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Khan SU, Ullah S, Li S, Mostafa AM, Bilal Riaz M, AlQahtani NF, Teklu SW. A novel simulation-based analysis of a stochastic HIV model with the time delay using high order spectral collocation technique. Sci Rep 2024; 14:7961. [PMID: 38575653 PMCID: PMC10994949 DOI: 10.1038/s41598-024-57073-3] [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: 01/06/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024] Open
Abstract
The economic impact of Human Immunodeficiency Virus (HIV) goes beyond individual levels and it has a significant influence on communities and nations worldwide. Studying the transmission patterns in HIV dynamics is crucial for understanding the tracking behavior and informing policymakers about the possible control of this viral infection. Various approaches have been adopted to explore how the virus interacts with the immune system. Models involving differential equations with delays have become prevalent across various scientific and technical domains over the past few decades. In this study, we present a novel mathematical model comprising a system of delay differential equations to describe the dynamics of intramural HIV infection. The model characterizes three distinct cell sub-populations and the HIV virus. By incorporating time delay between the viral entry into target cells and the subsequent production of new virions, our model provides a comprehensive understanding of the infection process. Our study focuses on investigating the stability of two crucial equilibrium states the infection-free and endemic equilibriums. To analyze the infection-free equilibrium, we utilize the LaSalle invariance principle. Further, we prove that if reproduction is less than unity, the disease free equilibrium is locally and globally asymptotically stable. To ensure numerical accuracy and preservation of essential properties from the continuous mathematical model, we use a spectral scheme having a higher-order accuracy. This scheme effectively captures the underlying dynamics and enables efficient numerical simulations.
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Affiliation(s)
- Sami Ullah Khan
- Department of Mathematics, City University of Science and Information Technology, Peshawar, KP, 25000, Pakistan
| | - Saif Ullah
- Department of Mathematics, University of Peshawar, Peshawar, KP, 25000, Pakistan
| | - Shuo Li
- School of Mathematics and Data Sciences, Changji University, Changji, Xinjiang, 831100, People's Republic of China.
| | - Almetwally M Mostafa
- Department of Information Systems, College of Computers and Information Science, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Bilal Riaz
- IT4Innovations, VSB- Technical University of Ostrava, Ostrava, Czech Republic
- Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon
| | - Nouf F AlQahtani
- IS Department, College of Education, King Saud University, Riyadh, Saudi Arabia
| | - Shewafera Wondimagegnhu Teklu
- Department of Mathematics, College of Natural and Computational Sciences, Debre Berhan University, 445, Debre Berhan, Ethiopia.
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2
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Liang Q, Yang J, Fan WTL, Lo WC. Patch formation driven by stochastic effects of interaction between viruses and defective interfering particles. PLoS Comput Biol 2023; 19:e1011513. [PMID: 37782667 PMCID: PMC10569632 DOI: 10.1371/journal.pcbi.1011513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 10/12/2023] [Accepted: 09/12/2023] [Indexed: 10/04/2023] Open
Abstract
Defective interfering particles (DIPs) are virus-like particles that occur naturally during virus infections. These particles are defective, lacking essential genetic materials for replication, but they can interact with the wild-type virus and potentially be used as therapeutic agents. However, the effect of DIPs on infection spread is still unclear due to complicated stochastic effects and nonlinear spatial dynamics. In this work, we develop a model with a new hybrid method to study the spatial-temporal dynamics of viruses and DIPs co-infections within hosts. We present two different scenarios of virus production and compare the results from deterministic and stochastic models to demonstrate how the stochastic effect is involved in the spatial dynamics of virus transmission. We compare the spread features of the virus in simulations and experiments, including the formation and the speed of virus spread and the emergence of stochastic patchy patterns of virus distribution. Our simulations simultaneously capture observed spatial spread features in the experimental data, including the spread rate of the virus and its patchiness. The results demonstrate that DIPs can slow down the growth of virus particles and make the spread of the virus more patchy.
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Affiliation(s)
- Qiantong Liang
- Department of Mathematics, City University of Hong Kong, Hong Kong, China
| | - Johnny Yang
- Department of Mathematics, Indiana University, Bloomington, Indiana, United States of America
| | - Wai-Tong Louis Fan
- Department of Mathematics, Indiana University, Bloomington, Indiana, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Wing-Cheong Lo
- Department of Mathematics, City University of Hong Kong, Hong Kong, China
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3
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Reyna RA, Maruyama J, Mantlo EK, Manning JT, Taniguchi S, Makishima T, Lukashevich IS, Paessler S. Depletion of CD4 and CD8 T Cells Reduces Acute Disease and Is Not Associated with Hearing Loss in ML29-Infected STAT1-/- Mice. Biomedicines 2022; 10:2433. [PMID: 36289695 PMCID: PMC9598517 DOI: 10.3390/biomedicines10102433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
Lassa virus (LASV) is a zoonotic virus endemic to western Africa that can cause a potentially lethal and hemorrhagic disease, Lassa fever (LF). Survivors suffer a myriad of sequelae, most notably sudden onset sensorineural hearing loss (SNHL), the mechanism of which remains unclear. Unfortunately, studies aiming to identify the mechanism of these sequelae are limited due to the biosafety level 4 (BSL4) requirements of LASV itself. ML29, a reassortant virus proposed as an experimental vaccine candidate against LASV, is potentially an ideal surrogate model of LF in STAT1-/- mice due to similar phenotype in these animals. We intended to better characterize ML29 pathogenesis and potential sequelae in this animal model. Our results indicate that while both CD4 and CD8 T cells are responsible for acute disease in ML29 infection, ML29 induces significant hearing loss in a mechanism independent of either CD4 or CD8 T cells. We believe that this model could provide valuable information for viral-associated hearing loss in general.
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Affiliation(s)
- Rachel A. Reyna
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Junki Maruyama
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Emily K. Mantlo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - John T. Manning
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Satoshi Taniguchi
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tomoko Makishima
- Department of Otolaryngology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Igor S. Lukashevich
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, USA
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
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4
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Bhat T, Cao A, Yin J. Virus-like Particles: Measures and Biological Functions. Viruses 2022; 14:383. [PMID: 35215979 PMCID: PMC8877645 DOI: 10.3390/v14020383] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022] Open
Abstract
Virus-like particles resemble infectious virus particles in size, shape, and molecular composition; however, they fail to productively infect host cells. Historically, the presence of virus-like particles has been inferred from total particle counts by microscopy, and infectious particle counts or plaque-forming-units (PFUs) by plaque assay; the resulting ratio of particles-to-PFUs is often greater than one, easily 10 or 100, indicating that most particles are non-infectious. Despite their inability to hijack cells for their reproduction, virus-like particles and the defective genomes they carry can exhibit a broad range of behaviors: interference with normal virus growth during co-infections, cell killing, and activation or inhibition of innate immune signaling. In addition, some virus-like particles become productive as their multiplicities of infection increase, a sign of cooperation between particles. Here, we review established and emerging methods to count virus-like particles and characterize their biological functions. We take a critical look at evidence for defective interfering virus genomes in natural and clinical isolates, and we review their potential as antiviral therapeutics. In short, we highlight an urgent need to better understand how virus-like genomes and particles interact with intact functional viruses during co-infection of their hosts, and their impacts on the transmission, severity, and persistence of virus-associated diseases.
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Affiliation(s)
| | | | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA; (T.B.); (A.C.)
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5
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Abstract
The success of many viruses depends upon cooperative interactions between viral genomes. However, whenever cooperation occurs, there is the potential for 'cheats' to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, the evolutionary theory of cheating could help us understand and manipulate viral dynamics, while viruses also offer new opportunities to study the evolution of cheating.
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Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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6
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Dziri S, Rodriguez C, Gerber A, Brichler S, Alloui C, Roulot D, Dény P, Pawlotsky JM, Gordien E, Le Gal F. Variable In Vivo Hepatitis D Virus (HDV) RNA Editing Rates According to the HDV Genotype. Viruses 2021; 13:v13081572. [PMID: 34452437 PMCID: PMC8402866 DOI: 10.3390/v13081572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/26/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022] Open
Abstract
Human hepatitis delta virus (HDV) is a small defective RNA satellite virus that requires hepatitis B virus (HBV) envelope proteins to form its own virions. The HDV genome possesses a single coding open reading frame (ORF), located on a replicative intermediate, the antigenome, encoding the small (s) and the large (L) isoforms of the delta antigen (s-HDAg and L-HDAg). The latter is produced following an editing process, changing the amber/stop codon on the s-HDAg-ORF into a tryptophan codon, allowing L-HDAg synthesis by the addition of 19 (or 20) C-terminal amino acids. The two delta proteins play different roles in the viral cell cycle: s-HDAg activates genome replication, while L-HDAg blocks replication and favors virion morphogenesis and propagation. L-HDAg has also been involved in HDV pathogenicity. Understanding the kinetics of viral editing rates in vivo is key to unravel the biology of the virus and understand its spread and natural history. We developed and validated a new assay based on next-generation sequencing and aimed at quantifying HDV RNA editing in plasma. We analyzed plasma samples from 219 patients infected with different HDV genotypes and showed that HDV editing capacity strongly depends on the genotype of the strain.
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Affiliation(s)
- Samira Dziri
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
| | - Christophe Rodriguez
- Centre National de référence des Hépatites Virales B, C et Delta, Département de Virologie, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris-Est, 94000 Créteil, France; (C.R.); (J.M.P.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Athenaïs Gerber
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
| | - Ségolène Brichler
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Chakib Alloui
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Dominique Roulot
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
- Unité d’hépatologie, Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris, Université Sorbonne-Paris-Cité, 93000 Bobigny, France
| | - Paul Dény
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052-UMR CNRS 5286, 69001 Lyon, France
| | - Jean Michel Pawlotsky
- Centre National de référence des Hépatites Virales B, C et Delta, Département de Virologie, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris-Est, 94000 Créteil, France; (C.R.); (J.M.P.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Emmanuel Gordien
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Frédéric Le Gal
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
- Correspondence:
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7
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López CB. Defective Viral Particles. Virology 2021. [DOI: 10.1002/9781119818526.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Johnson DM, Cubitt B, Pfeffer TL, de la Torre JC, Lukashevich IS. Lassa Virus Vaccine Candidate ML29 Generates Truncated Viral RNAs Which Contribute to Interfering Activity and Attenuation. Viruses 2021; 13:v13020214. [PMID: 33573250 PMCID: PMC7912207 DOI: 10.3390/v13020214] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/09/2021] [Accepted: 01/26/2021] [Indexed: 01/14/2023] Open
Abstract
Defective interfering particles (DIPs) are naturally occurring products during virus replication in infected cells. DIPs contain defective viral genomes (DVGs) and interfere with replication and propagation of their corresponding standard viral genomes by competing for viral and cellular resources, as well as promoting innate immune antiviral responses. Consequently, for many different viruses, including mammarenaviruses, DIPs play key roles in the outcome of infection. Due to their ability to broadly interfere with viral replication, DIPs are attractive tools for the development of a new generation of biologics to target genetically diverse and rapidly evolving viruses. Here, we provide evidence that in cells infected with the Lassa fever (LF) vaccine candidate ML29, a reassortant that carries the nucleoprotein (NP) and glycoprotein (GP) dominant antigens of the pathogenic Lassa virus (LASV) together with the L polymerase and Z matrix protein of the non-pathogenic genetically related Mopeia virus (MOPV), L-derived truncated RNA species are readily detected following infection at low multiplicity of infection (MOI) or in persistently-infected cells originally infected at high MOI. In the present study, we show that expression of green fluorescent protein (GFP) driven by a tri-segmented form of the mammarenavirus lymphocytic choriomeningitis virus (r3LCMV-GFP/GFP) was strongly inhibited in ML29-persistently infected cells, and that the magnitude of GFP suppression was dependent on the passage history of the ML29-persistently infected cells. In addition, we found that DIP-enriched ML29 was highly attenuated in immunocompetent CBA/J mice and in Hartley guinea pigs. Likewise, STAT-1-/- mice, a validated small animal model for human LF associated hearing loss sequelae, infected with DIP-enriched ML29 did not exhibit any hearing abnormalities throughout the observation period (62 days).
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Affiliation(s)
- Dylan M. Johnson
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
- Center for Predictive Medicine for Biodefense and Emerging Infectious diseases, University of Louisville, Louisville, KY 40202, USA;
- Correspondence: (D.M.J.); (I.S.L.)
| | - Beatrice Cubitt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (B.C.); (J.C.d.l.T.)
| | - Tia L. Pfeffer
- Center for Predictive Medicine for Biodefense and Emerging Infectious diseases, University of Louisville, Louisville, KY 40202, USA;
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, KY 402042, USA
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (B.C.); (J.C.d.l.T.)
| | - Igor S. Lukashevich
- Center for Predictive Medicine for Biodefense and Emerging Infectious diseases, University of Louisville, Louisville, KY 40202, USA;
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, KY 402042, USA
- Correspondence: (D.M.J.); (I.S.L.)
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9
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Ziegler CM, Botten JW. Defective Interfering Particles of Negative-Strand RNA Viruses. Trends Microbiol 2020; 28:554-565. [PMID: 32544442 PMCID: PMC7298151 DOI: 10.1016/j.tim.2020.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/27/2020] [Accepted: 02/25/2020] [Indexed: 12/14/2022]
Abstract
Viral defective interfering particles (DIPs) were intensely studied several decades ago but research waned leaving open many critical questions. New technologies and other advances led to a resurgence in DIP studies for negative-strand RNA viruses. While DIPs have long been recognized, their exact contribution to the outcome of acute or persistent viral infections has remained elusive. Recent studies have identified defective viral genomes (DVGs) in human infections, including respiratory syncytial virus and influenza, and growing evidence indicates that DVGs influence disease severity and may contribute to viral persistence. Further, several studies have advanced our understanding of key viral and host factors that regulate DIP formation and activity. Here we review these discoveries and highlight key questions moving forward.
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Affiliation(s)
- Christopher M Ziegler
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA
| | - Jason W Botten
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA; Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Vaccine Testing Center, University of Vermont, Burlington, VT 05405, USA.
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10
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Saad-Roy CM, McDermott AB, Grenfell BT. Dynamic Perspectives on the Search for a Universal Influenza Vaccine. J Infect Dis 2020; 219:S46-S56. [PMID: 30715467 DOI: 10.1093/infdis/jiz044] [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: 12/12/2022] Open
Abstract
A universal influenza vaccine (UIV) could considerably alleviate the public health burden of both seasonal and pandemic influenza. Although significant progress has been achieved in clarifying basic immunology and virology relating to UIV, several important questions relating to the dynamics of infection, immunity, and pathogen evolution remain unsolved. In this study, we review these gaps, which span integrative levels, from cellular to global and timescales from molecular events to decades. We argue that they can be best addressed by a tight integration of empirical (laboratory, epidemiological) research and theory and suggest fruitful areas for this synthesis. In particular, quantifying natural and vaccinal limitations on viral transmission are central to this effort.
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Affiliation(s)
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey.,Woodrow Wilson School of Public and International Affairs, Princeton University, New Jersey.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland
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11
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Mitarai N. How pirate phage interferes with helper phage: Comparison of the two distinct strategies. J Theor Biol 2019; 486:110096. [PMID: 31786182 DOI: 10.1016/j.jtbi.2019.110096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 11/26/2022]
Abstract
Pirate phages use the structural proteins encoded by unrelated helper phages to propagate. The best-studied example is the pirate P4 and helper P2 of coliphages, and it has been known that the Staphylococcus aureus pathogenicity islands (SaPIs) that can encode virulence factors act as pirate phages, too. When alone in the host, the pirate phages act as a prophage, but when the helper phage gene is also in the same host cell, the pirate phage has ability to exploit the helper phages structural proteins to produce pirate phage particles and spread, interfering with the helper phage production. The known helper phages in these systems are temperate phages. Interestingly, the interference of the pirate phage to the helper phage occurs in a different manner between the SaPI-helper system and the P4-P2 system. SaPIs cannot lyse a helper lysogen upon infection, while when a helper phage lyse a SaPI lysogen, most of the phage particles produced are the SaPI particles. On the contrary, in the P4-P2 system, a pirate phage P4 can lyse a helper P2 lysogen to produce mostly the P4 particles, while when P2 phage lyses a P4 lysogen, most of the produced phages are the P2 particles. Here, the consequences of these different strategies in the pirate and helper phage spreading among uninfected host is analyzed by using mathematical models. It is found that SaPI's strategy interferes with the helper phage spreading significantly more than the P4's strategy, because SaPI interferes with the helper phage's main reproduction step, while P4 interferes only by forcing the helper lysogens to lyse. However, the interference is found to be weaker in the spatially structured environment than in the well-mixed environment. This is because, in the spatial setting, the system tends to self-organize so that the helper phages take over the front of propagation due to the need of helper phage for the pirate phage spreading.
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Affiliation(s)
- Namiko Mitarai
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, 2100-DK, Denmark.
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12
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Abstract
Defective viral genomes (DVGs) are generated during viral replication and are unable to carry out a full replication cycle unless coinfected with a full-length virus. DVGs are produced by many viruses, and their presence correlates with alterations in infection outcomes. Historically, DVGs were studied for their ability to interfere with standard virus replication as well as for their association with viral persistence. More recently, a critical role for DVGs in inducing the innate immune response during infection was appreciated. Here we review the role of DVGs of RNA viruses in shaping outcomes of experimental as well as natural infections and explore the mechanisms by which DVGs impact infection outcome.
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Affiliation(s)
- Emmanuelle Genoyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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13
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Pinky L, Gonzalez-Parra G, Dobrovolny HM. Effect of stochasticity on coinfection dynamics of respiratory viruses. BMC Bioinformatics 2019; 20:191. [PMID: 30991939 PMCID: PMC6469119 DOI: 10.1186/s12859-019-2793-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/03/2019] [Indexed: 12/17/2022] Open
Abstract
Background Respiratory viral infections are a leading cause of mortality worldwide. As many as 40% of patients hospitalized with influenza-like illness are reported to be infected with more than one type of virus. However, it is not clear whether these infections are more severe than single viral infections. Mathematical models can be used to help us understand the dynamics of respiratory viral coinfections and their impact on the severity of the illness. Most models of viral infections use ordinary differential equations (ODE) that reproduce the average behavior of the infection, however, they might be inaccurate in predicting certain events because of the stochastic nature of viral replication cycle. Stochastic simulations of single virus infections have shown that there is an extinction probability that depends on the size of the initial viral inoculum and parameters that describe virus-cell interactions. Thus the coinfection dynamics predicted by the ODE might be difficult to observe in reality. Results In this work, a continuous-time Markov chain (CTMC) model is formulated to investigate probabilistic outcomes of coinfections. This CTMC model is based on our previous coinfection model, expressed in terms of a system of ordinary differential equations. Using the Gillespie method for stochastic simulation, we examine whether stochastic effects early in the infection can alter which virus dominates the infection. Conclusions We derive extinction probabilities for each virus individually as well as for the infection as a whole. We find that unlike the prediction of the ODE model, for similar initial growth rates stochasticity allows for a slower growing virus to out-compete a faster growing virus. Electronic supplementary material The online version of this article (10.1186/s12859-019-2793-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lubna Pinky
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, USA.,Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Hana M Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, USA.
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Attenuated Replication of Lassa Virus Vaccine Candidate ML29 in STAT-1 -/- Mice. Pathogens 2019; 8:pathogens8010009. [PMID: 30650607 PMCID: PMC6470856 DOI: 10.3390/pathogens8010009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 12/28/2018] [Accepted: 01/11/2019] [Indexed: 02/07/2023] Open
Abstract
Lassa virus (LASV), a highly prevalent mammalian arenavirus endemic in West Africa, can cause Lassa fever (LF), which is responsible for thousands of deaths annually. LASV is transmitted to humans from naturally infected rodents. At present, there is not an effective vaccine nor treatment. The genetic diversity of LASV is the greatest challenge for vaccine development. The reassortant ML29 carrying the L segment from the nonpathogenic Mopeia virus (MOPV) and the S segment from LASV is a vaccine candidate under current development. ML29 demonstrated complete protection in validated animal models against a Nigerian strain from clade II, which was responsible for the worst outbreak on record in 2018. This study demonstrated that ML29 was more attenuated than MOPV in STAT1-/- mice, a small animal model of human LF and its sequelae. ML29 infection of these mice resulted in more than a thousand-fold reduction in viremia and viral load in tissues and strong LASV-specific adaptive T cell responses compared to MOPV-infected mice. Persistent infection of Vero cells with ML29 resulted in generation of interfering particles (IPs), which strongly interfered with the replication of LASV, MOPV and LCMV, the prototype of the Arenaviridae. ML29 IPs induced potent cell-mediated immunity and were fully attenuated in STAT1-/- mice. Formulation of ML29 with IPs will improve the breadth of the host’s immune responses and further contribute to development of a pan-LASV vaccine with full coverage meeting the WHO requirements.
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