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Rezapour M, Walker SJ, Ornelles DA, McNutt PM, Atala A, Gurcan MN. Analysis of gene expression dynamics and differential expression in viral infections using generalized linear models and quasi-likelihood methods. Front Microbiol 2024; 15:1342328. [PMID: 38655085 PMCID: PMC11037428 DOI: 10.3389/fmicb.2024.1342328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Our study undertakes a detailed exploration of gene expression dynamics within human lung organ tissue equivalents (OTEs) in response to Influenza A virus (IAV), Human metapneumovirus (MPV), and Parainfluenza virus type 3 (PIV3) infections. Through the analysis of RNA-Seq data from 19,671 genes, we aim to identify differentially expressed genes under various infection conditions, elucidating the complexities of virus-host interactions. Methods We employ Generalized Linear Models (GLMs) with Quasi-Likelihood (QL) F-tests (GLMQL) and introduce the novel Magnitude-Altitude Score (MAS) and Relaxed Magnitude-Altitude Score (RMAS) algorithms to navigate the intricate landscape of RNA-Seq data. This approach facilitates the precise identification of potential biomarkers, highlighting the host's reliance on innate immune mechanisms. Our comprehensive methodological framework includes RNA extraction, library preparation, sequencing, and Gene Ontology (GO) enrichment analysis to interpret the biological significance of our findings. Results The differential expression analysis unveils significant changes in gene expression triggered by IAV, MPV, and PIV3 infections. The MAS and RMAS algorithms enable focused identification of biomarkers, revealing a consistent activation of interferon-stimulated genes (e.g., IFIT1, IFIT2, IFIT3, OAS1) across all viruses. Our GO analysis provides deep insights into the host's defense mechanisms and viral strategies exploiting host cellular functions. Notably, changes in cellular structures, such as cilium assembly and mitochondrial ribosome assembly, indicate a strategic shift in cellular priorities. The precision of our methodology is validated by a 92% mean accuracy in classifying respiratory virus infections using multinomial logistic regression, demonstrating the superior efficacy of our approach over traditional methods. Discussion This study highlights the intricate interplay between viral infections and host gene expression, underscoring the need for targeted therapeutic interventions. The stability and reliability of the MAS/RMAS ranking method, even under stringent statistical corrections, and the critical importance of adequate sample size for biomarker reliability are significant findings. Our comprehensive analysis not only advances our understanding of the host's response to viral infections but also sets a new benchmark for the identification of biomarkers, paving the way for the development of effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Mostafa Rezapour
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Stephen J. Walker
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - David A. Ornelles
- Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Patrick M. McNutt
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Metin Nafi Gurcan
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, United States
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Veronese A, Uršič T, Bizjak Vojinovič S, Rodman Berlot J. Exploring Clinical Predictors of Severe Human Metapneumovirus Respiratory Tract Infections in Children: Insights from a Recent Outbreak. Microorganisms 2024; 12:641. [PMID: 38674586 PMCID: PMC11052206 DOI: 10.3390/microorganisms12040641] [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: 02/25/2024] [Revised: 03/11/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Human metapneumovirus (hMPV) is an important pathogen that causes both upper (URTIs) and lower respiratory tract infections (LRTIs) in children. The virus can be implicated in severe bronchiolitis and pneumonia, necessitating hospitalization, with certain cases requiring intensive care unit intervention. As part of a retrospective observational study, we aimed to identify indicators of severe hMPV respiratory tract infections in children referred to the University Children's Hospital Ljubljana and the Department of Infectious Diseases Ljubljana, Slovenia, during a recent outbreak. We analyzed clinical data from November 2022 to January 2023 and compared the characteristics of children presenting with URTIs and LRTIs. We also examined the characteristics of children with hMPV LRTIs, distinguishing between children with and without LRTI-associated hypoxemia. Of 78 hMPV-PCR-positive pediatric patients (mean age 3.1 years; 60.3% boys), 36% had a URTI, and 64% had an LRTI. Hospitalization was required in 64% (50/78), with 42% (21/50) requiring oxygen therapy. LRTI-associated hypoxemia was more common in patients with atopy who showed dyspnea, tachypnea, crackles, and wheezing on lung auscultation. In a multivariable logistic regression analysis, wheezing detected on lung auscultation was a significant predictive factor for hypoxemic hMPV-LRTI. Specifically, children presenting with wheezing were found to be ten times more likely to experience hypoxemia. Prematurity and chronic conditions did not influence the presentation or severity of hMPV infection. This study highlights wheezing and atopy as crucial indicators of severe hMPV LRTI in children, emphasizing the importance of early recognition and intervention.
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Affiliation(s)
- Airin Veronese
- Department of Paediatric Pulmonology, University Children’s Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Tina Uršič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simona Bizjak Vojinovič
- Department of Infectious Diseases, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia;
| | - Jasna Rodman Berlot
- Department of Paediatric Pulmonology, University Children’s Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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Gan YZ, Yang P, Liu R, Wang YH, Hu YW, Yang Y. Changes in Spectrum of Respiratory Pathogen Infections and Disease Severity Among Children in Hohhot, China: Impact of COVID-19 Prevention Measures. Med Sci Monit 2024; 30:e942845. [PMID: 38451880 DOI: 10.12659/msm.942845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND This retrospective study evaluated the effects of specific COVID-19 preventive measures, including the use of medical masks, nucleic acid testing, and patient isolation, on respiratory infections, disease severity, and seasonal patterns among children in Hohhot, located in northern China. Understanding these alterations is pivotal in developing effective strategies to handle pediatric respiratory infections within the context of continuous public health initiatives. MATERIAL AND METHODS At the First Hospital of Hohhot, throat swabs were collected from 605 children with community-acquired respiratory between January 2022 and March 2023 for pathogen infection spectrum detection using microarray testing. RESULTS Among the patients, 56.03% were male, and their average age was 3.45 years. SARS-CoV-2 infections were highest between October 2022 and January 2023. Influenza A peaked in March 2023, and other pathogens such as respiratory syncytial virus and influenza B virus disappeared after December 2022. The proportion of mixed infections was 41.94% among SARS-CoV-2 patients, while other pathogens had mixed infection rates exceeding 57.14%. Before December 2022, the mean WBC count for Streptococcus pneumoniae and Haemophilus influenzae was 8.83×10⁹/L, CRP was 18.36 mg/L, and PCT was 1.11 ng/ml. After December 2022, these values decreased significantly. Coughing, difficulty breathing, running nose, and lower respiratory tract infection diagnoses decreased in December 2022, except for SARS-CoV-2 infections. CONCLUSIONS SARS-CoV-2 peaked around November 2022, influenza A peaked in March 2023, and other pathogens like respiratory syncytial virus and influenza B virus were greatly reduced after December 2022. Inflammatory markers and respiratory symptoms decreased after December 2022, except for SARS-CoV-2.
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Affiliation(s)
- Yan-Zi Gan
- Child Health Department, The First Hospital of Hohhot, Hohhot, Inner Mongolia, China (mainland)
| | - Peng Yang
- Neurophysiology Department, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China (mainland)
| | - Rui Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China (mainland)
| | - Yan-Hai Wang
- Child Health Department, The First Hospital of Hohhot, Hohhot, Inner Mongolia, China (mainland)
| | - Yu-Wei Hu
- Child Health Department, The First Hospital of Hohhot, Hohhot, Inner Mongolia, China (mainland)
| | - Yang Yang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China (mainland)
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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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Nadiger M, Sendi P, Martinez PA, Totapally BR. Epidemiology and Clinical Features of Human Metapneumovirus and Respiratory Syncytial Viral Infections in Children. Pediatr Infect Dis J 2023; 42:960-964. [PMID: 37523504 DOI: 10.1097/inf.0000000000004055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
BACKGROUND Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are 2 common causes of acute respiratory tract infections in infants and young children. The objective of this study is to compare the demographics and outcomes of children hospitalized with HMPV and RSV infections in the United States. METHODS We performed a retrospective cohort analysis of children 1 month to less than 3 years old discharged during 2016 with HMPV or RSV infection using the Kids' Inpatient Database. Children with HMPV and RSV coinfection were excluded. Data were weighted for national estimates. RESULTS There were 6585 children with HMPV infection and 70,824 with RSV infection discharged during the study period. The mean age of children with HMPV infection was higher than that of children with RSV infection (0.73 ± 0.8 vs. 0.42 ± 0.7 years; P < 0.05). The mortality rate was significantly higher in children with the presence of any complex chronic conditions compared to those without, in both HMPV [odds ratio (OR): 32.42; CI: 9.931-105.857; P < 0.05] as well as RSV (OR: 35.81; CI: 21.12-57.97; P < 0.05) groups. The adjusted median length of stay was longer (4.64 days; CI: 4.52-4.76 days vs. 3.33 days; CI: 3.31-3.35 days; P < 0.001) and total charges were higher ($44,358; CI: $42,145-$46,570 vs. $22,839; CI: $22,512-$23,166; P < 0.001), with HMPV infection. The mortality rate was similar in HMPV infection compared to RSV infection on multivariable analysis (OR: 1.48; P > 0.05). CONCLUSION In hospitalized children in the United States, HMPV infection is less common than RSV infection. Complex chronic conditions are more prevalent in children hospitalized with HMPV infection. Hospitalization with HMPV is associated with longer length of stay and higher hospital charges. The adjusted mortality is similar with both infections.
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Affiliation(s)
- Meghana Nadiger
- From the Division of Critical Care Medicine, Department of Pediatrics, University of Illinois College of Medicine, Peoria Illinois
| | - Prithvi Sendi
- Division of Critical Care Medicine, Nicklaus Children's Hospital, Miami, Florida
- Division of Critical Care Medicine, Department of Pediatrics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Paul A Martinez
- Division of Critical Care Medicine, Nicklaus Children's Hospital, Miami, Florida
- Division of Critical Care Medicine, Department of Pediatrics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Balagangadhar R Totapally
- Division of Critical Care Medicine, Nicklaus Children's Hospital, Miami, Florida
- Division of Critical Care Medicine, Department of Pediatrics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
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El Najjar F, Castillo SR, Moncman CL, Wu CY, Isla E, Velez Ortega AC, Frolenkov GI, Cifuentes-Munoz N, Dutch RE. Imaging analysis reveals budding of filamentous human metapneumovirus virions and direct transfer of inclusion bodies through intercellular extensions. mBio 2023; 14:e0158923. [PMID: 37681946 PMCID: PMC10653870 DOI: 10.1128/mbio.01589-23] [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: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 09/09/2023] Open
Abstract
IMPORTANCE Human metapneumovirus is an important respiratory pathogen that causes significant morbidity and mortality, particularly in the very young, the elderly, and the immunosuppressed. However, the molecular details of how this virus spreads to new target cells are unclear. This work provides important new information on the formation of filamentous structures that are consistent with virus particles and adds critical new insight into the structure of extensions between cells that form during infection. In addition, it demonstrates for the first time the movement of viral replication centers through these intercellular extensions, representing a new mode of direct cell-to-cell spread that may be applicable to other viral systems.
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Affiliation(s)
- Farah El Najjar
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Santiago Restrepo Castillo
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Carole L. Moncman
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Cheng-Yu Wu
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Eduardo Isla
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | | | - Gregory I. Frolenkov
- Department of Physiology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Nicolas Cifuentes-Munoz
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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O’Neill GK, Taylor J, Kok J, Dwyer DE, Dilcher M, Hua H, Levy A, Smith D, Minney-Smith CA, Wood T, Jelley L, Huang QS, Trenholme A, McAuliffe G, Barr I, Sullivan SG. Circulation of influenza and other respiratory viruses during the COVID-19 pandemic in Australia and New Zealand, 2020-2021. Western Pac Surveill Response J 2023; 14:1-9. [PMID: 37946717 PMCID: PMC10630701 DOI: 10.5365/wpsar.2023,14.3.948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Objective Circulation patterns of influenza and other respiratory viruses have been globally disrupted since the emergence of coronavirus disease (COVID-19) and the introduction of public health and social measures (PHSMs) aimed at reducing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Methods We reviewed respiratory virus laboratory data, Google mobility data and PHSMs in five geographically diverse regions in Australia and New Zealand. We also described respiratory virus activity from January 2017 to August 2021. Results We observed a change in the prevalence of circulating respiratory viruses following the emergence of SARS-CoV-2 in early 2020. Influenza activity levels were very low in all regions, lower than those recorded in 2017-2019, with less than 1% of laboratory samples testing positive for influenza virus. In contrast, rates of human rhinovirus infection were increased. Respiratory syncytial virus (RSV) activity was delayed; however, once it returned, most regions experienced activity levels well above those seen in 2017-2019. The timing of the resurgence in the circulation of both rhinovirus and RSV differed within and between the two countries. Discussion The findings of this study suggest that as domestic and international borders are opened up and other COVID-19 PHSMs are lifted, clinicians and public health professionals should be prepared for resurgences in influenza and other respiratory viruses. Recent patterns in RSV activity suggest that these resurgences in non-COVID-19 viruses have the potential to occur out of season and with increased impact.
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Affiliation(s)
- Genevieve K O’Neill
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Janette Taylor
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Meik Dilcher
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Harry Hua
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Avram Levy
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - David Smith
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | | | - Timothy Wood
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Lauren Jelley
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Q Sue Huang
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- Institute of Environmental Science and Research, Wellington, New Zealand
| | | | - Gary McAuliffe
- Virology and Immunology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Infectious Diseases and Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria, Australia
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Vectorial Release of Human RNA Viruses from Epithelial Cells. Viruses 2022; 14:v14020231. [PMID: 35215825 PMCID: PMC8875463 DOI: 10.3390/v14020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/07/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Epithelial cells are apico-basolateral polarized cells that line all tubular organs and are often targets for infectious agents. This review focuses on the release of human RNA virus particles from both sides of polarized human cells grown on transwells. Most viruses that infect the mucosa leave their host cells mainly via the apical side while basolateral release is linked to virus propagation within the host. Viruses do this by hijacking the cellular factors involved in polarization and trafficking. Thus, understanding epithelial polarization is essential for a clear understanding of virus pathophysiology.
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Kruglova N, Siniavin A, Gushchin V, Mazurov D. Different Neutralization Sensitivity of SARS-CoV-2 Cell-to-Cell and Cell-Free Modes of Infection to Convalescent Sera. Viruses 2021; 13:1133. [PMID: 34204732 PMCID: PMC8231521 DOI: 10.3390/v13061133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has posed a global threat to human lives and economics. One of the best ways to determine protection against the infection is to quantify the neutralizing activity of serum antibodies. Multiple assays have been developed to validate SARS-CoV-2 neutralization; most of them utilized lentiviral or vesicular stomatitis virus-based particles pseudotyped with the spike (S) protein, making them safe and acceptable to work with in many labs. However, these systems are only capable of measuring infection with purified particles. This study has developed a pseudoviral assay with replication-dependent reporter vectors that can accurately quantify the level of infection directly from the virus producing cell to the permissive target cell. Comparative analysis of cell-free and cell-to-cell infection revealed that the neutralizing activity of convalescent sera was more than tenfold lower in cell cocultures than in the cell-free mode of infection. As the pseudoviral system could not properly model the mechanisms of SARS-CoV-2 transmission, similar experiments were performed with replication-competent coronavirus, which detected nearly complete SARS-CoV-2 cell-to-cell infection resistance to neutralization by convalescent sera. These findings suggest that the cell-to-cell mode of SARS-CoV-2 transmission, for which the mechanisms are largely unknown, could be of great importance for treatment and prevention of COVID-19.
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Affiliation(s)
- Natalia Kruglova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia;
| | - Andrei Siniavin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (A.S.); (V.G.)
- Department of Molecular Neuroimmune Signalling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vladimir Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (A.S.); (V.G.)
| | - Dmitriy Mazurov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia;
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Host Components That Modulate the Disease Caused by hMPV. Viruses 2021; 13:v13030519. [PMID: 33809875 PMCID: PMC8004172 DOI: 10.3390/v13030519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Human metapneumovirus (hMPV) is one of the main pathogens responsible for acute respiratory infections in children up to 5 years of age, contributing substantially to health burden. The worldwide economic and social impact of this virus is significant and must be addressed. The structural components of hMPV (either proteins or genetic material) can be detected by several receptors expressed by host cells through the engagement of pattern recognition receptors. The recognition of the structural components of hMPV can promote the signaling of the immune response to clear the infection, leading to the activation of several pathways, such as those related to the interferon response. Even so, several intrinsic factors are capable of modulating the immune response or directly inhibiting the replication of hMPV. This article will discuss the current knowledge regarding the innate and adaptive immune response during hMPV infections. Accordingly, the host intrinsic components capable of modulating the immune response and the elements capable of restricting viral replication during hMPV infections will be examined.
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New Look at RSV Infection: Tissue Clearing and 3D Imaging of the Entire Mouse Lung at Cellular Resolution. Viruses 2021; 13:v13020201. [PMID: 33525646 PMCID: PMC7912480 DOI: 10.3390/v13020201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Respiratory Syncytial Virus (RSV) is the major cause of severe acute respiratory tract illness in young children worldwide and a main pathogen for the elderly and immune-compromised people. In the absence of vaccines or effective treatments, a better characterization of the pathogenesis of RSV infection is required. To date, the pathophysiology of the disease and its diagnosis has mostly relied on chest X-ray and genome detection in nasopharyngeal swabs. The development of new imaging approaches is instrumental to further the description of RSV spread, virus-host interactions and related acute respiratory disease, at the level of the entire lung. METHODS By combining tissue clearing, 3D microscopy and image processing, we developed a novel visualization tool of RSV infection in undissected mouse lungs. RESULTS Whole tissue analysis allowed the identification of infected cell subtypes, based on both morphological traits and position within the cellular network. Furthermore, 3D imaging was also valuable to detect the cytoplasmic viral factories, also called inclusion bodies, a hallmark of RSV infection. CONCLUSIONS Whole lung clearing and 3D deep imaging represents an unprecedented visualization method of infected lungs to allow insight into RSV pathophysiology and improve the 2D histology analyses.
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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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Abstract
A critical step in the life cycle of a virus is spread to a new target cell, which generally involves the release of new viral particles from the infected cell which can then initiate infection in the next target cell. While cell-free viral particles released into the extracellular environment are necessary for long distance spread, there are disadvantages to this mechanism. These include the presence of immune system components, the low success rate of infection by single particles, and the relative fragility of viral particles in the environment. Several mechanisms of direct cell-to-cell spread have been reported for animal viruses which would avoid the issues associated with cell-free particles. A number of viruses can utilize several different mechanisms of direct cell-to-cell spread, but our understanding of the differential usage by these pathogens is modest. Although the mechanisms of cell-to-cell spread differ among viruses, there is a common exploitation of key pathways and components of the cellular cytoskeleton. Remarkably, some of the viral mechanisms of cell-to-cell spread are surprisingly similar to those used by bacteria. Here we summarize the current knowledge of the conventional and non-conventional mechanisms of viral spread, the common methods used to detect viral spread, and the impact that these mechanisms can have on viral pathogenesis.
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Affiliation(s)
- Nicolas Cifuentes-Munoz
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, San Miguel, Santiago, Chile
| | - Farah El Najjar
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, United States.
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