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Arya RK, Verros GD, Thapliyal D. Towards a Mathematical Model for the Viral Progression in the Pharynx. Healthcare (Basel) 2021; 9:healthcare9121766. [PMID: 34946492 PMCID: PMC8701019 DOI: 10.3390/healthcare9121766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/03/2022] Open
Abstract
In this work, a comprehensive model for the viral progression in the pharynx has been developed. This one-dimension model considers both Fickian diffusion and convective flow coupled with chemical reactions, such as virus population growth, infected and uninfected cell accumulation as well as virus clearance. The effect of a sterilizing agent such as an alcoholic solution on the viral progression in the pharynx was taken into account and a parametric analysis for the effect of kinetic rate parameters on virus propagation was made. Moreover, different conditions caused by further medical treatment, such as a decrease in virus yield per infected cell, were examined. It is shown that the infection fails to establish by decreasing the virus yield per infected cell. It is believed that this work could be used to further investigate the medical treatment of viral progression in the pharynx.
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Affiliation(s)
- Raj Kumar Arya
- Department of Chemical Engineering, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar 144011, India;
- Correspondence: or
| | - George D. Verros
- Laboratory of Polymer and Colour Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki (AUTH), P.O. Box 454, Plagiari, Epanomi, 57500 Thessaloniki, Greece;
| | - Devyani Thapliyal
- Department of Chemical Engineering, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar 144011, India;
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2
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Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule. PLoS Comput Biol 2020; 16:e1007612. [PMID: 32986692 PMCID: PMC7544041 DOI: 10.1371/journal.pcbi.1007612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 10/08/2020] [Accepted: 08/03/2020] [Indexed: 11/27/2022] Open
Abstract
Interaction between filovirus glycoprotein (GP) and the Niemann-Pick C1 (NPC1) protein is essential for membrane fusion during virus entry. Some single-nucleotide polymorphism (SNPs) in two surface-exposed loops of NPC1 are known to reduce viral infectivity. However, the dependence of differences in entry efficiency on SNPs remains unclear. Using vesicular stomatitis virus pseudotyped with Ebola and Marburg virus GPs, we investigated the cell-to-cell spread of viruses in cultured cells expressing NPC1 or SNP derivatives. Eclipse and virus-producing phases were assessed by in vitro infection experiments, and we developed a mathematical model describing spatial-temporal virus spread. This mathematical model fit the plaque radius data well from day 2 to day 6. Based on the estimated parameters, we found that SNPs causing the P424A and D508N substitutions in NPC1 most effectively reduced the entry efficiency of Ebola and Marburg viruses, respectively. Our novel approach could be broadly applied to other virus plaque assays. Ebola (EBOV) and Marburg (MARV) viruses, which are included viruses of the family Filoviridae, cause severe hemorrhagic fever in humans. Filovirus particles is adsorbed to the cell through glycoprotein (GP), which is the only viral surface protein. Interaction between the filovirus sugar protein (GP) and the Niemann-Pick C1 (NPC1) protein plays a key role in membrane fusion during virus entry. Although some single-nucleotide polymorphism (SNPs) in two surface-exposed loops of NPC1 are known to reduce viral infectivity, the dependence of differences in entry efficiency on SNPs has not been studied. We therefore investigated the cell-to-cell spread of viruses in cultured cells expressing NPC1 or SNP derivatives. Using a mathematical model describing spatial-temporal virus spread, we quantitatively analyze viral entry efficiency and how this affected cell-to-cell spread. Our approach may be applied to not only understanding the roles of genetic polymorphisms in human susceptibility to filoviruses, but also other virus plaque assays.
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Dresp-Langley B, Wandeto JM. Pixel precise unsupervised detection of viral particle proliferation in cellular imaging data. INFORMATICS IN MEDICINE UNLOCKED 2020; 20:100433. [PMID: 32984498 PMCID: PMC7502244 DOI: 10.1016/j.imu.2020.100433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 11/20/2022] Open
Abstract
Cellular and molecular imaging techniques and models have been developed to characterize single stages of viral proliferation after focal infection of cells in vitro. The fast and automatic classification of cell imaging data may prove helpful prior to any further comparison of representative experimental data to mathematical models of viral propagation in host cells. Here, we use computer generated images drawn from a reproduction of an imaging model from a previously published study of experimentally obtained cell imaging data representing progressive viral particle proliferation in host cell monolayers. Inspired by experimental time-based imaging data, here in this study viral particle increase in time is simulated by a one-by-one increase, across images, in black or gray single pixels representing dead or partially infected cells, and hypothetical remission by a one-by-one increase in white pixels coding for living cells in the original image model. The image simulations are submitted to unsupervised learning by a Self-Organizing Map (SOM) and the Quantization Error in the SOM output (SOM-QE) is used for automatic classification of the image simulations as a function of the represented extent of viral particle proliferation or cell recovery. Unsupervised classification by SOM-QE of 160 model images, each with more than three million pixels, is shown to provide a statistically reliable, pixel precise, and fast classification model that outperforms human computer-assisted image classification by RGB image mean computation. The automatic classification procedure proposed here provides a powerful approach to understand finely tuned mechanisms in the infection and proliferation of virus in cell lines in vitro or other cells. Automatic classification of cell imaging data for in vitro viral propagation in host cells. Economical in terms of computation times for rapid change/no change detection in large image data prior to human decision making. Simulating viral proliferation/cell recovery by progressive and selective single pixel changes in contrast polarity and/or intensity.
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Affiliation(s)
| | - John Mwangi Wandeto
- Department of Information Technology, Dedan Kimathi University of Technology, Kenya
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4
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Abstract
When a virus infects a host cell, it hijacks the biosynthetic capacity of the cell to produce virus progeny, a process that may take less than an hour or more than a week. The overall time required for a virus to reproduce depends collectively on the rates of multiple steps in the infection process, including initial binding of the virus particle to the surface of the cell, virus internalization and release of the viral genome within the cell, decoding of the genome to make viral proteins, replication of the genome, assembly of progeny virus particles, and release of these particles into the extracellular environment. For a large number of virus types, much has been learned about the molecular mechanisms and rates of the various steps. However, in only relatively few cases during the last 50 years has an attempt been made-using mathematical modeling-to account for how the different steps contribute to the overall timing and productivity of the infection cycle in a cell. Here we review the initial case studies, which include studies of the one-step growth behavior of viruses that infect bacteria (Qβ, T7, and M13), human immunodeficiency virus, influenza A virus, poliovirus, vesicular stomatitis virus, baculovirus, hepatitis B and C viruses, and herpes simplex virus. Further, we consider how such models enable one to explore how cellular resources are utilized and how antiviral strategies might be designed to resist escape. Finally, we highlight challenges and opportunities at the frontiers of cell-level modeling of virus infections.
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Affiliation(s)
- John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jacob Redovich
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Timm AC, Warrick JW, Yin J. Quantitative profiling of innate immune activation by viral infection in single cells. Integr Biol (Camb) 2017; 9:782-791. [PMID: 28831492 PMCID: PMC5603422 DOI: 10.1039/c7ib00082k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cells infected by viruses can exhibit diverse patterns of viral and cellular gene expression. The patterns arise in part from the stochastic or noisy reaction kinetics associated with the small number of genomes, enzymes, and other molecules that typically initiate virus replication and activate cellular anti-viral defenses. It is not known what features, if any, of the early viral or cellular gene expression correlate with later processes of viral replication or cell survival. Here we used two fluorescent reporters to visualize innate immune activation of human prostate cancer (PC3) cells against infection by vesicular stomatitis virus. The cells were engineered to express green-fluorescent protein under control of the promoter for IFIT2, an interferon-sensitive component of the anti-viral response, while red-fluorescent protein was expressed as a byproduct of virus infection. To isolate and quantitatively analyze single-cells, we used a unique microwell array device and open-source image processing software. Kinetic analysis of viral and cellular reporter profiles from hundreds of cells revealed novel relationships between gene expression and the outcome of infection. Specifically, the relative timing rather than the magnitude of the viral gene expression and innate immune activation correlated with the infection outcome. Earlier viral or anti-viral gene expression favored or hindered virus growth, respectively. Further, analysis of kinetic parameters estimated from these data suggests a trade-off between robust antiviral signaling and cell death, as indicated by a higher rate of detectable cell lysis in infected cells with a detectable immune response. In short, cells that activate an immune response lyse at a higher rate. More broadly, we demonstrate how the intrinsic heterogeneity of individual cell behaviors can be exploited to discover features of viral and host gene expression that correlate with single-cell outcomes, which will ultimately impact whether or not infections spread.
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Affiliation(s)
- Andrea C Timm
- Systems Biology Theme, Wisconsin Institute for Discovery, Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, USA.
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6
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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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7
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Bocharov G, Meyerhans A, Bessonov N, Trofimchuk S, Volpert V. Spatiotemporal Dynamics of Virus Infection Spreading in Tissues. PLoS One 2016; 11:e0168576. [PMID: 27997613 PMCID: PMC5173377 DOI: 10.1371/journal.pone.0168576] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/03/2016] [Indexed: 12/21/2022] Open
Abstract
Virus spreading in tissues is determined by virus transport, virus multiplication in host cells and the virus-induced immune response. Cytotoxic T cells remove infected cells with a rate determined by the infection level. The intensity of the immune response has a bell-shaped dependence on the concentration of virus, i.e., it increases at low and decays at high infection levels. A combination of these effects and a time delay in the immune response determine the development of virus infection in tissues like spleen or lymph nodes. The mathematical model described in this work consists of reaction-diffusion equations with a delay. It shows that the different regimes of infection spreading like the establishment of a low level infection, a high level infection or a transition between both are determined by the initial virus load and by the intensity of the immune response. The dynamics of the model solutions include simple and composed waves, and periodic and aperiodic oscillations. The results of analytical and numerical studies of the model provide a systematic basis for a quantitative understanding and interpretation of the determinants of the infection process in target organs and tissues from the image-derived data as well as of the spatiotemporal mechanisms of viral disease pathogenesis, and have direct implications for a biopsy-based medical testing of the chronic infection processes caused by viruses, e.g. HIV, HCV and HBV.
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Affiliation(s)
- Gennady Bocharov
- Institute of Numerical Mathematics, Russian Academy of Sciences, Moscow, Russian Federation
- Gamaleya Center of Epidemiology and Microbiology, Moscow, Russian Federation
- RUDN University, Moscow, Russian Federation
| | - Andreas Meyerhans
- Institute of Numerical Mathematics, Russian Academy of Sciences, Moscow, Russian Federation
- Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | - Nickolai Bessonov
- Institute of Problems of Mechanical Engineering, Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Sergei Trofimchuk
- Instituto de Matemática y Fisica, Universidad de Talca, Talca, Chile
| | - Vitaly Volpert
- Institute of Numerical Mathematics, Russian Academy of Sciences, Moscow, Russian Federation
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, Villeurbanne, France
- INRIA Team Dracula, INRIA Lyon La Doua, Villeurbanne, France
- Laboratoire Poncelet, UMI 2615 CNRS, Moscow, Russian Federation
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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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Voigt EA, Swick A, Yin J. Rapid induction and persistence of paracrine-induced cellular antiviral states arrest viral infection spread in A549 cells. Virology 2016; 496:59-66. [PMID: 27254596 DOI: 10.1016/j.virol.2016.05.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 12/31/2022]
Abstract
The virus/host interaction is a complex interplay between pro- and anti-viral factors that ultimately determines the spread or halt of virus infections in tissues. This interplay develops over multiple rounds of infection. The purpose of this study was to determine how cellular-level processes combine to impact the spatial spread of infection. We measured the kinetics of virus replication (VSV), antiviral paracrine signal upregulation and secretion, spatial spread of virus and paracrine antiviral signaling, and inhibition of virus production in antiviral-exposed A549 human lung epithelial cells. We found that initially infected cells released antiviral signals 4-to-7h following production of virus. However, the subsequent rapid dissemination of signal and fast induction of a robust and persistent antiviral state ultimately led to a suppression of infection spread. This work shows how cellular responses to infection and activation of antiviral responses can integrate to ultimately control infection spread across host cell populations.
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Affiliation(s)
- Emily A Voigt
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam Swick
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - John Yin
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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de Rioja VL, Isern N, Fort J. A mathematical approach to virus therapy of glioblastomas. Biol Direct 2016; 11:1. [PMID: 26738889 PMCID: PMC4704393 DOI: 10.1186/s13062-015-0100-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/11/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND It is widely believed that the treatment of glioblastomas (GBM) could benefit from oncolytic virus therapy. Clinical research has shown that Vesicular Stomatitis Virus (VSV) has strong oncolytic properties. In addition, mathematical models of virus treatment of tumors have been developed in recent years. Some experiments in vitro and in vivo have been done and shown promising results, but have been never compared quantitatively with mathematical models. We use in vitro data of this virus applied to glioblastoma. RESULTS We describe three increasingly realistic mathematical models for the VSV-GBM in vitro experiment with progressive incorporation of time-delay effects. For the virus dynamics, we obtain results consistent with the in vitro experimental speed data only when applying the more complex and comprehensive model, with time-delay effects both in the reactive and diffusive terms. The tumor speed is given by the minimum of a very simple function that nonetheless yields results within the experimental measured range. CONCLUSIONS We have improved a previous model with new ideas and carefully incorporated concepts from experimental results. We have shown that the delay time τ is the crucial parameter in this kind of models. We have demonstrated that our new model can satisfactorily predict the front speed for the lytic action of oncolytic VSV on glioblastoma observed in vitro. We provide a basis that can be applied in the near future to realistically simulate in vivo virus treatments of several cancers.
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Affiliation(s)
- Victor Lopez de Rioja
- ICREA/Complex Systems Laboratory, Departament de Física, Universitat de Girona, Girona, 17071, Catalonia, Spain
| | - Neus Isern
- ICREA/Complex Systems Laboratory, Departament de Física, Universitat de Girona, Girona, 17071, Catalonia, Spain.
| | - Joaquim Fort
- ICREA/Complex Systems Laboratory, Departament de Física, Universitat de Girona, Girona, 17071, Catalonia, Spain.
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Swick A, Baltes A, Yin J. Visualizing infection spread: dual-color fluorescent reporting of virus-host interactions. Biotechnol Bioeng 2013; 111:1200-9. [PMID: 24338628 DOI: 10.1002/bit.25170] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/22/2013] [Accepted: 12/02/2013] [Indexed: 12/24/2022]
Abstract
Although the molecular mechanisms by which host cells defend themselves against viral infection have been studied in great depth, and countermeasures viruses employ to suppress such defensive responses have been widely documented, relatively little attention has been devoted toward elucidating how such interactions between virus and host are resolved over multiple rounds of infection. Here, we describe the design, synthesis, and validation of a dual-color fluorescent reporter system to study how viral infections spread through a host cell monolayer and how the cellular innate immune system mounts an antiviral response. We employed recombinant, red fluorescent protein expressing mutants of a prototypical RNA virus, vesicular stomatitis virus to enable identification and tracking of infected cells. Further, we generated stable reporter cells that use green fluorescent protein to report on the expression of IFIT2, an interferon stimulated gene involved in the interference of viral protein translation, and a marker of antiviral defense activation. The presence of the fluorescent protein reporters had minimal effects on the normal behavior of the cells or viruses. Moreover, expression of the virus and cell reporters correlated with the kinetics of viral replication and activation of an anti-viral response, respectively. This two-color system enabled us to track and quantify in live cells how viral replication and activation of host defensive responses play out over multiple rounds of infection. Initial study of propagating infections demonstrated that antiviral activation over multiple rounds was critical for slowing and ultimately halting the spread of infection.
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Affiliation(s)
- Adam Swick
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin, 53706-1607; Wisconsin Institute for Discovery-Systems Biology Theme, University of Wisconsin-Madison, Madison, Wisconsin
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12
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Liu D, Wang B, Guo S. Stability analysis of a novel epidemics model with vaccination and nonlinear infectious rate. APPLIED MATHEMATICS AND COMPUTATION 2013; 221:786-801. [PMID: 32287496 PMCID: PMC7132752 DOI: 10.1016/j.amc.2013.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this paper, by considering pathogen evolution and human interventions behaviors with vaccines or drugs, we build up a novel SEIRW model with the vaccination to the newborn children. The stability of the SEIRW model with time-varying perturbation to predict the evolution tendency of the disease is analyzed. Furthermore, we introduce a time-varying delay into the susceptible and infective stages in the model and give some global exponential stability criteria for the time-varying delay system. Finally, numerical simulations are presented to verify the results.
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Affiliation(s)
- Defang Liu
- College of Bioengineering, Chongqing University, Chongqing 400044, China
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Bochu Wang
- College of Bioengineering, Chongqing University, Chongqing 400044, China
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Songtao Guo
- College of Computer Science, Chongqing University, Chongqing 400044, China
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Voigt E, Inankur B, Baltes A, Yin J. A quantitative infection assay for human type I, II, and III interferon antiviral activities. Virol J 2013; 10:224. [PMID: 23829314 PMCID: PMC3716869 DOI: 10.1186/1743-422x-10-224] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 06/24/2013] [Indexed: 12/11/2022] Open
Abstract
Background Upon virus infection, cells secrete a diverse group of antiviral molecules that signal proximal cells to enter into an antiviral state, slowing or preventing viral spread. These paracrine signaling molecules can work synergistically, so measurement of any one antiviral molecule does not reflect the total antiviral activity of the system. Results We have developed an antiviral assay based on replication inhibition of an engineered fluorescent vesicular stomatitis virus reporter strain on A549 human lung epithelial cells. Our assay provides a quantitative functional readout of human type I, II, and III interferon activities, and it provides better sensitivity, intra-, and inter-assay reproducibility than the traditional crystal violet based assay. Further, it eliminates cell fixation, rinsing, and staining steps, and is inexpensive to implement. Conclusions A dsRed2-strain of vesicular stomatitis virus that is sensitive to type I, II, and III interferons was used to develop a convenient and sensitive assay for interferon antiviral activity. We demonstrate use of the assay to quantify the kinetics of paracrine antiviral signaling from human prostate cancer (PC3) cells in response to viral infection. The assay is applicable to high-throughput screening for anti-viral compounds as well as basic studies of cellular antiviral signaling.
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Affiliation(s)
- Emily Voigt
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, USA
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14
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Murillo LN, Murillo MS, Perelson AS. Towards multiscale modeling of influenza infection. J Theor Biol 2013; 332:267-90. [PMID: 23608630 DOI: 10.1016/j.jtbi.2013.03.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/19/2013] [Accepted: 03/27/2013] [Indexed: 02/05/2023]
Abstract
Aided by recent advances in computational power, algorithms, and higher fidelity data, increasingly detailed theoretical models of infection with influenza A virus are being developed. We review single scale models as they describe influenza infection from intracellular to global scales, and, in particular, we consider those models that capture details specific to influenza and can be used to link different scales. We discuss the few multiscale models of influenza infection that have been developed in this emerging field. In addition to discussing modeling approaches, we also survey biological data on influenza infection and transmission that is relevant for constructing influenza infection models. We envision that, in the future, multiscale models that capitalize on technical advances in experimental biology and high performance computing could be used to describe the large spatial scale epidemiology of influenza infection, evolution of the virus, and transmission between hosts more accurately.
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Affiliation(s)
- Lisa N Murillo
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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15
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Timm A, Yin J. Kinetics of virus production from single cells. Virology 2012; 424:11-7. [PMID: 22222212 PMCID: PMC3268887 DOI: 10.1016/j.virol.2011.12.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 10/03/2011] [Accepted: 12/07/2011] [Indexed: 11/28/2022]
Abstract
The production of virus by infected cells is an essential process for the spread and persistence of viral diseases, the effectiveness of live-viral vaccines, and the manufacture of viruses for diverse applications. Yet despite its importance, methods to precisely measure virus production from cells are lacking. Most methods test infected-cell populations, masking how individual cells behave. Here we measured the kinetics of virus production from single cells. We combined simple steps of liquid-phase infection, serial dilution, centrifugation, and harvesting, without specialized equipment, to track the production of virus particles from BHK cells infected with vesicular stomatitis virus. Remarkably, cell-to-cell differences in latent times to virus release were within a factor of two, while production rates and virus yields spanned over 300-fold, highlighting an extreme diversity in virus production for cells from the same population. These findings have fundamental and technological implications for health and disease.
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Affiliation(s)
- Andrea Timm
- Department of Chemical and Biological Engineering, Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin – Madison, 330 N Orchard Street, Madison WI, 53715, United States of America
| | - John Yin
- Department of Chemical and Biological Engineering, Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin – Madison, 330 N Orchard Street, Madison WI, 53715, United States of America
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16
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Hofacre A, Wodarz D, Komarova NL, Fan H. Early infection and spread of a conditionally replicating adenovirus under conditions of plaque formation. Virology 2011; 423:89-96. [PMID: 22192628 DOI: 10.1016/j.virol.2011.11.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 10/18/2011] [Accepted: 11/21/2011] [Indexed: 11/29/2022]
Abstract
Conditionally-replicating adenoviruses (CRAds) and other oncolytic viruses replicate selectively in tumor cells, presenting a potential cancer treatment approach. To optimize application of these viruses, understanding of early spread of these viruses in target cells is important. Here we used a recombinant adenovirus expressing enhanced jellyfish green fluorescent protein (EGFP) in place of the EIA and EIB genes (AdEGFPuci). Infection of susceptible cells (AD-293) under plaque formation conditions (MOI<<1) on gridded culture dishes and daily monitoring allowed visualization of initially infected cells, as well as spread to neighboring cells. We determined key parameters of early infection, including the rate and efficiency of spread from the initially infected cell to other cells. It was noteworthy that a minority of initially infected cells ultimately resulted in plaques. The approaches elucidated here will be useful for determining early infection parameters for CRAds of therapeutic interest.
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Affiliation(s)
- Andrew Hofacre
- Department of Molecular Biology and Biochemistry, Cancer Research Institute, University of California, Irvine, CA 92697, USA
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17
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18
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Gönci B, Németh V, Balogh E, Szabó B, Dénes Á, Környei Z, Vicsek T. Viral epidemics in a cell culture: novel high resolution data and their interpretation by a percolation theory based model. PLoS One 2010; 5:e15571. [PMID: 21187920 PMCID: PMC3004943 DOI: 10.1371/journal.pone.0015571] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 11/13/2010] [Indexed: 11/28/2022] Open
Abstract
Because of its relevance to everyday life, the spreading of viral infections has been of central interest in a variety of scientific communities involved in fighting, preventing and theoretically interpreting epidemic processes. Recent large scale observations have resulted in major discoveries concerning the overall features of the spreading process in systems with highly mobile susceptible units, but virtually no data are available about observations of infection spreading for a very large number of immobile units. Here we present the first detailed quantitative documentation of percolation-type viral epidemics in a highly reproducible in vitro system consisting of tens of thousands of virtually motionless cells. We use a confluent astroglial monolayer in a Petri dish and induce productive infection in a limited number of cells with a genetically modified herpesvirus strain. This approach allows extreme high resolution tracking of the spatio-temporal development of the epidemic. We show that a simple model is capable of reproducing the basic features of our observations, i.e., the observed behaviour is likely to be applicable to many different kinds of systems. Statistical physics inspired approaches to our data, such as fractal dimension of the infected clusters as well as their size distribution, seem to fit into a percolation theory based interpretation. We suggest that our observations may be used to model epidemics in more complex systems, which are difficult to study in isolation.
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Affiliation(s)
- Balázs Gönci
- Department of Biological Physics, Eötvös University, Budapest, Hungary
| | - Valéria Németh
- Department of Biological Physics, Eötvös University, Budapest, Hungary
| | - Emeric Balogh
- Department of Biological Physics, Eötvös University, Budapest, Hungary
- Department of Theoretical Physics, Babes-Bolyai University, Cluj-Napoca, Romania
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Bálint Szabó
- Department of Biological Physics, Eötvös University, Budapest, Hungary
| | - Ádám Dénes
- Institute of Experimental Medicine of the Hungarian Academy of Sciences, Budapest, Hungary
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Zsuzsanna Környei
- Institute of Experimental Medicine of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás Vicsek
- Department of Biological Physics, Eötvös University, Budapest, Hungary
- Statistical and Biological Physics Research Group of the Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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19
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Amor DR, Fort J. Virus infection speeds: theory versus experiment. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:061905. [PMID: 21230688 DOI: 10.1103/physreve.82.061905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Revised: 11/15/2010] [Indexed: 05/23/2023]
Abstract
In order to explain the speed of Vesicular Stomatitis Virus (VSV) infections, we develop a simple model that improves previous approaches to the propagation of virus infections. For VSV infections, we find that the delay time elapsed between the adsorption of a viral particle into a cell and the release of its progeny has a very important effect. Moreover, this delay time makes the adsorption rate essentially irrelevant in order to predict VSV infection speeds. Numerical simulations are in agreement with the analytical results. Our model satisfactorily explains the experimentally measured speeds of VSV infections.
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Affiliation(s)
- Daniel R Amor
- Complex Systems Laboratory, Departament de Física, Universitat de Girona, 17071 Girona, Catalonia, Spain
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20
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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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21
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Anekal SG, Zhu Y, Graham MD, Yin J. Dynamics of virus spread in the presence of fluid flow. Integr Biol (Camb) 2009; 1:664-71. [PMID: 20027375 PMCID: PMC2905057 DOI: 10.1039/b908197f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of viral infection spread, whether in laboratory cultures or in naturally infected hosts, reflects a coupling of biological and physical processes that remain to be fully elucidated. Biological processes include the kinetics of virus growth in infected cells while physical processes include transport of virus progeny from infected cells, where they are produced, to susceptible cells, where they initiate new infections. Mechanistic models of infection spread have been widely developed for systems where virus growth is coupled with transport of virus particles by diffusion, but they have yet to be developed for systems where viruses move under the influence of fluid flows. Recent experimental observations of flow-enhanced infection spread in laboratory cultures motivate here the development of initial continuum and discrete virus-particle models of infection spread. The magnitude of a dimensionless group, the Damköhler number, shows how parameters that characterize particle adsorption to cells, strain rates that reflect flow profiles, and diffusivities of virus particles combine to influence the spatial pattern of infection spread.
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Affiliation(s)
- Samartha G. Anekal
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 3706-1607, USA.; Tel: 608 265-3779
| | - Ying Zhu
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 3706-1607, USA.; Tel: 608 265-3779
| | - Michael D. Graham
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 3706-1607, USA.; Tel: 608 265-3779
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 3706-1607, USA.; Tel: 608 265-3779
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22
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Peng X, Chan EY, Li Y, Diamond DL, Korth MJ, Katze MG. Virus-host interactions: from systems biology to translational research. Curr Opin Microbiol 2009; 12:432-8. [PMID: 19576841 DOI: 10.1016/j.mib.2009.06.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 06/02/2009] [Accepted: 06/04/2009] [Indexed: 11/19/2022]
Abstract
Research embracing systems biology approaches and careful analysis of the critical host response has greatly expanded our understanding of infectious diseases. First-generation studies based on genomics and proteomics have made significant progress in establishing the foundation for network-based investigations on virus-host interactions. More recently, data from complementary high-throughput technologies, such as siRNA and microRNA screens and next-generation sequencing, are augmenting systems level analyses and are providing a more detailed and insightful multidimensional view of virus-host networks. Together with advances in data integration, systems biology approaches now have the potential to provide profound impacts on translational research, leading to the more rapid development of new therapeutics and vaccines for infectious diseases. In this review, we highlight new high-throughput technologies, a new philosophy for studying virus-host interactions, and discuss the potential of systems biology to facilitate bench-to-bedside research and create novel strategies to combat disease. Can we save the world using these approaches? Read on.
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Affiliation(s)
- Xinxia Peng
- Department of Microbiology, University of Washington, Seattle, WA 98195-8070, USA
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23
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Haseltine EL, Yin J, Rawlings JB. Implications of decoupling the intracellular and extracellular levels in multi-level models of virus growth. Biotechnol Bioeng 2008; 101:811-20. [PMID: 18512261 DOI: 10.1002/bit.21931] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Virus infections are characterized by two distinct levels of detail: the intracellular level describing how viruses hijack the host machinery to replicate, and the extracellular level describing how populations of virus and host cells interact. Deterministic, population balance models for viral infections permit incorporation of both the intracellular and extracellular levels of information. In this work, we identify assumptions that lead to exact, selective decoupling of the interaction between the intracellular and extracellular levels, effectively permitting solution of first the intracellular level, and subsequently the extracellular level. This decoupling leads to (1) intracellular and extracellular models of viral infections that have been previously reported and (2) a significant reduction in the computational expense required to solve the model. However, the decoupling restricts the behaviors that can be modeled. Simulation of a previously reported multi-level model demonstrates this decomposition when the intracellular level of description consists of numerous reaction events. Additionally, examples demonstrate that viruses can persist even when the intracellular level of description cannot sustain a steady-state production of virus (i.e., has only a trivial equilibrium). We expect the combination of this modeling framework with experimental data to result in a quantitative, systems-level understanding of viral infections and cellular antiviral strategies that will facilitate controlling both these infections and antiviral strategies.
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Affiliation(s)
- Eric L Haseltine
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706-1607, USA
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