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Rüdiger D, Piasecka J, Küchler J, Pontes C, Laske T, Kupke SY, Reichl U. Mathematical model calibrated to in vitro data predicts mechanisms of antiviral action of the influenza defective interfering particle "OP7". iScience 2024; 27:109421. [PMID: 38523782 PMCID: PMC10959662 DOI: 10.1016/j.isci.2024.109421] [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: 08/23/2023] [Revised: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
Defective interfering particles (DIPs) are regarded as potent broad-spectrum antivirals. We developed a mathematical model that describes intracellular co-infection dynamics of influenza standard virus (STV) and "OP7", a new type of influenza DIP discovered recently. Based on experimental data from in vitro studies to calibrate the model and confirm its predictions, we deduce OP7's mechanisms of interference, which were yet unknown. Simulations suggest that the "superpromoter" on OP7 genomic viral RNA enhances its replication and results in a depletion of viral proteins. This reduces STV genomic RNA replication, which appears to constitute an antiviral effect. Further, a defective viral protein (M1-OP7) likely causes the deficiency of OP7's replication. It appears unable to bind to genomic viral RNAs to facilitate their nuclear export, a critical step in the viral life cycle. An improved understanding of OP7's antiviral mechanism is crucial toward application in humans as a prospective antiviral treatment strategy.
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Affiliation(s)
- Daniel Rüdiger
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Julita Piasecka
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Jan Küchler
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Carolina Pontes
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Tanja Laske
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
- Institute for Computational Systems Biology, University of Hamburg, 20148 Hamburg, Germany
| | - Sascha Y. Kupke
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Udo Reichl
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
- Chair of Bioprocess Engineering, Otto-von-Guericke University, 39106 Magdeburg, Saxony-Anhalt, Germany
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2
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Noffel Z, Dobrovolny HM. Quantifying the effect of defective viral genomes in respiratory syncytial virus infections. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:12666-12681. [PMID: 37501460 DOI: 10.3934/mbe.2023564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Defective viral genomes (DVGs) are viral genomes that contain only a partial viral RNA and so cannot replicate within cells on their own. If a cell containing DVGs is subsequently infected with a complete viral genome, the DVG can then use the missing proteins expressed by the full genome in order to replicate itself. Since the cell is producing defective genomes, it has less resources to produce fully functional virions and thus release of complete virions is often suppressed. Here, we use data from challenge studies of respiratory syncytial virus (RSV) in healthy adults to quantify the effect of DVGs. We use a mathematical model to fit the data, finding that late onset of DVGs and prolonged DVG detection are associated with lower infection rates and higher clearance rates. This result could have implications for the use of DVGs as a therapeutic.
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Affiliation(s)
- Zakarya Noffel
- Department of Computer Science, University of Texas at Austin, Austin, TX, US
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, US
| | - Hana M Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, US
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3
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Franco EJ, Cella E, Tao X, Hanrahan KC, Azarian T, Brown AN. Favipiravir Suppresses Zika Virus (ZIKV) through Activity as a Mutagen. Microorganisms 2023; 11:1342. [PMID: 37317316 DOI: 10.3390/microorganisms11051342] [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: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
In a companion paper, we demonstrated that the nucleoside analogue favipiravir (FAV) suppressed Zika virus (ZIKV) replication in three human-derived cell lines-HeLa, SK-N-MC, and HUH-7. Our results revealed that FAV's effect was most pronounced in HeLa cells. In this work, we aimed to explain variation in FAV activity, investigating its mechanism of action and characterizing host cell factors relevant to tissue-specific differences in drug effect. Using viral genome sequencing, we show that FAV therapy was associated with an increase in the number of mutations and promoted the production of defective viral particles in all three cell lines. Our findings demonstrate that defective viral particles made up a larger portion of the viral population released from HeLa cells both at increasing FAV concentrations and at increasing exposure times. Taken together, our companion papers show that FAV acts via lethal mutagenesis against ZIKV and highlight the host cell's influence on the activation and antiviral activity of nucleoside analogues. Furthermore, the information gleaned from these companion papers can be applied to gain a more comprehensive understanding of the activity of nucleoside analogues and the impact of host cell factors against other viral infections for which we currently have no approved antiviral therapies.
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Affiliation(s)
- Evelyn J Franco
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, FL 32827, USA
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA
| | - Xun Tao
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, FL 32827, USA
| | - Kaley C Hanrahan
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA
| | - Ashley N Brown
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, FL 32827, USA
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Karki B, Bull JJ, Krone SM. Modeling the Therapeutic Potential of Defective Interfering Particles in the Presence of Immunity. Virus Evol 2022; 8:veac047. [PMID: 35799886 PMCID: PMC9255601 DOI: 10.1093/ve/veac047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/29/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Defective interfering particles (DIPs) are naturally occurring viruses that have evolved to parasitize other viruses. They suppress wild-type (WT) virus infections through their role as intracellular parasites. Because most encode few or no viral proteins, they have been entertained as possible safe antiviral therapies—something that might be given to patients infected with the WT virus. Adding to their safety, they cannot reproduce except when co-infecting the same cells as the WT, so they pose no danger of evolving into independent disease agents. But this dependence on the WT also limits their therapeutic utility by restricting the timing at which their administration can be effective. To develop a qualitative sense of these constraints for acute viral infections, we use ordinary differential equation models to study the mass-action dynamics of DIPs and WT virus in the presence of adaptive and innate immunity that will otherwise clear the infection. Our goal is to understand whether the therapeutic administration of DIPs will augment or interfere with the immune response and, in the former case, we seek to provide guidance on how virus suppression is affected by infection and clearance parameters, as well as by the timing of DIP introduction. Consistent with previous theoretical work, we find that DIPs can significantly suppress viral load. When immunity is present, the timing of DIP administration matters, with an intermediate optimum. When successful at viral suppression, DIPs even slow the immune response, but the combined effect of DIPs and immunity is still beneficial. Outcomes depend somewhat on whether immunity is elicited by and clears DIPs, but timing appears to have the greater effect.
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Affiliation(s)
- Bandita Karki
- Department of Mathematics and Statistical Science, University of Idaho , Moscow, ID 83844-1103 USA
| | - James J Bull
- Department of Biological Sciences, University of Idaho , Moscow, ID 83844-3051 USA
| | - Stephen M Krone
- Department of Mathematics and Statistical Science, University of Idaho , Moscow, ID 83844-1103 USA
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Feng H, Fu J, Zhang B, Xue T, Liu C. A Novel Virus-Like Agent Originated From Genome Rearrangement of Porcine Circovirus Type 2 (PCV2) Enhances PCV2 Replication and Regulates Intracellular Redox Status In Vitro. Front Cell Infect Microbiol 2022; 12:855920. [PMID: 35493731 PMCID: PMC9043654 DOI: 10.3389/fcimb.2022.855920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/22/2022] [Indexed: 01/31/2023] Open
Abstract
Genome rearrangement occurs to porcine circovirus type 2 (PCV2) during in vitro and in vivo infections, and a number of rearranged PCV2 genomes have been isolated and characterized. This study was conducted to investigate the role of the rearranged PCV2 (rPCV2) in PCV2 replication and the biological effect of rPCV2 in host cells. Two whole rPCV2 genome sequences (358 nt and 1125 nt in length) were synthesized and recombinant plasmids pBSK(+)-rPCV2 (pBSK(+)-1125 and pBSK(+)-358) were constructed. A novel virus-like agent (rPCV2-1125) was rescued by in vitro transfection of porcine kidney cell line (PK-15) and porcine alveolar macrophage 3D4/21 cells. The data indicate that rPCV2-1125 significantly enhanced PCV2 replication in vitro. Furthermore, rPCV2-1125 led to oxidative stress in host cells, as indicated by decreased intracellular glutathione (GSH) and total superoxide dismutase (SOD) activities, as well as increased malondialdehyde (MDA) levels. These results provide new insights into genome rearrangement of PCV2 and will contribute to future studies of PCV2 replication and associated mechanisms.
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Affiliation(s)
- Huicheng Feng
- School of Pharmacy, Linyi University, Linyi, Shandong, China
| | - Jinping Fu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, China
- Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bo Zhang
- School of Pharmacy, Linyi University, Linyi, Shandong, China
| | - Tao Xue
- School of Pharmacy, Linyi University, Linyi, Shandong, China
- *Correspondence: Chuanmin Liu, ; Tao Xue,
| | - Chuanmin Liu
- School of Pharmacy, Linyi University, Linyi, Shandong, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, China
- Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Chuanmin Liu, ; Tao Xue,
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Bhat T, Cao A, Yin J. Virus-like Particles: Measures and Biological Functions. Viruses 2022; 14:383. [PMID: 35215979 PMCID: PMC8877645 DOI: 10.3390/v14020383] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022] Open
Abstract
Virus-like particles resemble infectious virus particles in size, shape, and molecular composition; however, they fail to productively infect host cells. Historically, the presence of virus-like particles has been inferred from total particle counts by microscopy, and infectious particle counts or plaque-forming-units (PFUs) by plaque assay; the resulting ratio of particles-to-PFUs is often greater than one, easily 10 or 100, indicating that most particles are non-infectious. Despite their inability to hijack cells for their reproduction, virus-like particles and the defective genomes they carry can exhibit a broad range of behaviors: interference with normal virus growth during co-infections, cell killing, and activation or inhibition of innate immune signaling. In addition, some virus-like particles become productive as their multiplicities of infection increase, a sign of cooperation between particles. Here, we review established and emerging methods to count virus-like particles and characterize their biological functions. We take a critical look at evidence for defective interfering virus genomes in natural and clinical isolates, and we review their potential as antiviral therapeutics. In short, we highlight an urgent need to better understand how virus-like genomes and particles interact with intact functional viruses during co-infection of their hosts, and their impacts on the transmission, severity, and persistence of virus-associated diseases.
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Affiliation(s)
| | | | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA; (T.B.); (A.C.)
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Fatehi F, Bingham RJ, Dechant PP, Stockley PG, Twarock R. Therapeutic interfering particles exploiting viral replication and assembly mechanisms show promising performance: a modelling study. Sci Rep 2021; 11:23847. [PMID: 34903795 PMCID: PMC8668974 DOI: 10.1038/s41598-021-03168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/22/2021] [Indexed: 11/09/2022] Open
Abstract
Defective interfering particles arise spontaneously during a viral infection as mutants lacking essential parts of the viral genome. Their ability to replicate in the presence of the wild-type (WT) virus (at the expense of viable viral particles) is mimicked and exploited by therapeutic interfering particles. We propose a strategy for the design of therapeutic interfering RNAs (tiRNAs) against positive-sense single-stranded RNA viruses that assemble via packaging signal-mediated assembly. These tiRNAs contain both an optimised version of the virus assembly manual that is encoded by multiple dispersed RNA packaging signals and a replication signal for viral polymerase, but lack any protein coding information. We use an intracellular model for hepatitis C viral (HCV) infection that captures key aspects of the competition dynamics between tiRNAs and viral genomes for virally produced capsid protein and polymerase. We show that only a small increase in the assembly and replication efficiency of the tiRNAs compared with WT virus is required in order to achieve a treatment efficacy greater than 99%. This demonstrates that the proposed tiRNA design could be a promising treatment option for RNA viral infections.
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Affiliation(s)
- Farzad Fatehi
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
| | - Richard J Bingham
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Pierre-Philippe Dechant
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
- School of Science, Technology and Health, York St John University, York, YO31 7EX, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Reidun Twarock
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK.
- Department of Mathematics, University of York, York, YO10 5DD, UK.
- Department of Biology, University of York, York, YO10 5DD, UK.
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Shirogane Y, Rousseau E, Voznica J, Xiao Y, Su W, Catching A, Whitfield ZJ, Rouzine IM, Bianco S, Andino R. Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome. PLoS Pathog 2021; 17:e1009277. [PMID: 34570820 PMCID: PMC8496841 DOI: 10.1371/journal.ppat.1009277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/07/2021] [Accepted: 07/28/2021] [Indexed: 01/13/2023] Open
Abstract
During replication, RNA viruses accumulate genome alterations, such as mutations and deletions. The interactions between individual variants can determine the fitness of the virus population and, thus, the outcome of infection. To investigate the effects of defective interfering genomes (DI) on wild-type (WT) poliovirus replication, we developed an ordinary differential equation model, which enables exploring the parameter space of the WT and DI competition. We also experimentally examined virus and DI replication kinetics during co-infection, and used these data to infer model parameters. Our model identifies, and our experimental measurements confirm, that the efficiencies of DI genome replication and encapsidation are two most critical parameters determining the outcome of WT replication. However, an equilibrium can be established which enables WT to replicate, albeit to reduced levels.
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Affiliation(s)
- Yuta Shirogane
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Elsa Rousseau
- Department of Industrial and Applied Genomics, AI and Cognitive Software Division, IBM Almaden Research Center, San Jose, California, United States of America
- NSF Center for Cellular Construction, University of California, San Francisco, California, United States of America
| | - Jakub Voznica
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- ENS Cachan, Université Paris-Saclay, Cachan, France
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Weiheng Su
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Adam Catching
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Zachary J. Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Igor M. Rouzine
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Universite, Institut de Biologie Paris-Seine, Paris, France
| | - Simone Bianco
- Department of Industrial and Applied Genomics, AI and Cognitive Software Division, IBM Almaden Research Center, San Jose, California, United States of America
- NSF Center for Cellular Construction, University of California, San Francisco, California, United States of America
- * E-mail: (SB); (RA)
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- * E-mail: (SB); (RA)
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Tomaru Y, Yamaguchi H, Miki T. Growth Rate-dependent Cell Death of Diatoms due to Viral Infection and Their Subsequent Coexistence in a Semi-continuous Culture System. Microbes Environ 2021; 36. [PMID: 33390375 PMCID: PMC7966941 DOI: 10.1264/jsme2.me20116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Viral infections are a major factor in diatom cell death. However, the effects of viruses on diatom dynamics remain unclear. Based on laboratory studies, it is hypothesized that virus-induced diatom mortality is dependent on the diatom growth rate. The present study aimed to elucidate the relationship between the diatom growth rate and virus-induced mortality using model systems of the marine planktonic diatom, Chaetoceros tenuissimus and its infectious viruses. We also examined the fate of diatom populations in a semi-continuous dilution culture system, in which host growth rates were controlled at 0.69, 2.08, and 3.47 day–1. Diatom populations gradually decreased following the viral inoculation of each culture system, and virus-induced mortality inversely correlated with the diatom growth rate. Furthermore, the viral burst size was slightly higher in lower growth rate cultures. These results suggested that the host physiological status related to the growth rate affected viral infection and proliferation. Diatom populations were not completely lysed or washed out in any of the dilution systems; they showed steady growth in the presence of infectious viruses. This may be partially explained by defective interference particles from viruses and cell debris. The present results indicate that diatoms in dilution environments maintain their populations, even under viral pressure. Moreover, diatom populations with a low growth rate may partially sustain higher growth populations through nutrient recycling following virus-induced cell death. The results of the present study provide insights into diatom dynamics in natural environments in the presence of infectious viruses.
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Affiliation(s)
- Yuji Tomaru
- Hatsukaichi Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, National Research and Development Agency
| | | | - Takeshi Miki
- Ecology and Environmental Engineering, Faculty of Advanced Science and Technology, Ryukoku University
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Hein MD, Arora P, Marichal-Gallardo P, Winkler M, Genzel Y, Pöhlmann S, Schughart K, Kupke SY, Reichl U. Cell culture-based production and in vivo characterization of purely clonal defective interfering influenza virus particles. BMC Biol 2021; 19:91. [PMID: 33941189 PMCID: PMC8091782 DOI: 10.1186/s12915-021-01020-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/01/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Infections with influenza A virus (IAV) cause high morbidity and mortality in humans. Additional to vaccination, antiviral drugs are a treatment option. Besides FDA-approved drugs such as oseltamivir or zanamivir, virus-derived defective interfering (DI) particles (DIPs) are considered promising new agents. IAV DIPs typically contain a large internal deletion in one of their eight genomic viral RNA (vRNA) segments. Consequently, DIPs miss the genetic information necessary for replication and can usually only propagate by co-infection with infectious standard virus (STV), compensating for their defect. In such a co-infection scenario, DIPs interfere with and suppress STV replication, which constitutes their antiviral potential. RESULTS In the present study, we generated a genetically engineered MDCK suspension cell line for production of a purely clonal DIP preparation that has a large deletion in its segment 1 (DI244) and is not contaminated with infectious STV as egg-derived material. First, the impact of the multiplicity of DIP (MODIP) per cell on DI244 yield was investigated in batch cultivations in shake flasks. Here, the highest interfering efficacy was observed for material produced at a MODIP of 1E-2 using an in vitro interference assay. Results of RT-PCR suggested that DI244 material produced was hardly contaminated with other defective particles. Next, the process was successfully transferred to a stirred tank bioreactor (500 mL working volume) with a yield of 6.0E+8 PFU/mL determined in genetically modified adherent MDCK cells. The produced material was purified and concentrated about 40-fold by membrane-based steric exclusion chromatography (SXC). The DI244 yield was 92.3% with a host cell DNA clearance of 97.1% (99.95% with nuclease digestion prior to SXC) and a total protein reduction of 97.2%. Finally, the DIP material was tested in animal experiments in D2(B6).A2G-Mx1r/r mice. Mice infected with a lethal dose of IAV and treated with DIP material showed a reduced body weight loss and all animals survived. CONCLUSION In summary, experiments not only demonstrated that purely clonal influenza virus DIP preparations can be obtained with high titers from animal cell cultures but confirmed the potential of cell culture-derived DIPs as an antiviral agent.
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Affiliation(s)
- Marc D Hein
- Otto-von-Guericke-University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
| | - Prerna Arora
- German Primate Center-Leibniz Institute for Primate Research, Infection Biology Unit, Göttingen, Germany.,University Göttingen, Faculty of Biology and Psychology, Göttingen, Germany
| | - Pavel Marichal-Gallardo
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Michael Winkler
- German Primate Center-Leibniz Institute for Primate Research, Infection Biology Unit, Göttingen, Germany.,University Göttingen, Faculty of Biology and Psychology, Göttingen, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Stefan Pöhlmann
- German Primate Center-Leibniz Institute for Primate Research, Infection Biology Unit, Göttingen, Germany.,University Göttingen, Faculty of Biology and Psychology, Göttingen, Germany
| | - Klaus Schughart
- Helmholtz Centre for Infection Research, Department of Infection Genetics, Braunschweig, Germany.,University of Veterinary Medicine Hannover, Hannover, Germany.,University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, TN, USA
| | - Sascha Y Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Udo Reichl
- Otto-von-Guericke-University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
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11
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Das A, Dutta S, Sen M, Saxena A, Kumar J, Giri L, Murhammer DW, Chakraborty J. A detailed model and Monte Carlo simulation for predicting DIP genome length distribution in baculovirus infection of insect cells. Biotechnol Bioeng 2020; 118:238-252. [PMID: 32936454 DOI: 10.1002/bit.27566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/04/2020] [Accepted: 09/09/2020] [Indexed: 01/14/2023]
Abstract
Baculoviruses have enormous potential for use as biopesticides to control insect pest populations without the adverse environmental effects posed by the widespread use of chemical pesticides. However, continuous baculovirus production is susceptible to DNA mutation and the subsequent production of defective interfering particles (DIPs). The amount of DIPs produced and their genome length distribution are of great interest not only for baculoviruses but for many other DNA and RNA viruses. In this study, we elucidate this aspect of virus replication using baculovirus as an example system and both experimental and modeling studies. The existing mathematical models for the virus replication process consider DIPs as a lumped quantity and do not consider the genome length distribution of the DIPs. In this study, a detailed population balance model for the cell-virus culture is presented, which predicts the genome length distribution of the DIP population along with their relative proportion. The model is simulated using the kinetic Monte Carlo algorithm, and the results agree well with the experimental results. Using this model, a practical strategy to maintain the DIP fraction to near to its maximum and minimum limits has been demonstrated.
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Affiliation(s)
- Ashok Das
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Soumajit Dutta
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | | | - Abha Saxena
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, Telangana, India
| | - Jitendra Kumar
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, Telangana, India
| | - David W Murhammer
- Department of Chemical and Biochemical Engineering, The University of Iowa, Iowa City, California, USA
| | - Jayanta Chakraborty
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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12
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Ziegler CM, Botten JW. Defective Interfering Particles of Negative-Strand RNA Viruses. Trends Microbiol 2020; 28:554-565. [PMID: 32544442 PMCID: PMC7298151 DOI: 10.1016/j.tim.2020.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/27/2020] [Accepted: 02/25/2020] [Indexed: 12/14/2022]
Abstract
Viral defective interfering particles (DIPs) were intensely studied several decades ago but research waned leaving open many critical questions. New technologies and other advances led to a resurgence in DIP studies for negative-strand RNA viruses. While DIPs have long been recognized, their exact contribution to the outcome of acute or persistent viral infections has remained elusive. Recent studies have identified defective viral genomes (DVGs) in human infections, including respiratory syncytial virus and influenza, and growing evidence indicates that DVGs influence disease severity and may contribute to viral persistence. Further, several studies have advanced our understanding of key viral and host factors that regulate DIP formation and activity. Here we review these discoveries and highlight key questions moving forward.
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Affiliation(s)
- Christopher M Ziegler
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA
| | - Jason W Botten
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA; Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Vaccine Testing Center, University of Vermont, Burlington, VT 05405, USA.
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13
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Lathe R, Darlix JL. Prion protein PrP nucleic acid binding and mobilization implicates retroelements as the replicative component of transmissible spongiform encephalopathy. Arch Virol 2020; 165:535-556. [PMID: 32025859 PMCID: PMC7024060 DOI: 10.1007/s00705-020-04529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/21/2022]
Abstract
The existence of more than 30 strains of transmissible spongiform encephalopathy (TSE) and the paucity of infectivity of purified PrPSc, as well as considerations of PrP structure, are inconsistent with the protein-only (prion) theory of TSE. Nucleic acid is a strong contender as a second component. We juxtapose two key findings: (i) PrP is a nucleic-acid-binding antimicrobial protein that is similar to retroviral Gag proteins in its ability to trigger reverse transcription. (ii) Retroelement mobilization is widely seen in TSE disease. Given further evidence that PrP also mediates nucleic acid transport into and out of the cell, a strong case is to be made that a second element – retroelement nucleic acid – bound to PrP constitutes the second component necessary to explain the multiple strains of TSE.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh School of Medicine, Edinburgh, UK. .,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Moscow Region, Russia.
| | - Jean-Luc Darlix
- Faculté de Pharmacie, Centre Nationale de la Recherche Scientifique (CNRS) Laboratory of Bioimaging and Pathologies (Unité Mixte de Recherche 7021), Université de Strasbourg, Illkirch, France.
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14
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Bora M, Yousuf RW, Dhar P, Manu M, Zafir I, Mishra B, Rajak KK, Singh RP. Characterization of defective interfering (DI) particles of Pestedes petitsruminants vaccine virus Sungri/96 strain-implications in vaccine upscaling. Biologicals 2019; 62:57-64. [PMID: 31588012 DOI: 10.1016/j.biologicals.2019.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 08/03/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022] Open
Abstract
The present investigation deals with the characterization of defective interfering (DI) particles of Peste-des-petits ruminants (PPR) vaccine Sungri/96 strain generated as a result of high MOI in Vero cells. During the serial 10 passages, infectivity titres drastically reduced from 6.5 to 2.25 log10TCID50/ml at high MOI. Further, attenuation of CPE with high MOI indicated generation of DI particles that resulted in no/slow progression of CPE during the late passages. Monoclonal antibody based cell ELISA indicated normal protein (N & H) packaging in samples with DI activity. At genomic level, inconsistency in amplicon intensity of H gene was observed in RT-PCR, indicating a possible defect of H gene. Further analysis of copy number of PPRV by RT-qPCR indicated intermittent fluctuations of viral genomic RNA copies. The significant decline of viral RNA copies with MOI 3 (314 copies) compared to low MOI (512804 copies), proved that higher DI multiplicities cause more interference with the replication process of the standard virus. Therefore, MOI is critical for manufacturing of vaccines. These investigations will help in upscaling of PPR vaccines in view of ongoing National and Global PPR control and eradication programme.
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Affiliation(s)
- Mousumi Bora
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, India
| | - Raja Wasim Yousuf
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, India
| | - Pronab Dhar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, India
| | - M Manu
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, India
| | - Insha Zafir
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, India
| | - Rabindra Prasad Singh
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, India.
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15
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Brisse M, Ly H. Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5. Front Immunol 2019; 10:1586. [PMID: 31379819 PMCID: PMC6652118 DOI: 10.3389/fimmu.2019.01586] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. While RIG-I and MDA5 share many genetic, structural and functional similarities, there is increasing evidence that they can have significantly different strategies to recognize different pathogens, PAMPs, and in different host species. This review article discusses the similarities and differences between RIG-I and MDA5 from multiple perspectives, including their structures, evolution and functional relationships with other cellular proteins, their differential mechanisms of distinguishing between host and viral dsRNAs and interactions with host and viral protein factors, and their immunogenic signaling. A comprehensive comparative analysis can help inform future studies of RIG-I and MDA5 in order to fully understand their functions in order to optimize potential therapeutic approaches targeting them.
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Affiliation(s)
- Morgan Brisse
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Twin Cities, St. Paul, MN, United States
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
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16
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Koh C, Audsley MD, Di Giallonardo F, Kerton EJ, Young PR, Holmes EC, McGraw EA. Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture. Virus Evol 2019; 5:vez012. [PMID: 31191980 PMCID: PMC6555872 DOI: 10.1093/ve/vez012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Wolbachia is an intracellular endosymbiont of insects that inhibits the replication of a range of pathogens in its arthropod hosts. The release of Wolbachia into wild populations of mosquitoes is an innovative biocontrol effort to suppress the transmission of arthropod-borne viruses (arboviruses) to humans, most notably dengue virus. The success of the Wolbachia-based approach hinges upon the stable persistence of the ‘pathogen blocking’ effect, whose mechanistic basis is poorly understood. Evidence suggests that Wolbachia may affect viral replication via a combination of competition for host resources and activation of host immunity. The evolution of resistance against Wolbachia and pathogen blocking in the mosquito or the virus could reduce the public health impact of the symbiont releases. Here, we investigate if dengue 3 virus (DENV-3) is capable of accumulating adaptive mutations that improve its replicative capacity during serial passage in Wolbachia wMel-infected cells. During the passaging regime, viral isolates in Wolbachia-infected cells exhibited greater variation in viral loads compared to controls. The viral loads of these isolates declined rapidly during passaging due to the blocking effects of Wolbachia carriage, with several being lost all together and the remainder recovering to low but stable levels. We attempted to sequence the genomes of the surviving passaged isolates but, given their low abundance, were unable to obtain sufficient depth of coverage for evolutionary analysis. In contrast, viral loads in Wolbachia-free control cells were consistently high during passaging. The surviving isolates passaged in the presence of Wolbachia exhibited a reduced ability to replicate even in Wolbachia-free cells. These experiments demonstrate the challenge for dengue in evolving resistance to Wolbachia-mediated blocking.
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Affiliation(s)
- Cassandra Koh
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Michelle D Audsley
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Francesca Di Giallonardo
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia.,The Kirby Institute, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Emily J Kerton
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Paul R Young
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Elizabeth A McGraw
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Department of Entomology, Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, USA
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17
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Defective viral genomes are key drivers of the virus-host interaction. Nat Microbiol 2019; 4:1075-1087. [PMID: 31160826 PMCID: PMC7097797 DOI: 10.1038/s41564-019-0465-y] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 04/23/2019] [Indexed: 12/12/2022]
Abstract
Viruses survive often harsh host environments, yet we know little about the strategies they utilize to adapt and subsist given their limited genomic resources. We are beginning to appreciate the surprising versatility of viral genomes and how replication-competent and -defective virus variants can provide means for adaptation, immune escape and virus perpetuation. This Review summarizes current knowledge of the types of defective viral genomes generated during the replication of RNA viruses and the functions that they carry out. We highlight the universality and diversity of defective viral genomes during infections and discuss their predicted role in maintaining a fit virus population, their impact on human and animal health, and their potential to be harnessed as antiviral tools. This Review describes recent findings on the biogenesis and the role of defective viral genomes during replication of RNA viruses and discusses their impact on viral dynamics and evolution.
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18
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Abstract
Defective viral genomes (DVGs) are generated during viral replication and are unable to carry out a full replication cycle unless coinfected with a full-length virus. DVGs are produced by many viruses, and their presence correlates with alterations in infection outcomes. Historically, DVGs were studied for their ability to interfere with standard virus replication as well as for their association with viral persistence. More recently, a critical role for DVGs in inducing the innate immune response during infection was appreciated. Here we review the role of DVGs of RNA viruses in shaping outcomes of experimental as well as natural infections and explore the mechanisms by which DVGs impact infection outcome.
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Affiliation(s)
- Emmanuelle Genoyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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19
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Huff AL, Wongthida P, Kottke T, Thompson JM, Driscoll CB, Schuelke M, Shim KG, Harris RS, Molan A, Pulido JS, Selby PJ, Harrington KJ, Melcher A, Evgin L, Vile RG. APOBEC3 Mediates Resistance to Oncolytic Viral Therapy. Mol Ther Oncolytics 2018; 11:1-13. [PMID: 30294666 PMCID: PMC6169432 DOI: 10.1016/j.omto.2018.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/23/2018] [Indexed: 12/18/2022] Open
Abstract
Tumor cells frequently evade applied therapies through the accumulation of genomic mutations and rapid evolution. In the case of oncolytic virotherapy, understanding the mechanisms by which cancer cells develop resistance to infection and lysis is critical to the development of more effective viral-based platforms. Here, we identify APOBEC3 as an important factor that restricts the potency of oncolytic vesicular stomatitis virus (VSV). We show that VSV infection of B16 murine melanoma cells upregulated APOBEC3 in an IFN-β-dependent manner, which was responsible for the evolution of virus-resistant cell populations and suggested that APOBEC3 expression promoted the acquisition of a virus-resistant phenotype. Knockdown of APOBEC3 in B16 cells diminished their capacity to develop resistance to VSV infection in vitro and enhanced the therapeutic effect of VSV in vivo. Similarly, overexpression of human APOBEC3B promoted the acquisition of resistance to oncolytic VSV both in vitro and in vivo. Finally, we demonstrate that APOBEC3B expression had a direct effect on the fitness of VSV, an RNA virus that has not previously been identified as restricted by APOBEC3B. This research identifies APOBEC3 enzymes as key players to target in order to improve the efficacy of viral or broader nucleic acid-based therapeutic platforms.
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Affiliation(s)
- Amanda L. Huff
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Timothy Kottke
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jill M. Thompson
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Kevin G. Shim
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Reuben S. Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amy Molan
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jose S. Pulido
- Department of Ophthalmology, Mayo Clinic, Rochester, MN 55905, USA
| | - Peter J. Selby
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James’s University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | | | | | - Laura Evgin
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Richard G. Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James’s University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
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20
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Manzoni TB, López CB. Defective (interfering) viral genomes re-explored: impact on antiviral immunity and virus persistence. Future Virol 2018; 13:493-503. [PMID: 30245734 PMCID: PMC6136085 DOI: 10.2217/fvl-2018-0021] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/03/2018] [Indexed: 11/21/2022]
Abstract
Defective viral genomes (DVGs) are natural products of virus replication that occur in many positive and negative sense RNA viruses, including Ebola, dengue and respiratory syncytial virus. DVGs, which have severe genomic truncations and require a helper virus to replicate, have three well-described functions: interference with standard virus replication, immunostimulation, and establishment of virus persistence. These functions of DVGs were first described almost 50 years ago, yet only recent studies have shown the molecular intersection between their immunostimulatory and pro-persistence activities. Here, we review more than half a century of scientific literature on the immunostimulatory and pro-persistence functions of DVGs. We highlight recent advances in the field and the critical role DVGs have in both the acute and long-term virus-host interactions.
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Affiliation(s)
- Tomaz B Manzoni
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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An overview of process intensification and thermo stabilization for upscaling of Peste des petits ruminants vaccines in view of global control and eradication. Virusdisease 2018; 29:285-296. [PMID: 30159362 DOI: 10.1007/s13337-018-0455-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/03/2018] [Indexed: 12/22/2022] Open
Abstract
Peste des petits ruminants (PPR) has been recognized as a globally distributed disease affecting the small ruminant population. The disease results in severe economic losses mainly to small land holders and low input farming systems. The control of PPR is mainly achieved through vaccination with available live attenuated vaccines. The thermo labile nature of PPR virus poses a major constraint in production of quality vaccines which often results in vaccine failures. The lack of quality vaccine production jeopardize the wide vaccination coverage especially in countries with poor infrastructure due to which PPR persists endemically. The vaccine production system may require augmentation to attain consistent and quality vaccines through efforts of process intensification integrated with suitable stabilizer formulations with appropriate freeze drying cycles for improved thermo tolerance. Manufacturing of live attenuated PPR vaccines during batch cultures might introduce defective interfering particles (DIPs) as a result of high multiplicity of infection (MOI) of inoculums, which has a huge impact on virus dynamics and yield. Accumulation of DIPs adversely affects the quality of the manufactured vaccines which can be avoided through use of appropriate MOI of virus inoculums and quality control of working seed viruses. Therefore, adherence to critical manufacturing standard operating procedures in vaccine production and ongoing efforts on development of thermo tolerant vaccine will help a long way in PPR control and eradication programme globally. The present review focuses on the way forward to achieve the objectives of quality vaccine production and easy upscaling to help the global PPR control and eradication by mass vaccination as an important tool.
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22
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Wasik MA, Eichwald L, Genzel Y, Reichl U. Cell culture-based production of defective interfering particles for influenza antiviral therapy. Appl Microbiol Biotechnol 2017; 102:1167-1177. [PMID: 29204901 PMCID: PMC5778153 DOI: 10.1007/s00253-017-8660-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 11/28/2022]
Abstract
Defective interfering particles (DIPs) lack an essential portion of the virus genome, but retain signals for replication and packaging, and therefore, interfere with standard virus (STV) replication. Due to this property, DIPs can be potential antivirals. The influenza A virus DIP DI244, generated during propagation in chicken eggs, has been previously described as a potential candidate for influenza antiviral therapy. As a cell culture-based manufacturing process would be more suitable to fulfill large-scale production needs of an antiviral and enables full process control in closed systems, we investigated options to produce DI244 in the avian cell line AGE1.CR.pIX in chemically defined suspension culture. With a DI244 fraction of 55.8% compared to STV, the highest DI244 yield obtained from 50 million cells was 4.6 × 109 vRNA copies/mL at 12 h post infection. However, other defective genomes were also detected. Since these additionally produced defective particles are non-infectious, they might be still useful in antiviral therapies. In case they would interfere with quality of the final product, we examined the impact of virus seeds and selected process parameters on DI244 yield and contamination level with other defective particles. With a DI244 fraction of 5.5%, the yield obtained was 1.7 × 108 vRNA copies/mL but now without additional defective genomes. Although the DI244 yield might be decreased in this case, such controlled manufacturing conditions are not available in chicken eggs. Overall, the application of these findings can support design and optimization of a cell culture-based production process for DIPs to be used as antivirals.
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Affiliation(s)
- Milena A Wasik
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany.
| | - Luca Eichwald
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany.,Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitaetsplatz 2, 39106, Magdeburg, Germany
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23
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Liao LE, Iwami S, Beauchemin CAA. (In)validating experimentally derived knowledge about influenza A defective interfering particles. J R Soc Interface 2017; 13:rsif.2016.0412. [PMID: 27881801 PMCID: PMC5134007 DOI: 10.1098/rsif.2016.0412] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/27/2016] [Indexed: 11/28/2022] Open
Abstract
A defective interfering particle (DIP) in the context of influenza A virus is a virion with a significantly shortened RNA segment substituting one of eight full-length parent RNA segments, such that it is preferentially amplified. Hence, a cell co-infected with DIPs will produce mainly DIPs, suppressing infectious virus yields and affecting infection kinetics. Unfortunately, the quantification of DIPs contained in a sample is difficult because they are indistinguishable from standard virus (STV). Using a mathematical model, we investigated the standard experimental method for counting DIPs based on the reduction in STV yield (Bellett & Cooper, 1959, Journal of General Microbiology21, 498–509 (doi:10.1099/00221287-21-3-498)). We found the method is valid for counting DIPs provided that: (i) an STV-infected cell's co-infection window is approximately half its eclipse phase (it blocks infection by other virions before it begins producing progeny virions), (ii) a cell co-infected by STV and DIP produces less than 1 STV per 1000 DIPs and (iii) a high MOI of STV stock (more than 4 PFU per cell) is added to perform the assay. Prior work makes no mention of these criteria such that the method has been applied incorrectly in several publications discussed herein. We determined influenza A virus meets these criteria, making the method suitable for counting influenza A DIPs.
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Affiliation(s)
- Laura E Liao
- Department of Physics, Ryerson University, Toronto, Canada
| | - Shingo Iwami
- Department of Biology, Kyushu University, Fukuoka, Japan.,CREST and PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
| | - Catherine A A Beauchemin
- Department of Physics, Ryerson University, Toronto, Canada .,Interdisciplinary Theoretical Science (iTHES) Research Group at RIKEN, Wako, Japan
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24
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Xu J, Sun Y, Li Y, Ruthel G, Weiss SR, Raj A, Beiting D, López CB. Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence. Nat Commun 2017; 8:799. [PMID: 28986577 PMCID: PMC5630589 DOI: 10.1038/s41467-017-00909-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/02/2017] [Indexed: 12/03/2022] Open
Abstract
Replication defective viral genomes (DVGs) generated during virus replication are the primary triggers of antiviral immunity in many RNA virus infections. However, DVGs can also facilitate viral persistence. Why and how these two opposing functions of DVGs are achieved remain unknown. Here we report that during Sendai and respiratory syncytial virus infections DVGs selectively protect a subpopulation of cells from death, thereby promoting the establishment of persistent infections. We find that during Sendai virus infection this phenotype results from DVGs stimulating a mitochondrial antiviral-signaling (MAVS)-mediated TNF response that drives apoptosis of highly infected cells while extending the survival of cells enriched in DVGs. The pro-survival effect of TNF depends on the activity of the TNFR2/TRAF1 pathway that is regulated by MAVS signaling. These results identify TNF as a pivotal factor in determining cell fate during a viral infection and delineate a MAVS/TNFR2-mediated mechanism that drives the persistence of otherwise acute viruses. Replication defective viral genomes (DVGs) can facilitate persistence of paramyxoviruses, but the underlying mechanisms are unclear. Using FISH, Xu et al. here analyze the cellular response to DVGs on a single cell level and show that a MAVS-mediated TNF response specifically extends survival of cells enriched in DVGs.
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Affiliation(s)
- Jie Xu
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yan Sun
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gordon Ruthel
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arjun Raj
- Department of Bioengineering, School of Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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25
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A Virological and Phylogenetic Analysis of the Emergence of New Clades of Respiratory Syncytial Virus. Sci Rep 2017; 7:12232. [PMID: 28947776 PMCID: PMC5612963 DOI: 10.1038/s41598-017-12001-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/30/2017] [Indexed: 12/14/2022] Open
Abstract
The significant burden of Respiratory Syncytial Virus (RSV) in pediatric and elderly populations is well recognized. However, questions remain about transmission and evolution of RSV in the community, between seasons, and the role played by viral genetics in viral replication. Therefore, we integrated next generation sequencing, patient viral load, and viral replication analysis with surveillance of RSV to initiate a better understanding of viral adaptation in communities. RSV type-A and B infections were most closely related to RSV sequences from the USA and Asia, respectfully. The sample titres between RSV types-A and B were not significantly different. However, when the patient sample titre was compared to the phylogenetics of RSV, emergent clades were identified that we termed High Titre (HiT) clades of RSV. In conclusion, the correlation between patient viral load and replication kinetics of RSV patient isolates in culture indicated that viral genetics may determine virus replicative ability within patients. There was evolution or introduction of high-titre RSV type-A and B infections that seeded HiT clades in the subsequent year. Therefore, virological analysis of RSV isolates in conjunction with RSV phylogenetics may be a tool for predicting new clades of RSV in impending seasons.
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Baltes A, Akpinar F, Inankur B, Yin J. Inhibition of infection spread by co-transmitted defective interfering particles. PLoS One 2017; 12:e0184029. [PMID: 28915264 PMCID: PMC5600374 DOI: 10.1371/journal.pone.0184029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/16/2017] [Indexed: 11/18/2022] Open
Abstract
Although virus release from host cells and tissues propels the spread of many infectious diseases, most virus particles are not infectious; many are defective, lacking essential genetic information needed for replication. When defective and viable particles enter the same cell, the defective particles can multiply while interfering with viable particle production. Defective interfering particles (DIPs) occur in nature, but their role in disease pathogenesis and spread is not known. Here, we engineered an RNA virus and its DIPs to express different fluorescent reporters, and we observed how DIPs impact viral gene expression and infection spread. Across thousands of host cells, co-infected with infectious virus and DIPs, gene expression was highly variable, but average levels of viral reporter expression fell at higher DIP doses. In cell populations spatial patterns of infection spread provided the first direct evidence for the co-transmission of DIPs with infectious virus. Patterns of spread were highly sensitive to the behavior of initial or early co-infected cells, with slower overall spread stemming from higher early DIP doses. Under such conditions striking patterns of patchy gene expression reflected localized regions of DIP or virus enrichment. From a broader perspective, these results suggest DIPs contribute to the ecological and evolutionary persistence of viruses in nature.
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Affiliation(s)
- Ashley Baltes
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Fulya Akpinar
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Bahar Inankur
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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The brain parenchyma has a type I interferon response that can limit virus spread. Proc Natl Acad Sci U S A 2016; 114:E95-E104. [PMID: 27980033 DOI: 10.1073/pnas.1618157114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The brain has a tightly regulated environment that protects neurons and limits inflammation, designated "immune privilege." However, there is not an absolute lack of an immune response. We tested the ability of the brain to initiate an innate immune response to a virus, which was directly injected into the brain parenchyma, and to determine whether this response could limit viral spread. We injected vesicular stomatitis virus (VSV), a transsynaptic tracer, or naturally occurring VSV-derived defective interfering particles (DIPs), into the caudate-putamen (CP) and scored for an innate immune response and inhibition of virus spread. We found that the brain parenchyma has a functional type I interferon (IFN) response that can limit VSV spread at both the inoculation site and among synaptically connected neurons. Furthermore, we characterized the response of microglia to VSV infection and found that infected microglia produced type I IFN and uninfected microglia induced an innate immune response following virus injection.
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Spatial-Temporal Patterns of Viral Amplification and Interference Initiated by a Single Infected Cell. J Virol 2016; 90:7552-7566. [PMID: 27279621 PMCID: PMC4984635 DOI: 10.1128/jvi.00807-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/02/2016] [Indexed: 11/20/2022] Open
Abstract
When viruses infect their host cells, they can make defective virus-like particles along with intact virus. Cells coinfected with virus and defective particles often exhibit interference with virus growth caused by the competition for resources by defective genomes. Recent reports of the coexistence and cotransmission of such defective interfering particles (DIPs) in vivo, across epidemiological length and time scales, suggest a role in viral pathogenesis, but it is not known how DIPs impact infection spread, even under controlled culture conditions. Using fluorescence microscopy, we quantified coinfections of vesicular stomatitis virus (VSV) expressing a fluorescent reporter protein and its DIPs on BHK-21 host cell monolayers. We found that viral gene expression was more delayed, infections spread more slowly, and patterns of spread became more “patchy” with higher DIP inputs to the initial cell. To examine how infection spread might depend on the behavior of the initial coinfected cell, we built a computational model, adapting a cellular automaton (CA) approach to incorporate kinetic data on virus growth for the first time. Specifically, changes in observed patterns of infection spread could be directly linked to previous high-throughput single-cell measures of virus-DIP coinfection. The CA model also provided testable hypotheses on the spatial-temporal distribution of the DIPs, which remain governed by their predator-prey interaction. More generally, this work offers a data-driven computational modeling approach for better understanding of how single infected cells impact the multiround spread of virus infections across cell populations.
IMPORTANCE Defective interfering particles (DIPs) compete with intact virus, depleting host cell resources that are essential for virus growth and infection spread. However, it is not known how such competition, strong or weak, ultimately affects the way in which infections spread and cause disease. In this study, we address this unmet need by developing an integrated experimental-computational approach, which sheds new light on how infections spread. We anticipate that our approach will also be useful in the development of DIPs as therapeutic agents to manage the spread of viral infections.
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Akpinar F, Timm A, Yin J. High-Throughput Single-Cell Kinetics of Virus Infections in the Presence of Defective Interfering Particles. J Virol 2016; 90:1599-612. [PMID: 26608322 PMCID: PMC4719634 DOI: 10.1128/jvi.02190-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/18/2015] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Defective interfering particles (DIPs) are virus mutants that lack essential genes for growth. In coinfections with helper virus, the diversion of viral proteins to the replication and packaging of DIP genomes can interfere with virus production. Mounting cases of DIPs and DIP-like genomes in clinical and natural isolates, as well as growing interest in DIP-based therapies, underscore a need to better elucidate how DIPs work. DIP activity is primarily measured by its inhibition of virus infection yield, an endpoint that masks the dynamic and potentially diverse individual cell behaviors. Using vesicular stomatitis virus (VSV) as a model, we coinfected BHK cells with VSV DIPs and recombinant helper virus carrying a gene encoding a red fluorescent protein (RFP) whose expression correlates with the timing and level of virus release. For single cells within a monolayer, 10 DIPs per cell suppressed the reporter expression in only 1.2% of the cells. In most cells, it slowed and reduced viral gene expression, manifested as a shift in mean latent time from 4 to 6 h and reduced virus yields by 10-fold. For single cells isolated in microwells, DIP effects were more pronounced, reducing virus yields by 100-fold and extending latent times to 12 h, including individual instances above 20 h. Together, these results suggest that direct or indirect cell-cell interactions prevent most coinfected cells from being completely suppressed by DIPs. Finally, a gamma distribution model captures well how the infection kinetics quantitatively depends on the DIP dose. Such models will be useful for advancing a predictive biology of DIP-associated virus growth and infection spread. IMPORTANCE During the last century, basic studies in virology have focused on developing a molecular mechanistic understanding of how infectious viruses reproduce in their living host cells. However, over the last 10 years, the advent of deep sequencing and other powerful technologies has revealed in natural and patient infections that viruses do not act alone. Instead, viruses are often accompanied by defective virus-like particles that carry large deletions in their genomes and fail to replicate on their own. Coinfections of viable and defective viruses behave in unpredictable ways, but they often interfere with normal virus growth, potentially enabling infections to evade host immune surveillance. In the current study, controlled levels of defective viruses are coinfected with viable viruses that have been engineered to express a fluorescent reporter protein during infection. Unique profiles of reporter expression acquired from thousands of coinfected cells reveal how interference acts at multiple stages of infection.
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Affiliation(s)
- Fulya Akpinar
- Systems Biology Theme, Wisconsin Institute for Discovery, Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrea Timm
- Systems Biology Theme, Wisconsin Institute for Discovery, Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John Yin
- Systems Biology Theme, Wisconsin Institute for Discovery, Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Rabies viral vectors for monosynaptic tracing and targeted transgene expression in neurons. Cold Spring Harb Protoc 2015; 2015:375-85. [PMID: 25834254 DOI: 10.1101/pdb.prot072389] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Deletion-mutant rabies viral (RV) vectors are powerful tools for neuroscience, allowing monosynaptic tracing of inputs to defined populations and rapid, high-level transgene expression in neurons targeted by multiple routes. High titers and high purity are critical for the successful use of RV vectors in vivo. Here we present a protocol for producing high-quality viral stocks that can be concentrated by ultracentrifugation for final titers in excess of 10(10) infectious units per milliliter.
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Brown CM, Bidle KD. Attenuation of virus production at high multiplicities of infection in Aureococcus anophagefferens. Virology 2014; 466-467:71-81. [PMID: 25104555 DOI: 10.1016/j.virol.2014.07.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 01/16/2023]
Abstract
Infection dynamics (saturation kinetics, infection efficiency, adsorption and burst size) for the Aureococcus anophagefferens-Brown Tide virus (AaV) system were investigated using susceptible and resistant strains. Adsorption assays revealed that virus affinity to the cell surface is a key determinant of infectivity. Saturation of infection occurred at a multiplicity of infection (MOI) of 8 viruses per host and resulted in ~90-95% of infected cells, with burst sizes ranging from 164 to 191. Insight from the AaV genome implicates recycling of host nucleotides rather than de novo synthesis as a constraint on viral replication. Viral yields and mean burst sizes were significantly diminished with increasing MOI. This phenomenon, which was reminiscent of phage-induced 'lysis from without', appeared to be caused by viral contact and was unrelated to bacteria, signaling/toxic compounds, or defective interfering viruses. We posit that high-MOI effects attenuate viral proliferation in natural systems providing a negative feedback on virus-induced bloom collapse.
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Affiliation(s)
- Christopher M Brown
- Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ 08901, USA
| | - Kay D Bidle
- Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ 08901, USA.
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32
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Quantitative characterization of defective virus emergence by deep sequencing. J Virol 2013; 88:2623-32. [PMID: 24352442 DOI: 10.1128/jvi.02675-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Populations of RNA viruses can spontaneously produce variants that differ in genome size, sequence, and biological activity. Defective variants that lack essential genes can nevertheless reproduce by coinfecting cells with viable virus, a process that interferes with virus growth. How such defective interfering particles (DIPs) change in abundance and biological activity within a virus population is not known. Here, a prototype RNA virus, vesicular stomatitis virus (VSV), was cultured for three passages on BHK host cells, and passages were subjected to Illumina sequencing. Reads from the initial population, when aligned to the full-length viral sequence (11,161 nucleotides [nt]), distributed uniformly across the genome. However, during passages two plateaus in read counts appeared toward the 5' end of the negative-sense viral genome. Analysis by normalization and a simple sliding-window approach revealed plateau boundaries that suggested the emergence and enrichment of at least two truncated species having medium (∼5,900 nt) and short (∼4,000 nt) genomes. Relative measures of full-length and truncated species based on read counts were validated by quantitative reverse transcription-PCR (qRT-PCR). Limit-of-detection analysis suggests that deep sequencing can be more sensitive than complementary measures for detecting and quantifying defective particles in a population. Further, particle counts from transmission electron microscopy, coupled with infectivity assays, linked the rise in smaller genomes with an increase in truncated particles and interference activity. In summary, variation in deep sequencing coverage simultaneously shows the size, location, and relative level of truncated-genome variants, revealing a level of population heterogeneity that is masked by other measures of viral genomes and particles. IMPORTANCE We show how deep sequencing can be used to characterize the emergence, diversity, and relative abundance of truncated virus variants in virus populations. Adaptation of this approach to natural isolates may elucidate factors that influence the stability and persistence of virus populations in nature.
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Frensing T, Heldt FS, Pflugmacher A, Behrendt I, Jordan I, Flockerzi D, Genzel Y, Reichl U. Continuous influenza virus production in cell culture shows a periodic accumulation of defective interfering particles. PLoS One 2013; 8:e72288. [PMID: 24039749 PMCID: PMC3764112 DOI: 10.1371/journal.pone.0072288] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/13/2013] [Indexed: 01/02/2023] Open
Abstract
Influenza viruses are a major public health burden during seasonal epidemics and a continuous threat due to their potential to cause pandemics. Annual vaccination provides the best protection against the contagious respiratory illness caused by influenza viruses. However, the current production capacities for influenza vaccines are insufficient to meet the increasing demands. We explored the possibility to establish a continuous production process for influenza viruses using the duck-derived suspension cell line AGE1.CR. A two-stage bioreactor setup was designed in which cells were cultivated in a first stirred tank reactor where an almost constant cell concentration was maintained. Cells were then constantly fed to a second bioreactor where virus infection and replication took place. Using this two-stage reactor system, it was possible to continuously produce influenza viruses. Surprisingly, virus titers showed a periodic increase and decrease during the run-time of 17 days. These titer fluctuations were caused by the presence of defective interfering particles (DIPs), which we detected by PCR. Mathematical modeling confirmed this observation showing that constant virus titers can only emerge in the absence of DIPs. Even with very low amounts of DIPs in the seed virus and very low rates for de novo DIP generation, defective viruses rapidly accumulate and, therefore, represent a serious challenge for continuous vaccine production. Yet, the continuous replication of influenza virus using a two-stage bioreactor setup is a novel tool to study aspects of viral evolution and the impact of DIPs.
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Affiliation(s)
- Timo Frensing
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- * E-mail:
| | - Frank Stefan Heldt
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Antje Pflugmacher
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Ilona Behrendt
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | | | - Dietrich Flockerzi
- Systems and Control Theory, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Chair for Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
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Petterson E, Stormoen M, Evensen Ø, Mikalsen AB, Haugland Ø. Natural infection of Atlantic salmon (Salmo salar L.) with salmonid alphavirus 3 generates numerous viral deletion mutants. J Gen Virol 2013; 94:1945-1954. [PMID: 23704276 DOI: 10.1099/vir.0.052563-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Salmon pancreas disease virus (SPDV) also referred to as salmonid alphavirus (SAV) is a virus causing pancreas disease in Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss). Although the virus causes an economically important disease, relatively few full-length genome sequences of SAV strains are currently available. Here, we report full-length genome sequences of nine SAV3 strains from sites farming Atlantic salmon geographically spread along the Norwegian coastline. The virus genomes were sequenced directly from infected heart tissue, to avoid culture selection bias. Sequence analysis confirmed a high level of sequence identity within SAV3 strains, with a mean nucleotide diversity of 0.11 %. Sequence divergence was highest in 6K and E2, while lowest in the capsid protein and the non-structural proteins (nsP4 and nsP2). This study reports for the first time that numerous defective viruses containing genome deletions are generated during natural infection with SAV. Deletions occurred in all virus strains and were not distributed randomly throughout the genome but instead tended to aggregate in certain areas. We suggest imprecise homologous recombination as an explanation for generation of defective viruses with genome deletions. The presence of such viruses, provides a possible explanation for the difficulties in isolating SAV in cell culture. Primary virus isolation was successfully achieved for only two of eight strains, despite extensive attempts using three different cell lines. Both SAV isolates were easily propagated further and concomitant viral deletion mutants present in clinically infected heart tissue were maintained following serial passage in CHH-1 cells.
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Affiliation(s)
- Elin Petterson
- Norwegian School of Veterinary Science, Department of Basic Sciences and Aquatic Medicine, P.O. Box 8146 Dep., 0033 Oslo Norway
| | - Marit Stormoen
- Norwegian School of Veterinary Science, Department of Basic Sciences and Aquatic Medicine, P.O. Box 8146 Dep., 0033 Oslo Norway
| | - Øystein Evensen
- Norwegian School of Veterinary Science, Department of Basic Sciences and Aquatic Medicine, P.O. Box 8146 Dep., 0033 Oslo Norway
| | - Aase B Mikalsen
- Norwegian School of Veterinary Science, Department of Basic Sciences and Aquatic Medicine, P.O. Box 8146 Dep., 0033 Oslo Norway
| | - Øyvind Haugland
- Norwegian School of Veterinary Science, Department of Basic Sciences and Aquatic Medicine, P.O. Box 8146 Dep., 0033 Oslo Norway
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Ke R, Lloyd-Smith JO. Evolutionary analysis of human immunodeficiency virus type 1 therapies based on conditionally replicating vectors. PLoS Comput Biol 2012; 8:e1002744. [PMID: 23133349 PMCID: PMC3486895 DOI: 10.1371/journal.pcbi.1002744] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 08/31/2012] [Indexed: 12/15/2022] Open
Abstract
Efforts to reduce the viral load of human immunodeficiency virus type 1 (HIV-1) during long-term treatment are challenged by the evolution of anti-viral resistance mutants. Recent studies have shown that gene therapy approaches based on conditionally replicating vectors (CRVs) could have many advantages over anti-viral drugs and other approaches to therapy, potentially including the ability to circumvent the problem of evolved resistance. However, research to date has not explored the evolutionary consequences of long-term treatment of HIV-1 infections with conditionally replicating vectors. In this study, we analyze a computational model of the within-host co-evolutionary dynamics of HIV-1 and conditionally replicating vectors, using the recently proposed ‘therapeutic interfering particle’ as an example. The model keeps track of the stochastic process of viral mutation, and the deterministic population dynamics of T cells as well as different strains of CRV and HIV-1 particles. We show that early in the co-infection, mutant HIV-1 genotypes that escape suppression by CRV therapy appear; this is similar to the dynamics observed in drug treatments and other gene therapies. In contrast to other treatments, however, the CRV population is able to evolve and catch up with the dominant HIV-1 escape mutant and persist long-term in most cases. On evolutionary grounds, gene therapies based on CRVs appear to be a promising tool for long-term treatment of HIV-1. Our model allows us to propose design principles to optimize the efficacy of this class of gene therapies. In addition, because of the analogy between CRVs and naturally-occurring defective interfering particles, our results also shed light on the co-evolutionary dynamics of wild-type viruses and their defective interfering particles during natural infections. A long-standing challenge in efforts to control human immunodeficiency virus type 1 (HIV-1) is the rapid evolution of the virus. Any effective therapy quickly gives rise to so-called escape mutants of the virus, potentially resulting in treatment failure. A distinct class of gene therapy based on conditionally replicating vectors has been suggested to have potential to circumvent the problem of viral evolutionary escape. A conditionally replicating vector cannot replicate on its own, but when it coinfects the same cell with HIV-1, it is packaged into a virion-like particle and can be transmitted from cell to cell. Importantly, these vectors replicate using the same machinery that HIV-1 uses, and so they mutate at the same rate. This opens the possibility that conditionally replicating vectors could ‘keep up’ with HIV-1 evolution and prevent HIV-1 escape. In this study, we present mathematical analyses of the co-evolutionary dynamics of HIV-1 and conditionally replicating vectors within a patient. Our results show that with proper genetic design, conditionally replicating vectors can keep pace with HIV-1 evolution, leading to persistent reduction in HIV-1 viral loads. Therefore, this class of gene therapies shows potential for ‘evolution-proof’ control of HIV-1, and merits further investigation in laboratory trials.
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Affiliation(s)
- Ruian Ke
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA.
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36
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Lancaster KZ, Pfeiffer JK. Viral population dynamics and virulence thresholds. Curr Opin Microbiol 2012; 15:525-30. [PMID: 22658738 PMCID: PMC3424342 DOI: 10.1016/j.mib.2012.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 05/07/2012] [Accepted: 05/13/2012] [Indexed: 12/17/2022]
Abstract
Viral factors and host barriers influence virally induced disease, and asymptomatic versus symptomatic infection is governed by a 'virulence threshold'. Understanding modulation of virulence thresholds could lend insight into disease outcome and aid in rational therapeutic and vaccine design. RNA viruses are an excellent system to study virulence thresholds in the context of quasispecies population dynamics. RNA viruses have high error frequencies and our understanding of viral population dynamics has been shaped by quasispecies evolutionary theory. In turn, research using RNA viruses as replicons with short generation times and high mutation rates has been an invaluable tool to test models of quasispecies theory. The challenge and new frontier of RNA virus population dynamics research is to combine multiple theoretical models and experimental data to describe viral population behavior as it changes, moving within and between hosts, to predict disease and pathogen emergence. Several excellent studies have begun to undertake this challenge using novel approaches.
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Affiliation(s)
- Karen Z Lancaster
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA
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Pesko KN, Fitzpatrick KA, Ryan EM, Shi PY, Zhang B, Lennon NJ, Newman RM, Henn MR, Ebel GD. Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice. Virology 2012; 427:10-7. [PMID: 22365325 DOI: 10.1016/j.virol.2012.01.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/13/2011] [Accepted: 01/26/2012] [Indexed: 11/28/2022]
Abstract
Most RNA viruses exist in their hosts as a heterogeneous population of related variants. Due to error prone replication, mutants are constantly generated which may differ in individual fitness from the population as a whole. Here we characterize three WNV isolates that contain, along with full-length genomes, mutants with large internal deletions to structural and nonstructural protein-coding regions. The isolates were all obtained from lorikeets that died from WNV at the Rio Grande Zoo in Albuquerque, NM between 2005 and 2007. The deletions are approximately 2kb, in frame, and result in the elimination of the complete envelope, and portions of the prM and NS-1 proteins. In Vero cell culture, these internally deleted WNV genomes function as defective interfering particles, reducing the production of full-length virus when introduced at high multiplicities of infection. In mosquitoes, the shortened WNV genomes reduced infection and dissemination rates, and virus titers overall, and were not detected in legs or salivary secretions at 14 or 21 days post-infection. In mice, inoculation with internally deleted genomes did not attenuate pathogenesis relative to full-length or infectious clone derived virus, and shortened genomes were not detected in mice at the time of death. These observations provide evidence that large deletions may occur within flavivirus populations more frequently than has generally been appreciated and suggest that they impact population phenotype minimally. Additionally, our findings suggest that highly similar mutants may frequently occur in particular vertebrate hosts.
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Affiliation(s)
- Kendra N Pesko
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA.
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38
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Lancaster KZ, Pfeiffer JK. Mechanisms controlling virulence thresholds of mixed viral populations. J Virol 2011; 85:9778-88. [PMID: 21795346 PMCID: PMC3196390 DOI: 10.1128/jvi.00355-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 07/16/2011] [Indexed: 02/05/2023] Open
Abstract
The propensity of RNA viruses to revert attenuating mutations contributes to disease and complicates vaccine development. Despite the presence of virulent revertant viruses in some live-attenuated vaccines, disease from vaccination is rare. This suggests that in mixed viral populations, attenuated viruses may limit the pathogenesis of virulent viruses, thus establishing a virulence threshold. Here we examined virulence thresholds using mixtures of virulent and attenuated viruses in a transgenic mouse model of poliovirus infection. We determined that a 1,000-fold excess of the attenuated Sabin strain of poliovirus was protective against disease induced by the virulent Mahoney strain. Protection was induced locally, and inactivated virus conferred protection. Treatment with a poliovirus receptor-blocking antibody phenocopied the protective effect of inactivated viruses in vitro and in vivo, suggesting that one mechanism controlling virulence thresholds may be competition for a viral receptor. Additionally, the type I interferon response reduces poliovirus pathogenesis; therefore, we examined virulence thresholds in mice lacking the alpha/beta interferon receptor. We found that the attenuated virus was virulent in immunodeficient mice due to the enhanced replication and reversion of attenuating mutations. Therefore, while the type I interferon response limits the virulence of the attenuated strain by reducing replication, protection from disease conferred by the attenuated strain in immunocompetent mice can occur independently of replication. Our results identified mechanisms controlling the virulence of mixed viral populations and indicate that live-attenuated vaccines containing virulent virus may be safe, as long as virulent viruses are present at levels below a critical threshold.
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Affiliation(s)
| | - Julie K. Pfeiffer
- Corresponding author. Mailing address: Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9048. Phone: (214) 633-1377. Fax: (214) 648-5905. E-mail:
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Thompson KAS, Yin J. Population dynamics of an RNA virus and its defective interfering particles in passage cultures. Virol J 2010; 7:257. [PMID: 20920247 PMCID: PMC2955718 DOI: 10.1186/1743-422x-7-257] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 09/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Viruses can fall prey to their defective interfering (DI) particles. When viruses are cultured by serial passage on susceptible host cells, the presence of virus-like DI particles can cause virus populations to rise and fall, reflecting predator-prey interactions between DI and virus particles. The levels of virus and DI particles in each population passage can be determined experimentally by plaque and yield-reduction assays, respectively. RESULTS To better understand DI and virus particle interactions we measured vesicular stomatitis virus and DI particle production during serial-passage culture on BHK cells. When the multiplicity of infection (MOI, or ratio of infectious virus particles to cells) was fixed, virus yields followed a pattern of progressive decline, with higher MOI driving earlier and faster drops in virus level. These patterns of virus decline were consistent with predictions from a mathematical model based on single-passage behavior of cells co-infected with virus and DI particles. By contrast, the production of virus during fixed-volume passages exhibited irregular fluctuations that could not be described by either the steady-state or regular oscillatory dynamics of the model. However, these irregularities were, to a significant degree, reproduced when measured host-cell levels were incorporated into the model, revealing a high sensitivity of virus and DI particle populations to fluctuations in available cell resources. CONCLUSIONS This study shows how the development of mathematical models, when guided by quantitative experiments, can provide new insight into the dynamic behavior of virus populations.
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Affiliation(s)
- Kristen A Stauffer Thompson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1607, USA
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Abstract
The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the dynamics of the immune system. We describe how the immune system recognizes antigens by searching the large space of receptor molecules. We consider in some detail the theories that quantify the immune response to influenza and dengue fever. We review theoretical descriptions of the complementary evolution of pathogens that occurs in response to immune system pressure. Methods including bioinformatics, molecular simulation, random energy models, and quantum field theory contribute to a theoretical understanding of aspects of immunity.
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Affiliation(s)
- Michael W Deem
- Department of Bioengineering and Physics, Rice University, Houston, TX 77005, USA.
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