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Boender GJ, Hagenaars TJ, Holwerda M, Spierenburg MAH, van Rijn PA, van der Spek AN, Elbers ARW. Spatial Transmission Characteristics of the Bluetongue Virus Serotype 3 Epidemic in The Netherlands, 2023. Viruses 2024; 16:625. [PMID: 38675966 PMCID: PMC11054275 DOI: 10.3390/v16040625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
A devastating bluetongue (BT) epidemic caused by bluetongue virus serotype 3 (BTV-3) has spread throughout most of the Netherlands within two months since the first infection was officially confirmed in the beginning of September 2023. The epidemic comes with unusually strong suffering of infected cattle through severe lameness, often resulting in mortality or euthanisation for welfare reasons. In total, tens of thousands of sheep have died or had to be euthanised. By October 2023, more than 2200 locations with ruminant livestock were officially identified to be infected with BTV-3, and additionally, ruminants from 1300 locations were showing BTV-associated clinical symptoms (but not laboratory-confirmed BT). Here, we report on the spatial spread and dynamics of this BT epidemic. More specifically, we characterized the distance-dependent intensity of the between-holding transmission by estimating the spatial transmission kernel and by comparing it to transmission kernels estimated earlier for BTV-8 transmission in Northwestern Europe in 2006 and 2007. The 2023 BTV-3 kernel parameters are in line with those of the transmission kernel estimated previously for the between-holding spread of BTV-8 in Europe in 2007. The 2023 BTV-3 transmission kernel has a long-distance spatial range (across tens of kilometres), evidencing that in addition to short-distance dispersal of infected midges, other transmission routes such as livestock transports probably played an important role.
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Affiliation(s)
- Gert-Jan Boender
- Department of Epidemiology, Bioinformatics, Animal Studies and Vaccine Development, Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, The Netherlands; (G.-J.B.); (T.J.H.)
| | - Thomas J. Hagenaars
- Department of Epidemiology, Bioinformatics, Animal Studies and Vaccine Development, Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, The Netherlands; (G.-J.B.); (T.J.H.)
| | - Melle Holwerda
- Department of Virology, Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, The Netherlands; (M.H.); (P.A.v.R.)
| | - Marcel A. H. Spierenburg
- Incident- and Crisis Centre (NVIC), Netherlands Food and Consumer Product Safety Authority (NVWA), P.O. Box 43006, 3540 AA Utrecht, The Netherlands; (M.A.H.S.); (A.N.v.d.S.)
| | - Piet A. van Rijn
- Department of Virology, Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, The Netherlands; (M.H.); (P.A.v.R.)
- Department of Biochemistry, Centre for Human Metabolomics, North-West University, Private Bag X 6001, Potchefstroom 2520, South Africa
| | - Arco N. van der Spek
- Incident- and Crisis Centre (NVIC), Netherlands Food and Consumer Product Safety Authority (NVWA), P.O. Box 43006, 3540 AA Utrecht, The Netherlands; (M.A.H.S.); (A.N.v.d.S.)
| | - Armin R. W. Elbers
- Department of Epidemiology, Bioinformatics, Animal Studies and Vaccine Development, Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, The Netherlands; (G.-J.B.); (T.J.H.)
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Probst L, Laloli L, Licheri MF, Licheri M, Gultom M, Holwerda M, V’kovski P, Dijkman R. Generation and Characterization of an Influenza D Reporter Virus. Viruses 2023; 15:2444. [PMID: 38140686 PMCID: PMC10747006 DOI: 10.3390/v15122444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Influenza D virus (IDV) can infect various livestock animals, such as cattle, swine, and small ruminants, and was shown to have zoonotic potential. Therefore, it is important to identify viral factors involved in the broad host tropism and identify potential antiviral compounds that can inhibit IDV infection. Recombinant reporter viruses provide powerful tools for studying viral infections and antiviral drug discovery. Here we present the generation of a fluorescent reporter IDV using our previously established reverse genetic system for IDV. The mNeonGreen (mNG) fluorescent reporter gene was incorporated into the IDV non-structural gene segment as a fusion protein with the viral NS1 or NS2 proteins, or as a separate protein flanked by two autoproteolytic cleavage sites. We demonstrate that only recombinant reporter viruses expressing mNG as an additional separate protein or as an N-terminal fusion protein with NS1 could be rescued, albeit attenuated, compared to the parental reverse genetic clone. Serial passaging experiments demonstrated that the mNG gene is stably integrated for up to three passages, after which internal deletions accumulate. We conducted a proof-of-principle antiviral screening with the established fluorescent reporter viruses and identified two compounds influencing IDV infection. These results demonstrate that the newly established recombinant IDV reporter virus can be applied for antiviral drug discovery and monitoring viral replication, adding a new molecular tool for investigating IDV.
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Affiliation(s)
- Lukas Probst
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Laura Laloli
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Manon Flore Licheri
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Matthias Licheri
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Mitra Gultom
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Melle Holwerda
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Philip V’kovski
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Ronald Dijkman
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- European Virus Bioinformatics Center, 07743 Jena, Germany
- Microscope Imaging Center, University of Bern, 3012 Bern, Switzerland
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Kelly JN, Laloli L, V’kovski P, Holwerda M, Portmann J, Thiel V, Dijkman R. Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis. Front Immunol 2022; 13:978824. [PMID: 36268025 PMCID: PMC9576848 DOI: 10.3389/fimmu.2022.978824] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/01/2022] [Indexed: 12/04/2022] Open
Abstract
The respiratory epithelium constitutes the first line of defense against invading respiratory pathogens, such as the 2009 pandemic strain of influenza A virus (IAV, H1N1pdm09), and plays a crucial role in the host antiviral response to infection. Despite its importance, however, it remains unknown how individual cell types within the respiratory epithelium respond to IAV infection or how the latter may influence IAV disease progression and pathogenesis. Here, we used single cell RNA sequencing (scRNA-seq) to dissect the host response to IAV infection in its natural target cells. scRNA-seq was performed on human airway epithelial cell (hAEC) cultures infected with either wild-type pandemic IAV (WT) or with a mutant version of IAV (NS1R38A) that induced a robust innate immune response. We then characterized both the host and viral transcriptomes of more than 19,000 single cells across the 5 major cell types populating the human respiratory epithelium. For all cell types, we observed a wide spectrum of viral burden among single infected cells and a disparate host response between infected and bystander populations. Interestingly, we also identified multiple key differences in the host response to IAV among individual cell types, including high levels of pro-inflammatory cytokines and chemokines in secretory and basal cells and an important role for luminal cells in sensing and restricting incoming virus. Multiple infected cell types were shown to upregulate interferons (IFN), with type III IFNs clearly dominating the antiviral response. Transcriptional changes in genes related to cell differentiation, cell migration, and tissue repair were also identified. Strikingly, we also detected a shift in viral host cell tropism from non-ciliated cells to ciliated cells at later stages of infection and observed major changes in the cellular composition. Microscopic analysis of both WT and NS1R38A virus-infected hAECs at various stages of IAV infection revealed that the transcriptional changes we observed at 18 hpi were likely driving the downstream histopathological alterations in the airway epithelium. To our knowledge, this is the first study to provide a comprehensive analysis of the cell type-specific host antiviral response to influenza virus infection in its natural target cells – namely, the human respiratory epithelium.
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Affiliation(s)
- Jenna N. Kelly
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Laura Laloli
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philip V’kovski
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Ronald Dijkman
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center (EVBC), Jena, Germany
- *Correspondence: Ronald Dijkman,
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Laloli L, Licheri MF, Probst L, Licheri M, Gultom M, Holwerda M, V’kovski P, Dijkman R. Time-resolved characterization of the innate immune response in the respiratory epithelium of human, porcine, and bovine during influenza virus infection. Front Immunol 2022; 13:970325. [PMID: 36059535 PMCID: PMC9437644 DOI: 10.3389/fimmu.2022.970325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/27/2022] [Indexed: 11/15/2022] Open
Abstract
Viral cross-species transmission is recognized to be a major threat to both human and animal health, however detailed information on determinants underlying virus host tropism and susceptibility is missing. Influenza C and D viruses (ICV, IDV) are two respiratory viruses that share up to 50% genetic similarity, and both employ 9-O-acetylated sialic acids to enter a host cell. While ICV infections are mainly restricted to humans, IDV possesses a much broader host tropism and has shown to have a zoonotic potential. This suggests that additional virus–host interactions play an important role in the distinct host spectrum of ICV and IDV. In this study, we aimed to characterize the innate immune response of the respiratory epithelium of biologically relevant host species during influenza virus infection to identify possible determinants involved in viral cross-species transmission. To this end, we performed a detailed characterization of ICV and IDV infection in primary airway epithelial cell (AEC) cultures from human, porcine, and bovine origin. We monitored virus replication kinetics, cellular and host tropism, as well as the host transcriptional response over time at distinct ambient temperatures. We observed that both ICV and IDV predominantly infect ciliated cells, independently from host and temperature. Interestingly, temperature had a profound influence on ICV replication in both porcine and bovine AEC cultures, while IDV replicated efficiently irrespective of temperature and host. Detailed time-resolved transcriptome analysis revealed both species-specific and species uniform host responses and highlighted 34 innate immune-related genes with clear virus-specific and temperature-dependent profiles. These data provide the first comprehensive insights into important common and species-specific virus-host dynamics underlying the distinct host tropism of ICV and IDV, as well as possible determinants involved in viral cross-species transmission.
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Affiliation(s)
- Laura Laloli
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Lukas Probst
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Matthias Licheri
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Mitra Gultom
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Philip V’kovski
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Ronald Dijkman
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- *Correspondence: Ronald Dijkman,
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Martínez-Salazar B, Holwerda M, Stüdle C, Piragyte I, Mercader N, Engelhardt B, Rieben R, Döring Y. COVID-19 and the Vasculature: Current Aspects and Long-Term Consequences. Front Cell Dev Biol 2022; 10:824851. [PMID: 35242762 PMCID: PMC8887620 DOI: 10.3389/fcell.2022.824851] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/20/2022] [Indexed: 12/11/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first identified in December 2019 as a novel respiratory pathogen and is the causative agent of Corona Virus disease 2019 (COVID-19). Early on during this pandemic, it became apparent that SARS-CoV-2 was not only restricted to infecting the respiratory tract, but the virus was also found in other tissues, including the vasculature. Individuals with underlying pre-existing co-morbidities like diabetes and hypertension have been more prone to develop severe illness and fatal outcomes during COVID-19. In addition, critical clinical observations made in COVID-19 patients include hypercoagulation, cardiomyopathy, heart arrythmia, and endothelial dysfunction, which are indicative for an involvement of the vasculature in COVID-19 pathology. Hence, this review summarizes the impact of SARS-CoV-2 infection on the vasculature and details how the virus promotes (chronic) vascular inflammation. We provide a general overview of SARS-CoV-2, its entry determinant Angiotensin-Converting Enzyme II (ACE2) and the detection of the SARS-CoV-2 in extrapulmonary tissue. Further, we describe the relation between COVID-19 and cardiovascular diseases (CVD) and their impact on the heart and vasculature. Clinical findings on endothelial changes during COVID-19 are reviewed in detail and recent evidence from in vitro studies on the susceptibility of endothelial cells to SARS-CoV-2 infection is discussed. We conclude with current notions on the contribution of cardiovascular events to long term consequences of COVID-19, also known as “Long-COVID-syndrome”. Altogether, our review provides a detailed overview of the current perspectives of COVID-19 and its influence on the vasculature.
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Affiliation(s)
- Berenice Martínez-Salazar
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Melle Holwerda
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Chiara Stüdle
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Indre Piragyte
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.,Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Nadia Mercader
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.,Institute of Anatomy, University of Bern, Bern, Switzerland.,Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,Bern Center of Precision Medicine BCPM, University of Bern, Bern, Switzerland
| | | | - Robert Rieben
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Yvonne Döring
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.,Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich (LMU), Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
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Gultom M, Licheri M, Laloli L, Wider M, Strässle M, V'kovski P, Steiner S, Kratzel A, Thao TTN, Probst L, Stalder H, Portmann J, Holwerda M, Ebert N, Stokar-Regenscheit N, Gurtner C, Zanolari P, Posthaus H, Schuller S, Vicente-Santos A, Moreira-Soto A, Corrales-Aguilar E, Ruggli N, Tekes G, von Messling V, Sawatsky B, Thiel V, Dijkman R. Susceptibility of Well-Differentiated Airway Epithelial Cell Cultures from Domestic and Wild Animals to Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis 2021; 27:1811-1820. [PMID: 34152956 PMCID: PMC8237902 DOI: 10.3201/eid2707.204660] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, and the number of worldwide cases continues to rise. The zoonotic origins of SARS-CoV-2 and its intermediate and potential spillback host reservoirs, besides humans, remain largely unknown. Because of ethical and experimental constraints and more important, to reduce and refine animal experimentation, we used our repository of well-differentiated airway epithelial cell (AEC) cultures from various domesticated and wildlife animal species to assess their susceptibility to SARS-CoV-2. We observed that SARS-CoV-2 replicated efficiently only in monkey and cat AEC culture models. Whole-genome sequencing of progeny viruses revealed no obvious signs of nucleotide transitions required for SARS-CoV-2 to productively infect monkey and cat AEC cultures. Our findings, together with previous reports of human-to-animal spillover events, warrant close surveillance to determine the potential role of cats, monkeys, and closely related species as spillback reservoirs for SARS-CoV-2.
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Studer E, Schönecker L, Meylan M, Stucki D, Dijkman R, Holwerda M, Glaus A, Becker J. Prevalence of BRD-Related Viral Pathogens in the Upper Respiratory Tract of Swiss Veal Calves. Animals (Basel) 2021; 11:1940. [PMID: 34209718 PMCID: PMC8300226 DOI: 10.3390/ani11071940] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/17/2022] Open
Abstract
The prevention of bovine respiratory disease is important, as it may lead to impaired welfare, economic losses, and considerable antimicrobial use, which can be associated with antimicrobial resistance. The aim of this study was to describe the prevalence of respiratory viruses and to identify risk factors for their occurrence. A convenience sample of 764 deep nasopharyngeal swab samples from veal calves was screened by PCR for bovine respiratory syncytial virus (BRSV), bovine parainfluenza-3 virus (BPI3V), bovine coronavirus (BCoV), influenza D virus (IDV), and influenza C virus (ICV). The following prevalence rates were observed: BRSV, 2.1%; BPI3V, 3.3%; BCoV, 53.5%; IDV, 4.1%; ICV, 0%. Logistic mixed regression models were built for BCoV to explore associations with calf management and housing. Positive swab samples were more frequent in younger calves than older calves (>100 days; p < 0.001). The probability of detecting BCoV increased with increasing group size in young calves. Findings from this study suggested that young calves should be fattened in small groups to limit the risk of occurrence of BCoV, although an extended spectrum of risk factors for viral associated respiratory disorders such as nutritional aspects should be considered in future studies.
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Affiliation(s)
- Eveline Studer
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland; (E.S.); (L.S.); (M.M.); (D.S.)
| | - Lutz Schönecker
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland; (E.S.); (L.S.); (M.M.); (D.S.)
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland
| | - Mireille Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland; (E.S.); (L.S.); (M.M.); (D.S.)
| | - Dimitri Stucki
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland; (E.S.); (L.S.); (M.M.); (D.S.)
| | - Ronald Dijkman
- Institute of Virology and Immunology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland; (R.D.); (M.H.); (A.G.)
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland; (R.D.); (M.H.); (A.G.)
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
- Graduate School for Cellular and Biomedical Science, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland
| | - Anna Glaus
- Institute of Virology and Immunology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland; (R.D.); (M.H.); (A.G.)
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
| | - Jens Becker
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland; (E.S.); (L.S.); (M.M.); (D.S.)
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Holwerda M, Laloli L, Wider M, Schönecker L, Becker J, Meylan M, Dijkman R. Establishment of a Reverse Genetic System from a Bovine Derived Influenza D Virus Isolate. Viruses 2021; 13:v13030502. [PMID: 33803792 PMCID: PMC8003313 DOI: 10.3390/v13030502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/23/2022] Open
Abstract
The ruminant-associated influenza D virus (IDV) has a broad host tropism and was shown to have zoonotic potential. To identify and characterize molecular viral determinants influencing the host spectrum of IDV, a reverse genetic system is required. For this, we first performed 5′ and 3′ rapid amplification of cDNA ends (RACE) of all seven genomic segments, followed by assessment of the 5′ and 3′ NCR activity prior to constructing the viral genomic segments of a contemporary Swiss bovine IDV isolate (D/CN286) into the bidirectional pHW2000 vector. The bidirectional plasmids were transfected in HRT-18G cells followed by viral rescue on the same cell type. Analysis of the segment specific 5′ and 3′ non-coding regions (NCR) highlighted that the terminal 3′ end of all segments harbours an uracil instead of a cytosine nucleotide, similar to other influenza viruses. Subsequent analysis on the functionality of the 5′ and 3′ NCR in a minireplicon assay revealed that these sequences were functional and that the variable sequence length of the 5′ and 3′ NCR influences reporter gene expression. Thereafter, we evaluated the replication efficiency of the reverse genetic clone on conventional cell lines of human, swine and bovine origin, as well as by using an in vitro model recapitulating the natural replication site of IDV in bovine and swine. This revealed that the reverse genetic clone D/CN286 replicates efficiently in all cell culture models. Combined, these results demonstrate the successful establishment of a reverse genetic system from a contemporary bovine IDV isolate that can be used for future identification and characterization of viral determinants influencing the broad host tropism of IDV.
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Affiliation(s)
- Melle Holwerda
- Institute of Virology and Immunology, 3012 Bern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (L.L.); (M.W.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Laura Laloli
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (L.L.); (M.W.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Manon Wider
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (L.L.); (M.W.)
| | - Lutz Schönecker
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (J.B.); (M.M.)
- Department of Clinical Veterinary Science, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Jens Becker
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (J.B.); (M.M.)
- Department of Clinical Veterinary Science, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Mireille Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (J.B.); (M.M.)
- Department of Clinical Veterinary Science, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology, 3012 Bern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland; (L.L.); (M.W.)
- Correspondence: ; Tel.: +41-31-664-0783
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9
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V’kovski P, Gultom M, Kelly JN, Steiner S, Russeil J, Mangeat B, Cora E, Pezoldt J, Holwerda M, Kratzel A, Laloli L, Wider M, Portmann J, Tran T, Ebert N, Stalder H, Hartmann R, Gardeux V, Alpern D, Deplancke B, Thiel V, Dijkman R. Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium. PLoS Biol 2021; 19:e3001158. [PMID: 33780434 PMCID: PMC8032198 DOI: 10.1371/journal.pbio.3001158] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/08/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human upper and lower respiratory tract (33°C and 37°C, respectively) have been shown to affect the replication kinetics of several respiratory viruses, as well as host innate immune response dynamics, we investigated the impact of temperature on SARS-CoV-2 and SARS-CoV infection using the primary human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated to higher titers when infections were performed at 33°C rather than 37°C. Although both viruses were highly sensitive to type I and type III interferon pretreatment, a detailed time-resolved transcriptome analysis revealed temperature-dependent interferon and pro-inflammatory responses induced by SARS-CoV-2 that were inversely proportional to its replication efficiency at 33°C or 37°C. These data provide crucial insight on pivotal virus-host interaction dynamics and are in line with characteristic clinical features of SARS-CoV-2 and SARS-CoV, as well as their respective transmission efficiencies.
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Affiliation(s)
- Philip V’kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Mitra Gultom
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jenna N. Kelly
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Julie Russeil
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bastien Mangeat
- Gene Expression Core Facility (GECF), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elisa Cora
- Gene Expression Core Facility (GECF), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Joern Pezoldt
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Laura Laloli
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Manon Wider
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Thao Tran
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniel Alpern
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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10
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V'kovski P, Gultom M, Kelly JN, Steiner S, Russeil J, Mangeat B, Cora E, Pezoldt J, Holwerda M, Kratzel A, Laloli L, Wider M, Portmann J, Tran T, Ebert N, Stalder H, Hartmann R, Gardeux V, Alpern D, Deplancke B, Thiel V, Dijkman R. Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium. PLoS Biol 2021; 19:e3001158. [PMID: 33780434 DOI: 10.1101/2020.04.27.062315] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/08/2021] [Accepted: 02/25/2021] [Indexed: 05/23/2023] Open
Abstract
Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human upper and lower respiratory tract (33°C and 37°C, respectively) have been shown to affect the replication kinetics of several respiratory viruses, as well as host innate immune response dynamics, we investigated the impact of temperature on SARS-CoV-2 and SARS-CoV infection using the primary human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated to higher titers when infections were performed at 33°C rather than 37°C. Although both viruses were highly sensitive to type I and type III interferon pretreatment, a detailed time-resolved transcriptome analysis revealed temperature-dependent interferon and pro-inflammatory responses induced by SARS-CoV-2 that were inversely proportional to its replication efficiency at 33°C or 37°C. These data provide crucial insight on pivotal virus-host interaction dynamics and are in line with characteristic clinical features of SARS-CoV-2 and SARS-CoV, as well as their respective transmission efficiencies.
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Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Mitra Gultom
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Julie Russeil
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bastien Mangeat
- Gene Expression Core Facility (GECF), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elisa Cora
- Gene Expression Core Facility (GECF), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Joern Pezoldt
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Laura Laloli
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Manon Wider
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Thao Tran
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniel Alpern
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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11
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Gawryszuk A, Van der Laan H, Steenbakkers R, Van den Hoek J, Holwerda M, Leeuw IVD, Rinkel R, Bijl H, Langendijk J. PH-0042: Aspiration related OARs are relevant predictors of silent aspiration after (chemo)radiation. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)00068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Kratzel A, Todt D, V'kovski P, Steiner S, Gultom M, Thao TTN, Ebert N, Holwerda M, Steinmann J, Niemeyer D, Dijkman R, Kampf G, Drosten C, Steinmann E, Thiel V, Pfaender S. Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 by WHO-Recommended Hand Rub Formulations and Alcohols. Emerg Infect Dis 2020. [PMID: 32284092 DOI: 10.1101/2020.03.10.986711v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Infection control instructions call for use of alcohol-based hand rub solutions to inactivate severe acute respiratory syndrome coronavirus 2. We determined the virucidal activity of World Health Organization-recommended hand rub formulations, at full strength and multiple dilutions, and of the active ingredients. All disinfectants demonstrated efficient virus inactivation.
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13
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Kratzel A, Todt D, V'kovski P, Steiner S, Gultom M, Thao TTN, Ebert N, Holwerda M, Steinmann J, Niemeyer D, Dijkman R, Kampf G, Drosten C, Steinmann E, Thiel V, Pfaender S. Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 by WHO-Recommended Hand Rub Formulations and Alcohols. Emerg Infect Dis 2020; 26:1592-1595. [PMID: 32284092 PMCID: PMC7323537 DOI: 10.3201/eid2607.200915] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Infection control instructions call for use of alcohol-based hand rub solutions to inactivate severe acute respiratory syndrome coronavirus 2. We determined the virucidal activity of World Health Organization-recommended hand rub formulations, at full strength and multiple dilutions, and of the active ingredients. All disinfectants demonstrated efficient virus inactivation.
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14
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Thi Nhu Thao T, Labroussaa F, Ebert N, V'kovski P, Stalder H, Portmann J, Kelly J, Steiner S, Holwerda M, Kratzel A, Gultom M, Schmied K, Laloli L, Hüsser L, Wider M, Pfaender S, Hirt D, Cippà V, Crespo-Pomar S, Schröder S, Muth D, Niemeyer D, Corman VM, Müller MA, Drosten C, Dijkman R, Jores J, Thiel V. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature 2020; 582:561-565. [PMID: 32365353 DOI: 10.1038/s41586-020-2294-9] [Citation(s) in RCA: 281] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Reverse genetics has been an indispensable tool to gain insights into viral pathogenesis and vaccine development. The genomes of large RNA viruses, such as those from coronaviruses, are cumbersome to clone and manipulate in Escherichia coli owing to the size and occasional instability of the genome1-3. Therefore, an alternative rapid and robust reverse-genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses, including members of the Coronaviridae, Flaviviridae and Pneumoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples or synthetic DNA, and these fragments were then reassembled in one step in Saccharomyces cerevisiae using transformation-associated recombination cloning to maintain the genome as a yeast artificial chromosome. T7 RNA polymerase was then used to generate infectious RNA to rescue viable virus. Using this platform, we were able to engineer and generate chemically synthesized clones of the virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)4, which has caused the recent pandemic of coronavirus disease (COVID-19), in only a week after receipt of the synthetic DNA fragments. The technical advance that we describe here facilitates rapid responses to emerging viruses as it enables the real-time generation and functional characterization of evolving RNA virus variants during an outbreak.
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Affiliation(s)
- Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna Kelly
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Mitra Gultom
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Kimberly Schmied
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Laura Laloli
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Linda Hüsser
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Manon Wider
- Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Stephanie Pfaender
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Department for Molecular and Medical Virology, Ruhr-Universität Bochum, Bochum, Germany
| | - Dagny Hirt
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Valentina Cippà
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvia Crespo-Pomar
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Simon Schröder
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Doreen Muth
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. .,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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15
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Welkers MRA, Pawestri HA, Fonville JM, Sampurno OD, Pater M, Holwerda M, Han AX, Russell CA, Jeeninga RE, Setiawaty V, de Jong MD, Eggink D. Genetic diversity and host adaptation of avian H5N1 influenza viruses during human infection. Emerg Microbes Infect 2019; 8:262-271. [PMID: 30866780 PMCID: PMC6455201 DOI: 10.1080/22221751.2019.1575700] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The continuing pandemic threat posed by avian influenza A/H5N1 viruses calls for improved insights into their evolution during human infection. We performed whole genome deep sequencing of respiratory specimens from 44 H5N1-infected individuals from Indonesia and found substantial within-host viral diversity. At nearly 30% of genome positions multiple amino acids were observed within or across samples, including positions implicated in aerosol transmission between ferrets. Amino acid variants detected our cohort were often found more frequently in available H5N1 sequences of human than avian isolates. We additionally identified previously unreported amino acid variants and multiple variants that increased in proportion over time in available sequential samples. Given the importance of the polymerase complex for host adaptation, we tested 121 amino acid variants found in the PB2, PB1 and PA subunits for their effects on polymerase activity in human cells. We identified multiple single amino acid variants in all three polymerase subunits that substantially increase polymerase activity including some with effects comparable to that of the widely recognized adaption and virulence marker PB2-E627 K. These results indicate highly dynamic evolutionary processes during human H5N1 virus infection and the potential existence of previously undocumented adaptive pathways.
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Affiliation(s)
- Matthijs R A Welkers
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands
| | - Hana A Pawestri
- b National Institute of Health Research and Development, Ministry of Health , Jakarta , Indonesia
| | - Judy M Fonville
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands.,c Department of Zoology , University of Cambridge , Cambridge , UK.,e Department of Medical Microbiology , PAMM , Veldhoven , Netherlands
| | - Ondri D Sampurno
- b National Institute of Health Research and Development, Ministry of Health , Jakarta , Indonesia
| | - Maarten Pater
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands
| | - Melle Holwerda
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands
| | - Alvin X Han
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands.,d Bioinformatics Institute, A*STAR , Singapore , Singapore
| | - Colin A Russell
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands
| | - Rienk E Jeeninga
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands
| | - Vivi Setiawaty
- b National Institute of Health Research and Development, Ministry of Health , Jakarta , Indonesia
| | - Menno D de Jong
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands
| | - Dirk Eggink
- a Department of Medical Microbiology , Academic Medical Center , Amsterdam , Netherlands
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16
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Holwerda M, Kelly J, Laloli L, Stürmer I, Portmann J, Stalder H, Dijkman R. Determining the Replication Kinetics and Cellular Tropism of Influenza D Virus on Primary Well-Differentiated Human Airway Epithelial Cells. Viruses 2019; 11:v11040377. [PMID: 31022887 PMCID: PMC6521319 DOI: 10.3390/v11040377] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022] Open
Abstract
Influenza viruses are notorious pathogens that frequently cross the species barrier with often severe consequences for both animal and human health. In 2011, a novel member of the Orthomyxoviridae family, Influenza D virus (IDV), was identified in the respiratory tract of swine. Epidemiological surveys revealed that IDV is distributed worldwide among livestock and that IDV-directed antibodies are detected in humans with occupational exposure to livestock. To identify the transmission capability of IDV to humans, we determined the viral replication kinetics and cell tropism using an in vitro respiratory epithelium model of humans. The inoculation of IDV revealed efficient replication kinetics and apical progeny virus release at different body temperatures. Intriguingly, the replication characteristics of IDV revealed higher replication kinetics compared to Influenza C virus, despite sharing the cell tropism preference for ciliated cells. Collectively, these results might indicate why IDV-directed antibodies are detected among humans with occupational exposure to livestock.
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Affiliation(s)
- Melle Holwerda
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.
| | - Jenna Kelly
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Laura Laloli
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.
| | - Isabel Stürmer
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.
| | - Jasmine Portmann
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Hanspeter Stalder
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Ronald Dijkman
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
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17
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van Beek J, de Graaf M, Xia M, Jiang X, Vinjé J, Beersma M, de Bruin E, van de Vijver D, Holwerda M, van Houten M, Buisman AM, van Binnendijk R, Osterhaus ADME, van der Klis F, Vennema H, Koopmans MPG. Comparison of norovirus genogroup I, II and IV seroprevalence among children in the Netherlands, 1963, 1983 and 2006. J Gen Virol 2016; 97:2255-2264. [PMID: 27365054 PMCID: PMC5042128 DOI: 10.1099/jgv.0.000533] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Noroviruses are a major cause of acute gastroenteritis worldwide and are a genetically diverse group of viruses. Since 2002, an increasing number of norovirus outbreaks have been reported globally, but it is not clear whether this increase has been caused by a higher awareness or reflects the emergence of new genogroup II genotype 4 (GII.4) variants. The hypothesis that norovirus prevalence has increased post-2002 and is related to the emergence of GII.4 is tested in this study. Sera collected from children aged <5 years of three Dutch cross-sectional population based cohorts in 1963, 1983 and 2006/2007 (n=143, n=130 and n=376, respectively) were tested for specific serum IgG by protein array using antigens to GII.4 and a range of other antigens representing norovirus GI, GII and GIV genotypes. The protein array was validated by paired sera of norovirus infected patients and supernatants of B-cell cultures with single epitope specificity. Evidence for norovirus infection was found to be common among Dutch children in each cohort, but the prevalence towards different genotypes changed over time. At the genogroup level, GI seroprevalence decreased significantly between 1963 and 2006/2007, while a significant increase of GII and, in particular, specific antibodies of the genotype GII.4 was detected in the 2006/2007 cohort. There were no children with only GII.4 antibodies in the 1963 cohort. This study shows that the high GII.4 norovirus incidence in very young children is a recent phenomenon. These findings are of importance for vaccine development and trials that are currently focusing mostly on GII.4 viruses.
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Affiliation(s)
- Janko van Beek
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands.,Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Miranda de Graaf
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Ming Xia
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - Xi Jiang
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA
| | - Mathias Beersma
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Erwin de Bruin
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands.,Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - David van de Vijver
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Melle Holwerda
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Marlies van Houten
- Pediatric Department, Spaarne Hospital Hoofddorp, Hoofddorp, The Netherlands
| | - Annemarie M Buisman
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Rob van Binnendijk
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Fiona van der Klis
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Harry Vennema
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Marion P G Koopmans
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.,Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
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18
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Langereis MA, Rabouw HH, Holwerda M, Visser LJ, van Kuppeveld FJM. Knockout of cGAS and STING Rescues Virus Infection of Plasmid DNA-Transfected Cells. J Virol 2015; 89:11169-73. [PMID: 26311870 PMCID: PMC4621133 DOI: 10.1128/jvi.01781-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/19/2015] [Indexed: 11/20/2022] Open
Abstract
It is well known that plasmid DNA transfection, prior to virus infection, negatively affects infection efficiency. Here, we show that cytosolic plasmid DNA activates the cGAS/STING signaling pathway, which ultimately leads to the induction of an antiviral state of the cells. Using a transient one-plasmid clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, we generated cGAS/STING-knockout cells and show that these cells can be infected after plasmid DNA transfection as efficiently as nontransfected cells.
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Affiliation(s)
- Martijn A Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Huib H Rabouw
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Melle Holwerda
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Linda J Visser
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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19
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Canuti M, Deijs M, Jazaeri Farsani SM, Holwerda M, Jebbink MF, de Vries M, van Vugt S, Brugman C, Verheij T, Lammens C, Goossens H, Loens K, Ieven M, van der Hoek L. Metagenomic analysis of a sample from a patient with respiratory tract infection reveals the presence of a γ-papillomavirus. Front Microbiol 2014; 5:347. [PMID: 25071755 PMCID: PMC4086198 DOI: 10.3389/fmicb.2014.00347] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/23/2014] [Indexed: 01/19/2023] Open
Abstract
Previously unknown or unexpected pathogens may be responsible for that proportion of respiratory diseases in which a causative agent cannot be identified. The application of broad-spectrum, sequence independent virus discovery techniques may be useful to reduce this proportion and widen our knowledge about respiratory pathogens. Thanks to the availability of high-throughput sequencing (HTS) technology, it became today possible to detect viruses which are present at a very low load, but the clinical relevance of those viruses must be investigated. In this study we used VIDISCA-454, a restriction enzyme based virus discovery method that utilizes Roche 454 HTS system, on a nasal swab collected from a subject with respiratory complaints. A γ-papillomavirus was detected (complete genome: 7142 bp) and its role in disease was investigated. Respiratory samples collected both during the acute phase of the illness and 2 weeks after full recovery contained the virus. The patient presented antibodies directed against the virus but there was no difference between IgG levels in blood samples collected during the acute phase and 2 weeks after full recovery. We therefore concluded that the detected γ-papillomavirus is unlikely to be the causative agent of the respiratory complaints and its presence in the nose of the patient is not related to the disease. Although HTS based virus discovery techniques proved their great potential as a tool to clarify the etiology of some infectious diseases, the obtained information must be subjected to cautious interpretations. This study underlines the crucial importance of performing careful investigations on viruses identified when applying sensitive virus discovery techniques, since the mere identification of a virus and its presence in a clinical sample are not satisfactory proofs to establish a causative link with a disease.
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Affiliation(s)
- Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Seyed M Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Melle Holwerda
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Michel de Vries
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Saskia van Vugt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht Utrecht, Netherlands
| | - Curt Brugman
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht Utrecht, Netherlands
| | - Theo Verheij
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht Utrecht, Netherlands
| | - Christine Lammens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen-University Hospital Antwerp Antwerp, Belgium
| | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen-University Hospital Antwerp Antwerp, Belgium
| | - Katherine Loens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen-University Hospital Antwerp Antwerp, Belgium
| | - Margareta Ieven
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen-University Hospital Antwerp Antwerp, Belgium
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
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20
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van der Linden HJ, Jellema LC, Holwerda M, Verpoorte E. Stabilization of two-phase octanol/water flows inside poly(dimethylsiloxane) microchannels using polymer coatings. Anal Bioanal Chem 2006; 385:1376-83. [PMID: 16773299 DOI: 10.1007/s00216-006-0526-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Revised: 04/10/2006] [Accepted: 05/04/2006] [Indexed: 11/25/2022]
Abstract
In this paper we present our first results on the realization of stable water/octanol, two-phase flows inside poly(dimethylsiloxane) (PDMS) microchannels. Native PDMS microchannels were coated with high molecular weight polymers to change the surface properties of the microchannels and thus stabilize the laminar flow profile. The polymers poly(2-hydroxyethyl methacrylate), poly(vinyl pyrrolidone), poly(ethylene oxide), poly(ethylene glycol), and poly(vinyl alcohol) were assessed for their quality as stabilization coatings after deposition from flowing and stationary solutions. Additionally, the influence of coating the microchannels homogeneously with a single kind of polymer or heterogeneously with two different polymers was investigated. From the experimental observations, it can be concluded that homogeneous polymer coatings with poly(2-hydroxyethyl methacrylate) and poly(vinyl pyrrolidone) led to the effective stabilization of laminar water/octanol flows. Furthermore, heterogeneous coatings led to two-phase flows which had a better-defined and more stable interface over long distances (i.e., 40-mm-long microchannels). Finally, the partitioning of fuchsin dye in the coated microchannels was demonstrated, establishing the feasibility of the use of the polymer-coated PDMS microchannels for determination of logP values in laminar octanol/water flows.
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Affiliation(s)
- H J van der Linden
- Groningen Research Institute of Pharmacy, Groningen University, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands.
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