1
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Yamaguchi D, Shimizu R, Kubota R. Development of a SARS-CoV-2 viral dynamic model for patients with COVID-19 based on the amount of viral RNA and viral titer. CPT Pharmacometrics Syst Pharmacol 2024; 13:1354-1365. [PMID: 38783551 PMCID: PMC11330184 DOI: 10.1002/psp4.13164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/17/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
The target-cell limited model, which is one of the mathematical modeling approaches providing a quantitative understanding of viral dynamics, has been applied to describe viral RNA profiles of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in previous studies. However, these models have been developed mainly using patient data from the early phase of the pandemic. Furthermore, no reports focused on the profiles of the viral titer. In this study, the dynamics of both viral RNA and viral titer were characterized using data reflecting the current clinical situation in which the Omicron variant has become epidemic and vaccines for SARS-CoV-2 have become available. Consecutive data for 5212 viral RNA levels and 5216 viral titers were obtained from 720 patients with coronavirus disease 2019 (COVID-19) in a phase II/III study for ensitrelvir. Our model assumed that productively infected cells would produce only infectious viruses, which could be transformed into non-infectious viruses, and has been used to describe the dynamics of both viral RNA levels and viral titer. The time from infection to symptom onset (tinf) of unvaccinated patients was estimated to be 3.0 days, which was shorter than that of the vaccinated patients. The immune-related parameter as a power function for the vaccinated patients was 1.1 times stronger than that for the unvaccinated patients. Our model allows the prediction of the viral dynamics in patients with COVID-19 from the time of infection to symptom onset. Vaccination status was identified as a factor influencing tinf and the immune function.
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Affiliation(s)
- Daichi Yamaguchi
- Clinical Pharmacology & PharmacokineticsShionogi & Co., Ltd.OsakaJapan
| | - Ryosuke Shimizu
- Clinical Pharmacology & PharmacokineticsShionogi & Co., Ltd.OsakaJapan
| | - Ryuji Kubota
- Clinical Pharmacology & PharmacokineticsShionogi & Co., Ltd.OsakaJapan
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2
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Liyanage YR, Heitzman-Breen N, Tuncer N, Ciupe SM. Identifiability investigation of within-host models of acute virus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593464. [PMID: 38766177 PMCID: PMC11100786 DOI: 10.1101/2024.05.09.593464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Uncertainty in parameter estimates from fitting within-host models to empirical data limits the model's ability to uncover mechanisms of infection, disease progression, and to guide pharmaceutical interventions. Understanding the effect of model structure and data availability on model predictions is important for informing model development and experimental design. To address sources of uncertainty in parameter estimation, we use four mathematical models of influenza A infection with increased degrees of biological realism. We test the ability of each model to reveal its parameters in the presence of unlimited data by performing structural identifiability analyses. We then refine the results by predicting practical identifiability of parameters under daily influenza A virus titers alone or together with daily adaptive immune cell data. Using these approaches, we present insight into the sources of uncertainty in parameter estimation and provide guidelines for the types of model assumptions, optimal experimental design, and biological information needed for improved predictions.
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Affiliation(s)
- Yuganthi R Liyanage
- Department of Mathematics and Statistics, Florida Atlantic University, Boca Raton, FL, USA
| | - Nora Heitzman-Breen
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Necibe Tuncer
- Department of Mathematics and Statistics, Florida Atlantic University, Boca Raton, FL, USA
| | - Stanca M Ciupe
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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3
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Ciupe SM, Conway JM. Incorporating Intracellular Processes in Virus Dynamics Models. Microorganisms 2024; 12:900. [PMID: 38792730 PMCID: PMC11124127 DOI: 10.3390/microorganisms12050900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
In-host models have been essential for understanding the dynamics of virus infection inside an infected individual. When used together with biological data, they provide insight into viral life cycle, intracellular and cellular virus-host interactions, and the role, efficacy, and mode of action of therapeutics. In this review, we present the standard model of virus dynamics and highlight situations where added model complexity accounting for intracellular processes is needed. We present several examples from acute and chronic viral infections where such inclusion in explicit and implicit manner has led to improvement in parameter estimates, unification of conclusions, guidance for targeted therapeutics, and crossover among model systems. We also discuss trade-offs between model realism and predictive power and highlight the need of increased data collection at finer scale of resolution to better validate complex models.
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Affiliation(s)
- Stanca M. Ciupe
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Penn State University, State College, PA 16802, USA
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4
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Zitzmann C, Ke R, Ribeiro RM, Perelson AS. How robust are estimates of key parameters in standard viral dynamic models? PLoS Comput Biol 2024; 20:e1011437. [PMID: 38626190 PMCID: PMC11051641 DOI: 10.1371/journal.pcbi.1011437] [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: 08/17/2023] [Revised: 04/26/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Mathematical models of viral infection have been developed, fitted to data, and provide insight into disease pathogenesis for multiple agents that cause chronic infection, including HIV, hepatitis C, and B virus. However, for agents that cause acute infections or during the acute stage of agents that cause chronic infections, viral load data are often collected after symptoms develop, usually around or after the peak viral load. Consequently, we frequently lack data in the initial phase of viral growth, i.e., when pre-symptomatic transmission events occur. Missing data may make estimating the time of infection, the infectious period, and parameters in viral dynamic models, such as the cell infection rate, difficult. However, having extra information, such as the average time to peak viral load, may improve the robustness of the estimation. Here, we evaluated the robustness of estimates of key model parameters when viral load data prior to the viral load peak is missing, when we know the values of some parameters and/or the time from infection to peak viral load. Although estimates of the time of infection are sensitive to the quality and amount of available data, particularly pre-peak, other parameters important in understanding disease pathogenesis, such as the loss rate of infected cells, are less sensitive. Viral infectivity and the viral production rate are key parameters affecting the robustness of data fits. Fixing their values to literature values can help estimate the remaining model parameters when pre-peak data is missing or limited. We find a lack of data in the pre-peak growth phase underestimates the time to peak viral load by several days, leading to a shorter predicted growth phase. On the other hand, knowing the time of infection (e.g., from epidemiological data) and fixing it results in good estimates of dynamical parameters even in the absence of early data. While we provide ways to approximate model parameters in the absence of early viral load data, our results also suggest that these data, when available, are needed to estimate model parameters more precisely.
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Affiliation(s)
- Carolin Zitzmann
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ruian Ke
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Alan S. Perelson
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
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5
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Nguyen BT, Marc A, Suñer C, Marks M, Ubals M, Hernández-Rodríguez Á, Melendez MÁ, Hruby DE, Russo AT, Mentré F, Mitjà O, Grosenbach DW, Guedj J. Early administration of tecovirimat shortens the time to mpox clearance in a model of human infection. PLoS Biol 2023; 21:e3002249. [PMID: 38127878 PMCID: PMC10734935 DOI: 10.1371/journal.pbio.3002249] [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: 07/03/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Despite use of tecovirimat since the beginning of the 2022 outbreak, few data have been published on its antiviral effect in humans. We here predict tecovirimat efficacy using a unique set of data in nonhuman primates (NHPs) and humans. We analyzed tecovirimat antiviral activity on viral kinetics in NHP to characterize its concentration-effect relationship in vivo. Next, we used a pharmacological model developed in healthy volunteers to project its antiviral efficacy in humans. Finally, a viral dynamic model was applied to characterize mpox kinetics in skin lesions from 54 untreated patients, and we used this modeling framework to predict the impact of tecovirimat on viral clearance in skin lesions. At human-recommended doses, tecovirimat could inhibit viral replication from infected cells by more than 90% after 3 to 5 days of drug administration and achieved over 97% efficacy at drug steady state. With an estimated mpox within-host basic reproduction number, R0, equal to 5.6, tecovirimat could therefore shorten the time to viral clearance if given before viral peak. We predicted that initiating treatment at symptom onset, which on average occurred 2 days before viral peak, could reduce the time to viral clearance by about 6 days. Immediate postexposure prophylaxis could not only reduce time to clearance but also lower peak viral load by more than 1.0 log10 copies/mL and shorten the duration of positive viral culture by about 7 to 10 days. These findings support the early administration of tecovirimat against mpox infection, ideally starting from the infection day as a postexposure prophylaxis.
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Affiliation(s)
| | - Aurélien Marc
- Université Paris Cité, INSERM, IAME, F-75018, Paris, France
| | - Clara Suñer
- Skin Neglected Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
| | - Michael Marks
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Hospital for Tropical Diseases, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Maria Ubals
- Skin Neglected Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
- Facultat de Medicina, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - Águeda Hernández-Rodríguez
- Microbiology Department, Clinical Laboratory North Metropolitan Area, University Hospital Germans Trias I Pujol, Badalona, Spain
- Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain
| | - María Ángeles Melendez
- Microbiology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | | | - Dennis E. Hruby
- SIGA Technologies, Inc., Corvallis, Oregon, United States of America
| | - Andrew T. Russo
- SIGA Technologies, Inc., Corvallis, Oregon, United States of America
| | - France Mentré
- Université Paris Cité, INSERM, IAME, F-75018, Paris, France
- Unité de Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Oriol Mitjà
- Skin Neglected Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
- School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | | | - Jérémie Guedj
- Université Paris Cité, INSERM, IAME, F-75018, Paris, France
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6
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Korosec CS, Betti MI, Dick DW, Ooi HK, Moyles IR, Wahl LM, Heffernan JM. Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: Parameter estimates, identifiability, sensitivity and the eclipse phase profile. J Theor Biol 2023; 564:111449. [PMID: 36894132 PMCID: PMC9990894 DOI: 10.1016/j.jtbi.2023.111449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 03/09/2023]
Abstract
Within-host SARS-CoV-2 modelling studies have been published throughout the COVID-19 pandemic. These studies contain highly variable numbers of individuals and capture varying timescales of pathogen dynamics; some studies capture the time of disease onset, the peak viral load and subsequent heterogeneity in clearance dynamics across individuals, while others capture late-time post-peak dynamics. In this study, we curate multiple previously published SARS-CoV-2 viral load data sets, fit these data with a consistent modelling approach, and estimate the variability of in-host parameters including the basic reproduction number, R0, as well as the best-fit eclipse phase profile. We find that fitted dynamics can be highly variable across data sets, and highly variable within data sets, particularly when key components of the dynamic trajectories (e.g. peak viral load) are not represented in the data. Further, we investigated the role of the eclipse phase time distribution in fitting SARS-CoV-2 viral load data. By varying the shape parameter of an Erlang distribution, we demonstrate that models with either no eclipse phase, or with an exponentially-distributed eclipse phase, offer significantly worse fits to these data, whereas models with less dispersion around the mean eclipse time (shape parameter two or more) offered the best fits to the available data across all data sets used in this work. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".
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Affiliation(s)
- Chapin S Korosec
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, M3J 1P3, ON, Canada; Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, M3J 1P3, ON, Canada.
| | - Matthew I Betti
- Department of Mathematics and Computer Science, Mount Allison University, 62 York St, Sackville, E4L 1E2, NB, Canada.
| | - David W Dick
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, M3J 1P3, ON, Canada; Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, M3J 1P3, ON, Canada.
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, 222 College Street, Toronto, M5T 3J1, ON, Canada.
| | - Iain R Moyles
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, M3J 1P3, ON, Canada; Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, M3J 1P3, ON, Canada.
| | - Lindi M Wahl
- Mathematics, Western University, 1151 Richmond St, London, N6A 5B7, ON, Canada.
| | - Jane M Heffernan
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, M3J 1P3, ON, Canada; Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, M3J 1P3, ON, Canada.
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7
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Xu Z, Wei D, Zhang H, Demongeot J. A Novel Mathematical Model That Predicts the Protection Time of SARS-CoV-2 Antibodies. Viruses 2023; 15:v15020586. [PMID: 36851801 PMCID: PMC9962246 DOI: 10.3390/v15020586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Infectious diseases such as SARS-CoV-2 pose a considerable threat to public health. Constructing a reliable mathematical model helps us quantitatively explain the kinetic characteristics of antibody-virus interactions. A novel and robust model is developed to integrate antibody dynamics with virus dynamics based on a comprehensive understanding of immunology principles. This model explicitly formulizes the pernicious effect of the antibody, together with a positive feedback stimulation of the virus-antibody complex on the antibody regeneration. Besides providing quantitative insights into antibody and virus dynamics, it demonstrates good adaptivity in recapturing the virus-antibody interaction. It is proposed that the environmental antigenic substances help maintain the memory cell level and the corresponding neutralizing antibodies secreted by those memory cells. A broader application is also visualized in predicting the antibody protection time caused by a natural infection. Suitable binding antibodies and the presence of massive environmental antigenic substances would prolong the protection time against breakthrough infection. The model also displays excellent fitness and provides good explanations for antibody selection, antibody interference, and self-reinfection. It helps elucidate how our immune system efficiently develops neutralizing antibodies with good binding kinetics. It provides a reasonable explanation for the lower SARS-CoV-2 mortality in the population that was vaccinated with other vaccines. It is inferred that the best strategy for prolonging the vaccine protection time is not repeated inoculation but a directed induction of fast-binding antibodies. Eventually, this model will inform the future construction of an optimal mathematical model and help us fight against those infectious diseases.
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Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou 253023, China
- Correspondence: (Z.X.); (J.D.)
| | - Dongqing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hongmei Zhang
- Department of Life Science, Dezhou University, Dezhou 253023, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France
- Correspondence: (Z.X.); (J.D.)
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8
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Nande A, Hill AL. The risk of drug resistance during long-acting antimicrobial therapy. Proc Biol Sci 2022; 289:20221444. [PMID: 36350211 PMCID: PMC9653236 DOI: 10.1098/rspb.2022.1444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The emergence of drug resistance during antimicrobial therapy is a major global health problem, especially for chronic infections like human immunodeficiency virus, hepatitis B and C, and tuberculosis. Sub-optimal adherence to long-term treatment is an important contributor to resistance risk. New long-acting drugs are being developed for weekly, monthly or less frequent dosing to improve adherence, but may lead to long-term exposure to intermediate drug levels. In this study, we analyse the effect of dosing frequency on the risk of resistance evolving during time-varying drug levels. We find that long-acting therapies can increase, decrease or have little effect on resistance, depending on the source (pre-existing or de novo) and degree of resistance, and rates of drug absorption and clearance. Long-acting therapies with rapid drug absorption, slow clearance and strong wild-type inhibition tend to reduce resistance caused by partially resistant strains in the early stages of treatment even if they do not improve adherence. However, if subpopulations of microbes persist and can reactivate during sub-optimal treatment, longer-acting therapies may substantially increase the resistance risk. Our results show that drug kinetics affect selection for resistance in a complicated manner, and that pathogen-specific models are needed to evaluate the benefits of new long-acting therapies.
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Affiliation(s)
- Anjalika Nande
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alison L. Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
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9
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Marlin R, Desjardins D, Contreras V, Lingas G, Solas C, Roques P, Naninck T, Pascal Q, Behillil S, Maisonnasse P, Lemaitre J, Kahlaoui N, Delache B, Pizzorno A, Nougairede A, Ludot C, Terrier O, Dereuddre-Bosquet N, Relouzat F, Chapon C, Ho Tsong Fang R, van der Werf S, Rosa Calatrava M, Malvy D, de Lamballerie X, Guedj J, Le Grand R. Antiviral efficacy of favipiravir against Zika and SARS-CoV-2 viruses in non-human primates. Nat Commun 2022; 13:5108. [PMID: 36042198 PMCID: PMC9427089 DOI: 10.1038/s41467-022-32565-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/05/2022] [Indexed: 12/02/2022] Open
Abstract
The COVID-19 pandemic has exemplified that rigorous evaluation in large animal models is key for translation from promising in vitro results to successful clinical implementation. Among the drugs that have been largely tested in clinical trials but failed so far to bring clear evidence of clinical efficacy is favipiravir, a nucleoside analogue with large spectrum activity against several RNA viruses in vitro and in small animal models. Here, we evaluate the antiviral activity of favipiravir against Zika or SARS-CoV-2 virus in cynomolgus macaques. In both models, high doses of favipiravir are initiated before infection and viral kinetics are evaluated during 7 to 15 days after infection. Favipiravir leads to a statistically significant reduction in plasma Zika viral load compared to untreated animals. However, favipiravir has no effects on SARS-CoV-2 viral kinetics, and 4 treated animals have to be euthanized due to rapid clinical deterioration, suggesting a potential role of favipiravir in disease worsening in SARS-CoV-2 infected animals. To summarize, favipiravir has an antiviral activity against Zika virus but not against SARS-CoV-2 infection in the cynomolgus macaque model. Our results support the clinical evaluation of favipiravir against Zika virus but they advocate against its use against SARS-CoV-2 infection. Repurposed antiviral drugs present as a valuable resource in the defence during outbreaks, with rigorous evaluation in large animal models keys for translation to clinical implementation. Here, the authors explore the antiviral activity of favipiravir against Zika virus and SARS-CoV-2 in cynomolgus macaques, in order to support future clinical investigations into this RNA polymerase inhibitor.
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Affiliation(s)
- Romain Marlin
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Delphine Desjardins
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Vanessa Contreras
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | | | - Caroline Solas
- Aix-Marseille Univ, APHM, Unité des Virus Emergents (UVE) IRD 190, INSERM 1207, Laboratoire de Pharmacocinétique et Toxicologie, Hôpital La Timone, 13005, Marseille, France
| | - Pierre Roques
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France.,Virology Unit, Institut Pasteur de Guinée, Conakry, Guinée
| | - Thibaut Naninck
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Quentin Pascal
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Sylvie Behillil
- Unité de Génétique Moléculaire des Virus à ARN, GMVR, Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France.,Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Pauline Maisonnasse
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Julien Lemaitre
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Nidhal Kahlaoui
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Benoit Delache
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Antoine Nougairede
- Unité des Virus Emergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection, 13005, Marseille, France
| | - Camille Ludot
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Francis Relouzat
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Catherine Chapon
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Raphael Ho Tsong Fang
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, GMVR, Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France.,Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Manuel Rosa Calatrava
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,VirNext, Université Claude Bernard Lyon 1, Faculté de Médecine Laennec, Lyon, France
| | - Denis Malvy
- Department of infectious ad tropical diseases, University hopsital, Bordeaux & Inserm 1219/IRD, Bordeaux University, Bordeaux, France
| | - Xavier de Lamballerie
- Unité des Virus Emergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection, 13005, Marseille, France
| | - Jeremie Guedj
- Université de Paris, INSERM, IAME, F-75018, Paris, France.
| | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases » (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France.
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10
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Identifiability of parameters in mathematical models of SARS-CoV-2 infections in humans. Sci Rep 2022; 12:14637. [PMID: 36030320 PMCID: PMC9418662 DOI: 10.1038/s41598-022-18683-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/16/2022] [Indexed: 12/12/2022] Open
Abstract
Determining accurate estimates for the characteristics of the severe acute respiratory syndrome coronavirus 2 in the upper and lower respiratory tracts, by fitting mathematical models to data, is made difficult by the lack of measurements early in the infection. To determine the sensitivity of the parameter estimates to the noise in the data, we developed a novel two-patch within-host mathematical model that considered the infection of both respiratory tracts and assumed that the viral load in the lower respiratory tract decays in a density dependent manner and investigated its ability to match population level data. We proposed several approaches that can improve practical identifiability of parameters, including an optimal experimental approach, and found that availability of viral data early in the infection is of essence for improving the accuracy of the estimates. Our findings can be useful for designing interventions.
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11
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Jeong YD, Ejima K, Kim KS, Joohyeon W, Iwanami S, Fujita Y, Jung IH, Aihara K, Shibuya K, Iwami S, Bento AI, Ajelli M. Designing isolation guidelines for COVID-19 patients with rapid antigen tests. Nat Commun 2022; 13:4910. [PMID: 35987759 PMCID: PMC9392070 DOI: 10.1038/s41467-022-32663-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 08/10/2022] [Indexed: 12/18/2022] Open
Abstract
Appropriate isolation guidelines for COVID-19 patients are warranted. Currently, isolating for fixed time is adopted in most countries. However, given the variability in viral dynamics between patients, some patients may no longer be infectious by the end of isolation, whereas others may still be infectious. Utilizing viral test results to determine isolation length would minimize both the risk of prematurely ending isolation of infectious patients and the unnecessary individual burden of redundant isolation of noninfectious patients. In this study, we develop a data-driven computational framework to compute the population-level risk and the burden of different isolation guidelines with rapid antigen tests (i.e., lateral flow tests). Here, we show that when the detection limit is higher than the infectiousness threshold values, additional consecutive negative results are needed to ascertain infectiousness status. Further, rapid antigen tests should be designed to have lower detection limits than infectiousness threshold values to minimize the length of prolonged isolation. Utilizing viral test results to determine isolation length would minimize both the risk of prematurely ending isolation of infectious patients and the unnecessary individual burden of redundant isolation of noninfectious patients. Here, the authors develop a framework to compute the population-level risk of different isolation guidelines with rapid antigen tests.
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12
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Chen C, Lavezzi SM, Iavarone L. The area under the effect curve as an efficacy determinant for anti‐infectives. CPT Pharmacometrics Syst Pharmacol 2022; 11:1029-1044. [PMID: 35638366 PMCID: PMC9381909 DOI: 10.1002/psp4.12811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022] Open
Abstract
Pharmacokinetic/pharmacodynamic (PK/PD) indices making use of area under the curve, maximum concentration, and the duration that in vivo drug concentration is maintained above a critical level are commonly applied to clinical dose prediction from animal efficacy experiments in the infectious disease arena. These indices make suboptimal use of the nonclinical data, and the prediction depends on the shape of the PK profiles in the animals, determined by the species‐specific absorption, distribution, metabolism, and elimination properties, and the dosing regimen used in the efficacy experiments. Motivated by the principle that efficacy is driven by pharmacology, we conducted simulations using a generalized pathogen dynamic model, to assess the properties of an alternative efficacy predictor: the area under the effect curve (AUEC), computed using in vitro PD and in vivo PK. Across a wide range of hypothetical scenarios, the AUEC consistently showed regimen‐independent strong correlation (R2 0.76–0.98) with in vivo efficacy, superior to all other indices. These findings serve as proof of concept that AUEC should be considered in practice as a translation tool for cross‐species dose prediction. Using AUEC for clinical dose prediction could also potentially cut down animal use by reducing or avoiding dose fractionation experiments.
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Affiliation(s)
- Chao Chen
- Clinical Pharmacology Modelling and Simulation GlaxoSmithKline London UK
| | - Silvia Maria Lavezzi
- Clinical Pharmacology, Modelling, and Simulation, Parexel International Dublin Ireland
| | - Laura Iavarone
- Clinical Pharmacology, Modelling, and Simulation Parexel International London UK
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13
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Desikan R, Padmanabhan P, Kierzek AM, van der Graaf PH. Mechanistic Models of COVID-19: Insights into Disease Progression, Vaccines, and Therapeutics. Int J Antimicrob Agents 2022; 60:106606. [PMID: 35588969 PMCID: PMC9110059 DOI: 10.1016/j.ijantimicag.2022.106606] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/27/2022] [Accepted: 05/08/2022] [Indexed: 12/02/2022]
Abstract
The COVID-19 pandemic has severely impacted health systems and economies worldwide. Significant global efforts are therefore ongoing to improve vaccine efficacies, optimize vaccine deployment, and develop new antiviral therapies to combat the pandemic. Mechanistic viral dynamics and quantitative systems pharmacology models of SARS-CoV-2 infection, vaccines, immunomodulatory agents, and antiviral therapeutics have played a key role in advancing our understanding of SARS-CoV-2 pathogenesis and transmission, the interplay between innate and adaptive immunity to influence the outcomes of infection, effectiveness of treatments, mechanisms and performance of COVID-19 vaccines, and the impact of emerging SARS-CoV-2 variants. Here, we review some of the critical insights provided by these models and discuss the challenges ahead.
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Affiliation(s)
- Rajat Desikan
- Quantitative Systems Pharmacology (QSP) group, Certara, Sheffield and Canterbury, United Kingdom.
| | - Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Andrzej M Kierzek
- Quantitative Systems Pharmacology (QSP) group, Certara, Sheffield and Canterbury, United Kingdom; School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Piet H van der Graaf
- Quantitative Systems Pharmacology (QSP) group, Certara, Sheffield and Canterbury, United Kingdom; Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.
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14
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Frank TD. Eigenvalue analysis of SARS-CoV-2 viral load data: illustration for eight COVID-19 patients. INTERNATIONAL JOURNAL OF DATA SCIENCE AND ANALYTICS 2022; 15:281-290. [PMID: 35399335 PMCID: PMC8978770 DOI: 10.1007/s41060-022-00319-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
Abstract
Eigenvalue analysis is an important tool in economics and nonlinear physics to analyze industrial processes and instability phenomena, respectively. A model-based eigenvalue analysis of viral load data from eight symptomatic COVID-19 patients was conducted. The eigenvalues and eigenvectors of the instabilities were determined that give rise to COVID-19. For all eight patients, it was found that the virus dynamics followed the unstable eigenvectors until the viral load reached the respective peak values. At the peak virus values, the virus dynamics branched off from the directions specified by the eigenvectors. The temporal course of the unstable eigenvalues was determined as well. For all patients, it was found that the eigenvalues switched from positive to negative values just when the virus load reached peak values. These findings suggest that the fixed, instability-related eigenvalues and eigenvectors determine initial stages of SARS-CoV-2 infections during which virus load increases. In contrast, the time-dependent eigenvalues show a sign-switching phenomenon that indicates when the virus dynamics switches from the growth stage (increasing virus load) to the decay stage (decreasing virus load). The virus dynamics model was a standard three-variable virus dynamics model frequently used in the literature.
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Affiliation(s)
- Till D. Frank
- Department of Psychological Sciences, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269 USA
- Department of Physics, University of Connecticut, 196 Auditorium Road, Storrs, CT 06269 USA
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15
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Frank T. SARS-coronavirus-2 infections: biological instabilities characterized by order parameters. Phys Biol 2022; 19. [PMID: 35108687 DOI: 10.1088/1478-3975/ac5155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/02/2022] [Indexed: 11/12/2022]
Abstract
A four-variable virus dynamics TIIV model was considered that involves infected cells in an eclipse phase. The state space description of the model was transferred into an amplitude space description which is the appropriate general, nonlinear physics framework to describe instabilities. In this context, the unstable eigenvector or order parameter of the model was determined. Subsequently, a model-based analysis of viral load data from eight symptomatic COVID-19 patients was conducted. For all patients, it was found that the initial SARS-CoV-2 infection evolved along the respective patient-specific order parameter, as expected by theoretical considerations. The order parameter amplitude that described the initial virus multiplication showed doubling times between 30 minutes and 3 hours. Peak viral loads of patients were linearly related to the amplitudes of the patient order parameters. Finally, it was found that the patient order parameters determined qualitatively and quantitatively the relationships between the increases in virus-producing infected cells and infected cells in the eclipse phase. Overall, the study echoes the 40 years old suggestion by Mackey and Glass to consider diseases as instabilities.
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Affiliation(s)
- Till Frank
- University of Connecticut, 406 Babbidge Road, Storrs, Connecticut, 06269, UNITED STATES
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16
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Heitzman-Breen N, Golden J, Vazquez A, Kuchinsky SC, Duggal NK, Ciupe SM. Modeling the dynamics of Usutu virus infection in birds. J Theor Biol 2021; 531:110896. [PMID: 34506809 DOI: 10.1016/j.jtbi.2021.110896] [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: 05/13/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 02/08/2023]
Abstract
Usutu virus is an emerging zoonotic flavivirus causing high avian mortality rates and occasional severe neurological disorders in humans. Several virus strains are co-circulating and the differences in their characteristics and avian pathogenesis levels are still unknown. In this study, we use within-host mathematical models to characterize the mechanisms responsible for virus expansion and clearance in juvenile chickens challenged with four Usutu virus strains. We find heterogeneity between the virus strains, with the time between cell infection and viral production varying between 16 h and 23 h, the infected cell lifespan varying between 48 min and 9.5 h, and the basic reproductive number R0 varying between 12.05 and 19.49. The strains with high basic reproductive number have short infected cell lifespan, indicative of immune responses. The virus strains with low basic reproductive number have lower viral peaks and longer lasting viremia, due to lower infection rates and high infected cell lifespan. We discuss how the host and virus heterogeneities may differently impact the public health threat presented by these virus strains.
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Affiliation(s)
- Nora Heitzman-Breen
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jacob Golden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Ana Vazquez
- National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Epidemiology and Public Health Network of Biomedical Research Centre (CIBERESP), Madrid, Spain
| | - Sarah C Kuchinsky
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Nisha K Duggal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Stanca M Ciupe
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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17
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Tuncer N, Martcheva M. Determining reliable parameter estimates for within-host and within-vector models of Zika virus. JOURNAL OF BIOLOGICAL DYNAMICS 2021; 15:430-454. [PMID: 34463605 DOI: 10.1080/17513758.2021.1970261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
In this paper, we introduce three within-host and one within-vector models of Zika virus. The within-host models are the target cell limited model, the target cell limited model with natural killer (NK) cells class, and a within-host-within-fetus model of a pregnant individual. The within-vector model includes the Zika virus dynamics in the midgut and salivary glands. The within-host models are not structurally identifiable with respect to data on viral load and NK cell counts. After rescaling, the scaled within-host models are locally structurally identifiable. The within-vector model is structurally identifiable with respect to viremia data in the midgut and salivary glands. Using Monte Carlo Simulations, we find that target cell limited model is practically identifiable from data on viremia; the target cell limited model with NK cell class is practically identifiable, except for the rescaled half saturation constant. The within-host-within-fetus model has all fetus-related parameters not practically identifiable without data on the fetus, as well as the rescaled half saturation constant is also not practically identifiable. The remaining parameters are practically identifiable. Finally we find that none of the parameters of the within-vector model is practically identifiable.
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Affiliation(s)
- Necibe Tuncer
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Maia Martcheva
- Department of Mathematics, University of Florida, Gainesville, FL, USA
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18
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Ren M, Wang Y, Luo Y, Yao X, Yang Z, Zhang P, Zhao W, Jiang D. Functionalized Nanoparticles in Prevention and Targeted Therapy of Viral Diseases With Neurotropism Properties, Special Insight on COVID-19. Front Microbiol 2021; 12:767104. [PMID: 34867899 PMCID: PMC8634613 DOI: 10.3389/fmicb.2021.767104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Neurotropic viruses have neural-invasive and neurovirulent properties to damage the central nervous system (CNS), leading to humans' fatal symptoms. Neurotropic viruses comprise a lot of viruses, such as Zika virus (ZIKV), herpes simplex virus (HSV), rabies virus (RABV), and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Effective therapy is needed to prevent infection by these viruses in vivo and in vitro. However, the blood-brain barrier (BBB) usually prevents macromolecules from entering the CNS, which challenges the usage of the traditional probes, antiviral drugs, or neutralizing antibodies in the CNS. Functionalized nanoparticles (NPs) have been increasingly reported in the targeted therapy of neurotropic viruses due to their sensitivity and targeting characteristics. Therefore, the present review outlines efficient functionalized NPs to further understand the recent trends, challenges, and prospects of these materials.
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Affiliation(s)
| | - Yin Wang
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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19
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Marc A, Kerioui M, Blanquart F, Bertrand J, Mitjà O, Corbacho-Monné M, Marks M, Guedj J. Quantifying the relationship between SARS-CoV-2 viral load and infectiousness. eLife 2021; 10:e69302. [PMID: 34569939 PMCID: PMC8476126 DOI: 10.7554/elife.69302] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 09/01/2021] [Indexed: 12/16/2022] Open
Abstract
The relationship between SARS-CoV-2 viral load and infectiousness is poorly known. Using data from a cohort of cases and high-risk contacts, we reconstructed viral load at the time of contact and inferred the probability of infection. The effect of viral load was larger in household contacts than in non-household contacts, with a transmission probability as large as 48% when the viral load was greater than 1010 copies per mL. The transmission probability peaked at symptom onset, with a mean probability of transmission of 29%, with large individual variations. The model also projects the effects of variants on disease transmission. Based on the current knowledge that viral load is increased by two- to eightfold with variants of concern and assuming no changes in the pattern of contacts across variants, the model predicts that larger viral load levels could lead to a relative increase in the probability of transmission of 24% to 58% in household contacts, and of 15% to 39% in non-household contacts.
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Affiliation(s)
| | | | - François Blanquart
- Université de Paris, IAME, INSERMParisFrance
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research UniversityParisFrance
| | | | - Oriol Mitjà
- Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i PujolBadalonaSpain
- Lihir Medical Centre, International SOSLondolovitPapua New Guinea
| | - Marc Corbacho-Monné
- Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i PujolBadalonaSpain
- Hospital Universitari Parc TaulíSabadellSpain
- Facultat de Medicina–Universitat de BarcelonaBarcelonaSpain
| | - Michael Marks
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
- Hospital for Tropical DiseasesLondonUnited Kingdom
- Division of infection and Immunity, University College LondonLondonUnited Kingdom
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20
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Huang Y, Xiao S, Yuan Z. Comparison and Evaluation of Real-Time Taqman PCR for Detection and Quantification of Ebolavirus. Viruses 2021; 13:1575. [PMID: 34452440 PMCID: PMC8402893 DOI: 10.3390/v13081575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 01/12/2023] Open
Abstract
Given that ebolavirus causes severe and frequently lethal disease, its rapid and accurate detection using available and validated methods is essential for controlling infection. Real-time reverse-transcription PCR (RT-PCR) has proven to be an invaluable tool for ebolaviruses diagnostics. Many assays with different targets have been developed, but they have not been externally compared or validated, and limits of detection are not uniformly reported. Here we compared and evaluated the sensitivity, reproducibility and specificity of 23 in-house assays under the same conditions. Our results showed that these assays were highly gene- and species- specific when evaluated using in vitro RNA transcripts and viral RNA, and the potential limits of detection were uniformly reported ranging from 102 to 106 in vitro synthesized RNA transcripts copies perμL and 1-100 TCID50/mL. The comparison of these assays indicated that those targeting the more conservative NP gene could be the better option for EVD case definition and quantitative measurement because of its higher sensitivity for the same species. Our analysis could contribute to the standardization of ebolavirus detection and quantification assays, which can offer a better understanding of the meaning of results across laboratories and time points, as well as make them easy to implement, especially under outbreak conditions.
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Affiliation(s)
- Yi Huang
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan 430020, China
| | - Shuqi Xiao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430020, China;
| | - Zhiming Yuan
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan 430020, China
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21
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Jeong YD, Ejima K, Kim KS, Iwanami S, Bento AI, Fujita Y, Jung IH, Aihara K, Watashi K, Miyazaki T, Wakita T, Iwami S, Ajelli M. Revisiting the guidelines for ending isolation for COVID-19 patients. eLife 2021; 10:e69340. [PMID: 34311842 PMCID: PMC8315804 DOI: 10.7554/elife.69340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/02/2021] [Indexed: 12/20/2022] Open
Abstract
Since the start of the COVID-19 pandemic, two mainstream guidelines for defining when to end the isolation of SARS-CoV-2-infected individuals have been in use: the one-size-fits-all approach (i.e. patients are isolated for a fixed number of days) and the personalized approach (i.e. based on repeated testing of isolated patients). We use a mathematical framework to model within-host viral dynamics and test different criteria for ending isolation. By considering a fixed time of 10 days since symptom onset as the criterion for ending isolation, we estimated that the risk of releasing an individual who is still infectious is low (0-6.6%). However, this policy entails lengthy unnecessary isolations (4.8-8.3 days). In contrast, by using a personalized strategy, similar low risks can be reached with shorter prolonged isolations. The obtained findings provide a scientific rationale for policies on ending the isolation of SARS-CoV-2-infected individuals.
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Affiliation(s)
- Yong Dam Jeong
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
- Department of Mathematics, Pusan National UniversityBusanRepublic of Korea
| | - Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-BloomingtonBloomingtonUnited States
| | - Kwang Su Kim
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - Shoya Iwanami
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-BloomingtonBloomingtonUnited States
| | - Yasuhisa Fujita
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - Il Hyo Jung
- Department of Mathematics, Pusan National UniversityBusanRepublic of Korea
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of TokyoTokyoJapan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious DiseasesTokyoJapan
- Research Center for Drug and Vaccine Development, National Institute of Infectious DiseasesTokyoJapan
- Department of Applied Biological Science, Tokyo University of ScienceNodaJapan
| | - Taiga Miyazaki
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical SciencesNagasakiJapan
- Division of Respirology, Rheumatology, Infectious Diseases, and Neurology, Department of Internal Medicine, Faculty of Medicine, University of MiyazakiMiyazakiJapan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious DiseasesTokyoJapan
| | - Shingo Iwami
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
- Institute of Mathematics for Industry, Kyushu UniversityFukuokaJapan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto UniversityKyotoJapan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR)TokyoJapan
- Science Groove IncFukuokaJapan
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-BloomingtonBloomingtonUnited States
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern UniversityBostonUnited States
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22
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Shi H, Yin J. Kinetics of Asian and African Zika virus lineages over single-cycle and multi-cycle growth in culture: Gene expression, cell killing, virus production, and mathematical modeling. Biotechnol Bioeng 2021; 118:4231-4245. [PMID: 34270089 DOI: 10.1002/bit.27892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 11/07/2022]
Abstract
Since 2014, an Asian lineage of Zika virus has caused outbreaks, and it has been associated with neurological disorders in adults and congenital defects in newborns. The resulting threat of the Zika virus to human health has prompted the development of new vaccines, which have yet to be approved for human use. Vaccines based on the attenuated or chemically inactivated virus will require large-scale production of the intact virus to meet potential global demands. Intact viruses are produced by infecting cultures of susceptible cells, a dynamic process that spans from hours to days and has yet to be optimized. Here, we infected Vero cells adhesively cultured in well-plates with two Zika virus strains: a recently isolated strain from the Asian lineage, and a cell-culture-adapted strain from the African lineage. At different time points post-infection, virus particles in the supernatant were quantified; further, microscopy images were used to quantify cell density and the proportion of cells expressing viral protein. These measurements were performed across multiple replicate samples of one-step infections every four hours over 60 h and for multi-step infections every four to 24 h over 144 h, generating a rich data set. For each set of data, mathematical models were developed to estimate parameters associated with cell infection and virus production. The African-lineage strain was found to produce a 14-fold higher yield than the Asian-lineage strain in one-step growth and a sevenfold higher titer in multi-step growth, suggesting a benefit of cell-culture adaptation for developing a vaccine strain. We found that image-based measurements were critical for discriminating among different models, and different parameters for the two strains could account for the experimentally observed differences. An exponential-distributed delay model performed best in accounting for multi-step infection of the Asian strain, and it highlighted the significant sensitivity of virus titer to the rate of viral degradation, with implications for optimization of vaccine production. More broadly, this study highlights how image-based measurements can contribute to the discrimination of virus-culture models for the optimal production of inactivated and attenuated whole-virus vaccines.
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Affiliation(s)
- Huicheng Shi
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
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23
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Iwanami S, Ejima K, Kim KS, Noshita K, Fujita Y, Miyazaki T, Kohno S, Miyazaki Y, Morimoto S, Nakaoka S, Koizumi Y, Asai Y, Aihara K, Watashi K, Thompson RN, Shibuya K, Fujiu K, Perelson AS, Iwami S, Wakita T. Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study. PLoS Med 2021; 18:e1003660. [PMID: 34228712 PMCID: PMC8259968 DOI: 10.1371/journal.pmed.1003660] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 05/18/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Development of an effective antiviral drug for Coronavirus Disease 2019 (COVID-19) is a global health priority. Although several candidate drugs have been identified through in vitro and in vivo models, consistent and compelling evidence from clinical studies is limited. The lack of evidence from clinical trials may stem in part from the imperfect design of the trials. We investigated how clinical trials for antivirals need to be designed, especially focusing on the sample size in randomized controlled trials. METHODS AND FINDINGS A modeling study was conducted to help understand the reasons behind inconsistent clinical trial findings and to design better clinical trials. We first analyzed longitudinal viral load data for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) without antiviral treatment by use of a within-host virus dynamics model. The fitted viral load was categorized into 3 different groups by a clustering approach. Comparison of the estimated parameters showed that the 3 distinct groups were characterized by different virus decay rates (p-value < 0.001). The mean decay rates were 1.17 d-1 (95% CI: 1.06 to 1.27 d-1), 0.777 d-1 (0.716 to 0.838 d-1), and 0.450 d-1 (0.378 to 0.522 d-1) for the 3 groups, respectively. Such heterogeneity in virus dynamics could be a confounding variable if it is associated with treatment allocation in compassionate use programs (i.e., observational studies). Subsequently, we mimicked randomized controlled trials of antivirals by simulation. An antiviral effect causing a 95% to 99% reduction in viral replication was added to the model. To be realistic, we assumed that randomization and treatment are initiated with some time lag after symptom onset. Using the duration of virus shedding as an outcome, the sample size to detect a statistically significant mean difference between the treatment and placebo groups (1:1 allocation) was 13,603 and 11,670 (when the antiviral effect was 95% and 99%, respectively) per group if all patients are enrolled regardless of timing of randomization. The sample size was reduced to 584 and 458 (when the antiviral effect was 95% and 99%, respectively) if only patients who are treated within 1 day of symptom onset are enrolled. We confirmed the sample size was similarly reduced when using cumulative viral load in log scale as an outcome. We used a conventional virus dynamics model, which may not fully reflect the detailed mechanisms of viral dynamics of SARS-CoV-2. The model needs to be calibrated in terms of both parameter settings and model structure, which would yield more reliable sample size calculation. CONCLUSIONS In this study, we found that estimated association in observational studies can be biased due to large heterogeneity in viral dynamics among infected individuals, and statistically significant effect in randomized controlled trials may be difficult to be detected due to small sample size. The sample size can be dramatically reduced by recruiting patients immediately after developing symptoms. We believe this is the first study investigated the study design of clinical trials for antiviral treatment using the viral dynamics model.
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Affiliation(s)
- Shoya Iwanami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Indiana, United States of America
| | - Kwang Su Kim
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Koji Noshita
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhisa Fujita
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Taiga Miyazaki
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | | | - Yoshitsugu Miyazaki
- Department of Chemotherapy & Mycoses and Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Shinji Nakaoka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Yoshiki Koizumi
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Yusuke Asai
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Robin N. Thompson
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Kenji Shibuya
- Institute for Population Health, King’s College London, London, United Kingdom
| | - Katsuhito Fujiu
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Advanced Cardiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Alan S. Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
- Science Groove Inc., Fukuoka, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
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24
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Ejima K, Kim KS, Iwanami S, Fujita Y, Li M, Zoh RS, Aihara K, Miyazaki T, Wakita T, Iwami S. Time variation in the probability of failing to detect a case of polymerase chain reaction testing for SARS-CoV-2 as estimated from a viral dynamics model. J R Soc Interface 2021; 18:20200947. [PMID: 33878277 PMCID: PMC8086922 DOI: 10.1098/rsif.2020.0947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Viral tests including polymerase chain reaction (PCR) tests are recommended to diagnose COVID-19 infection during the acute phase of infection. A test should have high sensitivity; however, the sensitivity of the PCR test is highly influenced by viral load, which changes over time. Because it is difficult to collect data before the onset of symptoms, the current literature on the sensitivity of the PCR test before symptom onset is limited. In this study, we used a viral dynamics model to track the probability of failing to detect a case of PCR testing over time, including the presymptomatic period. The model was parametrized by using longitudinal viral load data collected from 30 hospitalized patients. The probability of failing to detect a case decreased toward symptom onset, and the lowest probability was observed 2 days after symptom onset and increased afterwards. The probability on the day of symptom onset was 1.0% (95% CI: 0.5 to 1.9) and that 2 days before symptom onset was 60.2% (95% CI: 57.1 to 63.2). Our study suggests that the diagnosis of COVID-19 by PCR testing should be done carefully, especially when the test is performed before or way after symptom onset. Further study is needed of patient groups with potentially different viral dynamics, such as asymptomatic cases.
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Affiliation(s)
- Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN 47405, USA
| | - Kwang Su Kim
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Shoya Iwanami
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Yasuhisa Fujita
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN 47405, USA
| | - Roger S Zoh
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN 47405, USA
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo, Japan
| | - Taiga Miyazaki
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan.,MIRAI, JST, Saitama, Japan.,Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Science Groove Inc., Fukuoka, Japan
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25
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Forde JE, Ciupe SM. Quantification of the Tradeoff between Test Sensitivity and Test Frequency in a COVID-19 Epidemic-A Multi-Scale Modeling Approach. Viruses 2021; 13:457. [PMID: 33799660 PMCID: PMC7999334 DOI: 10.3390/v13030457] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/20/2022] Open
Abstract
Control strategies that employ real time polymerase chain reaction (RT-PCR) tests for the diagnosis and surveillance of COVID-19 epidemic are inefficient in fighting the epidemic due to high cost, delays in obtaining results, and the need of specialized personnel and equipment for laboratory processing. Cheaper and faster alternatives, such as antigen and paper-strip tests, have been proposed. They return results rapidly, but have lower sensitivity thresholds for detecting virus. To quantify the effects of the tradeoffs between sensitivity, cost, testing frequency, and delay in test return on the overall course of an outbreak, we built a multi-scale immuno-epidemiological model that connects the virus profile of infected individuals with transmission and testing at the population level. We investigated various randomized testing strategies and found that, for fixed testing capacity, lower sensitivity tests with shorter return delays slightly flatten the daily incidence curve and delay the time to the peak daily incidence. However, compared with RT-PCR testing, they do not always reduce the cumulative case count at half a year into the outbreak. When testing frequency is increased to account for the lower cost of less sensitive tests, we observe a large reduction in cumulative case counts, from 55.4% to as low as 1.22% half a year into the outbreak. The improvement is preserved even when the testing budget is reduced by one half or one third. Our results predict that surveillance testing that employs low-sensitivity tests at high frequency is an effective tool for epidemic control.
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Affiliation(s)
- Jonathan E. Forde
- Department of Mathematics and Computer Sciences, Hobart and William Smith Colleges, Geneva, NY 14456, USA
| | - Stanca M. Ciupe
- Department of Mathematics, Virginia Tech, Blacksburg, VA 24060, USA;
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26
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Perelson AS, Ke R. Mechanistic Modeling of SARS-CoV-2 and Other Infectious Diseases and the Effects of Therapeutics. Clin Pharmacol Ther 2021; 109:829-840. [PMID: 33410134 DOI: 10.1002/cpt.2160] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022]
Abstract
Modern viral kinetic modeling and its application to therapeutics is a field that attracted the attention of the medical, pharmaceutical, and modeling communities during the early days of the AIDS epidemic. Its successes led to applications of modeling methods not only to HIV but a plethora of other viruses, such as hepatitis C virus (HCV), hepatitis B virus and cytomegalovirus, which along with HIV cause chronic diseases, and viruses such as influenza, respiratory syncytial virus, West Nile virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which generally cause acute infections. Here we first review the historical development of mathematical models to understand HIV and HCV infections and the effects of treatment by fitting the models to clinical data. We then focus on recent efforts and contributions of applying these models towards understanding SARS-CoV-2 infection and highlight outstanding questions where modeling can provide crucial insights and help to optimize nonpharmaceutical and pharmaceutical interventions of the coronavirus disease 2019 (COVID-19) pandemic. The review is written from our personal perspective emphasizing the power of simple target cell limited models that provided important insights and then their evolution into more complex models that captured more of the virology and immunology. To quote Albert Einstein, "Everything should be made as simple as possible, but not simpler," and this idea underlies the modeling we describe below.
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Affiliation(s)
- Alan S Perelson
- Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, New Mexico, USA.,New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Ruian Ke
- Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, New Mexico, USA.,New Mexico Consortium, Los Alamos, New Mexico, USA
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27
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Gonçalves A, Maisonnasse P, Donati F, Albert M, Behillil S, Contreras V, Naninck T, Marlin R, Solas C, Pizzorno A, Lemaitre J, Kahlaoui N, Terrier O, Ho Tsong Fang R, Enouf V, Dereuddre-Bosquet N, Brisebarre A, Touret F, Chapon C, Hoen B, Lina B, Rosa Calatrava M, de Lamballerie X, Mentré F, Le Grand R, van der Werf S, Guedj J. SARS-CoV-2 viral dynamics in non-human primates. PLoS Comput Biol 2021; 17:e1008785. [PMID: 33730053 PMCID: PMC8007039 DOI: 10.1371/journal.pcbi.1008785] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/29/2021] [Accepted: 02/11/2021] [Indexed: 01/08/2023] Open
Abstract
Non-human primates infected with SARS-CoV-2 exhibit mild clinical signs. Here we used a mathematical model to characterize in detail the viral dynamics in 31 cynomolgus macaques for which nasopharyngeal and tracheal viral load were frequently assessed. We identified that infected cells had a large burst size (>104 virus) and a within-host reproductive basic number of approximately 6 and 4 in nasopharyngeal and tracheal compartment, respectively. After peak viral load, infected cells were rapidly lost with a half-life of 9 hours, with no significant association between cytokine elevation and clearance, leading to a median time to viral clearance of 10 days, consistent with observations in mild human infections. Given these parameter estimates, we predict that a prophylactic treatment blocking 90% of viral production or viral infection could prevent viral growth. In conclusion, our results provide estimates of SARS-CoV-2 viral kinetic parameters in an experimental model of mild infection and they provide means to assess the efficacy of future antiviral treatments.
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Affiliation(s)
| | - Pauline Maisonnasse
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Flora Donati
- Unité de Génétique Moléculaire des Virus à ARN, GMVR: Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France
- Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Mélanie Albert
- Unité de Génétique Moléculaire des Virus à ARN, GMVR: Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France
- Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Sylvie Behillil
- Unité de Génétique Moléculaire des Virus à ARN, GMVR: Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France
- Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Vanessa Contreras
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Thibaut Naninck
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Romain Marlin
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Caroline Solas
- Aix-Marseille Univ, APHM, Unité des Virus Emergents (UVE) IRD 190, INSERM 1207, Laboratoire de Pharmacocinétique et Toxicologie, Hôpital La Timone, Marseille, France
| | - Andres Pizzorno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Julien Lemaitre
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Nidhal Kahlaoui
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Raphael Ho Tsong Fang
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Vincent Enouf
- Unité de Génétique Moléculaire des Virus à ARN, GMVR: Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France
- Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
- Plate-forme de microbiologie mutualisée (P2M), Pasteur International Bioresources Network (PIBnet), Institut Pasteur, Paris, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Angela Brisebarre
- Unité de Génétique Moléculaire des Virus à ARN, GMVR: Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France
- Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Franck Touret
- Unité des Virus Emergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection, Marseille, France
| | - Catherine Chapon
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Bruno Hoen
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France
| | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Laboratoire de Virologie, Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Manuel Rosa Calatrava
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Xavier de Lamballerie
- Unité des Virus Emergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection, Marseille, France
| | | | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, GMVR: Institut Pasteur, UMR CNRS 3569, Université de Paris, Paris, France
- Centre National de Référence des Virus des infections respiratoires (dont la grippe), Institut Pasteur, Paris, France
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28
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Kim KS, Ejima K, Iwanami S, Fujita Y, Ohashi H, Koizumi Y, Asai Y, Nakaoka S, Watashi K, Aihara K, Thompson RN, Ke R, Perelson AS, Iwami S. A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2. PLoS Biol 2021; 19:e3001128. [PMID: 33750978 PMCID: PMC7984623 DOI: 10.1371/journal.pbio.3001128] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
The scientific community is focused on developing antiviral therapies to mitigate the impacts of the ongoing novel coronavirus disease 2019 (COVID-19) outbreak. This will be facilitated by improved understanding of viral dynamics within infected hosts. Here, using a mathematical model in combination with published viral load data, we compare within-host viral dynamics of SARS-CoV-2 with analogous dynamics of MERS-CoV and SARS-CoV. Our quantitative analyses using a mathematical model revealed that the within-host reproduction number at symptom onset of SARS-CoV-2 was statistically significantly larger than that of MERS-CoV and similar to that of SARS-CoV. In addition, the time from symptom onset to the viral load peak for SARS-CoV-2 infection was shorter than those of MERS-CoV and SARS-CoV. These findings suggest the difficulty of controlling SARS-CoV-2 infection by antivirals. We further used the viral dynamics model to predict the efficacy of potential antiviral drugs that have different modes of action. The efficacy was measured by the reduction in the viral load area under the curve (AUC). Our results indicate that therapies that block de novo infection or virus production are likely to be effective if and only if initiated before the viral load peak (which appears 2-3 days after symptom onset), but therapies that promote cytotoxicity of infected cells are likely to have effects with less sensitivity to the timing of treatment initiation. Furthermore, combining a therapy that promotes cytotoxicity and one that blocks de novo infection or virus production synergistically reduces the AUC with early treatment. Our unique modeling approach provides insights into the pathogenesis of SARS-CoV-2 and may be useful for development of antiviral therapies.
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Affiliation(s)
- Kwang Su Kim
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health–Bloomington, Bloomington, Indiana, United States of America
| | - Shoya Iwanami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhisa Fujita
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Hirofumi Ohashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiki Koizumi
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Yusuke Asai
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinji Nakaoka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- JST-Mirai, Japan Science and Technology Agency, Saitama, Japan
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, University of Tokyo Institutes for Advanced Study, University of Tokyo, Tokyo, Japan
| | - Robin N. Thompson
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Ruian Ke
- New Mexico Consortium, Los Alamos, New Mexico, United States of America
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Perelson
- New Mexico Consortium, Los Alamos, New Mexico, United States of America
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
- JST-Mirai, Japan Science and Technology Agency, Saitama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
- Science Groove, Fukuoka, Japan
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29
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Maisonnasse P, Aldon Y, Marc A, Marlin R, Dereuddre-Bosquet N, Kuzmina NA, Freyn AW, Snitselaar JL, Gonçalves A, Caniels TG, Burger JA, Poniman M, Chesnais V, Diry S, Iershov A, Ronk AJ, Jangra S, Rathnasinghe R, Brouwer P, Bijl T, van Schooten J, Brinkkemper M, Liu H, Yuan M, Mire CE, van Breemen MJ, Contreras V, Naninck T, Lemaître J, Kahlaoui N, Relouzat F, Chapon C, Ho Tsong Fang R, McDanal C, Osei-Twum M, St-Amant N, Gagnon L, Montefiori DC, Wilson IA, Ginoux E, de Bree GJ, García-Sastre A, Schotsaert M, Coughlan L, Bukreyev A, van der Werf S, Guedj J, Sanders RW, van Gils MJ, Le Grand R. COVA1-18 neutralizing antibody protects against SARS-CoV-2 in three preclinical models. RESEARCH SQUARE 2021:rs.3.rs-235272. [PMID: 33619476 PMCID: PMC7899470 DOI: 10.21203/rs.3.rs-235272/v1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
One year into the Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), effective treatments are still needed 1-3 . Monoclonal antibodies, given alone or as part of a therapeutic cocktail, have shown promising results in patients, raising the hope that they could play an important role in preventing clinical deterioration in severely ill or in exposed, high risk individuals 4-6 . Here, we evaluated the prophylactic and therapeutic effect of COVA1-18 in vivo , a neutralizing antibody isolated from a convalescent patient 7 and highly potent against the B.1.1.7. isolate 8,9 . In both prophylactic and therapeutic settings, SARS-CoV-2 remained undetectable in the lungs of COVA1-18 treated hACE2 mice. Therapeutic treatment also caused a dramatic reduction in viral loads in the lungs of Syrian hamsters. When administered at 10 mg kg - 1 one day prior to a high dose SARS-CoV-2 challenge in cynomolgus macaques, COVA1-18 had a very strong antiviral activity in the upper respiratory compartments with an estimated reduction in viral infectivity of more than 95%, and prevented lymphopenia and extensive lung lesions. Modelling and experimental findings demonstrate that COVA1-18 has a strong antiviral activity in three different preclinical models and could be a valuable candidate for further clinical evaluation.
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Affiliation(s)
- P Maisonnasse
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Y Aldon
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - A Marc
- Université de Paris, INSERM, IAME, F-75018 Paris, France
| | - R Marlin
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - N Dereuddre-Bosquet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - N A Kuzmina
- Department of Pathology, University of Texas Medical Branch at Galveston, Texas, USA
- Galveston National Laboratory, Texas, USA
| | - A W Freyn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York (NY), USA
| | - J L Snitselaar
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - A Gonçalves
- Université de Paris, INSERM, IAME, F-75018 Paris, France
| | - T G Caniels
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - J A Burger
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - M Poniman
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - V Chesnais
- Life and Soft, 92350 Le Plessis-Robinson, France
| | - S Diry
- Life and Soft, 92350 Le Plessis-Robinson, France
| | - A Iershov
- Life and Soft, 92350 Le Plessis-Robinson, France
| | - A J Ronk
- Department of Pathology, University of Texas Medical Branch at Galveston, Texas, USA
- Galveston National Laboratory, Texas, USA
| | - S Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York (NY), USA
| | - R Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York (NY), USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (NY), USA
| | - Pjm Brouwer
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - Tpl Bijl
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - J van Schooten
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - M Brinkkemper
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - H Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - M Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - C E Mire
- Galveston National Laboratory, Texas, USA
- Department of Microbiology, University of Texas Medical Branch at Galveston, Texas, USA
| | - M J van Breemen
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - V Contreras
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - T Naninck
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - J Lemaître
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - N Kahlaoui
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - F Relouzat
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - C Chapon
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - R Ho Tsong Fang
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - C McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | | | | | - D C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - I A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - E Ginoux
- Life and Soft, 92350 Le Plessis-Robinson, France
| | - G J de Bree
- Internal Medicine of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - A García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York (NY), USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York (NY), USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York (NY), USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York (NY), USA
| | - M Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York (NY), USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York (NY), USA
| | - L Coughlan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York (NY), USA
- University of Maryland School of Medicine, Department of Microbiology and Immunology and Center for Vaccine Development and Global Health (CVD), 685 W. Baltimore Street, HSF1, Office #380E, Baltimore, MD 21201
| | - A Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, Texas, USA
- Galveston National Laboratory, Texas, USA
- Department of Microbiology, University of Texas Medical Branch at Galveston, Texas, USA
| | - S van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - J Guedj
- Université de Paris, INSERM, IAME, F-75018 Paris, France
| | - R W Sanders
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - M J van Gils
- Departments of Medical Microbiology of the Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ, Amsterdam, The Netherlands
| | - R Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
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Best K, Barouch DH, Guedj J, Ribeiro RM, Perelson AS. Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference. PLoS Comput Biol 2021; 17:e1008564. [PMID: 33471814 PMCID: PMC7817008 DOI: 10.1371/journal.pcbi.1008564] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/27/2020] [Indexed: 12/11/2022] Open
Abstract
Experimental Zika virus infection in non-human primates results in acute viral load dynamics that can be well-described by mathematical models. The inoculum dose that would be received in a natural infection setting is likely lower than the experimental infections and how this difference affects the viral dynamics and immune response is unclear. Here we study a dataset of experimental infection of non-human primates with a range of doses of Zika virus. We develop new models of infection incorporating both an innate immune response and viral interference with that response. We find that such a model explains the data better than models with no interaction between virus and the immune response. We also find that larger inoculum doses lead to faster dynamics of infection, but approximately the same total amount of viral production. The relationship between the infecting dose of a pathogen and the subsequent viral dynamics is unclear in many disease settings, and this relationship has implications for both the timing and the required efficacy of antiviral therapy. Since experimental challenge studies often employ higher doses of virus than would generally be present in natural infection assessment of this relationship is particularly important for translation of findings. In this study we used mathematical modelling of viral load data from a multi-dose study of Zika virus infection in a macaque model to describe the impact of varying the dose of Zika virus on model parameters, and developed a novel mathematical model incorporating viral interference with the innate immune response.
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Affiliation(s)
- Katharine Best
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Laboratório de Biomatemática, Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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Patel K, Dodds M, Gonçalves A, Kamal MA, Rayner CR, Kirkpatrick CM, Smith PF. Using in silico viral kinetic models to guide therapeutic strategies during a pandemic: An example in SARS-CoV-2. Br J Clin Pharmacol 2021; 87:3425-3438. [PMID: 33373059 DOI: 10.1111/bcp.14718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/01/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022] Open
Abstract
AIMS We propose the use of in silico mathematical models to provide insights that optimize therapeutic interventions designed to effectively treat respiratory infection during a pandemic. A modelling and simulation framework is provided using SARS-CoV-2 as an example, considering applications for both treatment and prophylaxis. METHODS A target cell-limited model was used to quantify the viral infection dynamics of SARS-CoV-2 in a pooled population of 105 infected patients. Parameter estimates from the resulting model were used to simulate and compare the impact of various interventions against meaningful viral load endpoints. RESULTS Robust parameter estimates were obtained for the basic reproduction number, viral release rate and infected-cell mortality from the infection model. These estimates were informed by the largest dataset currently available for SARS-CoV-2 viral time course. The utility of this model was demonstrated using simulations, which hypothetically introduced inhibitory or stimulatory drug mechanisms at various target sites within the viral life-cycle. We show that early intervention is crucial to achieving therapeutic benefit when monotherapy is administered. In contrast, combination regimens of two or three drugs may provide improved outcomes if treatment is initiated late. The latter is relevant to SARS-CoV-2, where the period between infection and symptom onset is relatively long. CONCLUSIONS The use of in silico models can provide viral load predictions that can rationalize therapeutic strategies against an emerging viral pathogen.
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Lingas G, Rosenke K, Safronetz D, Guedj J. Lassa viral dynamics in non-human primates treated with favipiravir or ribavirin. PLoS Comput Biol 2021; 17:e1008535. [PMID: 33411731 PMCID: PMC7817048 DOI: 10.1371/journal.pcbi.1008535] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 01/20/2021] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Lassa fever is an haemorrhagic fever caused by Lassa virus (LASV). There is no vaccine approved against LASV and the only recommended antiviral treatment relies on ribavirin, despite limited evidence of efficacy. Recently, the nucleotide analogue favipiravir showed a high antiviral efficacy, with 100% survival obtained in an otherwise fully lethal non-human primate (NHP) model of Lassa fever. However the mechanism of action of the drug is not known and the absence of pharmacokinetic data limits the translation of these results to the human setting. Here we aimed to better understand the antiviral effect of favipiravir by developping the first mathematical model recapitulating Lassa viral dynamics and treatment. We analyzed the viral dynamics in 24 NHPs left untreated or treated with ribavirin or favipiravir, and we put the results in perspective with those obtained with the same drugs in the context of Ebola infection. Our model estimates favipiravir EC50 in vivo to 2.89 μg.mL-1, which is much lower than what was found against Ebola virus. The main mechanism of action of favipiravir was to decrease virus infectivity, with an efficacy of 91% at the highest dose. Based on our knowledge acquired on the drug pharmacokinetics in humans, our model predicts that favipiravir doses larger than 1200 mg twice a day should have the capability to strongly reduce the production infectious virus and provide a milestone towards a future use in humans.
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Affiliation(s)
| | - Kyle Rosenke
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, USA
| | - David Safronetz
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Zou X, Yuan M, Zhang T, Zheng N, Wu Z. EVs Containing Host Restriction Factor IFITM3 Inhibited ZIKV Infection of Fetuses in Pregnant Mice through Trans-placenta Delivery. Mol Ther 2021; 29:176-190. [PMID: 33002418 PMCID: PMC7791082 DOI: 10.1016/j.ymthe.2020.09.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 08/09/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Zika virus (ZIKV) infection can lead to neurological complications and fetal defects, and it has attracted global public health concerns. Effective treatment for ZIKV infection remains elusive, and a preventative vaccine is not yet available. Therapeutics for fetuses need to overcome placenta barriers to reach the fetuses and require higher safety standards. In the present study, we engineered mammalian extracellular vesicles (EVs) to deliver a host restriction factor, interferon-induced transmembrane protein 3 (IFITM3), for the treatment of ZIKV infection. Our results demonstrated that the IFITM3-containing EVs (IFITM3-Exos) suppressed ZIKV viremia by a 2-log reduction in pregnant mice. Moreover, the engineered EVs effectively delivered IFITM3 protein across the placental barrier and suppressed ZIKV in the fetuses with significant reduction of viremia in key fetal organs as measured by quantitative real-time PCR. Mechanistic study showed that IFITM3 was delivered to late endosomes/lysosomes where it inhibited viral entry into the host cells. Our study demonstrated that EVs could act as a cross-placenta drug delivery vehicle to the fetus, and IFITM3, an endogenous restriction factor, is a potential treatment for ZIKV infection during pregnancy.
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Affiliation(s)
- Xue Zou
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Meng Yuan
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Tongyu Zhang
- Model Animal Research Center, Nanjing University, Nanjing, China
| | - Nan Zheng
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China; Medical School, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China.
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China; Medical School, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China.
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Lord JS, Bonsall MB. The evolutionary dynamics of viruses: virion release strategies, time delays and fitness minima. Virus Evol 2021; 7:veab039. [PMID: 34221452 PMCID: PMC8242231 DOI: 10.1093/ve/veab039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viruses exhibit a diverse array of strategies for infecting host cells and for virion release after replication. Cell exit strategies generally involve either budding from the cell membrane or killing the host cell. The conditions under which either is at a selective advantage is a key question in the evolutionary theory of viruses, with the outcome having potentially important impacts on the course of infection and pathogenicity. Although a plethora of external factors will influence the fitness of either strategy; here, we focus just on the effects of the physical properties of the system. We develop theoretical approaches to assess the effects of the time delays between initial infection and virion release. We show that the length of the delay before apoptosis is an important trait in virus evolutionary dynamics. Our results show that for a fixed time to apoptosis, intermediate delays lead to virus fitness that is lower than short times to apoptosis - leading to an apoptotic strategy - and long times to apoptosis - leading to a budding strategy at the between-cell level. At fitness minima, selection is expected to be disruptive and the potential for adaptive radiation in virus strategies is feasible. Hence, the physical properties of the system are sufficient to explain the existence of both budding and virus-induced apoptosis. The fitness functions presented here provide a formal basis for further work focusing on the evolutionary implications of trade-offs between time delays, intracellular replication and resulting mutation rates.
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Affiliation(s)
- Jennifer S Lord
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Michael B Bonsall
- Mathematical Ecology Research Group, Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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Lequime S, Dehecq JS, Matheus S, de Laval F, Almeras L, Briolant S, Fontaine A. Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus. PLoS Pathog 2020; 16:e1009068. [PMID: 33382858 PMCID: PMC7774846 DOI: 10.1371/journal.ppat.1009068] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/14/2020] [Indexed: 01/01/2023] Open
Abstract
Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can transmit ZIKV experimentally and was suspected to be a ZIKV vector in Central Africa, the potential of this species to sustain virus transmission was yet to be uncovered until the end of 2019, when several autochthonous transmissions of the virus vectored by Ae. albopictus occurred in France. Aside from these few locally acquired ZIKV infections, most territories colonized by Ae. albopictus have been spared so far. The risk level of ZIKV emergence in these areas remains however an open question. To assess Ae. albopictus' vector potential for ZIKV and identify key virus outbreak predictors, we built a complete framework using the complementary combination of (i) dose-dependent experimental Ae. albopictus exposure to ZIKV followed by time-dependent assessment of infection and systemic infection rates, (ii) modeling of intra-human ZIKV viremia dynamics, and (iii) in silico epidemiological simulations using an Agent-Based Model. The highest risk of transmission occurred during the pre-symptomatic stage of the disease, at the peak of viremia. At this dose, mosquito infection probability was estimated to be 20%, and 21 days were required to reach the median systemic infection rates. Mosquito population origin, either temperate or tropical, had no impact on infection rates or intra-host virus dynamic. Despite these unfavorable characteristics for transmission, Ae. albopictus was still able to trigger and yield large outbreaks in a simulated environment in the presence of sufficiently high mosquito biting rates. Our results reveal a low but existing epidemic potential of Ae. albopictus for ZIKV, that might explain the absence of large scale ZIKV epidemics so far in territories occupied only by Ae. albopictus. They nevertheless support active surveillance and eradication programs in these territories to maintain the risk of emergence to a low level.
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Affiliation(s)
- Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Jean-Sébastien Dehecq
- French Ministry of Health, Agence Régionale de Santé de La Réunion, Vector control Unit, La Reunion Island, Saint-Denis, France
| | - Séverine Matheus
- Laboratory of Virology, National Reference Center for Arboviruses, Institut Pasteur, Guyane Française, Cayenne, France
- Environment and infections risks unit, Institut Pasteur, Paris, France
| | - Franck de Laval
- SSA, Service de Santé des Armées, CESPA, Centre d’épidémiologie et de santé publique des armées, Marseille, France
- Aix Marseille Univ, INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, Marseille, France
| | - Lionel Almeras
- Unité Parasitologie et Entomologie, Département Microbiologie et maladies infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, UMR Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sébastien Briolant
- Unité Parasitologie et Entomologie, Département Microbiologie et maladies infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, UMR Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Albin Fontaine
- Unité Parasitologie et Entomologie, Département Microbiologie et maladies infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, UMR Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Pharmacokinetic Basis of the Hydroxychloroquine Response in COVID-19: Implications for Therapy and Prevention. Eur J Drug Metab Pharmacokinet 2020; 45:715-723. [PMID: 32780273 PMCID: PMC7418279 DOI: 10.1007/s13318-020-00640-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND OBJECTIVES Chloroquine/hydroxychloroquine has recently been the subject of intense debate regarding its potential antiviral activity against SARS-Cov-2, the etiologic agent of COVID-19. Some report possible curative effects; others do not. Therefore, the objective of this study was to simulate possible scenarios of response to hydroxychloroquine in COVID-19 patients using mathematical modeling. METHODS To shed some light on this controversial topic, we simulated hydroxychloroquine-based interventions on virus/host cell dynamics using a basic system of previously published differential equations. Mathematical modeling was implemented using Python programming language v 3.7. RESULTS According to mathematical modeling, hydroxychloroquine may have an impact on the amplitude of the viral load peak and viral clearance if the drug is administered early enough (i.e., when the virus is still confined within the pharyngeal cavity). The effects of chloroquine/hydroxychloroquine may be fully explained only when also considering the capacity of this drug to increase the death rate of SARS-CoV-2-infected cells, in this case by enhancing the cell-mediated immune response. CONCLUSIONS These considerations may not only be applied to chloroquine/hydroxychloroquine but may have more general implications for development of anti-COVID-19 combination therapies and prevention strategies through an increased death rate of the infected cells.
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Low Aedes aegypti Vector Competence for Zika Virus from Viremic Rhesus Macaques. Viruses 2020; 12:v12121345. [PMID: 33255150 PMCID: PMC7759330 DOI: 10.3390/v12121345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/13/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
Despite worldwide efforts to understand the transmission dynamics of Zika virus (ZIKV), scanty evaluation has been made on the vector competence of Aedes aegypti fed directly on viremic human and non-human primates (NHPs). We blood-fed Ae. aegypti from two districts in Rio de Janeiro on six ZIKV infected pregnant rhesus macaques at several time points, half of which were treated with Sofosbuvir (SOF). Mosquitoes were analyzed for vector competence after 3, 7 and 14 days of incubation. Although viremia extended up to eight days post monkey inoculation, only mosquitoes fed on the day of the peak of viremia, recorded on day two, became infected. The influence of SOF treatment could not be assessed because the drug was administered just after mosquito feeding on day two. The global infection, dissemination and transmission rates were quite low (4.09%, 1.91% and 0.54%, respectively); no mosquito was infected when viremia was below 1.26 × 105 RNA copies/mL. In conclusion, Ae. aegypti vector competence for ZIKV from macaques is low, likely to be due to low viral load and the short duration of ZIKV viremia in primates suitable for infecting susceptible mosquitoes. If ZIKV infection in human and macaques behaves similarly, transmission of the Zika virus in nature is most strongly affected by vector density.
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Liao LE, Carruthers J, Smither SJ, Weller SA, Williamson D, Laws TR, García-Dorival I, Hiscox J, Holder BP, Beauchemin CAA, Perelson AS, López-García M, Lythe G, Barr JN, Molina-París C. Quantification of Ebola virus replication kinetics in vitro. PLoS Comput Biol 2020; 16:e1008375. [PMID: 33137116 PMCID: PMC7660928 DOI: 10.1371/journal.pcbi.1008375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 11/12/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
Mathematical modelling has successfully been used to provide quantitative descriptions of many viral infections, but for the Ebola virus, which requires biosafety level 4 facilities for experimentation, modelling can play a crucial role. Ebola virus modelling efforts have primarily focused on in vivo virus kinetics, e.g., in animal models, to aid the development of antivirals and vaccines. But, thus far, these studies have not yielded a detailed specification of the infection cycle, which could provide a foundational description of the virus kinetics and thus a deeper understanding of their clinical manifestation. Here, we obtain a diverse experimental data set of the Ebola virus infection in vitro, and then make use of Bayesian inference methods to fully identify parameters in a mathematical model of the infection. Our results provide insights into the distribution of time an infected cell spends in the eclipse phase (the period between infection and the start of virus production), as well as the rate at which infectious virions lose infectivity. We suggest how these results can be used in future models to describe co-infection with defective interfering particles, which are an emerging alternative therapeutic.
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Affiliation(s)
- Laura E. Liao
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA 87545
| | - Jonathan Carruthers
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | | | | | - Simon A. Weller
- Defence Science and Technology Laboratory, Salisbury SP4 0JQ, UK
| | - Diane Williamson
- Defence Science and Technology Laboratory, Salisbury SP4 0JQ, UK
| | - Thomas R. Laws
- Defence Science and Technology Laboratory, Salisbury SP4 0JQ, UK
| | - Isabel García-Dorival
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Julian Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Benjamin P. Holder
- Department of Physics, Grand Valley State University, Allendale, MI, USA 49401
| | - Catherine A. A. Beauchemin
- Department of Physics, Ryerson University, Toronto, ON, Canada M5B 2K3
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) Research Program at RIKEN, Wako, Saitama, Japan, 351-0198
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA 87545
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - John N. Barr
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
- * E-mail:
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39
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Wang S, Pan Y, Wang Q, Miao H, Brown AN, Rong L. Modeling the viral dynamics of SARS-CoV-2 infection. Math Biosci 2020; 328:108438. [PMID: 32771304 PMCID: PMC7409942 DOI: 10.1016/j.mbs.2020.108438] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19), an infectious disease caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading and causing the global coronavirus pandemic. The viral dynamics of SARS-CoV-2 infection have not been quantitatively investigated. In this paper, we use mathematical models to study the pathogenic features of SARS-CoV-2 infection by examining the interaction between the virus, cells and immune responses. Models are fit to the data of SARS-CoV-2 infection in patients and non-human primates. Data fitting and numerical simulation show that viral dynamics of SARS-CoV-2 infection have a few distinct stages. In the initial stage, viral load increases rapidly and reaches the peak, followed by a plateau phase possibly generated by lymphocytes as a secondary target of infection. In the last stage, viral load declines due to the emergence of adaptive immune responses. When the initiation of seroconversion is late or slow, the model predicts viral rebound and prolonged viral persistence, consistent with the observation in non-human primates. Using the model we also evaluate the effect of several potential therapeutic interventions for SARS-CoV-2 infection. Model simulation shows that anti-inflammatory treatments or antiviral drugs combined with interferon are effective in reducing the duration of the viral plateau phase and diminishing the time to recovery. These results provide insights for understanding the infection dynamics and might help develop treatment strategies against COVID-19.
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Affiliation(s)
- Sunpeng Wang
- Department of Biology, New York University, New York, NY 10012, United States of America
| | - Yang Pan
- Beijing Center for Disease Prevention and Control, Beijing 100013, China; Beijing Research Center for Preventive Medicine, Beijing, China; School of Public Health, Capital Medical University, Beijing, China
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing 100013, China; Beijing Research Center for Preventive Medicine, Beijing, China
| | - Hongyu Miao
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center at Houston, TX, 77030, United States of America
| | - Ashley N Brown
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, United States of America
| | - Libin Rong
- Department of Mathematics, University of Florida, Gainesville, FL 32611, United States of America.
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40
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Gonçalves A, Bertrand J, Ke R, Comets E, de Lamballerie X, Malvy D, Pizzorno A, Terrier O, Rosa Calatrava M, Mentré F, Smith P, Perelson AS, Guedj J. Timing of Antiviral Treatment Initiation is Critical to Reduce SARS-CoV-2 Viral Load. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2020; 9:509-514. [PMID: 32558354 PMCID: PMC7323384 DOI: 10.1002/psp4.12543] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022]
Abstract
We modeled the viral dynamics of 13 untreated patients infected with severe acute respiratory syndrome‐coronavirus 2 to infer viral growth parameters and predict the effects of antiviral treatments. In order to reduce peak viral load by more than two logs, drug efficacy needs to be > 90% if treatment is administered after symptom onset; an efficacy of 60% could be sufficient if treatment is initiated before symptom onset. Given their pharmacokinetic/pharmacodynamic properties, current investigated drugs may be in a range of 6–87% efficacy. They may help control virus if administered very early, but may not have a major effect in severely ill patients.
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Affiliation(s)
| | | | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Xavier de Lamballerie
- Institut Hospitalo-Universitaire Méditerranée Infection, UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Marseille, France
| | - Denis Malvy
- Inserm, UMR 1219, Université de Bordeaux, Bordeaux, France.,Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Manuel Rosa Calatrava
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | | | - Patrick Smith
- Certara, Integrated Drug Development, Princeton, New Jersey, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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41
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Vijayvargiya P, Esquer Garrigos Z, Castillo Almeida NE, Gurram PR, Stevens RW, Razonable RR. Treatment Considerations for COVID-19: A Critical Review of the Evidence (or Lack Thereof). Mayo Clin Proc 2020; 95:1454-1466. [PMID: 32561148 PMCID: PMC7190528 DOI: 10.1016/j.mayocp.2020.04.027] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 01/08/2023]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 is causing a worldwide pandemic that may lead to a highly morbid and potentially fatal coronavirus disease 2019 (COVID-19). There is currently no drug that has been proven as an effective therapy for COVID-19. Several candidate drugs are being considered and evaluated for treatment. This includes clinically available drugs, such as chloroquine, hydroxychloroquine, and lopinavir/ritonavir, which are being repurposed for the treatment of COVID-19. Novel experimental therapies, such as remdesivir and favipiravir, are also actively being investigated for antiviral efficacy. Clinically available and investigational immunomodulators, such as the interleukin 6 inhibitors tocilizumab and sarilumab and the anti-granulocyte-macrophage colony-stimulating factor lenzilumab, are being tested for their anticipated effect in counteracting the pro-inflammatory cytokine environment that characterizes severe and critical COVID-19. This review article examines the evidence behind the potential use of these leading drug candidates for the treatment of COVID-19. The authors conclude, based on this review, that there is still no high-quality evidence to support any of these proposed drug therapies. The authors, therefore, encourage the enrollment of eligible patients to multiple ongoing clinical trials that assess the efficacy and safety of these candidate therapies. Until the results of controlled trials are available, none of the suggested therapeutics is clinically proven as an effective therapy for COVID-19.
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Key Words
- ace2, angiotensin-converting enzyme 2
- ards, acute respiratory distress syndrome
- cc, 50% cytotoxic concentration
- covid-19, coronavirus disease 2019
- crp, c-reactive protein
- ec50, half-maximal effective concentration
- fda, us food and drug administration
- gm-csf, granulocyte-macrophage colony-stimulating factor
- hiv, human immunodeficiency viruses
- ifn-α, interferon-alpha
- ifn-β, interferon-beta
- il-6, interleukin 6
- lpv, lopinavir
- lpv/r, lopinavir/ritonavir
- mers-cov, middle east respiratory syndrome–related coronavirus
- sars, severe acute respiratory syndrome
- sars-cov, severe acute respiratory syndrome coronavirus
- sars-cov-2, severe acute respiratory syndrome coronavirus 2
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Affiliation(s)
- Prakhar Vijayvargiya
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Zerelda Esquer Garrigos
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Natalia E Castillo Almeida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Pooja R Gurram
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Ryan W Stevens
- Department of Pharmacy Services, Mayo Clinic, Rochester, MN
| | - Raymund R Razonable
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN.
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42
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Gonçalves A, Bertrand J, Ke R, Comets E, de Lamballerie X, Malvy D, Pizzorno A, Terrier O, Calatrava MR, Mentré F, Smith P, Perelson AS, Guedj J. Timing of antiviral treatment initiation is critical to reduce SARS-CoV-2 viral load. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020. [PMID: 32511641 DOI: 10.1101/2020.04.04.20047886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer viral growth parameters and predict the effects of antiviral treatments. In order to reduce peak viral load by more than 2 logs, drug efficacy needs to be greater than 80% if treatment is administered after symptom onset; an efficacy of 50% could be sufficient if treatment is initiated before symptom onset. Given their pharmacokinetic/pharmacodynamic properties, current investigated drugs may be in a range of 20-70% efficacy. They may help control virus if administered very early, but may not have a major effect in severe patients.
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43
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Haddow AD, Perez-Sautu U, Wiley MR, Miller LJ, Kimmel AE, Principe LM, Wollen-Roberts SE, Shamblin JD, Valdez SM, Cazares LH, Pratt WD, Rossi FD, Lugo-Roman L, Bavari S, Palacios GF, Nalca A, Nasar F, Pitt MLM. Modeling mosquito-borne and sexual transmission of Zika virus in an enzootic host, the African green monkey. PLoS Negl Trop Dis 2020; 14:e0008107. [PMID: 32569276 PMCID: PMC7343349 DOI: 10.1371/journal.pntd.0008107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 07/08/2020] [Accepted: 02/01/2020] [Indexed: 01/08/2023] Open
Abstract
Mosquito-borne and sexual transmission of Zika virus (ZIKV), a TORCH pathogen, recently initiated a series of large epidemics throughout the Tropics. Animal models are necessary to determine transmission risk and study pathogenesis, as well screen antivirals and vaccine candidates. In this study, we modeled mosquito and sexual transmission of ZIKV in the African green monkey (AGM). Following subcutaneous, intravaginal or intrarectal inoculation of AGMs with ZIKV, we determined the transmission potential and infection dynamics of the virus. AGMs inoculated by all three transmission routes exhibited viremia and viral shedding followed by strong virus neutralizing antibody responses, in the absence of clinical illness. All four of the subcutaneously inoculated AGMs became infected (mean peak viremia: 2.9 log10 PFU/mL, mean duration: 4.3 days) and vRNA was detected in their oral swabs, with infectious virus being detected in a subset of these specimens. Although all four of the intravaginally inoculated AGMs developed virus neutralizing antibody responses, only three had detectable viremia (mean peak viremia: 4.0 log10 PFU/mL, mean duration: 3.0 days). These three AGMs also had vRNA and infectious virus detected in both oral and vaginal swabs. Two of the four intrarectally inoculated AGMs became infected (mean peak viremia: 3.8 log10 PFU/mL, mean duration: 3.5 days). vRNA was detected in oral swabs collected from both of these infected AGMs, and infectious virus was detected in an oral swab from one of these AGMs. Notably, vRNA and infectious virus were detected in vaginal swabs collected from the infected female AGM (peak viral load: 7.5 log10 copies/mL, peak titer: 3.8 log10 PFU/mL, range of detection: 5-21 days post infection). Abnormal clinical chemistry and hematology results were detected and acute lymphadenopathy was observed in some AGMs. Infection dynamics in all three AGM ZIKV models are similar to those reported in the majority of human ZIKV infections. Our results indicate that the AGM can be used as a surrogate to model mosquito or sexual ZIKV transmission and infection. Furthermore, our results suggest that AGMs are likely involved in the enzootic maintenance and amplification cycle of ZIKV.
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Affiliation(s)
- Andrew D. Haddow
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Unai Perez-Sautu
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Michael R. Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Lynn J. Miller
- Veterinary Medicine Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Adrienne E. Kimmel
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Lucia M. Principe
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Suzanne E. Wollen-Roberts
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Joshua D. Shamblin
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Stephanie M. Valdez
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Lisa H. Cazares
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - William D. Pratt
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Franco D. Rossi
- Aerobiology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Luis Lugo-Roman
- Veterinary Medicine Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Sina Bavari
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Gustavo F. Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Aysegul Nalca
- Aerobiology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Farooq Nasar
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - M. Louise M. Pitt
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
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44
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Hart WS, Maini PK, Yates CA, Thompson RN. A theoretical framework for transitioning from patient-level to population-scale epidemiological dynamics: influenza A as a case study. J R Soc Interface 2020; 17:20200230. [PMID: 32400267 DOI: 10.1098/rsif.2020.0230] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Multi-scale epidemic forecasting models have been used to inform population-scale predictions with within-host models and/or infection data collected in longitudinal cohort studies. However, most multi-scale models are complex and require significant modelling expertise to run. We formulate an alternative multi-scale modelling framework using a compartmental model with multiple infected stages. In the large-compartment limit, our easy-to-use framework generates identical results compared to previous more complicated approaches. We apply our framework to the case study of influenza A in humans. By using a viral dynamics model to generate synthetic patient-level data, we explore the effects of limited and inaccurate patient data on the accuracy of population-scale forecasts. If infection data are collected daily, we find that a cohort of at least 40 patients is required for a mean population-scale forecasting error below 10%. Forecasting errors may be reduced by including more patients in future cohort studies or by increasing the frequency of observations for each patient. Our work, therefore, provides not only an accessible epidemiological modelling framework but also an insight into the data required for accurate forecasting using multi-scale models.
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Affiliation(s)
- W S Hart
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
| | - P K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
| | - C A Yates
- Centre for Mathematical Biology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - R N Thompson
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK.,Christ Church, University of Oxford, Saint Aldate's, Oxford OX1 1DP, UK
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45
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Madelain V, Mentré F, Baize S, Anglaret X, Laouénan C, Oestereich L, Nguyen THT, Malvy D, Piorkowski G, Graw F, Günther S, Raoul H, de Lamballerie X, Guedj J. Modeling Favipiravir Antiviral Efficacy Against Emerging Viruses: From Animal Studies to Clinical Trials. CPT Pharmacometrics Syst Pharmacol 2020; 9:258-271. [PMID: 32198838 PMCID: PMC7239338 DOI: 10.1002/psp4.12510] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/30/2019] [Indexed: 12/14/2022] Open
Abstract
In 2014, our research network was involved in the evaluation of favipiravir, an anti-influenza polymerase inhibitor, against Ebola virus. In this review, we discuss how mathematical modeling was used, first to propose a relevant dosing regimen in humans, and then to optimize its antiviral efficacy in a nonhuman primate (NHP) model. The data collected in NHPs were finally used to develop a model of Ebola pathogenesis integrating the interactions among the virus, the innate and adaptive immune response, and the action of favipiravir. We conclude the review of this work by discussing how these results are of relevance for future human studies in the context of Ebola virus, but also for other emerging viral diseases for which no therapeutics are available.
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Affiliation(s)
| | | | - Sylvain Baize
- UBIVEInstitut PasteurCentre International de Recherche en InfectiologieLyonFrance
| | - Xavier Anglaret
- INSERMUMR 1219Université de BordeauxBordeauxFrance
- Programme PACCI/site ANRS de Côte d’IvoireAbidjanCôte d’Ivoire
| | | | - Lisa Oestereich
- Bernhard‐Nocht‐Institute for Tropical MedicineHamburgGermany
- German Center for Infection Research (DZIF)Partner Site HamburgGermany
| | | | - Denis Malvy
- INSERMUMR 1219Université de BordeauxBordeauxFrance
- Centre Hospitalier Universitaire de BordeauxBordeauxFrance
| | - Géraldine Piorkowski
- UMR "Emergence des Pathologies Virales" (EPV: Aix‐Marseille University – IRD 190 – Inserm 1207 – EHESP) – Institut Hospitalo‐Universitaire Méditerranée InfectionMarseilleFrance
| | - Frederik Graw
- Center for Modeling and Simulation in the Biosciences (BIOMS)BioQuant‐CenterHeidelberg UniversityHeidelbergGermany
| | - Stephan Günther
- Bernhard‐Nocht‐Institute for Tropical MedicineHamburgGermany
- German Center for Infection Research (DZIF)Partner Site HamburgGermany
| | - Hervé Raoul
- Laboratoire P4 Inserm‐Jean MérieuxUS003 InsermLyonFrance
| | - Xavier de Lamballerie
- UMR "Emergence des Pathologies Virales" (EPV: Aix‐Marseille University – IRD 190 – Inserm 1207 – EHESP) – Institut Hospitalo‐Universitaire Méditerranée InfectionMarseilleFrance
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46
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Tang B, Xiao Y, Sander B, Kulkarni MA, RADAM-LAC Research Team, Wu J. Modelling the impact of antibody-dependent enhancement on disease severity of Zika virus and dengue virus sequential and co-infection. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191749. [PMID: 32431874 PMCID: PMC7211844 DOI: 10.1098/rsos.191749] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/12/2020] [Indexed: 05/22/2023]
Abstract
Human infections with viruses of the genus Flavivirus, including dengue virus (DENV) and Zika virus (ZIKV), are of increasing global importance. Owing to antibody-dependent enhancement (ADE), secondary infection with one Flavivirus following primary infection with another Flavivirus can result in a significantly larger peak viral load with a much higher risk of severe disease. Although several mathematical models have been developed to quantify the virus dynamics in the primary and secondary infections of DENV, little progress has been made regarding secondary infection of DENV after a primary infection of ZIKV, or DENV-ZIKV co-infection. Here, we address this critical gap by developing compartmental models of virus dynamics. We first fitted the models to published data on dengue viral loads of the primary and secondary infections with the observation that the primary infection reaches its peak much more gradually than the secondary infection. We then quantitatively show that ADE is the key factor determining a sharp increase/decrease of viral load near the peak time in the secondary infection. In comparison, our simulations of DENV and ZIKV co-infection (simultaneous rather than sequential) show that ADE has very limited influence on the peak DENV viral load. This indicates pre-existing immunity to ZIKV is the determinant of a high level of ADE effect. Our numerical simulations show that (i) in the absence of ADE effect, a subsequent co-infection is beneficial to the second virus; and (ii) if ADE is feasible, then a subsequent co-infection can induce greater damage to the host with a higher peak viral load and a much earlier peak time for the second virus, and for the second peak for the first virus.
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Affiliation(s)
- Biao Tang
- Laboratory for Industrial and Applied Mathematics (LIAM), York University, Toronto, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
- Toronto Health Economics and Technology Assessment, Toronto, Ontario, Canada
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Beate Sander
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
- Toronto Health Economics and Technology Assessment, Toronto, Ontario, Canada
| | - Manisha A. Kulkarni
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Canada
| | | | - Jianhong Wu
- Laboratory for Industrial and Applied Mathematics (LIAM), York University, Toronto, Canada
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47
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Moore JR, Ahmed H, Manicassamy B, Garcia-Sastre A, Handel A, Antia R. Varying Inoculum Dose to Assess the Roles of the Immune Response and Target Cell Depletion by the Pathogen in Control of Acute Viral Infections. Bull Math Biol 2020; 82:35. [PMID: 32125535 DOI: 10.1007/s11538-020-00711-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/19/2020] [Indexed: 02/05/2023]
Abstract
It is difficult to determine whether an immune response or target cell depletion by the infectious agent is most responsible for the control of acute primary infection. Both mechanisms can explain the basic dynamics of an acute infection-exponential growth of the pathogen followed by control and clearance-and can also be represented by many different differential equation models. Consequently, traditional model comparison techniques using time series data can be ambiguous or inconclusive. We propose that varying the inoculum dose and measuring the subsequent infectious load can rule out target cell depletion by the pathogen as the main control mechanism. Infectious load can be any measure that is proportional to the number of infected cells, such as viraemia. We show that a twofold or greater change in infectious load is unlikely when target cell depletion controls infection, regardless of the model details. Analyzing previously published data from mice infected with influenza, we find the proportion of lung epithelial cells infected was 21-fold greater (95% confidence interval 14-32) in the highest dose group than in the lowest. This provides evidence in favor of an alternative to target cell depletion, such as innate immunity, in controlling influenza infections in this experimental system. Data from other experimental animal models of acute primary infection have a similar pattern.
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Affiliation(s)
- James R Moore
- Division of Vaccines and Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, USA.
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, USA
| | - Balaji Manicassamy
- Department of Microbiology and Immunology, University of Iowa School College of Medicine, Iowa City, USA
| | | | - Andreas Handel
- Epidemiology and Biostatistics, University of Georgia, Athens, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, USA
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48
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Gonçalves A, Mentré F, Lemenuel-Diot A, Guedj J. Model Averaging in Viral Dynamic Models. AAPS JOURNAL 2020; 22:48. [PMID: 32060662 DOI: 10.1208/s12248-020-0426-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022]
Abstract
The paucity of experimental data makes both inference and prediction particularly challenging in viral dynamic models. In the presence of several candidate models, a common strategy is model selection (MS), in which models are fitted to the data but only results obtained with the "best model" are presented. However, this approach ignores model uncertainty, which may lead to inaccurate predictions. When several models provide a good fit to the data, another approach is model averaging (MA) that weights the predictions of each model according to its consistency to the data. Here, we evaluated by simulations in a nonlinear mixed-effect model framework the performances of MS and MA in two realistic cases of acute viral infection, i.e., (1) inference in the presence of poorly identifiable parameters, namely, initial viral inoculum and eclipse phase duration, (2) uncertainty on the mechanisms of action of the immune response. MS was associated in some scenarios with a large rate of false selection. This led to a coverage rate lower than the nominal coverage rate of 0.95 in the majority of cases and below 0.50 in some scenarios. In contrast, MA provided better estimation of parameter uncertainty, with coverage rates ranging from 0.72 to 0.98 and mostly comprised within the nominal coverage rate. Finally, MA provided similar predictions than those obtained with MS. In conclusion, parameter estimates obtained with MS should be taken with caution, especially when several models well describe the data. In this situation, MA has better performances and could be performed to account for model uncertainty.
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Affiliation(s)
- Antonio Gonçalves
- Université de Paris, IAME, INSERM, Henri Huchard, F-75018, Paris, France.
| | - France Mentré
- Université de Paris, IAME, INSERM, Henri Huchard, F-75018, Paris, France
| | - Annabelle Lemenuel-Diot
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | - Jérémie Guedj
- Université de Paris, IAME, INSERM, Henri Huchard, F-75018, Paris, France
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Wethington D, Harder O, Uppulury K, Stewart WCL, Chen P, King T, Reynolds SD, Perelson AS, Peeples ME, Niewiesk S, Das J. Mathematical modelling identifies the role of adaptive immunity as a key controller of respiratory syncytial virus in cotton rats. J R Soc Interface 2019; 16:20190389. [PMID: 31771450 DOI: 10.1098/rsif.2019.0389] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a common virus that can have varying effects ranging from mild cold-like symptoms to mortality depending on the age and immune status of the individual. We combined mathematical modelling using ordinary differential equations (ODEs) with measurement of RSV infection kinetics in primary well-differentiated human bronchial epithelial cultures in vitro and in immunocompetent and immunosuppressed cotton rats to glean mechanistic details that underlie RSV infection kinetics in the lung. Quantitative analysis of viral titre kinetics in our mathematical model showed that the elimination of infected cells by the adaptive immune response generates unique RSV titre kinetic features including a faster timescale of viral titre clearance than viral production, and a monotonic decrease in the peak RSV titre with decreasing inoculum dose. Parameter estimation in the ODE model using a nonlinear mixed effects approach revealed a very low rate (average single-cell lifetime > 10 days) of cell lysis by RSV before the adaptive immune response is initiated. Our model predicted negligible changes in the RSV titre kinetics at early times post-infection (less than 5 dpi) but a slower decay in RSV titre in immunosuppressed cotton rats compared to that in non-suppressed cotton rats at later times (greater than 5 dpi) in silico. These predictions were in excellent agreement with the experimental results. Our combined approach quantified the importance of the adaptive immune response in suppressing RSV infection in cotton rats, which could be useful in testing RSV vaccine candidates.
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Affiliation(s)
- Darren Wethington
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Olivia Harder
- College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Karthik Uppulury
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - William C L Stewart
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA.,Department of Statistics, The Ohio State University, Columbus, OH 43210, USA
| | - Phylip Chen
- Vaccines and Immunity, Abigail Wexner Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Tiffany King
- Vaccines and Immunity, Abigail Wexner Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Susan D Reynolds
- Center for Perinatal Research, Abigail Wexner Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Mark E Peeples
- Vaccines and Immunity, Abigail Wexner Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Stefan Niewiesk
- College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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50
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High susceptibility, viral dynamics and persistence of South American Zika virus in New World monkey species. Sci Rep 2019; 9:14495. [PMID: 31601848 PMCID: PMC6787206 DOI: 10.1038/s41598-019-50918-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/16/2019] [Indexed: 12/18/2022] Open
Abstract
South American Zika virus (ZIKV) recently emerged as a novel human pathogen, linked with neurological disorders. However, comparative ZIKV infectivity studies in New World primates are lacking. Two members of the Callitrichidae family, common marmosets (Callithrix jacchus) and red-bellied tamarins (Saguinus labiatus), were highly susceptible to sub-cutaneous challenge with the Puerto Rico-origin ZIKVPRVABC59 strain. Both exhibited rapid, high, acute viraemia with early neuroinvasion (3 days) in peripheral and central nervous tissue. ZIKV RNA levels in blood and tissues were significantly higher in New World hosts compared to Old World species (Macaca mulatta, Macaca fascicularis). Tamarins and rhesus macaques exhibited loss of zonal occludens-1 (ZO-1) staining, indicative of a compromised blood-brain barrier 3 days post-ZIKV exposure. Early, widespread dissemination across multiple anatomical sites distant to the inoculation site preceded extensive ZIKV persistence after 100 days in New and Old World lineages, especially lymphoid, neurological and reproductive sites. Prolonged persistence in brain tissue has implications for otherwise resolved human ZIKV infection. High susceptibility of distinct New World species underscores possible establishment of ZIKV sylvatic cycles in primates indigenous to ZIKV endemic regions. Tamarins and marmosets represent viable New World models for ZIKV pathogenesis and therapeutic intervention studies, including vaccines, with contemporary strains.
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