218 NHLBI NIH HHS
- U01 HL120393 NHLBI NIH HHS
- HL117004 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL135156 NHLBI NIH HHS
- T32 GM007546 NIGMS NIH HHS
- MD010443 U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)
- R01 HL128439 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- P60 MD006902 NIMHD NIH HHS
- HHSN268201600032C NHLBI NIH HHS
- U24 HG008956 NHGRI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- R01 MD010443 NIMHD NIH HHS
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Affiliation(s)
- Satria P Sajuthi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Peter DeFord
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Yingchun Li
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Michael T Montgomery
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Cydney L Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Elmar Pruesse
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - James D Nolin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Elizabeth G Plender
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | | | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sandra Salazar
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vivian Medina
- Centro de Neumología Pediátrica, San Juan, Puerto Rico
| | - Eric M Wohlford
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of Pediatric Allergy and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Northwest Genomics Center, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | | | | | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hyun Min Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Rajesh Kumar
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University, Chicago, IL, USA
| | - Sam Oh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
- Department of Pediatrics, National Jewish Health, Denver, CO, USA.
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado-AMC, Aurora, CO, USA.
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19
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Kuek LE, Lee RJ. First contact: the role of respiratory cilia in host-pathogen interactions in the airways. Am J Physiol Lung Cell Mol Physiol 2020; 319:L603-L619. [PMID: 32783615 PMCID: PMC7516383 DOI: 10.1152/ajplung.00283.2020] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Respiratory cilia are the driving force of the mucociliary escalator, working in conjunction with secreted airway mucus to clear inhaled debris and pathogens from the conducting airways. Respiratory cilia are also one of the first contact points between host and inhaled pathogens. Impaired ciliary function is a common pathological feature in patients with chronic airway diseases, increasing susceptibility to respiratory infections. Common respiratory pathogens, including viruses, bacteria, and fungi, have been shown to target cilia and/or ciliated airway epithelial cells, resulting in a disruption of mucociliary clearance that may facilitate host infection. Despite being an integral component of airway innate immunity, the role of respiratory cilia and their clinical significance during airway infections are still poorly understood. This review examines the expression, structure, and function of respiratory cilia during pathogenic infection of the airways. This review also discusses specific known points of interaction of bacteria, fungi, and viruses with respiratory cilia function. The emerging biological functions of motile cilia relating to intracellular signaling and their potential immunoregulatory roles during infection will also be discussed.
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Affiliation(s)
- Li Eon Kuek
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Robert J Lee
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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20
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Respiratory Syncytial Virus and Human Metapneumovirus Infections in Three-Dimensional Human Airway Tissues Expose an Interesting Dichotomy in Viral Replication, Spread, and Inhibition by Neutralizing Antibodies. J Virol 2020; 94:JVI.01068-20. [PMID: 32759319 DOI: 10.1128/jvi.01068-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are two of the leading causes of respiratory infections in children and elderly and immunocompromised patients worldwide. There is no approved treatment for HMPV and only one prophylactic treatment against RSV, palivizumab, for high-risk infants. Better understanding of the viral lifecycles in a more relevant model system may help identify novel therapeutic targets. By utilizing three-dimensional (3-D) human airway tissues to examine viral infection in a physiologically relevant model system, we showed that RSV infects and spreads more efficiently than HMPV, with the latter requiring higher multiplicities of infection (MOIs) to yield similar levels of infection. Apical ciliated cells were the target for both viruses, but RSV apical release was significantly more efficient than HMPV. In RSV- or HMPV-infected cells, cytosolic inclusion bodies containing the nucleoprotein, phosphoprotein, and respective viral genomic RNA were clearly observed in human airway epithelial (HAE) culture. In HMPV-infected cells, actin-based filamentous extensions were more common (35.8%) than those found in RSV-infected cells (4.4%). Interestingly, neither RSV nor HMPV formed syncytia in HAE tissues. Palivizumab and nirsevimab effectively inhibited entry and spread of RSV in HAE tissues, with nirsevimab displaying significantly higher potency than palivizumab. In contrast, 54G10 completely inhibited HMPV entry but only modestly reduced viral spread, suggesting HMPV may use alternative mechanisms for spread. These results represent the first comparative analysis of infection by the two pneumoviruses in a physiologically relevant model, demonstrating an interesting dichotomy in the mechanisms of infection, spread, and consequent inhibition of the viral lifecycles by neutralizing monoclonal antibodies.IMPORTANCE Respiratory syncytial virus and human metapneumovirus are leading causes of respiratory illness worldwide, but limited treatment options are available. To better target these viruses, we examined key aspects of the viral life cycle in three-dimensional (3-D) human airway tissues. Both viruses establish efficient infection through the apical surface, but efficient spread and apical release were seen for respiratory syncytial virus (RSV) but not human metapneumovirus (HMPV). Both viruses form inclusion bodies, minimally composed of nucleoprotein (N), phosphoprotein (P), and viral RNA (vRNA), indicating that these structures are critical for replication in this more physiological model. HMPV formed significantly more long, filamentous actin-based extensions in human airway epithelial (HAE) tissues than RSV, suggesting HMPV may promote cell-to-cell spread via these extensions. Lastly, RSV entry and spread were fully inhibited by neutralizing antibodies palivizumab and the novel nirsevimab. In contrast, while HMPV entry was fully inhibited by 54G10, a neutralizing antibody, spread was only modestly reduced, further supporting a cell-to-cell spread mechanism.
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21
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Funnell SGP, Dowling WE, Muñoz-Fontela C, Gsell PS, Ingber DE, Hamilton GA, Delang L, Rocha-Pereira J, Kaptein S, Dallmeier KH, Neyts J, Rosenke K, de Wit E, Feldmann H, Maisonnasse P, Le Grand R, Frieman MB, Coleman CM. Emerging preclinical evidence does not support broad use of hydroxychloroquine in COVID-19 patients. Nat Commun 2020; 11:4253. [PMID: 32848158 PMCID: PMC7450055 DOI: 10.1038/s41467-020-17907-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/25/2020] [Indexed: 11/17/2022] Open
Abstract
There is an urgent need for drugs, therapies and vaccines to be available to protect the human population against COVID-19. One of the first approaches taken in the COVID-19 global response was to consider repurposing licensed drugs. This commentary highlights an extraordinary international collaborative effort of independent researchers who have recently all come to the same conclusion—that chloroquine or hydroxchloroquine are unlikely to provide clinical benefit against COVID-19.
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Affiliation(s)
- S G P Funnell
- National Infection Service, Public Health England, Porton Down, Manor Farm Road, Salisbury, Wiltshire, SP40JG, UK.
| | - W E Dowling
- Coalition for Epidemic Preparedness Innovations, 1901 Pennsylvania Avenue, NW, Suite 1003, Washington, DC, 20006, USA
| | - C Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Strasse. 74, 20359, Hamburg, Germany
| | - P-S Gsell
- World Health Organisation, Avenue Appia, 1211, Geneva, Switzerland
| | - D E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, CLSB5, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - G A Hamilton
- Emulate Inc., 27 Drydock Avenue, 5th Floor, Boston, MA, 02210, USA
| | - L Delang
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, Global Virus Network, KU Leuven, 3000, Leuven, Belgium
| | - J Rocha-Pereira
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, Global Virus Network, KU Leuven, 3000, Leuven, Belgium
| | - S Kaptein
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, Global Virus Network, KU Leuven, 3000, Leuven, Belgium
| | - K H Dallmeier
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, Global Virus Network, KU Leuven, 3000, Leuven, Belgium
| | - J Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, Global Virus Network, KU Leuven, 3000, Leuven, Belgium
| | - K Rosenke
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, 59840, MT, USA
| | - E de Wit
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, 59840, MT, USA
| | - H Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, 59840, MT, USA
| | - P Maisonnasse
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, 92265, France
| | - R Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, 92265, France
| | - M B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - C M Coleman
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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22
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Nicolas De Lamballerie C, Pizzorno A, Dubois J, Padey B, Julien T, Traversier A, Carbonneau J, Orcel E, Lina B, Hamelin ME, Roche M, Textoris J, Boivin G, Legras-Lachuer C, Terrier O, Rosa-Calatrava M. Human Respiratory Syncytial Virus-Induced Immune Signature of Infection Revealed by Transcriptome Analysis of Clinical Pediatric Nasopharyngeal Swab Samples. J Infect Dis 2020; 223:1052-1061. [PMID: 32726438 DOI: 10.1093/infdis/jiaa468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/24/2020] [Indexed: 11/12/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) constitutes one the main causes of respiratory infection in neonates and infants worldwide. Transcriptome analysis of clinical samples using high-throughput technologies remains an important tool to better understand virus-host complex interactions in the real-life setting but also to identify new diagnosis/prognosis markers or therapeutics targets. A major challenge when exploiting clinical samples such as nasal swabs, washes, or bronchoalveolar lavages is the poor quantity and integrity of nucleic acids. In this study, we applied a tailored transcriptomics workflow to exploit nasal wash samples from children who tested positive for HRSV. Our analysis revealed a characteristic immune signature as a direct reflection of HRSV pathogenesis and highlighted putative biomarkers of interest such as IP-10, TMEM190, MCEMP1, and TIMM23.
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Affiliation(s)
- Claire Nicolas De Lamballerie
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,Viroscan3D SAS, Lyon, France
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Julia Dubois
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Blandine Padey
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Thomas Julien
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Aurélien Traversier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Julie Carbonneau
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | | | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Marie-Eve Hamelin
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | | | - Julien Textoris
- Pathophysiology of Injury-Induced Immunosuppression, Hospices Civils de Lyon, bioMérieux, Université Claude Bernard Lyon 1, Hôpital Edouard Herriot, Lyon, France
| | - Guy Boivin
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | - Catherine Legras-Lachuer
- Viroscan3D SAS, Lyon, France.,Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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23
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Maisonnasse P, Guedj J, Contreras V, Behillil S, Solas C, Marlin R, Naninck T, Pizzorno A, Lemaitre J, Gonçalves A, Kahlaoui N, Terrier O, Fang RHT, Enouf V, Dereuddre-Bosquet N, Brisebarre A, Touret F, Chapon C, Hoen B, Lina B, Calatrava MR, van der Werf S, de Lamballerie X, Le Grand R. Hydroxychloroquine use against SARS-CoV-2 infection in non-human primates. Nature 2020; 585:584-587. [PMID: 32698191 DOI: 10.1038/s41586-020-2558-4] [Citation(s) in RCA: 228] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) has rapidly become a global pandemic and no antiviral drug or vaccine is yet available for the treatment of this disease1-3. Several clinical studies are ongoing to evaluate the efficacy of repurposed drugs that have demonstrated antiviral efficacy in vitro. Among these candidates, hydroxychloroquine (HCQ) has been given to thousands of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the virus that causes COVID-19-worldwide but there is no definitive evidence that HCQ is effective for treating COVID-194-7. Here we evaluated the antiviral activity of HCQ both in vitro and in SARS-CoV-2-infected macaques. HCQ showed antiviral activity in African green monkey kidney cells (Vero E6) but not in a model of reconstituted human airway epithelium. In macaques, we tested different treatment strategies in comparison to a placebo treatment, before and after peak viral load, alone or in combination with azithromycin (AZTH). Neither HCQ nor the combination of HCQ and AZTH showed a significant effect on viral load in any of the analysed tissues. When the drug was used as a pre-exposure prophylaxis treatment, HCQ did not confer protection against infection with SARS-CoV-2. Our findings do not support the use of HCQ, either alone or in combination with AZTH, as an antiviral drug for the treatment of COVID-19 in humans.
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Affiliation(s)
- Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | - Vanessa Contreras
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Sylvie Behillil
- Unité de Génétique Moléculaire des Virus à ARN, GMVR, Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France.,Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Caroline Solas
- Laboratoire de Pharmacocinétique et Toxicologie, Aix-Marseille Université, APHM, Unité des Virus Emergents (UVE) IRD 190, INSERM 1207, Hôpital La Timone, Marseille, France
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Andres Pizzorno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Julien Lemaitre
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Raphael Ho Tsong Fang
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Vincent Enouf
- Unité de Génétique Moléculaire des Virus à ARN, GMVR, Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France.,Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France.,Plate-forme de microbiologie mutualisée (P2M), Pasteur International Bioresources Network (PIBnet), Institut Pasteur, Paris, France
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Angela Brisebarre
- Unité de Génétique Moléculaire des Virus à ARN, GMVR, Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France.,Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Franck Touret
- Unité des Virus Emergents (UVE), Aix-Marseille Université, IRD 190, INSERM 1207, IHU Méditerranée Infection, Marseille, France
| | - Catherine Chapon
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Bruno Hoen
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France
| | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France.,Laboratoire de Virologie, Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Manuel Rosa Calatrava
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, GMVR, Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France.,Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Emergents (UVE), Aix-Marseille Université, IRD 190, INSERM 1207, IHU Méditerranée Infection, Marseille, France
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France.
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24
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Pizzorno A, Padey B, Julien T, Trouillet-Assant S, Traversier A, Errazuriz-Cerda E, Fouret J, Dubois J, Gaymard A, Lescure FX, Dulière V, Brun P, Constant S, Poissy J, Lina B, Yazdanpanah Y, Terrier O, Rosa-Calatrava M. Characterization and Treatment of SARS-CoV-2 in Nasal and Bronchial Human Airway Epithelia. Cell Rep Med 2020; 1:100059. [PMID: 32835306 DOI: 10.1101/2020.03.31.017889] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/01/2020] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
In the current COVID-19 pandemic context, proposing and validating effective treatments represents a major challenge. However, the scarcity of biologically relevant pre-clinical models of SARS-CoV-2 infection imposes a significant barrier for scientific and medical progress, including the rapid transition of potentially effective treatments to the clinical setting. We use reconstituted human airway epithelia to isolate and then characterize the viral infection kinetics, tissue-level remodeling of the cellular ultrastructure, and transcriptional early immune signatures induced by SARS-CoV-2 in a physiologically relevant model. Our results emphasize distinctive transcriptional immune signatures between nasal and bronchial HAE, both in terms of kinetics and intensity, hence suggesting putative intrinsic differences in the early response to SARS-CoV-2 infection. Most important, we provide evidence in human-derived tissues on the antiviral efficacy of remdesivir monotherapy and explore the potential of the remdesivir-diltiazem combination as an option worthy of further investigation to respond to the still-unmet COVID-19 medical need.
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Affiliation(s)
- Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Blandine Padey
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Signia Therapeutics SAS, Lyon, France
| | - Thomas Julien
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Sophie Trouillet-Assant
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Laboratoire Commun de Recherche HCL-bioMérieux, Centre Hospitalier Lyon-Sud, Pierre-Bénite, France
| | - Aurélien Traversier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | | | | | - Julia Dubois
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Alexandre Gaymard
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Laboratoire de Virologie, Centre National de Référence des Virus Influenza Sud, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - François-Xavier Lescure
- AP-HP, Infectious and Tropical Diseases Department, Bichat-Claude Bernard University Hospital, Paris, France
- University of Paris, French Institute for Health and Medical Research (INSERM), IAME U1137, Team DesCID, Paris, France
| | - Victoria Dulière
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Pauline Brun
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | | | - Julien Poissy
- Pôle de Réanimation, Hôpital Roger Salengro, Centre Hospitalier Régional et Universitaire de Lille, Université de Lille 2, Lille, France
| | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Laboratoire de Virologie, Centre National de Référence des Virus Influenza Sud, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Yazdan Yazdanpanah
- AP-HP, Infectious and Tropical Diseases Department, Bichat-Claude Bernard University Hospital, Paris, France
- University of Paris, French Institute for Health and Medical Research (INSERM), IAME U1137, Team DesCID, Paris, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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25
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Pizzorno A, Padey B, Julien T, Trouillet-Assant S, Traversier A, Errazuriz-Cerda E, Fouret J, Dubois J, Gaymard A, Lescure FX, Dulière V, Brun P, Constant S, Poissy J, Lina B, Yazdanpanah Y, Terrier O, Rosa-Calatrava M. Characterization and Treatment of SARS-CoV-2 in Nasal and Bronchial Human Airway Epithelia. CELL REPORTS MEDICINE 2020; 1:100059. [PMID: 32835306 PMCID: PMC7373044 DOI: 10.1016/j.xcrm.2020.100059] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/01/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023]
Abstract
In the current COVID-19 pandemic context, proposing and validating effective treatments represents a major challenge. However, the scarcity of biologically relevant pre-clinical models of SARS-CoV-2 infection imposes a significant barrier for scientific and medical progress, including the rapid transition of potentially effective treatments to the clinical setting. We use reconstituted human airway epithelia to isolate and then characterize the viral infection kinetics, tissue-level remodeling of the cellular ultrastructure, and transcriptional early immune signatures induced by SARS-CoV-2 in a physiologically relevant model. Our results emphasize distinctive transcriptional immune signatures between nasal and bronchial HAE, both in terms of kinetics and intensity, hence suggesting putative intrinsic differences in the early response to SARS-CoV-2 infection. Most important, we provide evidence in human-derived tissues on the antiviral efficacy of remdesivir monotherapy and explore the potential of the remdesivir-diltiazem combination as an option worthy of further investigation to respond to the still-unmet COVID-19 medical need. We use reconstituted human airway epithelia to characterize SARS-CoV-2 infection kinetics SARS-CoV-2 induces characteristic remodeling of the respiratory epithelium cellular ultrastructure SARS-CoV-2 induces differential early immune responses in nasal and bronchial HAE We evaluate the antiviral activity of remdesivir and remdesivir-diltiazem in both Vero E6 and HAE models
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Affiliation(s)
- Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Blandine Padey
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Signia Therapeutics SAS, Lyon, France
| | - Thomas Julien
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Sophie Trouillet-Assant
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Laboratoire Commun de Recherche HCL-bioMérieux, Centre Hospitalier Lyon-Sud, Pierre-Bénite, France
| | - Aurélien Traversier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | | | | | - Julia Dubois
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Alexandre Gaymard
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Laboratoire de Virologie, Centre National de Référence des Virus Influenza Sud, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - François-Xavier Lescure
- AP-HP, Infectious and Tropical Diseases Department, Bichat-Claude Bernard University Hospital, Paris, France
- University of Paris, French Institute for Health and Medical Research (INSERM), IAME U1137, Team DesCID, Paris, France
| | - Victoria Dulière
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Pauline Brun
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | | | - Julien Poissy
- Pôle de Réanimation, Hôpital Roger Salengro, Centre Hospitalier Régional et Universitaire de Lille, Université de Lille 2, Lille, France
| | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Laboratoire de Virologie, Centre National de Référence des Virus Influenza Sud, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Yazdan Yazdanpanah
- AP-HP, Infectious and Tropical Diseases Department, Bichat-Claude Bernard University Hospital, Paris, France
- University of Paris, French Institute for Health and Medical Research (INSERM), IAME U1137, Team DesCID, Paris, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Corresponding author
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- Corresponding author
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Ballegeer M, Saelens X. Cell-Mediated Responses to Human Metapneumovirus Infection. Viruses 2020; 12:v12050542. [PMID: 32423043 PMCID: PMC7290942 DOI: 10.3390/v12050542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 12/29/2022] Open
Abstract
Viruses are the most common cause of acute respiratory tract infections (ARTI). Human metapneumovirus (hMPV) frequently causes viral pneumonia which can become life-threatening if the virus spreads to the lungs. Even though hMPV was only isolated in 2001, this negative-stranded RNA virus has probably been circulating in the human population for many decades. Interestingly, almost all adults have serologic evidence of hMPV infection. A well-established host immune response is evoked when hMPV infection occurs. However, the virus has evolved to circumvent and even exploit the host immune response. Further, infection with hMPV induces a weak memory response, and re-infections during life are common. In this review, we provide a comprehensive overview of the different cell types involved in the immune response in order to better understand the immunopathology induced by hMPV. Such knowledge may contribute to the development of vaccines and therapeutics directed against hMPV.
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Affiliation(s)
- Marlies Ballegeer
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium;
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium;
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
- Correspondence:
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27
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Cell-Mediated Responses to Human Metapneumovirus Infection. Viruses 2020; 12:542. [PMID: 32423043 PMCID: PMC7290942 DOI: 10.3390/v12050542&set/a 882111696+808152660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Viruses are the most common cause of acute respiratory tract infections (ARTI). Human metapneumovirus (hMPV) frequently causes viral pneumonia which can become life-threatening if the virus spreads to the lungs. Even though hMPV was only isolated in 2001, this negative-stranded RNA virus has probably been circulating in the human population for many decades. Interestingly, almost all adults have serologic evidence of hMPV infection. A well-established host immune response is evoked when hMPV infection occurs. However, the virus has evolved to circumvent and even exploit the host immune response. Further, infection with hMPV induces a weak memory response, and re-infections during life are common. In this review, we provide a comprehensive overview of the different cell types involved in the immune response in order to better understand the immunopathology induced by hMPV. Such knowledge may contribute to the development of vaccines and therapeutics directed against hMPV.
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28
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Cell-Mediated Responses to Human Metapneumovirus Infection. Viruses 2020. [DOI: 10.3390/v12050542
expr 836379838 + 819716165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Viruses are the most common cause of acute respiratory tract infections (ARTI). Human metapneumovirus (hMPV) frequently causes viral pneumonia which can become life-threatening if the virus spreads to the lungs. Even though hMPV was only isolated in 2001, this negative-stranded RNA virus has probably been circulating in the human population for many decades. Interestingly, almost all adults have serologic evidence of hMPV infection. A well-established host immune response is evoked when hMPV infection occurs. However, the virus has evolved to circumvent and even exploit the host immune response. Further, infection with hMPV induces a weak memory response, and re-infections during life are common. In this review, we provide a comprehensive overview of the different cell types involved in the immune response in order to better understand the immunopathology induced by hMPV. Such knowledge may contribute to the development of vaccines and therapeutics directed against hMPV.
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29
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Sajuthi SP, DeFord P, Jackson ND, Montgomery MT, Everman JL, Rios CL, Pruesse E, Nolin JD, Plender EG, Wechsler ME, Mak ACY, Eng C, Salazar S, Medina V, Wohlford EM, Huntsman S, Nickerson DA, Germer S, Zody MC, Abecasis G, Kang HM, Rice KM, Kumar R, Oh S, Rodriguez-Santana J, Burchard EG, Seibold MA. Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.09.034454. [PMID: 32511326 PMCID: PMC7239056 DOI: 10.1101/2020.04.09.034454] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) outcomes vary from asymptomatic infection to death. This disparity may reflect different airway levels of the SARS-CoV-2 receptor, ACE2, and the spike protein activator, TMPRSS2. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci (eQTL) for both ACE2 and TMPRSS2, that vary in frequency across world populations. Importantly, we find TMPRSS2 is part of a mucus secretory network, highly upregulated by T2 inflammation through the action of interleukin-13, and that interferon response to respiratory viruses highly upregulates ACE2 expression. Finally, we define airway responses to coronavirus infections in children, finding that these infections upregulate IL6 while also stimulating a more pronounced cytotoxic immune response relative to other respiratory viruses. Our results reveal mechanisms likely influencing SARS-CoV-2 infectivity and COVID-19 clinical outcomes.
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Affiliation(s)
- Satria P. Sajuthi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Peter DeFord
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Nathan D. Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Michael T. Montgomery
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Jamie L. Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Cydney L. Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Elmar Pruesse
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - James D. Nolin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Elizabeth G. Plender
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | | | - Angel CY Mak
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Celeste Eng
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Sandra Salazar
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Vivian Medina
- Centro de Neumología Pediátrica, San Juan, Puerto Rico
| | - Eric M. Wohlford
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
- Division of Pediatric Allergy and Immunology, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Scott Huntsman
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Northwest Genomics Center, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | | | | | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hyun Min Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kenneth M. Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, III
| | - Sam Oh
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | | | - Esteban G. Burchard
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
- Department of Bioengineering and Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Max A. Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
- Department of Pediatrics, National Jewish Health, Denver, CO, 80206 USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado-AMC, Aurora, CO, 80045 USA
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30
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Dubois J, Pizzorno A, Cavanagh MH, Padey B, Nicolas de Lamballerie C, Uyar O, Venable MC, Carbonneau J, Traversier A, Julien T, Lavigne S, Couture C, Lina B, Hamelin MÈ, Terrier O, Rosa-Calatrava M, Boivin G. Strain-Dependent Impact of G and SH Deletions Provide New Insights for Live-Attenuated HMPV Vaccine Development. Vaccines (Basel) 2019; 7:vaccines7040164. [PMID: 31671656 PMCID: PMC6963613 DOI: 10.3390/vaccines7040164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 01/15/2023] Open
Abstract
Human metapneumovirus (HMPV) is a major pediatric respiratory pathogen with currently no specific treatment or licensed vaccine. Different strategies to prevent this infection have been evaluated, including live-attenuated vaccines (LAV) based on SH and/or G protein deletions. This approach showed promising outcomes but has not been evaluated further using different viral strains. In that regard, we previously showed that different HMPV strains harbor distinct in vitro fusogenic and in vivo pathogenic phenotypes, possibly influencing the selection of vaccine strains. In this study, we investigated the putative contribution of the low conserved SH or G accessory proteins in such strain-dependent phenotypes and generated recombinant wild type (WT) and SH- or G-deleted viruses derived from two different patient-derived HMPV strains, A1/C-85473 and B2/CAN98-75. The ΔSH and ΔG deletions led to different strain-specific phenotypes in both LLC-MK2 cell and reconstituted human airway epithelium models. More interestingly, the ΔG-85473 and especially ΔSH-C-85473 recombinant viruses conferred significant protection against HMPV challenge and induced immunogenicity against a heterologous strain. In conclusion, our results show that the viral genetic backbone should be considered in the design of live-attenuated HMPV vaccines, and that a SH-deleted virus based on the A1/C-85473 HMPV strain could be a promising LAV candidate as it is both attenuated and protective in mice while being efficiently produced in a cell-based system.
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Affiliation(s)
- Julia Dubois
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
- Centre de Recherche en Infectiologie of the Centre Hospitalier Universitaire de Québec and Université Laval, QC G1V 4G2, Canada.
| | - Andrés Pizzorno
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
| | - Marie-Hélène Cavanagh
- Centre de Recherche en Infectiologie of the Centre Hospitalier Universitaire de Québec and Université Laval, QC G1V 4G2, Canada.
| | - Blandine Padey
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
| | - Claire Nicolas de Lamballerie
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
| | - Olus Uyar
- Centre de Recherche en Infectiologie of the Centre Hospitalier Universitaire de Québec and Université Laval, QC G1V 4G2, Canada.
| | - Marie-Christine Venable
- Centre de Recherche en Infectiologie of the Centre Hospitalier Universitaire de Québec and Université Laval, QC G1V 4G2, Canada.
| | - Julie Carbonneau
- Centre de Recherche en Infectiologie of the Centre Hospitalier Universitaire de Québec and Université Laval, QC G1V 4G2, Canada.
| | - Aurélien Traversier
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
| | - Thomas Julien
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
| | - Sophie Lavigne
- Quebec Heart and Lung Institute, Laval University, Quebec City, QC G1V 4G5, Canada.
| | - Christian Couture
- Quebec Heart and Lung Institute, Laval University, Quebec City, QC G1V 4G5, Canada.
| | - Bruno Lina
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
- Laboratoire de Virologie, Centre National de Référence des virus Influenza, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, 69004 Lyon, France.
| | - Marie-Ève Hamelin
- Centre de Recherche en Infectiologie of the Centre Hospitalier Universitaire de Québec and Université Laval, QC G1V 4G2, Canada.
| | - Olivier Terrier
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
| | - Manuel Rosa-Calatrava
- Laboratoire de Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France.
| | - Guy Boivin
- Centre de Recherche en Infectiologie of the Centre Hospitalier Universitaire de Québec and Université Laval, QC G1V 4G2, Canada.
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