1
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Smith AM. Decoding immune kinetics: unveiling secrets using custom-built mathematical models. Nat Methods 2024; 21:744-747. [PMID: 38710785 DOI: 10.1038/s41592-024-02265-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Affiliation(s)
- Amber M Smith
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA.
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2
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Schäfer PSL, Dimitrov D, Villablanca EJ, Saez-Rodriguez J. Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system. Nat Immunol 2024; 25:405-417. [PMID: 38413722 DOI: 10.1038/s41590-024-01768-2] [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: 05/31/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
The immune system comprises diverse specialized cell types that cooperate to defend the host against a wide range of pathogenic threats. Recent advancements in single-cell and spatial multi-omics technologies provide rich information about the molecular state of immune cells. Here, we review how the integration of single-cell and spatial multi-omics data with prior knowledge-gathered from decades of detailed biochemical studies-allows us to obtain functional insights, focusing on gene regulatory processes and cell-cell interactions. We present diverse applications in immunology and critically assess underlying assumptions and limitations. Finally, we offer a perspective on the ongoing technological and algorithmic developments that promise to get us closer to a systemic mechanistic understanding of the immune system.
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Affiliation(s)
- Philipp Sven Lars Schäfer
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Daniel Dimitrov
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Julio Saez-Rodriguez
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany.
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3
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Reeves DB, Bacchus-Souffan C, Fitch M, Abdel-Mohsen M, Hoh R, Ahn H, Stone M, Hecht F, Martin J, Deeks SG, Hellerstein MK, McCune JM, Schiffer JT, Hunt PW. Estimating the contribution of CD4 T cell subset proliferation and differentiation to HIV persistence. Nat Commun 2023; 14:6145. [PMID: 37783718 PMCID: PMC10545742 DOI: 10.1038/s41467-023-41521-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
Persistence of HIV in people living with HIV (PWH) on suppressive antiretroviral therapy (ART) has been linked to physiological mechanisms of CD4+ T cells. Here, in the same 37 male PWH on ART we measure longitudinal kinetics of HIV DNA and cell turnover rates in five CD4 cell subsets: naïve (TN), stem-cell- (TSCM), central- (TCM), transitional- (TTM), and effector-memory (TEM). HIV decreases in TTM and TEM but not in less-differentiated subsets. Cell turnover is ~10 times faster than HIV clearance in memory subsets, implying that cellular proliferation consistently creates HIV DNA. The optimal mathematical model for these integrated data sets posits HIV DNA also passages between CD4 cell subsets via cellular differentiation. Estimates are heterogeneous, but in an average participant's year ~10 (in TN and TSCM) and ~104 (in TCM, TTM, TEM) proviruses are generated by proliferation while ~103 proviruses passage via cell differentiation (per million CD4). In simulations, therapies blocking proliferation and/or enhancing differentiation could reduce HIV DNA by 1-2 logs over 3 years. In summary, HIV exploits cellular proliferation and differentiation to persist during ART but clears faster in more proliferative/differentiated CD4 cell subsets and the same physiological mechanisms sustaining HIV might be temporarily modified to reduce it.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
- Department of Global Health, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA.
| | | | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | | | - Rebecca Hoh
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Haelee Ahn
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Mars Stone
- Vitalant Research Institute, 360 Spear St Suite 200, San Francisco, CA, 94105, USA
| | - Frederick Hecht
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Jeffrey Martin
- Epidemiology & Biostatistics, University of California San Francisco School of Medicine, 550 16th Street, San Francisco, CA, 94158, USA
| | - Steven G Deeks
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Marc K Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | - Joseph M McCune
- HIV Frontiers, Global Health Accelerator, Bill & Melinda Gates Foundation, 500 5th Ave N, Seattle, WA, 98109, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA
| | - Peter W Hunt
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
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4
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Zhdanov VP. Extracellular interplay of amyloid fibrils and neural cells. Biosystems 2023; 231:104971. [PMID: 37429375 DOI: 10.1016/j.biosystems.2023.104971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023]
Abstract
Some neurological disorders such e.g. as Alzheimer disease are accompanied by the appearance of amyloid fibrils inside and outside cells. Herein, I present a generic coarse-grained kinetic mean-field model describing at the extracellular level the interplay of fibrils and cells. It includes the formation and degradation of fibrils, activation of healthy cells with respect to the fabrication of fibrils, and death of activated cells. The corresponding analysis indicates that the disease development can occur in two qualitatively different regimes. The first one is controlled primarily by the intrinsic factors resulting in slow increase of fibril production inside cells. The second one implies faster self-promoted growth of the fibril population by analogy with explosion. This prediction reported as a hypothesis is of interest for conceptual understanding of the neurological disorders.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Nano and Biophysics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
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5
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Chin JL, Chan LC, Yeaman MR, Meyer AS. Tensor-based insights into systems immunity and infectious disease. Trends Immunol 2023; 44:329-332. [PMID: 36997459 PMCID: PMC10411872 DOI: 10.1016/j.it.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023]
Abstract
Profiling immune responses across several dimensions, including time, patients, molecular features, and tissue sites, can deepen our understanding of immunity as an integrated system. These studies require new analytical approaches to realize their full potential. We highlight recent applications of tensor methods and discuss several future opportunities.
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Affiliation(s)
- Jackson L Chin
- Department of Bioengineering, University of California Los Angeles (UCLA), Los Angeles, CA 90024, USA
| | - Liana C Chan
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Division of Molecular Medicine, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Michael R Yeaman
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Division of Molecular Medicine, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Aaron S Meyer
- Department of Bioengineering, University of California Los Angeles (UCLA), Los Angeles, CA 90024, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90024, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90024, USA.
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6
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Fu J, Zhu F, Xu CJ, Li Y. Metabolomics meets systems immunology. EMBO Rep 2023; 24:e55747. [PMID: 36916532 PMCID: PMC10074123 DOI: 10.15252/embr.202255747] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/24/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Metabolic processes play a critical role in immune regulation. Metabolomics is the systematic analysis of small molecules (metabolites) in organisms or biological samples, providing an opportunity to comprehensively study interactions between metabolism and immunity in physiology and disease. Integrating metabolomics into systems immunology allows the exploration of the interactions of multilayered features in the biological system and the molecular regulatory mechanism of these features. Here, we provide an overview on recent technological developments of metabolomic applications in immunological research. To begin, two widely used metabolomics approaches are compared: targeted and untargeted metabolomics. Then, we provide a comprehensive overview of the analysis workflow and the computational tools available, including sample preparation, raw spectra data preprocessing, data processing, statistical analysis, and interpretation. Third, we describe how to integrate metabolomics with other omics approaches in immunological studies using available tools. Finally, we discuss new developments in metabolomics and its prospects for immunology research. This review provides guidance to researchers using metabolomics and multiomics in immunity research, thus facilitating the application of systems immunology to disease research.
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Affiliation(s)
- Jianbo Fu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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7
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Schuurman AR, Sloot PMA, Wiersinga WJ, van der Poll T. Embracing complexity in sepsis. Crit Care 2023; 27:102. [PMID: 36906606 PMCID: PMC10007743 DOI: 10.1186/s13054-023-04374-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/19/2023] [Indexed: 03/13/2023] Open
Abstract
Sepsis involves the dynamic interplay between a pathogen, the host response, the failure of organ systems, medical interventions and a myriad of other factors. This together results in a complex, dynamic and dysregulated state that has remained ungovernable thus far. While it is generally accepted that sepsis is very complex indeed, the concepts, approaches and methods that are necessary to understand this complexity remain underappreciated. In this perspective we view sepsis through the lens of complexity theory. We describe the concepts that support viewing sepsis as a state of a highly complex, non-linear and spatio-dynamic system. We argue that methods from the field of complex systems are pivotal for a fuller understanding of sepsis, and we highlight the progress that has been made over the last decades in this respect. Still, despite these considerable advancements, methods like computational modelling and network-based analyses continue to fly under the general scientific radar. We discuss what barriers contribute to this disconnect, and what we can do to embrace complexity with regards to measurements, research approaches and clinical applications. Specifically, we advocate a focus on longitudinal, more continuous biological data collection in sepsis. Understanding the complexity of sepsis will require a huge multidisciplinary effort, in which computational approaches derived from complex systems science must be supported by, and integrated with, biological data. Such integration could finetune computational models, guide validation experiments, and identify key pathways that could be targeted to modulate the system to the benefit of the host. We offer an example for immunological predictive modelling, which may inform agile trials that could be adjusted throughout the trajectory of disease. Overall, we argue that we should expand our current mental frameworks of sepsis, and embrace nonlinear, system-based thinking in order to move the field forward.
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Affiliation(s)
- Alex R Schuurman
- Centre for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centres - Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Peter M A Sloot
- Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands
| | - W Joost Wiersinga
- Centre for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centres - Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Tom van der Poll
- Centre for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centres - Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. .,Division of Infectious Diseases, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands.
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8
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Toptygina A, Grebennikov D, Bocharov G. Prediction of Specific Antibody- and Cell-Mediated Responses Using Baseline Immune Status Parameters of Individuals Received Measles-Mumps-Rubella Vaccine. Viruses 2023; 15:v15020524. [PMID: 36851738 PMCID: PMC9960117 DOI: 10.3390/v15020524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
A successful vaccination implies the induction of effective specific immune responses. We intend to find biomarkers among various immune cell subpopulations, cytokines and antibodies that could be used to predict the levels of specific antibody- and cell-mediated responses after measles-mumps-rubella vaccination. We measured 59 baseline immune status parameters (frequencies of 42 immune cell subsets, levels of 13 cytokines, immunoglobulins) before vaccination and 13 response variables (specific IgA and IgG, antigen-induced IFN-γ production, CD107a expression on CD8+ T lymphocytes, and cellular proliferation levels by CFSE dilution) 6 weeks after vaccination for 19 individuals. Statistically significant Spearman correlations between some baseline parameters and response variables were found for each response variable (p < 0.05). Because of the low number of observations relative to the number of baseline parameters and missing data for some observations, we used three feature selection strategies to select potential predictors of the post-vaccination responses among baseline variables: (a) screening of the variables based on correlation analysis; (b) supervised screening based on the information of changes of baseline variables at day 7; and (c) implicit feature selection using regularization-based sparse regression. We identified optimal multivariate linear regression models for predicting the effectiveness of vaccination against measles-mumps-rubella using the baseline immune status parameters. It turned out that the sufficient number of predictor variables ranges from one to five, depending on the response variable of interest.
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Affiliation(s)
- Anna Toptygina
- Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia
- Correspondence: (A.T.); (D.G.); (G.B.)
| | - Dmitry Grebennikov
- Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences, (INM RAS), 119333 Moscow, Russia
- Moscow Center for Fundamental and Applied Mathematics, INM RAS, 119333 Moscow, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Correspondence: (A.T.); (D.G.); (G.B.)
| | - Gennady Bocharov
- Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences, (INM RAS), 119333 Moscow, Russia
- Moscow Center for Fundamental and Applied Mathematics, INM RAS, 119333 Moscow, Russia
- Institute of Computer Science and Mathematical Modelling, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Correspondence: (A.T.); (D.G.); (G.B.)
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9
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Costa B, Vale N. Modulating Immune Response in Viral Infection for Quantitative Forecasts of Drug Efficacy. Pharmaceutics 2023; 15:pharmaceutics15010167. [PMID: 36678799 PMCID: PMC9867121 DOI: 10.3390/pharmaceutics15010167] [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: 11/10/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
The antiretroviral drug, the total level of viral production, and the effectiveness of immune responses are the main topics of this review because they are all dynamically interrelated. Immunological and viral processes interact in extremely complex and non-linear ways. For reliable analysis and quantitative forecasts that may be used to follow the immune system and create a disease profile for each patient, mathematical models are helpful in characterizing these non-linear interactions. To increase our ability to treat patients and identify individual differences in disease development, immune response profiling might be useful. Identifying which patients are moving from mild to severe disease would be more beneficial using immune system parameters. Prioritize treatments based on their inability to control the immune response and prevent T cell exhaustion. To increase treatment efficacy and spur additional research in this field, this review intends to provide examples of the effects of modelling immune response in viral infections, as well as the impact of pharmaceuticals on immune response.
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Affiliation(s)
- Bárbara Costa
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
- Correspondence: ; Tel.: +351-220426537
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10
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Namilae S, Wu Y, Mubayi A, Srinivasan A, Scotch M. Reply to comments on "Identifying mitigation strategies for COVID-19 superspreading on flights using models that account for passenger movement". Travel Med Infect Dis 2023; 51:102453. [PMID: 36162716 PMCID: PMC9500346 DOI: 10.1016/j.tmaid.2022.102453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/12/2023]
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A Hybrid Discrete–Continuum Modelling Approach to Explore the Impact of T-Cell Infiltration on Anti-tumour Immune Response. Bull Math Biol 2022; 84:141. [DOI: 10.1007/s11538-022-01095-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/06/2022] [Indexed: 11/02/2022]
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12
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Mechanistic models of Rift Valley fever virus transmission: A systematic review. PLoS Negl Trop Dis 2022; 16:e0010339. [PMID: 36399500 PMCID: PMC9718419 DOI: 10.1371/journal.pntd.0010339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 12/02/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
Rift Valley fever (RVF) is a zoonotic arbovirosis which has been reported across Africa including the northernmost edge, South West Indian Ocean islands, and the Arabian Peninsula. The virus is responsible for high abortion rates and mortality in young ruminants, with economic impacts in affected countries. To date, RVF epidemiological mechanisms are not fully understood, due to the multiplicity of implicated vertebrate hosts, vectors, and ecosystems. In this context, mathematical models are useful tools to develop our understanding of complex systems, and mechanistic models are particularly suited to data-scarce settings. Here, we performed a systematic review of mechanistic models studying RVF, to explore their diversity and their contribution to the understanding of this disease epidemiology. Researching Pubmed and Scopus databases (October 2021), we eventually selected 48 papers, presenting overall 49 different models with numerical application to RVF. We categorized models as theoretical, applied, or grey, depending on whether they represented a specific geographical context or not, and whether they relied on an extensive use of data. We discussed their contributions to the understanding of RVF epidemiology, and highlighted that theoretical and applied models are used differently yet meet common objectives. Through the examination of model features, we identified research questions left unexplored across scales, such as the role of animal mobility, as well as the relative contributions of host and vector species to transmission. Importantly, we noted a substantial lack of justification when choosing a functional form for the force of infection. Overall, we showed a great diversity in RVF models, leading to important progress in our comprehension of epidemiological mechanisms. To go further, data gaps must be filled, and modelers need to improve their code accessibility.
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13
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Christian DA, Adams TA, Shallberg LA, Phan AT, Smith TE, Abraha M, Perry J, Ruthel G, Clark JT, Pritchard GH, Aronson LR, Gossa S, McGavern DB, Kedl RM, Hunter CA. cDC1 coordinate innate and adaptive responses in the omentum required for T cell priming and memory. Sci Immunol 2022; 7:eabq7432. [PMID: 36179012 PMCID: PMC9835709 DOI: 10.1126/sciimmunol.abq7432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In the peritoneal cavity, the omentum contains fat-associated lymphoid clusters (FALCs) whose role in response to infection is poorly understood. After intraperitoneal immunization with Toxoplasma gondii, conventional type 1 dendritic cells (cDC1s) were critical to induce innate sources of IFN-γ and cellular changes in the FALCs. Unexpectedly, infected peritoneal macrophages that migrated into the FALCs primed CD8+ T cells. Although T cell priming was cDC1 independent, these DCs were required for maximal CD8+ T cell expansion. An agent-based computational model and experimental data highlighted that cDC1s affected the magnitude of the proliferative burst and promoted CD8+ T cell expression of nutrient uptake receptors and cell survival. Thus, although FALCs lack the organization of secondary lymphoid organs, cDC1s resident in this tissue coordinate innate responses to microbial challenge and provide secondary signals required for T cell expansion and memory formation.
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Affiliation(s)
- David A. Christian
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Thomas A. Adams
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario
| | | | - Anthony T. Phan
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Tony E. Smith
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Mosana Abraha
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario
| | - Joseph Perry
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Gordon Ruthel
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Joseph T. Clark
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Lillian R. Aronson
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104
- Section of Surgery, Department of Clinical Studies, University of Pennsylvania, Philadelphia, PA 19104
| | - Selamawit Gossa
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814
| | - Dorian B. McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814
| | - Ross M. Kedl
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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Atitey K, Anchang B. Mathematical Modeling of Proliferative Immune Response Initiated by Interactions Between Classical Antigen-Presenting Cells Under Joint Antagonistic IL-2 and IL-4 Signaling. Front Mol Biosci 2022; 9:777390. [PMID: 35155574 PMCID: PMC8831889 DOI: 10.3389/fmolb.2022.777390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
During an adaptive immune response from pathogen invasion, multiple cytokines are produced by various immune cells interacting jointly at the cellular level to mediate several processes. For example, studies have shown that regulation of interleukin-4 (IL-4) correlates with interleukin-2 (IL-2) induced lymphocyte proliferation. This motivates the need to better understand and model the mechanisms driving the dynamic interplay of proliferation of lymphocytes with the complex interaction effects of cytokines during an immune response. To address this challenge, we adopt a hybrid computational approach comprising of continuous, discrete and stochastic non-linear model formulations to predict a system-level immune response as a function of multiple dependent signals and interacting agents including cytokines and targeted immune cells. We propose a hybrid ordinary differential equation-based (ODE) multicellular model system with a stochastic component of antigen microscopic states denoted as Multiscale Multicellular Quantitative Evaluator (MMQE) implemented using MATLAB. MMQE combines well-defined immune response network-based rules and ODE models to capture the complex dynamic interactions between the proliferation levels of different types of communicating lymphocyte agents mediated by joint regulation of IL-2 and IL-4 to predict the emergent global behavior of the system during an immune response. We model the activation of the immune system in terms of different activation protocols of helper T cells by the interplay of independent biological agents of classic antigen-presenting cells (APCs) and their joint activation which is confounded by the exposure time to external pathogens. MMQE quantifies the dynamics of lymphocyte proliferation during pathogen invasion as bivariate distributions of IL-2 and IL-4 concentration levels. Specifically, by varying activation agents such as dendritic cells (DC), B cells and their joint mechanism of activation, we quantify how lymphocyte activation and differentiation protocols boost the immune response against pathogen invasion mediated by a joint downregulation of IL-4 and upregulation of IL-2. We further compare our in-silico results to in-vivo and in-vitro experimental studies for validation. In general, MMQE combines intracellular and extracellular effects from multiple interacting systems into simpler dynamic behaviors for better interpretability. It can be used to aid engineering of anti-infection drugs or optimizing drug combination therapies against several diseases.
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15
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Zhang L, Li R, Song G, Scholes GD, She ZS. Impairment of T cells' antiviral and anti-inflammation immunities may be critical to death from COVID-19. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211606. [PMID: 34950497 PMCID: PMC8692966 DOI: 10.1098/rsos.211606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/25/2021] [Indexed: 05/02/2023]
Abstract
Clarifying dominant factors determining the immune heterogeneity from non-survivors to survivors is crucial for developing therapeutics and vaccines against COVID-19. The main difficulty is quantitatively analysing the multi-level clinical data, including viral dynamics, immune response and tissue damages. Here, we adopt a top-down modelling approach to quantify key functional aspects and their dynamical interplay in the battle between the virus and the immune system, yielding an accurate description of real-time clinical data involving hundreds of patients for the first time. The quantification of antiviral responses gives that, compared to antibodies, T cells play a more dominant role in virus clearance, especially for mild patients (96.5%). Moreover, the anti-inflammatory responses, namely the cytokine inhibition and tissue repair rates, also positively correlate with T cell number and are significantly suppressed in non-survivors. Simulations show that the lack of T cells can lead to more significant inflammation, proposing an explanation for the monotonic increase of COVID-19 mortality with age and higher mortality for males. We propose that T cells play a crucial role in the immunity against COVID-19, which provides a new direction-improvement of T cell number for advancing current prevention and treatment.
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Affiliation(s)
- Luhao Zhang
- Institute of Health System Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Rong Li
- Institute of Health System Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
- State Key Laboratory for Turbulence and Complex Systems, Peking University, Beijing 100871, People's Republic of China
| | - Gang Song
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | | | - Zhen-Su She
- Institute of Health System Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
- State Key Laboratory for Turbulence and Complex Systems, Peking University, Beijing 100871, People's Republic of China
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16
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Zhdanov VP. How nanoparticles can induce dimerization and aggregation of cells in blood or lymph. Biosystems 2021; 210:104551. [PMID: 34597710 DOI: 10.1016/j.biosystems.2021.104551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/24/2022]
Abstract
By analogy with virions, the binding of biologically-inspired nanoparticles (NPs) with ligands to the cellular membrane containing receptors depends on the multivalent ligand-receptor interaction, membrane bending, and cytoskeleton deformation. The interplay of these factors results in the existence of the potential minimum and activation barrier on the pathway towards full absorption of a NP. Herein, I hypothesize and show theoretically that the interaction of a NP, bound to one cell, with another cell can stabilize the potential minimum and increase the corresponding activation barrier, i.e., NPs can mediate the formation of long-living pairs of cells and aggregates containing a few cells inside blood and lymphatic vessels.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Nano and Biophysics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
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17
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Zhdanov VP. Virology from the perspective of theoretical colloid and interface science. Curr Opin Colloid Interface Sci 2021; 53:101450. [PMID: 36568530 PMCID: PMC9761319 DOI: 10.1016/j.cocis.2021.101450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Viral infections occur at very different length and time scales and include various processes, which can often be described using the models developed and/or employed in colloid and interface science. Bearing in mind the currently active COVID-19, I discuss herein the models aimed at viral transmission via respiratory droplets and the contact of virions with the epithelium. In a more general context, I outline the models focused on penetration of virions via the cellular membrane, initial stage of viral genome replication, and formation of viral capsids in cells. In addition, the models related to a new generation of drug delivery vehicles, for example, lipid nanoparticles with size about 100-200 nm, are discussed as well. Despite the high current interest in all these processes, their understanding is still limited, and this area is open for new theoretical studies.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Nano and Biological Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden
- Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia
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18
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Zhdanov VP. Kinetic aspects of virus targeting by nanoparticles in vivo. J Biol Phys 2021; 47:95-101. [PMID: 34080098 PMCID: PMC8184910 DOI: 10.1007/s10867-021-09570-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 01/29/2023] Open
Abstract
One of the suggested ways of the use of nanoparticles in virology implies their association with and subsequent deactivation of virions. The conditions determining the efficiency of this approach in vivo are now not clear. Herein, I propose the first kinetic model describing the corresponding processes and clarifying these conditions. My analysis indicates that nanoparticles can decrease concentration of infected cells by a factor of one order of magnitude, but this decrease itself (without feedback of the immune system) is insufficient for full eradication of infection. It can, however, induce delay in the progress of infection, and this delay can help to form sufficient feedback of the immune system.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Nano and Biophysics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden.
- Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
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19
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Hwang W, Lei W, Katritsis NM, MacMahon M, Chapman K, Han N. Current and prospective computational approaches and challenges for developing COVID-19 vaccines. Adv Drug Deliv Rev 2021; 172:249-274. [PMID: 33561453 PMCID: PMC7871111 DOI: 10.1016/j.addr.2021.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2, which causes COVID-19, was first identified in humans in late 2019 and is a coronavirus which is zoonotic in origin. As it spread around the world there has been an unprecedented effort in developing effective vaccines. Computational methods can be used to speed up the long and costly process of vaccine development. Antigen selection, epitope prediction, and toxicity and allergenicity prediction are areas in which computational tools have already been applied as part of reverse vaccinology for SARS-CoV-2 vaccine development. However, there is potential for computational methods to assist further. We review approaches which have been used and highlight additional bioinformatic approaches and PK modelling as in silico methods which may be useful for SARS-CoV-2 vaccine design but remain currently unexplored. As more novel viruses with pandemic potential are expected to arise in future, these techniques are not limited to application to SARS-CoV-2 but also useful to rapidly respond to novel emerging viruses.
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Affiliation(s)
- Woochang Hwang
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Winnie Lei
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Nicholas M Katritsis
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Méabh MacMahon
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Centre for Therapeutics Discovery, LifeArc, Stevenage, UK
| | - Kathryn Chapman
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
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20
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Zhdanov VP, Kasemo B. Virions and respiratory droplets in air: Diffusion, drift, and contact with the epithelium. Biosystems 2020; 198:104241. [PMID: 32896576 PMCID: PMC9991016 DOI: 10.1016/j.biosystems.2020.104241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 01/07/2023]
Abstract
Some infections, including e.g. influenza and currently active COVID 19, may be transmitted via air during sneezing, coughing, and talking. This pathway occurs via diffusion and gravity-induced drift of single virions and respiratory droplets consisting primarily of water, including small fraction of nonvolatile matter, and containing virions. These processes are accompanied by water evaporation resulting in reduction of the droplet size. The manifold of information concerning these steps is presented in textbooks and articles not related to virology and the focus is there frequently on biologically irrelevant conditions and/or droplet sizes. In this brief review, we systematically describe the behavior of virions and virion-carrying droplets in air with emphasis on various regimes of diffusion, drift, and evaporation, and estimate the rates of all these steps under virologically relevant conditions. In addition, we discuss the kinetic aspects of the first steps of infection after attachment of virions or virion-carrying droplets to the epithelium, i.e., virion diffusion in the mucus and periciliary layers, penetration into the cells, and the early stage of replication. The presentation is oriented to virologists who are interested in the corresponding physics and to physicists who are interested in application of the physics to virology.
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Affiliation(s)
- Vladimir P Zhdanov
- Sections of Nano and Biological Physics and Chemical Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
| | - Bengt Kasemo
- Sections of Nano and Biological Physics and Chemical Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden
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21
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Hausmann A, Hardt WD. Elucidating host-microbe interactions in vivo by studying population dynamics using neutral genetic tags. Immunology 2020; 162:341-356. [PMID: 32931019 PMCID: PMC7968395 DOI: 10.1111/imm.13266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/21/2020] [Accepted: 08/29/2020] [Indexed: 12/14/2022] Open
Abstract
Host–microbe interactions are highly dynamic in space and time, in particular in the case of infections. Pathogen population sizes, microbial phenotypes and the nature of the host responses often change dramatically over time. These features pose particular challenges when deciphering the underlying mechanisms of these interactions experimentally, as traditional microbiological and immunological methods mostly provide snapshots of population sizes or sparse time series. Recent approaches – combining experiments using neutral genetic tags with stochastic population dynamic models – allow more precise quantification of biologically relevant parameters that govern the interaction between microbe and host cell populations. This is accomplished by exploiting the patterns of change of tag composition in the microbe or host cell population under study. These models can be used to predict the effects of immunodeficiencies or therapies (e.g. antibiotic treatment) on populations and thereby generate hypotheses and refine experimental designs. In this review, we present tools to study population dynamics in vivo using genetic tags, explain examples for their implementation and briefly discuss future applications.
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Affiliation(s)
- Annika Hausmann
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
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22
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Zhdanov VP, Jackman JA. Analysis of the initiation of viral infection under flow conditions with applications to transmission in feed. Biosystems 2020; 196:104184. [PMID: 32531420 PMCID: PMC7282798 DOI: 10.1016/j.biosystems.2020.104184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/07/2020] [Accepted: 06/07/2020] [Indexed: 02/07/2023]
Abstract
While kinetic models are widely used to describe viral infection at various levels, most of them are focused on temporal aspects and understanding of corresponding spatio-temporal aspects remains limited. In this work, our attention is focused on the initial stage of infection of immobile cells by virus particles ("virions") under flow conditions with diffusion. A practical example of this scenario occurs when humans or animals consume food from virion-containing sources. Mathematically, such situations can be described by using a model constructed in analogy with those employed in chemical engineering for analysis of the function of a plug-flow reactor with dispersion. As in the temporal case, the corresponding spatio-temporal model predicts either the transition to a steady state or exponential growth of the populations of virions and infected cells. The spatial distributions of these species are similar in both of these regimes. In particular, the maximums of the populations are shifted to the upper boundary of the infected region. The results illustrating these conclusions were obtained analytically and by employing numerical calculations without and with the dependence of the kinetic parameters on the coordinate. The model proposed has also been used in order to illustrate the effect of antiviral feed additives on feedborne infection towards curbing disease transmission.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Biological Physics, Department of Physics, Chalmers University of Technology, S-41296 Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Joshua A Jackman
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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