1
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Porthiyas J, Nussey D, Beauchemin CAA, Warren DC, Quirouette C, Wilkie KP. Practical parameter identifiability and handling of censored data with Bayesian inference in mathematical tumour models. NPJ Syst Biol Appl 2024; 10:89. [PMID: 39143084 PMCID: PMC11324876 DOI: 10.1038/s41540-024-00409-6] [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: 09/27/2023] [Accepted: 07/21/2024] [Indexed: 08/16/2024] Open
Abstract
Mechanistic mathematical models (MMs) are a powerful tool to help us understand and predict the dynamics of tumour growth under various conditions. In this work, we use 5 MMs with an increasing number of parameters to explore how certain (often overlooked) decisions in estimating parameters from data of experimental tumour growth affect the outcome of the analysis. In particular, we propose a framework for including tumour volume measurements that fall outside the upper and lower limits of detection, which are normally discarded. We demonstrate how excluding censored data results in an overestimation of the initial tumour volume and the MM-predicted tumour volumes prior to the first measurements, and an underestimation of the carrying capacity and the MM-predicted tumour volumes beyond the latest measurable time points. We show in which way the choice of prior for the MM parameters can impact the posterior distributions, and illustrate that reporting the most likely parameters and their 95% credible interval can lead to confusing or misleading interpretations. We hope this work will encourage others to carefully consider choices made in parameter estimation and to adopt the approaches we put forward herein.
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Affiliation(s)
- Jamie Porthiyas
- Department of Mathematics, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Daniel Nussey
- Department of Mathematics, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Catherine A A Beauchemin
- Department of Physics, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) Program, RIKEN, Wako-shi, Saitama, 351-0198, Japan
| | - Donald C Warren
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) Program, RIKEN, Wako-shi, Saitama, 351-0198, Japan
- Florida Institute of Technology, Melbourne, FL, 32901, USA
| | - Christian Quirouette
- Department of Physics, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Kathleen P Wilkie
- Department of Mathematics, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada.
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2
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Bagdonaite I, Abdurahman S, Mirandola M, Pasqual D, Frank M, Narimatsu Y, Joshi HJ, Vakhrushev SY, Salata C, Mirazimi A, Wandall HH. Targeting host O-linked glycan biosynthesis affects Ebola virus replication efficiency and reveals differential GalNAc-T acceptor site preferences on the Ebola virus glycoprotein. J Virol 2024; 98:e0052424. [PMID: 38757972 PMCID: PMC11237518 DOI: 10.1128/jvi.00524-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Ebola virus glycoprotein (EBOV GP) is one of the most heavily O-glycosylated viral glycoproteins, yet we still lack a fundamental understanding of the structure of its large O-glycosylated mucin-like domain and to what degree the host O-glycosylation capacity influences EBOV replication. Using tandem mass spectrometry, we identified 47 O-glycosites on EBOV GP and found similar glycosylation signatures on virus-like particle- and cell lysate-derived GP. Furthermore, we performed quantitative differential O-glycoproteomics on proteins produced in wild-type HEK293 cells and cell lines ablated for the three key initiators of O-linked glycosylation, GalNAc-T1, -T2, and -T3. The data show that 12 out of the 47 O-glycosylated sites were regulated, predominantly by GalNAc-T1. Using the glycoengineered cell lines for authentic EBOV propagation, we demonstrate the importance of O-linked glycan initiation and elongation for the production of viral particles and the titers of progeny virus. The mapped O-glycan positions and structures allowed to generate molecular dynamics simulations probing the largely unknown spatial arrangements of the mucin-like domain. The data highlight targeting GALNT1 or C1GALT1C1 as a possible way to modulate O-glycan density on EBOV GP for novel vaccine designs and tailored intervention approaches.IMPORTANCEEbola virus glycoprotein acquires its extensive glycan shield in the host cell, where it is decorated with N-linked glycans and mucin-type O-linked glycans. The latter is initiated by a family of polypeptide GalNAc-transferases that have different preferences for optimal peptide substrates resulting in a spectrum of both very selective and redundant substrates for each isoform. In this work, we map the exact locations of O-glycans on Ebola virus glycoprotein and identify subsets of sites preferentially initiated by one of the three key isoforms of GalNAc-Ts, demonstrating that each enzyme contributes to the glycan shield integrity. We further show that altering host O-glycosylation capacity has detrimental effects on Ebola virus replication, with both isoform-specific initiation and elongation playing a role. The combined structural and functional data highlight glycoengineered cell lines as useful tools for investigating molecular mechanisms imposed by specific glycans and for steering the immune responses in future vaccine designs.
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Affiliation(s)
- Ieva Bagdonaite
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Mattia Mirandola
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Denis Pasqual
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Sweden
- Department of Laboratory Medicine (LABMED), Karolinska Institute, Stockholm, Sweden
- National Veterinary Institute, Uppsala, Sweden
| | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
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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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Williams B, Carruthers J, Gillard JJ, Lythe G, Perelson AS, Ribeiro RM, Molina-París C, López-García M. The reproduction number and its probability distribution for stochastic viral dynamics. J R Soc Interface 2024; 21:20230400. [PMID: 38264928 PMCID: PMC10806437 DOI: 10.1098/rsif.2023.0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
We consider stochastic models of individual infected cells. The reproduction number, R, is understood as a random variable representing the number of new cells infected by one initial infected cell in an otherwise susceptible (target cell) population. Variability in R results partly from heterogeneity in the viral burst size (the number of viral progeny generated from an infected cell during its lifetime), which depends on the distribution of cellular lifetimes and on the mechanism of virion release. We analyse viral dynamics models with an eclipse phase: the period of time after a cell is infected but before it is capable of releasing virions. The duration of the eclipse, or the subsequent infectious, phase is non-exponential, but composed of stages. We derive the probability distribution of the reproduction number for these viral dynamics models, and show it is a negative binomial distribution in the case of constant viral release from infectious cells, and under the assumption of an excess of target cells. In a deterministic model, the ultimate in-host establishment or extinction of the viral infection depends entirely on whether the mean reproduction number is greater than, or less than, one, respectively. Here, the probability of extinction is determined by the probability distribution of R, not simply its mean value. In particular, we show that in some cases the probability of infection is not an increasing function of the mean reproduction number.
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Affiliation(s)
- Bevelynn Williams
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | | | - Joseph J. Gillard
- CBR Division, Defence Science and Technology Laboratory, Salisbury, UK
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | - Alan S. Perelson
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ruy M. Ribeiro
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Carmen Molina-París
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
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5
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Quirouette C, Cresta D, Li J, Wilkie KP, Liang H, Beauchemin CAA. The effect of random virus failure following cell entry on infection outcome and the success of antiviral therapy. Sci Rep 2023; 13:17243. [PMID: 37821517 PMCID: PMC10567758 DOI: 10.1038/s41598-023-44180-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/04/2023] [Indexed: 10/13/2023] Open
Abstract
A virus infection can be initiated with very few or even a single infectious virion, and as such can become extinct, i.e. stochastically fail to take hold or spread significantly. There are many ways that a fully competent infectious virion, having successfully entered a cell, can fail to cause a productive infection, i.e. one that yields infectious virus progeny. Though many stochastic models (SMs) have been developed and used to estimate a virus infection's establishment probability, these typically neglect infection failure post virus entry. The SM presented herein introduces parameter [Formula: see text] which corresponds to the probability that a virion's entry into a cell will result in a productive cell infection. We derive an expression for the likelihood of infection establishment in this new SM, and find that prophylactic therapy with an antiviral reducing [Formula: see text] is at least as good or better at decreasing the establishment probability, compared to antivirals reducing the rates of virus production or virus entry into cells, irrespective of the SM parameters. We investigate the difference in the fraction of cells consumed by so-called extinct versus established virus infections, and find that this distinction becomes biologically meaningless as the probability of establishment approaches zero. We explain why the release of virions continuously over an infectious cell's lifespan, rather than as a single burst at the end of the cell's lifespan, does not result in an increased risk of infection extinction. We show, instead, that the number of virus released, not the timing of the release, affects infection establishment and associated critical antiviral efficacy.
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Affiliation(s)
| | - Daniel Cresta
- Department of Physics, Toronto Metropolitan University, Toronto, Canada
| | - Jizhou Li
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Wako, Japan
| | - Kathleen P Wilkie
- Department of Mathematics, Toronto Metropolitan University, Toronto, Canada
| | - Haozhao Liang
- Nishina Center for Accelerator-Based Science (RNC), RIKEN, Wako, Japan
- Department of Physics, University of Tokyo, Tokyo, Japan
| | - Catherine A A Beauchemin
- Department of Physics, Toronto Metropolitan University, Toronto, Canada.
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Wako, Japan.
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6
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Guterres A. Viral load: We need a new look at an old problem? J Med Virol 2023; 95:e29061. [PMID: 37638475 DOI: 10.1002/jmv.29061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/22/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
The concept of viral load was introduced in the 1980s to measure the amount of viral genetic material in a person's blood, primarily for human immunodeficiency virus (HIV). It has since become crucial for monitoring HIV infection progression and assessing the efficacy of antiretroviral therapy. However, during the coronavirus disease 2019 pandemic, the term "viral load" became widely popularized, not only for the scientific community but for the general population. Viral load plays a critical role in both clinical patient management and research, providing valuable insights for antiviral treatment strategies, vaccination efforts, and epidemiological control measures. As measuring viral load is so important, why don't researchers discuss the best way to do it? Is it simply acceptable to use raw Ct values? Relying solely on Ct values for viral load estimation can be problematic due to several reasons. First, Ct values can vary between different quantitative polymerase chain reaction assays, platforms, and laboratories, making it difficult to compare data across studies. Second, Ct values do not directly measure the quantity of viral particles in a sample and they can be influenced by various factors such as initial viral load, sample quality, and assay sensitivity. Moreover, variations in viral RNA extraction and reverse-transcription steps can further impact the accuracy of viral load estimation, emphasizing the need for careful interpretation of Ct values in viral load assessment. Interestingly, we did not observe scientific articles addressing different strategies to quantify viral load. The absence of standardized and validated methods impedes the implementation of viral load monitoring in clinical management. The variability in cell quantities within samples and the variation in viral particle numbers within infected cells further challenge accurate viral load measurement and interpretation. To advance the field and improve patient outcomes, there is an urgent need for the development and validation of tailored, standardized methods for precise viral load quantification.
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Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
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7
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Boytz R, Seitz S, Gaudiano E, Patten JJ, Keiser PT, Connor JH, Sharpe AH, Davey RA. Inactivation of Ebola Virus and SARS-CoV-2 in Cell Culture Supernatants and Cell Pellets by Gamma Irradiation. Viruses 2022; 15:43. [PMID: 36680083 PMCID: PMC9866162 DOI: 10.3390/v15010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Viral pathogens with the potential to cause widespread disruption to human health and society continue to emerge or re-emerge around the world. Research on such viruses often involves high biocontainment laboratories (BSL3 or BSL4), but the development of diagnostics, vaccines and therapeutics often uses assays that are best performed at lower biocontainment. Reliable inactivation is necessary to allow removal of materials to these spaces and to ensure personnel safety. Here, we validate the use of gamma irradiation to inactivate culture supernatants and pellets of cells infected with a representative member of the Filovirus and Coronavirus families. We show that supernatants and cell pellets containing SARS-CoV-2 are readily inactivated with 1.9 MRad, while Ebola virus requires higher doses of 2.6 MRad for supernatants and 3.8 MRad for pellets. While these doses of radiation inactivate viruses, proinflammatory cytokines that are common markers of virus infection are still detected with low losses. The doses required for virus inactivation of supernatants are in line with previously reported values, but the inactivation of cell pellets has not been previously reported and enables new approaches for analysis of protein-based host responses to infection.
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Affiliation(s)
- RuthMabel Boytz
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Scott Seitz
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Emily Gaudiano
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - J. J. Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Patrick T. Keiser
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - John H. Connor
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Arlene H. Sharpe
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A. Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
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8
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Amidei A, Dobrovolny HM. Estimation of virus-mediated cell fusion rate of SARS-CoV-2. Virology 2022; 575:91-100. [PMID: 36088794 PMCID: PMC9449781 DOI: 10.1016/j.virol.2022.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/27/2022] [Accepted: 08/28/2022] [Indexed: 12/22/2022]
Abstract
Several viruses have the ability to form large multinucleated cells known as syncytia. Many properties of syncytia and the role they play in the evolution of a viral infection are not well understood. One basic question that has not yet been answered is how quickly syncytia form. We use a novel mathematical model of cell-cell fusion assays and apply it to experimental data from SARS-CoV-2 fusion assays to provide the first estimates of virus-mediated cell fusion rate. We find that for SARS-CoV2, the fusion rate is in the range of 6 × 10−4–12×10−4/h. We also use our model to compare fusion rates when the protease TMPRSS2 is overexpressed (2–4 times larger fusion rate), when the protease furin is removed (one third the original fusion rate), and when the spike protein is altered (1/10th the original fusion rate). The use of mathematical models allows us to provide additional quantitative information about syncytia formation.
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Affiliation(s)
- Ava Amidei
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, TX, USA
| | - Hana M Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, USA.
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9
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Sim JR, Shin DH, Park PG, Park SH, Bae JY, Lee Y, Kang DY, Kim YJ, Aum S, Noh SH, Hwang SJ, Cha HR, Kim CB, Ko SH, Park S, Jeon D, Cho S, Lee GE, Kim J, Moon YH, Kim JO, Nam JS, Kim CH, Moon S, Chung YW, Park MS, Ryu JH, Namkung W, Lee JM, Lee MG. Amelioration of SARS-CoV-2 infection by ANO6 phospholipid scramblase inhibition. Cell Rep 2022; 40:111117. [PMID: 35839776 PMCID: PMC9250890 DOI: 10.1016/j.celrep.2022.111117] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 05/27/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
As an enveloped virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delivers its viral genome into host cells via fusion of the viral and cell membranes. Here, we show that ANO6/TMEM16F-mediated cell surface exposure of phosphatidylserine is critical for SARS-CoV-2 entry and that ANO6-selective inhibitors are effective against SARS-CoV-2 infections. Application of the SARS-CoV-2 Spike pseudotyped virus (SARS2-PsV) evokes a cytosolic Ca2+ elevation and ANO6-dependent phosphatidylserine externalization in ACE2/TMPRSS2-positive mammalian cells. A high-throughput screening of drug-like chemical libraries identifies three different structural classes of chemicals showing ANO6 inhibitory effects. Among them, A6-001 displays the highest potency and ANO6 selectivity and it inhibits the single-round infection of SARS2-PsV in ACE2/TMPRSS2-positive HEK 293T cells. More importantly, A6-001 strongly inhibits authentic SARS-CoV-2-induced phosphatidylserine scrambling and SARS-CoV-2 viral replications in Vero, Calu-3, and primarily cultured human nasal epithelial cells. These results provide mechanistic insights into the viral entry process and offer a potential target for pharmacological intervention to protect against coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Ju-Ri Sim
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dong Hoon Shin
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Pil-Gu Park
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - So-Hyeon Park
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Youngchae Lee
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dha-Yei Kang
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ye Jin Kim
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sowon Aum
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Shin Hye Noh
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea; Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Su Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hye-Ran Cha
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Cheong Bi Kim
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Si Hwan Ko
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sunghoon Park
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dongkyu Jeon
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Sungwoo Cho
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Gee Eun Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Jeonghun Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Young-Hye Moon
- Science Unit, International Vaccine Institute, Seoul 08826, Korea
| | - Jae-Ouk Kim
- Science Unit, International Vaccine Institute, Seoul 08826, Korea
| | - Jae-Sung Nam
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Chang-Hoon Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sungmin Moon
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Youn Wook Chung
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Ji-Hwan Ryu
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
| | - Wan Namkung
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea.
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
| | - Min Goo Lee
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea; Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
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10
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Widerspick L, Vázquez CA, Niemetz L, Heung M, Olal C, Bencsik A, Henkel C, Pfister A, Brunetti JE, Kucinskaite-Kodze I, Lawrence P, Muñoz Fontela C, Diederich S, Escudero-Pérez B. Inactivation Methods for Experimental Nipah Virus Infection. Viruses 2022; 14:v14051052. [PMID: 35632791 PMCID: PMC9145063 DOI: 10.3390/v14051052] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/29/2022] [Accepted: 05/12/2022] [Indexed: 02/07/2023] Open
Abstract
Nipah virus (NiV) is an emerging zoonotic paramyxovirus that causes severe disease in humans and livestock. Due to its high pathogenicity in humans and the lack of available vaccines and therapeutics, NiV needs to be handled in biosafety level 4 (BSL-4) laboratories. Safe inactivation of samples containing NiV is thus necessary to allow further processing in lower containment areas. To date, there is only limited information available on NiV inactivation methods validated by BSL-4 facilities that can be used as a reference. Here, we compare some of the most common inactivation methods in order to evaluate their efficacy at inactivating NiV in infected cells, supernatants and organs. Thus, several physical and chemical inactivation methods, and combinations thereof, were assessed. Viral replication was monitored for 3 weeks and NiV presence was assessed by RT-qPCR, plaque assay and indirect immunofluorescence. A total of nineteen methods were shown to reduce NiV infectious particles in cells, supernatants and organs to undetectable levels. Therefore, we provide a list of methods for the safe and efficient inactivation of NiV.
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Affiliation(s)
- Lina Widerspick
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Cecilia Alejandra Vázquez
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires 1428, Argentina;
| | - Linda Niemetz
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Michelle Heung
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Catherine Olal
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - András Bencsik
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Christoph Henkel
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Anneke Pfister
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Jesús Emanuel Brunetti
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | | | - Philip Lawrence
- Science and Humanities Confluence Research Center (EA 1598), Catholic University of Lyon (UCLy), 69002 Lyon, France;
| | - César Muñoz Fontela
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Sandra Diederich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany;
| | - Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; (L.W.); (L.N.); (M.H.); (C.O.); (A.B.); (C.H.); (A.P.); (J.E.B.); (C.M.F.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
- Correspondence:
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11
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Khan S, Dobrovolny HM. A study of the effects of age on the dynamics of RSV in animal models. Virus Res 2021; 304:198524. [PMID: 34329697 DOI: 10.1016/j.virusres.2021.198524] [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: 01/27/2021] [Revised: 06/24/2021] [Accepted: 07/17/2021] [Indexed: 01/18/2023]
Abstract
Respiratory syncytial virus can cause severe illness and even death, particularly in infants. The increased severity of disease in young children is thought to be due to a lack of previous exposure to the virus as well as the limited immune response in infants. While studies have examined the clinical differences in disease between infants and adults, there has been limited examination of how the viral dynamics differ as infants develop. In this study, we apply a mathematical model to data from cotton rats and ferrets of different ages to assess how viral kinetics parameters change as the animals age. We find no clear trend in the viral decay rate, infecting time, and basic reproduction number as the animals age. We discuss possible reasons for the null result including the limited data, lack of detail of the mathematical model, and the limitations of animal models.
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Affiliation(s)
- Shaheer Khan
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX USA
| | - Hana M Dobrovolny
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX USA.
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