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Modeling and Optimization of Continuous Viral Vaccine Production. Processes (Basel) 2022. [DOI: 10.3390/pr10112426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A model that captures realistic viral growth dynamics has been developed based on a continuous and semi-continuous production model of an influenza A virus. This model considers viral growth parameters such as viral latency. It also captures the lag observed during the early production of viruses in a culture and explains later-phase growth dynamics. Furthermore, a sensitivity analysis was performed to investigate the effects of each input on each output. This revealed that production of defective interfering particles (DIPs) highly depends on the number of cells introduced to the viral reactor. The rationale for this is, as per the model, that a reduction in number of cells to be infected causes a reduction in DIPs formed as rate of viral infection decreases. Finally, a flowsheet model was created to optimize the continuous platform, including number of cells supplied to the viral reactor. From this, it was observed that the peak number of DIPs formed could be reduced by one-third. Finally, this model is tailorable to different viral particles using parameter estimation. Therefore, the proposed mathematical model provides a versatile, comprehensive platform that can be tailored to various viral cultures with or without a latent phase.
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Efficient numerical schemes for population balance models. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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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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Ali Q, Mustafa IH, Elkamel A, Touboul E, Gruy F, Lambert C. Mathematical modelling of T-cells activation dynamics for CD3 molecules recycling process. CAN J CHEM ENG 2016. [DOI: 10.1002/cjce.22607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qasim Ali
- Department of Applied Mathematics; University of Western Ontario; London ON Canada
| | - Ibrahim H. Mustafa
- Biomedical Engineering Department; Helwan University; Cairo Egypt
- Department of Chemical Engineering; University of Waterloo; Waterloo ON Canada
| | - Ali Elkamel
- Department of Chemical Engineering; University of Waterloo; Waterloo ON Canada
| | - Eric Touboul
- Henry Fayol Institute; ENSM - Saint Étienne France
| | - Frederic Gruy
- Center for Biomedical and Healthcare Engineering; ENSM - Saint Étienne France
| | - Claude Lambert
- CHU - Saint Etienne, Immunology Lab; University Hospital; F 42055, Saint-Étienne France
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Ali Q, Elkamel A, Gruy F, Lambert C, Touboul E. Population balances in case of crossing characteristic curves: Application to T-cells immune response. CAN J CHEM ENG 2016. [DOI: 10.1002/cjce.22497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qasim Ali
- Department of Applied Mathematics; University of Western Ontario; London ON Canada
- Center for Biomedical and Healthcare Engineering; ENSM - Saint Etienne; France
| | - Ali Elkamel
- Department of Chemical Engineering; University of Waterloo; Waterloo ON Canada
| | - Frédéric Gruy
- Center for Biomedical and Healthcare Engineering; ENSM - Saint Etienne; France
| | - Claude Lambert
- CHU - Saint Etienne, Immunology Lab; University Hospital; F 42055, Saint-Etienne France
| | - Eric Touboul
- Henry Fayol Institute; ENSM - Saint Etienne; France
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Nasir W, Bally M, Zhdanov VP, Larson G, Höök F. Interaction of Virus-Like Particles with Vesicles Containing Glycolipids: Kinetics of Detachment. J Phys Chem B 2015; 119:11466-72. [PMID: 26260011 DOI: 10.1021/acs.jpcb.5b04160] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many viruses interact with their host cells via glycosphingolipids (GSLs) and/or glycoproteins present on the outer cell membrane. This highly specific interaction includes virion attachment and detachment. The residence time determined by the detachment is particularly interesting, since it is directly related to internalization and infection as well as to virion egress and spreading. In an attempt to deepen the understanding of virion detachment kinetics, we have used total internal reflection fluorescence (TIRF) microscopy to probe the interaction between individual fluorescently labeled GSL-containing lipid vesicles and surface-bound virus-like particles (VLPs) of a norovirus genotype II.4 strain. The distribution of the VLP-vesicle residence time was investigated for seven naturally occurring GSLs, all of which are candidates for the not yet identified receptor(s) mediating norovirus entry into host cells. As expected for interactions involving multiple GSL binding sites at a viral capsid, the detachment kinetics displayed features typical for a broad activation-energy distribution for all GSLs. Detailed inspection of these distributions revealed significant differences among the different GSLs. The results are discussed in terms of strength of the interaction, vesicle size, as well as spatial distribution and clustering of GSLs in the vesicle membrane.
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Affiliation(s)
- Waqas Nasir
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg, Sweden
| | - Marta Bally
- Department of Applied Physics, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden.,Institut Curie, Centre de Recherche, CNRS, UMR 168, Physico-Chimie Curie, F-75248 Paris, France
| | - Vladimir P Zhdanov
- Department of Applied Physics, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden.,Boreskov Institute of Catalysis, Russian Academy of Sciences , Novosibirsk 630090, Russia
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
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Rational design of medium supplementation strategy for improved influenza viruses production based on analyzing nutritional requirements of MDCK Cells. Vaccine 2014; 32:7091-7. [DOI: 10.1016/j.vaccine.2014.10.067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/25/2014] [Accepted: 10/27/2014] [Indexed: 11/22/2022]
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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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Müller T, Dürr R, Isken B, Schulze-Horsel J, Reichl U, Kienle A. Distributed modeling of human influenza a virus-host cell interactions during vaccine production. Biotechnol Bioeng 2013; 110:2252-66. [DOI: 10.1002/bit.24878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/20/2012] [Accepted: 02/14/2013] [Indexed: 11/06/2022]
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Isken B, Genzel Y, Reichl U. Productivity, apoptosis, and infection dynamics of influenza A/PR/8 strains and A/PR/8-based reassortants. Vaccine 2012; 30:5253-61. [PMID: 22698452 DOI: 10.1016/j.vaccine.2012.05.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 05/16/2012] [Accepted: 05/25/2012] [Indexed: 01/18/2023]
Abstract
In cell culture-based influenza vaccine production significant efforts are directed towards virus seed optimization for maximum yields. Typically, high growth reassortants (HGR) containing backbones of six gene segments of e.g. influenza A/PR/8, are generated from wild type strains. Often, however, HA and TCID₅₀ titres obtained do not meet expectations and further optimization measures are required. Flow cytometry is an invaluable tool to improve our understanding of mechanism related to progress of infection, virus-induced apoptosis, and cell-specific productivity. In this study, we performed infections with two influenza A/PR/8 variants (from NIBSC and RKI) and two A/PR/8-based HGRs (Wisconsin-like and Uruguay-like) to investigate virus replication, apoptosis and virus titres at different multiplicities of infection (MOI 0.0001, 0.1, 3). Flow cytometric analyses showed similar dynamics in the time course of infected and apoptotic cell populations for all four tested strains at MOI 0.0001. Interestingly, higher MOI resulted in an earlier increase of the populations of infected and apoptotic cells and showed strain-specific differences. Infections with A/PR/8 NIBSC resulted in an earlier increase in both cell populations compared to A/PR/8 RKI. The Uruguay-like reassortant showed the earliest increase in the concentration of infected cells and a late induction of apoptosis at all tested MOIs. In contrast, the Wisconsin-like reassortant showed strong apoptosis induction at high MOIs resulting in reduced titres compared to lower MOI. Maximum HA titres were unaffected by changes in the MOI for the two A/PR/8 and the Uruguay-like reassortant. Maximum TCID₅₀ titres, however, decreased with increasing MOI for all strains. Overall, infections at very low MOI (0.0001) resulted not only in similar dynamics concerning progress of infection and induction of apoptosis but also in maximum virus yields. Highest HA titres were obtained for virus seed strains combining a fast progress in infection with a late onset of apoptosis. Therefore, both factors should be considered for the establishment of robust influenza vaccine production processes.
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Affiliation(s)
- B Isken
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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Petiot E, Jacob D, Lanthier S, Lohr V, Ansorge S, Kamen AA. Metabolic and kinetic analyses of influenza production in perfusion HEK293 cell culture. BMC Biotechnol 2011; 11:84. [PMID: 21884612 PMCID: PMC3175177 DOI: 10.1186/1472-6750-11-84] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 09/01/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cell culture-based production of influenza vaccine remains an attractive alternative to egg-based production. Short response time and high production yields are the key success factors for the broader adoption of cell culture technology for industrial manufacturing of pandemic and seasonal influenza vaccines. Recently, HEK293SF cells have been successfully used to produce influenza viruses, achieving hemagglutinin (HA) and infectious viral particle (IVP) titers in the highest ranges reported to date. In the same study, it was suggested that beyond 4 × 10(6) cells/mL, viral production was limited by a lack of nutrients or an accumulation of toxic products. RESULTS To further improve viral titers at high cell densities, perfusion culture mode was evaluated. Productivities of both perfusion and batch culture modes were compared at an infection cell density of 6 × 10(6) cells/mL. The metabolism, including glycolysis, glutaminolysis and amino acids utilization as well as physiological indicators such as viability and apoptosis were extensively documented for the two modes of culture before and after viral infection to identify potential metabolic limitations. A 3 L bioreactor with a perfusion rate of 0.5 vol/day allowed us to reach maximal titers of 3.3 × 10(11) IVP/mL and 4.0 logHA units/mL, corresponding to a total production of 1.0 × 10(15) IVP and 7.8 logHA units after 3 days post-infection. Overall, perfusion mode titers were higher by almost one order of magnitude over the batch culture mode of production. This improvement was associated with an activation of the cell metabolism as seen by a 1.5-fold and 4-fold higher consumption rates of glucose and glutamine respectively. A shift in the viral production kinetics was also observed leading to an accumulation of more viable cells with a higher specific production and causing an increase in the total volumetric production of infectious influenza particles. CONCLUSIONS These results confirm that the HEK293SF cell is an excellent substrate for high yield production of influenza virus. Furthermore, there is great potential in further improving the production yields through better control of the cell culture environment and viral production kinetics. Once accomplished, this cell line can be promoted as an industrial platform for cost-effective manufacturing of the influenza seasonal vaccine as well as for periods of peak demand during pandemics.
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Affiliation(s)
- Emma Petiot
- Biotechnology Research Institute, 6100 Royalmount Avenue, Montreal, H4P 2R2 Québec, Canada
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Intracellular viral kinetics limited by the supply of amino acids for synthesis of viral proteins. Biosystems 2009; 97:117-20. [DOI: 10.1016/j.biosystems.2009.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2008] [Revised: 05/12/2009] [Accepted: 05/12/2009] [Indexed: 11/20/2022]
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Infection dynamics and virus-induced apoptosis in cell culture-based influenza vaccine production—Flow cytometry and mathematical modeling. Vaccine 2009; 27:2712-22. [DOI: 10.1016/j.vaccine.2009.02.027] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 02/01/2009] [Accepted: 02/05/2009] [Indexed: 11/24/2022]
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Time Dependent Virus Replication in Cell Cultures. LECTURE NOTES OF THE INSTITUTE FOR COMPUTER SCIENCES, SOCIAL INFORMATICS AND TELECOMMUNICATIONS ENGINEERING 2009. [DOI: 10.1007/978-3-642-02466-5_63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Sidorenko Y, Voigt A, Schulze-Horsel J, Reichl U, Kienle A. Stochastic population balance modeling of influenza virus replication in vaccine production processes. II. Detailed description of the replication mechanism. Chem Eng Sci 2008. [DOI: 10.1016/j.ces.2007.12.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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