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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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Liang Q, Yang J, Fan WTL, Lo WC. Patch formation driven by stochastic effects of interaction between viruses and defective interfering particles. PLoS Comput Biol 2023; 19:e1011513. [PMID: 37782667 PMCID: PMC10569632 DOI: 10.1371/journal.pcbi.1011513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 10/12/2023] [Accepted: 09/12/2023] [Indexed: 10/04/2023] Open
Abstract
Defective interfering particles (DIPs) are virus-like particles that occur naturally during virus infections. These particles are defective, lacking essential genetic materials for replication, but they can interact with the wild-type virus and potentially be used as therapeutic agents. However, the effect of DIPs on infection spread is still unclear due to complicated stochastic effects and nonlinear spatial dynamics. In this work, we develop a model with a new hybrid method to study the spatial-temporal dynamics of viruses and DIPs co-infections within hosts. We present two different scenarios of virus production and compare the results from deterministic and stochastic models to demonstrate how the stochastic effect is involved in the spatial dynamics of virus transmission. We compare the spread features of the virus in simulations and experiments, including the formation and the speed of virus spread and the emergence of stochastic patchy patterns of virus distribution. Our simulations simultaneously capture observed spatial spread features in the experimental data, including the spread rate of the virus and its patchiness. The results demonstrate that DIPs can slow down the growth of virus particles and make the spread of the virus more patchy.
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Affiliation(s)
- Qiantong Liang
- Department of Mathematics, City University of Hong Kong, Hong Kong, China
| | - Johnny Yang
- Department of Mathematics, Indiana University, Bloomington, Indiana, United States of America
| | - Wai-Tong Louis Fan
- Department of Mathematics, Indiana University, Bloomington, Indiana, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Wing-Cheong Lo
- Department of Mathematics, City University of Hong Kong, Hong Kong, China
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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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Cecilia H, Vriens R, Wichgers Schreur PJ, de Wit MM, Métras R, Ezanno P, ten Bosch QA. Heterogeneity of Rift Valley fever virus transmission potential across livestock hosts, quantified through a model-based analysis of host viral load and vector infection. PLoS Comput Biol 2022; 18:e1010314. [PMID: 35867712 PMCID: PMC9348665 DOI: 10.1371/journal.pcbi.1010314] [Citation(s) in RCA: 7] [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: 11/15/2021] [Revised: 08/03/2022] [Accepted: 06/16/2022] [Indexed: 01/17/2023] Open
Abstract
Quantifying the variation of pathogens’ life history traits in multiple host systems is crucial to understand their transmission dynamics. It is particularly important for arthropod-borne viruses (arboviruses), which are prone to infecting several species of vertebrate hosts. Here, we focus on how host-pathogen interactions determine the ability of host species to transmit a virus to susceptible vectors upon a potentially infectious contact. Rift Valley fever (RVF) is a viral, vector-borne, zoonotic disease, chosen as a case study. The relative contributions of livestock species to RVFV transmission has not been previously quantified. To estimate their potential to transmit the virus over the course of their infection, we 1) fitted a within-host model to viral RNA and infectious virus measures, obtained daily from infected lambs, calves, and young goats, 2) estimated the relationship between vertebrate host infectious titers and probability to infect mosquitoes, and 3) estimated the net infectiousness of each host species over the duration of their infectious periods, taking into account different survival outcomes for lambs. Our results indicate that the efficiency of viral replication, along with the lifespan of infectious particles, could be sources of heterogeneity between hosts. Given available data on RVFV competent vectors, we found that, for similar infectious titers, infection rates in the Aedes genus were on average higher than in the Culex genus. Consequently, for Aedes-mediated infections, we estimated the net infectiousness of lambs to be 2.93 (median) and 3.65 times higher than that of calves and goats, respectively. In lambs, we estimated the overall infectiousness to be 1.93 times higher in individuals which eventually died from the infection than in those recovering. Beyond infectiousness, the relative contributions of host species to transmission depend on local ecological factors, including relative abundances and vector host-feeding preferences. Quantifying these contributions will ultimately help design efficient, targeted, surveillance and vaccination strategies. Viruses spread by mosquitoes present a major threat to animal and public health worldwide. When these pathogenic viruses can infect multiple species, controlling their spread becomes difficult. Rift Valley fever virus (RVFV) is such a virus. It spreads predominantly among ruminant livestock but can also spill over and cause severe disease in humans. Understanding which of these ruminant species are most important for the transmission of RVFV can help for effective control. One piece of this puzzle is to assess how effective infected animals are at transmitting RVFV to mosquitoes. To answer this question, we combine mathematical models with observations from experimental infections in cattle, sheep, and goats, and model changes in viremia over time within individuals. We then quantify the relationship between hosts’ viremia and the probability to infect mosquitoes. In combining these two analyses, we estimate the overall transmission potential of sheep, when in contact with mosquitoes, to be 3 to 5 times higher than that of goats and cattle. Further, sheep that experience a lethal infection have an even larger overall transmission potential. Once applied at the level of populations, with setting-specific herd composition and exposure to mosquitoes, these results will help unravel species’ role in RVF outbreaks.
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Affiliation(s)
- Hélène Cecilia
- INRAE, Oniris, BIOEPAR, Nantes, France
- * E-mail: (HC); (QAtB)
| | - Roosmarie Vriens
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Mariken M. de Wit
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Raphaëlle Métras
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Paris, France
| | | | - Quirine A. ten Bosch
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, The Netherlands
- * E-mail: (HC); (QAtB)
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Aguiar M, Anam V, Blyuss KB, Estadilla CDS, Guerrero BV, Knopoff D, Kooi BW, Srivastav AK, Steindorf V, Stollenwerk N. Mathematical models for dengue fever epidemiology: A 10-year systematic review. Phys Life Rev 2022; 40:65-92. [PMID: 35219611 PMCID: PMC8845267 DOI: 10.1016/j.plrev.2022.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/11/2023]
Abstract
Mathematical models have a long history in epidemiological research, and as the COVID-19 pandemic progressed, research on mathematical modeling became imperative and very influential to understand the epidemiological dynamics of disease spreading. Mathematical models describing dengue fever epidemiological dynamics are found back from 1970. Dengue fever is a viral mosquito-borne infection caused by four antigenically related but distinct serotypes (DENV-1 to DENV-4). With 2.5 billion people at risk of acquiring the infection, it is a major international public health concern. Although most of the cases are asymptomatic or mild, the disease immunological response is complex, with severe disease linked to the antibody-dependent enhancement (ADE) - a disease augmentation phenomenon where pre-existing antibodies to previous dengue infection do not neutralize but rather enhance the new infection. Here, we present a 10-year systematic review on mathematical models for dengue fever epidemiology. Specifically, we review multi-strain frameworks describing host-to-host and vector-host transmission models and within-host models describing viral replication and the respective immune response. Following a detailed literature search in standard scientific databases, different mathematical models in terms of their scope, analytical approach and structural form, including model validation and parameter estimation using empirical data, are described and analyzed. Aiming to identify a consensus on infectious diseases modeling aspects that can contribute to public health authorities for disease control, we revise the current understanding of epidemiological and immunological factors influencing the transmission dynamics of dengue. This review provide insights on general features to be considered to model aspects of real-world public health problems, such as the current epidemiological scenario we are living in.
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Affiliation(s)
- Maíra Aguiar
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Dipartimento di Matematica, Università degli Studi di Trento, Via Sommarive 14, Povo, Trento, 38123, Italy; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - Vizda Anam
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Konstantin B Blyuss
- VU University, Faculty of Science, De Boelelaan 1085, NL 1081, HV Amsterdam, the Netherlands
| | - Carlo Delfin S Estadilla
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Bruno V Guerrero
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Damián Knopoff
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Centro de Investigaciones y Estudios de Matemática CIEM, CONICET, Medina Allende s/n, Córdoba, 5000, Argentina
| | - Bob W Kooi
- University of Sussex, Department of Mathematics, Falmer, Brighton, UK
| | - Akhil Kumar Srivastav
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Vanessa Steindorf
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Nico Stollenwerk
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Dipartimento di Matematica, Università degli Studi di Trento, Via Sommarive 14, Povo, Trento, 38123, Italy
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Sweilam N, AL-Mekhlafi S, Shatta S. Optimal bang-bang control for variable-order dengue virus; numerical studies. J Adv Res 2021; 32:37-44. [PMID: 34484824 PMCID: PMC8408335 DOI: 10.1016/j.jare.2021.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/14/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Introduction Dengue and Malaria are the most important mosquito-borne viral diseases affecting humans. Fever is transmitted between human hosts by infected female aedes mosquitoes. The modeling study of viral infections is very useful to show how the virus replicates in an infected individual and how the human antibody response acts to control that replication, which antibody playing a key role in controlling infection. Objectives Optimal control of a novel variable-order nonlinear model of dengue virus is studied in the present work. Bang-bang control is suggested to minimize the viral infection as well as quick clearance of the virus from the host. Necessary conditions for the control problem are given. The variable-order derivatives are given in the sense of Caputo. Moreover, the parameters of the proposed model are dependent on the same variable-order fractional power. Two numerical schemes are constructed for solving the optimality systems. Comparative studies and numerical simulations are implemented. The variable-order fractional derivative can be describe the effects of long variable memory of time dependent systems than the integer order and fractional order derivatives. Methods Both the nonstandard generalized fourth order Runge-Kutta and the nonstandard generalized Euler methods are presented. Results We have successfully applied a kind of Pontryagin's maximum principle with bang-bang control and were able to reduce the viraemia level by adding the dose of DI particles. The nonstandard generalized fourth order Runge-Kutta method has the best results than nonstandard generalized Euler method. Conclusion The combination of the variable-order fractional derivative and bang-bang control in the Dengue mathematical model improves the dynamics of the model. The nonstandard generalized Euler method and the nonstandard generalized fourth order Runge-Kutta method can be used to study the variable order fractional optimal control problem simply.
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Affiliation(s)
- N.H. Sweilam
- Department of Mathematics, Faculty of Science, Cairo University, Giza, Egypt
- Academy of Scientific Research &Technology, 101 Al Kasr El Aini, Cairo, Egypt
| | - S.M. AL-Mekhlafi
- Department of Mathematics, Faculty of Science, Cairo University, Giza, Egypt
- Academy of Scientific Research &Technology, 101 Al Kasr El Aini, Cairo, Egypt
| | - S.A. Shatta
- Department of Mathematics, Faculty of Science, Helwan University, Cairo, Egypt
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Mapder T, Aaskov J, Burrage K. Administration of Defective Virus Inhibits Dengue Transmission into Mosquitoes. Viruses 2020; 12:v12050558. [PMID: 32443524 PMCID: PMC7290595 DOI: 10.3390/v12050558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/22/2020] [Accepted: 05/09/2020] [Indexed: 11/16/2022] Open
Abstract
The host-vector shuttle and the bottleneck in dengue transmission is a significant aspect with regard to the study of dengue outbreaks. As mosquitoes require 100–1000 times more virus to become infected than human, the transmission of dengue virus from human to mosquito is a vulnerability that can be targeted to improve disease control. In order to capture the heterogeneity in the infectiousness of an infected patient population towards the mosquito population, we calibrate a population of host-to-vector virus transmission models based on an experimentally quantified infected fraction of a mosquito population. Once the population of models is well-calibrated, we deploy a population of controls that helps to inhibit the human-to-mosquito transmission of the dengue virus indirectly by reducing the viral load in the patient body fluid. We use an optimal bang-bang control on the administration of the defective virus (transmissible interfering particles (TIPs)) to symptomatic patients in the course of their febrile period and observe the dynamics in successful reduction of dengue spread into mosquitoes.
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Affiliation(s)
- Tarunendu Mapder
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia;
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Correspondence:
| | - John Aaskov
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia;
| | - Kevin Burrage
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia;
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Department of Computer Science, University of Oxford, Oxford OX1 3QD, UK
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