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Embregts CWE, Farag EABA, Bansal D, Boter M, van der Linden A, Vaes VP, van Middelkoop-van den Berg I, IJpelaar J, Ziglam H, Coyle PV, Ibrahim I, Mohran KA, Alrajhi MMS, Islam MM, Abdeen R, Al-Zeyara AA, Younis NM, Al-Romaihi HE, AlThani MHJ, Sikkema RS, Koopmans MPG, Oude Munnink BB, GeurtsvanKessel CH. Rabies Virus Populations in Humans and Mice Show Minor Inter-Host Variability within Various Central Nervous System Regions and Peripheral Tissues. Viruses 2022; 14:v14122661. [PMID: 36560665 PMCID: PMC9781572 DOI: 10.3390/v14122661] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Rabies virus (RABV) has a broad host range and infects multiple cell types throughout the infection cycle. Next-generation sequencing (NGS) and minor variant analysis are powerful tools for studying virus populations within specific hosts and tissues, leading to novel insights into the mechanisms of host-switching and key factors for infecting specific cell types. In this study we investigated RABV populations and minor variants in both original (non-passaged) samples and in vitro-passaged isolates of various CNS regions (hippocampus, medulla oblongata and spinal cord) of a fatal human rabies case, and of multiple CNS and non-CNS tissues of experimentally infected mice. No differences in virus populations were detected between the human CNS regions, and only one non-synonymous single nucleotide polymorphism (SNP) was detected in the fifth in vitro passage of virus isolated from the spinal cord. However, the appearance of this SNP shows the importance of sequencing newly passaged virus stocks before further use. Similarly, we did not detect apparent differences in virus populations isolated from different CNS and non-CNS tissues of experimentally infected mice. Sequencing of viruses obtained from pharyngeal swab and salivary gland proved difficult, and we propose methods for improving sampling.
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Affiliation(s)
- Carmen W. E. Embregts
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
- Correspondence:
| | | | | | - Marjan Boter
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Anne van der Linden
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Vincent P. Vaes
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | | | - Jeroen. IJpelaar
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Hisham Ziglam
- Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | | | - Imad Ibrahim
- Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
- Biomedical Research Centre, Qatar University, Doha P.O. Box 2713, Qatar
| | - Khaled A. Mohran
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
- Biotechnology Departments ERC, Animal Health Research Institute, Dokki 12611, Egypt
| | | | - Md. Mazharul Islam
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
| | - Randa Abdeen
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
| | - Abdul Aziz Al-Zeyara
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
| | - Nidal Mahmoud Younis
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
| | | | | | - Reina S. Sikkema
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Bas B. Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
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Spronken MI, Short KR, Herfst S, Bestebroer TM, Vaes VP, van der Hoeven B, Koster AJ, Kremers GJ, Scott DP, Gultyaev AP, Sorell EM, de Graaf M, Bárcena M, Rimmelzwaan GF, Fouchier RA. Optimisations and Challenges Involved in the Creation of Various Bioluminescent and Fluorescent Influenza A Virus Strains for In Vitro and In Vivo Applications. PLoS One 2015; 10:e0133888. [PMID: 26241861 PMCID: PMC4524686 DOI: 10.1371/journal.pone.0133888] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 05/07/2015] [Accepted: 07/03/2015] [Indexed: 01/15/2023] Open
Abstract
Bioluminescent and fluorescent influenza A viruses offer new opportunities to study influenza virus replication, tropism and pathogenesis. To date, several influenza A reporter viruses have been described. These strategies typically focused on a single reporter gene (either bioluminescent or fluorescent) in a single virus backbone. However, whilst bioluminescence is suited to in vivo imaging, fluorescent viruses are more appropriate for microscopy. Therefore, the idea l reporter virus varies depending on the experiment in question, and it is important that any reporter virus strategy can be adapted accordingly. Herein, a strategy was developed to create five different reporter viruses in a single virus backbone. Specifically, enhanced green fluorescent protein (eGFP), far-red fluorescent protein (fRFP), near-infrared fluorescent protein (iRFP), Gaussia luciferase (gLUC) and firefly luciferase (fLUC) were inserted into the PA gene segment of A/PR/8/34 (H1N1). This study provides a comprehensive characterisation of the effects of different reporter genes on influenza virus replication and reporter activity. In vivo reporter gene expression, in lung tissues, was only detected for eGFP, fRFP and gLUC expressing viruses. In vitro, the eGFP-expressing virus displayed the best reporter stability and could be used for correlative light electron microscopy (CLEM). This strategy was then used to create eGFP-expressing viruses consisting entirely of pandemic H1N1, highly pathogenic avian influenza (HPAI) H5N1 and H7N9. The HPAI H5N1 eGFP-expressing virus infected mice and reporter gene expression was detected, in lung tissues, in vivo. Thus, this study provides new tools and insights for the creation of bioluminescent and fluorescent influenza A reporter viruses.
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Affiliation(s)
- Monique I. Spronken
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Kirsty R. Short
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- School of Biomedical Sciences, University of Queensland, Brisbane, Australia
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Vincent P. Vaes
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Barbara van der Hoeven
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Centre, Leiden, the Netherlands
| | - Abraham J. Koster
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Centre, Leiden, the Netherlands
| | - Gert-Jan Kremers
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Dana P. Scott
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Alexander P. Gultyaev
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, the Netherlands
| | - Erin M. Sorell
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- Milken Institute School of Public Health, Department of Health Policy and Management, George Washington University, Washington, DC, United States of America
| | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Montserrat Bárcena
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Centre, Leiden, the Netherlands
| | - Guus F. Rimmelzwaan
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Ron A. Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- * E-mail:
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