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Kakish JE, Mehrani Y, Kodeeswaran A, Geronimo K, Clark ME, van Vloten JP, Karimi K, Mallard BA, Meng B, Bridle BW, Knapp JP. Investigating the effect of reduced temperatures on the efficacy of rhabdovirus-based viral vector platforms. J Gen Virol 2024; 105. [PMID: 39172037 DOI: 10.1099/jgv.0.002010] [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] [Indexed: 08/23/2024] Open
Abstract
Rhabdoviral vectors can induce lysis of cancer cells. While studied almost exclusively at 37 °C, viruses are subject to a range of temperatures in vivo, including temperatures ≤31 °C. Despite potential implications, the effect of temperatures <37 °C on the performance of rhabdoviral vectors is unknown. We investigated the effect of low anatomical temperatures on two rhabdoviruses, vesicular stomatitis virus (VSV) and Maraba virus (MG1). Using a metabolic resazurin assay, VSV- and MG1-mediated oncolysis was characterized in a panel of cell lines at 28, 31, 34 and 37 °C. The oncolytic ability of both viruses was hindered at 31 and 28 °C. Cold adaptation of both viruses was attempted as a mitigation strategy. Viruses were serially passaged at decreasing temperatures in an attempt to induce mutations. Unfortunately, the cold-adaptation strategies failed to potentiate the oncolytic activity of the viruses at temperatures <37 °C. Interestingly, we discovered that viral replication was unaffected at low temperatures despite the abrogation of oncolytic activity. In contrast, the proliferation of cancer cells was reduced at low temperatures. Equivalent oncolytic effects could be achieved if cells at low temperatures were treated with viruses for longer times. This suggests that rhabdovirus-mediated oncolysis could be compromised at low temperatures in vivo where therapeutic windows are limited.
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Affiliation(s)
- Julia E Kakish
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Yeganeh Mehrani
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Arthane Kodeeswaran
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Katrina Geronimo
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mary Ellen Clark
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Jacob P van Vloten
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Khalil Karimi
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Bonnie A Mallard
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Byram W Bridle
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Jason P Knapp
- Department of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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2
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Aouadi W, Najburg V, Legendre R, Varet H, Kergoat L, Tangy F, Larrous F, Komarova AV, Bourhy H. Comparative analysis of rabies pathogenic and vaccine strains detection by RIG-I-like receptors. Microbes Infect 2024; 26:105321. [PMID: 38461968 DOI: 10.1016/j.micinf.2024.105321] [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: 11/21/2023] [Revised: 02/25/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Rabies virus (RABV) is a lethal neurotropic virus that causes 60,000 human deaths every year globally. RABV infection is characterized by the suppression of the interferon (IFN)-mediated antiviral response. However, molecular mechanisms leading to RABV sensing by RIG-I-like receptors (RLR) that initiates IFN signaling currently remain elusive. Here, we showed that RABV RNAs are primarily recognized by the RIG-I RLR, resulting in an IFN response in the infected cells, but this response varied according to the type of RABV used. Pathogenic RABV strain RNAs, Tha, were poorly detected in the cytosol by RIG-I and therefore caused a weak antiviral response. However, we revealed a strong IFN activity triggered by the attenuated RABV vaccine strain RNAs, SAD, mediated by RIG-I. We characterized two major 5' copy-back defective interfering (5'cb DI) genomes generated during SAD replication. Furthermore, we identified an interaction between 5'cb DI genomes, and RIG-I correlated with a high stimulation of the type I IFN signaling. This study indicates that wild-type RABV RNAs poorly activate the RIG-I pathway, while the presence of 5'cb DIs in the live-attenuated vaccine strain serves as an intrinsic adjuvant that strengthens its efficiency by enhancing RIG-I detection thus strongly stimulates the IFN response.
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Affiliation(s)
- Wahiba Aouadi
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, 75015 Paris, France
| | - Valérie Najburg
- Institut Pasteur, Université Paris Cité, Vaccines-innovation Laboratory, 75015 Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Hub Bioinformatics, and Biostatistics, 75015 Paris, France
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité, Hub Bioinformatics, and Biostatistics, 75015 Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, 75015 Paris, France
| | - Frédéric Tangy
- Institut Pasteur, Université Paris Cité, Vaccines-innovation Laboratory, 75015 Paris, France
| | - Florence Larrous
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, 75015 Paris, France
| | - Anastassia V Komarova
- Institut Pasteur, Université Paris Cité, Interactomics, RNA and Immunity Laboratory, 75015 Paris, France.
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, 75015 Paris, France.
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3
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Rüdiger D, Piasecka J, Küchler J, Pontes C, Laske T, Kupke SY, Reichl U. Mathematical model calibrated to in vitro data predicts mechanisms of antiviral action of the influenza defective interfering particle "OP7". iScience 2024; 27:109421. [PMID: 38523782 PMCID: PMC10959662 DOI: 10.1016/j.isci.2024.109421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
Defective interfering particles (DIPs) are regarded as potent broad-spectrum antivirals. We developed a mathematical model that describes intracellular co-infection dynamics of influenza standard virus (STV) and "OP7", a new type of influenza DIP discovered recently. Based on experimental data from in vitro studies to calibrate the model and confirm its predictions, we deduce OP7's mechanisms of interference, which were yet unknown. Simulations suggest that the "superpromoter" on OP7 genomic viral RNA enhances its replication and results in a depletion of viral proteins. This reduces STV genomic RNA replication, which appears to constitute an antiviral effect. Further, a defective viral protein (M1-OP7) likely causes the deficiency of OP7's replication. It appears unable to bind to genomic viral RNAs to facilitate their nuclear export, a critical step in the viral life cycle. An improved understanding of OP7's antiviral mechanism is crucial toward application in humans as a prospective antiviral treatment strategy.
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Affiliation(s)
- Daniel Rüdiger
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Julita Piasecka
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Jan Küchler
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Carolina Pontes
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Tanja Laske
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
- Institute for Computational Systems Biology, University of Hamburg, 20148 Hamburg, Germany
| | - Sascha Y. Kupke
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Udo Reichl
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
- Chair of Bioprocess Engineering, Otto-von-Guericke University, 39106 Magdeburg, Saxony-Anhalt, Germany
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4
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Chen BJ, Lin CH, Wu HY, Cai JJ, Chao DY. Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer. Microbiol Spectr 2024; 12:e0395423. [PMID: 38483513 PMCID: PMC10986531 DOI: 10.1128/spectrum.03954-23] [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: 11/15/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
Coronaviruses (CoVs), including severe acute respiratory syndrome coronavirus 2, can infect a variety of mammalian and avian hosts with significant medical and economic consequences. During the life cycle of CoV, a coordinated series of subgenomic RNAs, including canonical subgenomic messenger RNA and non-canonical defective viral genomes (DVGs), are generated with different biological implications. Studies that adopted the Nanopore sequencer (ONT) to investigate the landscape and dynamics of viral RNA subgenomic transcriptomes applied arbitrary bioinformatics parameters without justification or experimental validation. The current study used bovine coronavirus (BCoV), which can be performed under biosafety level 2 for library construction and experimental validation using traditional colony polymerase chain reaction and Sanger sequencing. Four different ONT protocols, including RNA direct and cDNA direct sequencing with or without exonuclease treatment, were used to generate RNA transcriptomic libraries from BCoV-infected cell lysates. Through rigorously examining the k-mer, gap size, segment size, and bin size, the optimal cutoffs for the bioinformatic pipeline were determined to remove the sequence noise while keeping the informative DVG reads. The sensitivity and specificity of identifying DVG reads using the proposed pipeline can reach 82.6% and 99.6% under the k-mer size cutoff of 15. Exonuclease treatment reduced the abundance of RNA transcripts; however, it was not necessary for future library preparation. Additional recovery of clipped BCoV nucleotide sequences with experimental validation expands the landscape of the CoV discontinuous RNA transcriptome, whose biological function requires future investigation. The results of this study provide the benchmarks for library construction and bioinformatic parameters for studying the discontinuous CoV RNA transcriptome.IMPORTANCEFunctional defective viral genomic RNA, containing all the cis-acting elements required for translation or replication, may play different roles in triggering cell innate immune signaling, interfering with the canonical subgenomic messenger RNA transcription/translation or assisting in establishing persistence infection. This study does not only provide benchmarks for library construction and bioinformatic parameters for studying the discontinuous coronavirus RNA transcriptome but also reveals the complexity of the bovine coronavirus transcriptome, whose functional assays will be critical in future studies.
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Affiliation(s)
- Bo-Jia Chen
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - James J. Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Day-Yu Chao
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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5
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Xu Z, Peng Q, Song J, Zhang H, Wei D, Demongeot J, Zeng Q. Bioinformatic analysis of defective viral genomes in SARS-CoV-2 and its impact on population infection characteristics. Front Immunol 2024; 15:1341906. [PMID: 38348041 PMCID: PMC10859446 DOI: 10.3389/fimmu.2024.1341906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
DVGs (Defective Viral Genomes) are prevalent in RNA virus infections. In this investigation, we conducted an analysis of high-throughput sequencing data and observed widespread presence of DVGs in SARS-CoV-2. Comparative analysis between SARS-CoV-2 and diverse DNA viruses revealed heightened susceptibility to damage and increased sequencing sample heterogeneity within the SARS-CoV-2 genome. Whole-genome sequencing depth variability analysis exhibited a higher coefficient of variation for SARS-CoV-2, while DVG analysis indicated a significant proportion of recombination sites, signifying notable genome heterogeneity and suggesting that a large proportion of assembled virus particles contain incomplete RNA sequences. Moreover, our investigation explored the sequencing depth and DVG content differences among various strains. Our findings revealed that as the virus evolves, there is a notable increase in the proportion of intact genomes within virus particles, as evidenced by third-generation sequencing data. Specifically, the proportion of intact genome in the Omicron strain surpassed that of the Delta and Alpha strains. This observation effectively elucidates the heightened infectiousness of the Omicron strain compared to the Delta and Alpha strains. We also postulate that this improvement in completeness stems from enhanced virus assembly capacity, as the Omicron strain can promptly facilitate the binding of RNA and capsid protein, thereby reducing the exposure time of vulnerable virus RNA in the host environment and significantly mitigating its degradation. Finally, employing mathematical modeling, we simulated the impact of DVG effects under varying environmental factors on infection characteristics and population evolution. Our findings provide an explanation for the close association between symptom severity and the extent of virus invasion, as well as the substantial disparity in population infection characteristics caused by the same strain under distinct environmental conditions. This study presents a novel approach for future virus research and vaccine development.
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Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou, China
| | - Qingzhi Peng
- Department of Life Science, Dezhou University, Dezhou, China
| | - Jian Song
- Department of Life Science, Dezhou University, Dezhou, China
| | - Hongmei Zhang
- Department of Life Science, Dezhou University, Dezhou, China
| | - Dongqing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, China
- Peng Cheng National Laboratory, Shenzhen, Guangdong, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), F-38700 La Tronche, France
| | - Qiangcheng Zeng
- Department of Life Science, Dezhou University, Dezhou, China
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6
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Andres FGM, Pfaller CK. Molecular Analysis of Copy-Back Defective Interfering RNAs of Morbilliviruses. Methods Mol Biol 2024; 2808:71-88. [PMID: 38743363 DOI: 10.1007/978-1-0716-3870-5_6] [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] [Indexed: 05/16/2024]
Abstract
Copy-back defective interfering RNAs are major contaminants of viral stock preparations of morbilliviruses and other negative strand RNA viruses. They are hybrid molecules of positive sense antigenome and negative sense genome. They possess perfectly complementary ends allowing the formation of extremely stable double-stranded RNA panhandle structures. The presence of the 3'-terminal promoter allows replication of these molecules by the viral polymerase. They thereby negatively interfere with replication of standard genomes. In addition, the double-stranded RNA stem structures are highly immunostimulatory and activate antiviral cell-intrinsic innate immune responses. Thus, copy-back defective interfering RNAs severely affect the virulence and pathogenesis of morbillivirus stocks. We describe two biochemical methods to analyze copy-back defective interfering RNAs in virus-infected samples, or purified viral RNA. First, we present our Northern blotting protocol that allows accurate size determination of defective interfering RNA molecules and estimation of the relative contamination level of virus preparations. Second, we describe a PCR approach to amplify defective interfering RNAs specifically, which allows detailed sequence analysis.
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Affiliation(s)
- Felix G M Andres
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | - Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany.
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
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7
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Cheng H, Zhang H, Cai H, Liu M, Wen S, Ren J. Molecular biology of canine parainfluenza virus V protein and its potential applications in tumor immunotherapy. Front Microbiol 2023; 14:1282112. [PMID: 38173672 PMCID: PMC10761501 DOI: 10.3389/fmicb.2023.1282112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Canine parainfluenza virus (CPIV) is a zoonotic virus that is widely distributed and is the main pathogen causing canine infectious respiratory disease (CIRD), also known as "kennel cough," in dogs. The CPIV-V protein is the only nonstructural protein of the virus and plays an important role in multiple stages of the virus life cycle by inhibiting apoptosis, altering the host cell cycle and interfering with the interferon response. In addition, studies have shown that the V protein has potential applications in the field of immunotherapy in oncolytic virus therapy or self-amplifying RNA vaccines. In this review, the biosynthesis, structural characteristics and functions of the CPIV-V protein are reviewed with an emphasis on how it facilitates viral immune escape and its potential applications in the field of immunotherapy. Therefore, this review provides a scientific basis for research into the CPIV-V protein and its potential applications.
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Affiliation(s)
- Huai Cheng
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Hewei Zhang
- College of Food and Drugs, Luoyang Polytechnic, Luoyang, China
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang, China
| | - Huanchang Cai
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Min Liu
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Shubo Wen
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China
| | - Jingqiang Ren
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang, China
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8
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Dogra T, Pelz L, Boehme JD, Kuechler J, Kershaw O, Marichal-Gallardo P, Baelkner M, Hein MD, Gruber AD, Benndorf D, Genzel Y, Bruder D, Kupke SY, Reichl U. Generation of "OP7 chimera" defective interfering influenza A particle preparations free of infectious virus that show antiviral efficacy in mice. Sci Rep 2023; 13:20936. [PMID: 38017026 PMCID: PMC10684881 DOI: 10.1038/s41598-023-47547-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023] Open
Abstract
Influenza A virus (IAV) defective interfering particles (DIPs) are considered as new promising antiviral agents. Conventional DIPs (cDIPs) contain a deletion in the genome and can only replicate upon co-infection with infectious standard virus (STV), during which they suppress STV replication. We previously discovered a new type of IAV DIP "OP7" that entails genomic point mutations and displays higher antiviral efficacy than cDIPs. To avoid safety concerns for the medical use of OP7 preparations, we developed a production system that does not depend on infectious IAV. We reconstituted a mixture of DIPs consisting of cDIPs and OP7 chimera DIPs, in which both harbor a deletion in their genome. To complement the defect, the deleted viral protein is expressed by the suspension cell line used for production in shake flasks. Here, DIP preparations harvested are not contaminated with infectious virions, and the fraction of OP7 chimera DIPs depended on the multiplicity of infection. Intranasal administration of OP7 chimera DIP material was well tolerated in mice. A rescue from an otherwise lethal IAV infection and no signs of disease upon OP7 chimera DIP co-infection demonstrated the remarkable antiviral efficacy. The clinical development of this new class of broad-spectrum antiviral may contribute to pandemic preparedness.
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Affiliation(s)
- Tanya Dogra
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Lars Pelz
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Julia D Boehme
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto Von Guericke University Magdeburg, Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jan Kuechler
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Olivia Kershaw
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Pavel Marichal-Gallardo
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Maike Baelkner
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto Von Guericke University Magdeburg, Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marc D Hein
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Magdeburg, Germany
| | - Achim D Gruber
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Dirk Benndorf
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Dunja Bruder
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto Von Guericke University Magdeburg, Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sascha Y Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Magdeburg, Germany
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9
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Hackbart M, López CB. S RNA Intergenic Deletions Drive Viral Interference during Arenavirus Infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564889. [PMID: 37961573 PMCID: PMC10635013 DOI: 10.1101/2023.10.31.564889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Arenaviruses, a family of negative-sense RNA viruses spread by rodents, are a leading cause of severe hemorrhagic fever in humans. Due to a paucity of antivirals and vaccines for arenaviruses, there is a need to identify new mechanisms for interfering with arenavirus replication. In several negative-sense RNA viruses, natural viral interference results from the production of non-standard viral genomes (nsVGs) that activate the innate immune system and/or compete for essential viral products. Although it is well established that arenaviruses produce strong interfering activities, it is unknown if they produce interfering nsVGs. Here we show that arenaviruses produce deletions within the intergenic region of their Small (S) RNA genome, which prevents the production of viral mRNA and protein. These deletions are more abundant when arenaviruses are grown in high-interfering conditions and are associated with inhibited viral replication. Overall, we found that arenaviruses produce internal deletions within the S RNA intergenic region that are produced by arenaviruses and can block viral replication. These natural arenavirus interfering molecules provide a new target for the generation of antivirals as well as an alternative strategy for producing attenuated arenaviruses for vaccines.
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Affiliation(s)
- Matthew Hackbart
- Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine, St. MO
| | - Carolina B. López
- Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine, St. MO
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10
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Pelz L, Piagnani E, Marsall P, Wynserski N, Hein MD, Marichal-Gallardo P, Kupke SY, Reichl U. Broad-Spectrum Antiviral Activity of Influenza A Defective Interfering Particles against Respiratory Syncytial, Yellow Fever, and Zika Virus Replication In Vitro. Viruses 2023; 15:1872. [PMID: 37766278 PMCID: PMC10537524 DOI: 10.3390/v15091872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
New broadly acting and readily available antiviral agents are needed to combat existing and emerging viruses. Defective interfering particles (DIPs) of influenza A virus (IAV) are regarded as promising options for the prevention and treatment of IAV infections. Interestingly, IAV DIPs also inhibit unrelated viral infections by stimulating antiviral innate immunity. Here, we tested the ability of IAV DIPs to suppress respiratory syncytial, yellow fever and Zika virus infections in vitro. In human lung (A549) cells, IAV DIP co-infection inhibited the replication and spread of all three viruses. In contrast, we observed no antiviral activity in Vero cells, which are deficient in the production of interferon (IFN), demonstrating its importance for the antiviral effect. Further, in A549 cells, we observed an enhanced type-I and type-III IFN response upon co-infection that appears to explain the antiviral potential of IAV DIPs. Finally, a lack of antiviral activity in the presence of the Janus kinase 1/2 (JAK1/2) inhibitor ruxolitinib was detected. This revealed a dependency of the antiviral activity on the JAK/signal transducers and activators of transcription (STAT) signaling pathway. Overall, this study supports the notion that IAV DIPs may be used as broad-spectrum antivirals to treat infections with a variety of IFN-sensitive viruses, particularly respiratory viruses.
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Affiliation(s)
- Lars Pelz
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Elena Piagnani
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Patrick Marsall
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Nancy Wynserski
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Marc Dominique Hein
- Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Pavel Marichal-Gallardo
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Sascha Young Kupke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
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11
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Noffel Z, Dobrovolny HM. Quantifying the effect of defective viral genomes in respiratory syncytial virus infections. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:12666-12681. [PMID: 37501460 DOI: 10.3934/mbe.2023564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Defective viral genomes (DVGs) are viral genomes that contain only a partial viral RNA and so cannot replicate within cells on their own. If a cell containing DVGs is subsequently infected with a complete viral genome, the DVG can then use the missing proteins expressed by the full genome in order to replicate itself. Since the cell is producing defective genomes, it has less resources to produce fully functional virions and thus release of complete virions is often suppressed. Here, we use data from challenge studies of respiratory syncytial virus (RSV) in healthy adults to quantify the effect of DVGs. We use a mathematical model to fit the data, finding that late onset of DVGs and prolonged DVG detection are associated with lower infection rates and higher clearance rates. This result could have implications for the use of DVGs as a therapeutic.
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Affiliation(s)
- Zakarya Noffel
- Department of Computer Science, University of Texas at Austin, Austin, TX, US
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, US
| | - Hana M Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, US
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12
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Delima GK, Ganti K, Holmes KE, Shartouny JR, Lowen AC. Influenza A virus coinfection dynamics are shaped by distinct virus-virus interactions within and between cells. PLoS Pathog 2023; 19:e1010978. [PMID: 36862762 PMCID: PMC10013887 DOI: 10.1371/journal.ppat.1010978] [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: 11/07/2022] [Revised: 03/14/2023] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
When multiple viral populations propagate within the same host environment, they often shape each other's dynamics. These interactions can be positive or negative and can occur at multiple scales, from coinfection of a cell to co-circulation at a global population level. For influenza A viruses (IAVs), the delivery of multiple viral genomes to a cell substantially increases burst size. However, despite its relevance for IAV evolution through reassortment, the implications of this positive density dependence for coinfection between distinct IAVs has not been explored. Furthermore, the extent to which these interactions within the cell shape viral dynamics at the level of the host remains unclear. Here we show that, within cells, diverse coinfecting IAVs strongly augment the replication of a focal strain, irrespective of their homology to the focal strain. Coinfecting viruses with a low intrinsic reliance on multiple infection offer the greatest benefit. Nevertheless, virus-virus interactions at the level of the whole host are antagonistic. This antagonism is recapitulated in cell culture when the coinfecting virus is introduced several hours prior to the focal strain or under conditions conducive to multiple rounds of viral replication. Together, these data suggest that beneficial virus-virus interactions within cells are counterbalanced by competition for susceptible cells during viral propagation through a tissue. The integration of virus-virus interactions across scales is critical in defining the outcomes of viral coinfection.
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Affiliation(s)
- Gabrielle K. Delima
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Katie E. Holmes
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jessica R. Shartouny
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
- * E-mail:
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13
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Budzyńska D, Zwart MP, Hasiów-Jaroszewska B. Defective RNA Particles of Plant Viruses-Origin, Structure and Role in Pathogenesis. Viruses 2022; 14:v14122814. [PMID: 36560818 PMCID: PMC9786237 DOI: 10.3390/v14122814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The genomes of RNA viruses may be monopartite or multipartite, and sub-genomic particles such as defective RNAs (D RNAs) or satellite RNAs (satRNAs) can be associated with some of them. D RNAs are small, deletion mutants of a virus that have lost essential functions for independent replication, encapsidation and/or movement. D RNAs are common elements associated with human and animal viruses, and they have been described for numerous plant viruses so far. Over 30 years of studies on D RNAs allow for some general conclusions to be drawn. First, the essential condition for D RNA formation is prolonged passaging of the virus at a high cellular multiplicity of infection (MOI) in one host. Second, recombination plays crucial roles in D RNA formation. Moreover, during virus propagation, D RNAs evolve, and the composition of the particle depends on, e.g., host plant, virus isolate or number of passages. Defective RNAs are often engaged in transient interactions with full-length viruses-they can modulate accumulation, infection dynamics and virulence, and are widely used, i.e., as a tool for research on cis-acting elements crucial for viral replication. Nevertheless, many questions regarding the generation and role of D RNAs in pathogenesis remain open. In this review, we summarise the knowledge about D RNAs of plant viruses obtained so far.
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Affiliation(s)
- Daria Budzyńska
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Wl Wegorka 20, 60-318 Poznan, Poland
| | - Mark P. Zwart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Wl Wegorka 20, 60-318 Poznan, Poland
- Correspondence:
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Defective Interfering Particles of Influenza Virus and Their Characteristics, Impacts, and Use in Vaccines and Antiviral Strategies: A Systematic Review. Viruses 2022; 14:v14122773. [PMID: 36560777 PMCID: PMC9781619 DOI: 10.3390/v14122773] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Defective interfering particles (DIPs) are particles containing defective viral genomes (DVGs) generated during viral replication. DIPs have been found in various RNA viruses, especially in influenza viruses. Evidence indicates that DIPs interfere with the replication and encapsulation of wild-type viruses, namely standard viruses (STVs) that contain full-length viral genomes. DIPs may also activate the innate immune response by stimulating interferon synthesis. In this review, the underlying generation mechanisms and characteristics of influenza virus DIPs are summarized. We also discuss the potential impact of DIPs on the immunogenicity of live attenuated influenza vaccines (LAIVs) and development of influenza vaccines based on NS1 gene-defective DIPs. Finally, we review the antiviral strategies based on influenza virus DIPs that have been used against both influenza virus and SARS-CoV-2. This review provides systematic insights into the theory and application of influenza virus DIPs.
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15
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Wen Y, Xu H, Wan W, Shang W, Jin R, Zhou F, Mei H, Wang J, Xiao G, Chen H, Wu X, Zhang L. Visualizing lymphocytic choriomeningitis virus infection in cells and living mice. iScience 2022; 25:105090. [PMID: 36185356 PMCID: PMC9519613 DOI: 10.1016/j.isci.2022.105090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/31/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Mammarenavirus are a large family of enveloped negative-strand RNA viruses that include several agents responsible for severe hemorrhagic fevers. Until now, no FDA-licensed drug has been admitted for treating an arenavirus infection, and only few effective anti-arenavirus drugs have been tested in vivo. In this work, we designed a recombinant reporter arenavirus lymphocytic choriomeningitis virus that stably expressed nanoluciferase (LCMV-Nluc). The LCMV-Nluc was proved to share similar biological properties with wild-type LCMV and the Nluc intensity reliably reflected viral replication both in vitro and in vivo. Replication of the Nluc-encoding virus in living mice can be visualized by real-time bioluminescent imaging, and bioluminescence can be detected in a variety of organs of infected mice. This work provides a novel approach that enables real-time study of the arenavirus infection and is a convenient and valuable tool for screening of compounds that are active against arenaviruses in vitro and in living mice. LCMV-Nluc was constructed and shared similar biological properties with LCMV-WT Replication of the LCMV-Nluc can be visualized by real-time bioluminescent imaging LCMV-Nluc is a valuable tool for screening antiviral compounds in vitro LCMV-Nluc is successfully applied for screening antiviral compounds in vivo
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Affiliation(s)
- Yuxi Wen
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Huan Xu
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Weiwei Wan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Runming Jin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Fen Zhou
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Heng Mei
- Institute of Haematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Clinical and Research Centre of Thrombosis and Haemostasis, Wuhan, China
| | - Jingshi Wang
- Department of Hematology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongbo Chen
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiaoyan Wu
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Hubei Jiangxia Laboratory,Wuhan 430000, China
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16
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Zadeh VR, Afowowe TO, Abe H, Urata S, Yasuda J. Potential and action mechanism of favipiravir as an antiviral against Junin virus. PLoS Pathog 2022; 18:e1010689. [PMID: 35816544 PMCID: PMC9302769 DOI: 10.1371/journal.ppat.1010689] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 07/21/2022] [Accepted: 06/19/2022] [Indexed: 12/26/2022] Open
Abstract
Favipiravir is a nucleoside analogue that inhibits the replication and transcription of a broad spectrum of RNA viruses, including pathogenic arenaviruses. In this study, we isolated a favipiravir-resistant mutant of Junin virus (JUNV), which is the causative agent of Argentine hemorrhagic fever, and analyzed the antiviral mechanism of favipiravir against JUNV. Two amino acid substitutions, N462D in the RNA-dependent RNA polymerase (RdRp) and A168T in the glycoprotein precursor GPC, were identified in the mutant. GPC-A168T substitution enhanced the efficiency of JUNV internalization, which explains the robust replication kinetics of the mutant in the virus growth analysis. Although RdRp-N462D substitution did not affect polymerase activity levels in a minigenome system, comparisons of RdRp error frequencies showed that the virus with RdRp-D462 possessed a significantly higher fidelity. Our next generation sequence (NGS) analysis showed a gradual accumulation of both mutations as we passaged the virus in presence of favipiravir. We also provided experimental evidence for the first time that favipiravir inhibited JUNV through the accumulation of transition mutations, confirming its role as a purine analogue against arenaviruses. Moreover, we showed that treatment with a combination of favipiravir and either ribavirin or remdesivir inhibited JUNV replication in a synergistic manner, blocking the generation of the drug-resistant mutant. Our findings provide new insights for the clinical management and treatment of Argentine hemorrhagic fever. Development of antivirals requires cautious and extensive assessment of action mechanism as well as potential for emergence of resistant phenotype of the virus. In recent years, favipiravir has been put forward as a promising candidate for the treatment of Argentine hemorrhagic fever (AHF) caused by Junin virus (JUNV). We, therefore, aimed to provide experimental evidence on action mechanism of favipiravir to help guide its clinical use. Here we show that favipiravir causes lethal mutation that impairs virus infectivity. More importantly, we demonstrate that the virus has the capability to escape favipiravir selective pressure by acquiring two amino acid substitutions on glycoprotein precursor and polymerase proteins. This observation raises concern over the use of only favipiravir in therapeutic regimens. To overcome this risk, we show that combination of favipiravir with other nucleoside analogues demonstrates a synergistic effect and suppresses the ability of JUNV to escape drug pressure. Favipiravir, ribavirin, and remdesivir have a broad spectrum of antiviral activity. Therefore, combination therapies of these drugs would be expected to have potential therapeutic effects for not only AHF but also the diseases caused by a variety of viruses, including emerging RNA viruses.
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Affiliation(s)
- Vahid Rajabali Zadeh
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Tosin Oladipo Afowowe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Shuzo Urata
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
- * E-mail:
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17
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A Virus Is a Community: Diversity within Negative-Sense RNA Virus Populations. Microbiol Mol Biol Rev 2022; 86:e0008621. [PMID: 35658541 DOI: 10.1128/mmbr.00086-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Negative-sense RNA virus populations are composed of diverse viral components that interact to form a community and shape the outcome of virus infections. At the genomic level, RNA virus populations consist not only of a homogeneous population of standard viral genomes but also of an extremely large number of genome variants, termed viral quasispecies, and nonstandard viral genomes, which include copy-back viral genomes, deletion viral genomes, mini viral RNAs, and hypermutated RNAs. At the particle level, RNA virus populations are composed of pleomorphic particles, particles missing or having additional genomes, and single particles or particle aggregates. As we continue discovering more about the components of negative-sense RNA virus populations and their crucial functions during virus infection, it will become more important to study RNA virus populations as a whole rather than their individual parts. In this review, we will discuss what is known about the components of negative-sense RNA virus communities, speculate how the components of the virus community interact, and summarize what vaccines and antiviral therapies are being currently developed to target or harness these components.
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18
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Olmo-Uceda MJ, Muñoz-Sánchez JC, Lasso-Giraldo W, Arnau V, Díaz-Villanueva W, Elena SF. DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data. Viruses 2022; 14:v14051114. [PMID: 35632855 PMCID: PMC9144107 DOI: 10.3390/v14051114] [Citation(s) in RCA: 2] [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: 05/02/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing (HTS) data has become an interesting computational problem. Several algorithms have been proposed to accomplish this goal, though all incur false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. We present a metasearch tool, DVGfinder, that wraps the two most commonly used DVG search algorithms in a single workflow for the identification of the DVGs in HTS data. DVGfinder processes the results of ViReMa-a and DI-tector and uses a gradient boosting classifier machine learning algorithm to reduce the number of false-positive events. The program also generates output files in user-friendly HTML format, which can help users to explore the DVGs identified in the sample. We evaluated the performance of DVGfinder compared to the two search algorithms used separately and found that it slightly improves sensitivities for low-coverage synthetic HTS data and DI-tector precision for high-coverage samples. The metasearch program also showed higher sensitivity on a real sample for which a set of copy-backs were previously validated.
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Affiliation(s)
- Maria J. Olmo-Uceda
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Juan C. Muñoz-Sánchez
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Wilberth Lasso-Giraldo
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Vicente Arnau
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Wladimiro Díaz-Villanueva
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Correspondence: ; Tel.: +34-963-544-779
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19
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Data-driven models for replication kinetics of Orthohantavirus infections. Math Biosci 2022; 349:108834. [DOI: 10.1016/j.mbs.2022.108834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/16/2022]
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20
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Defective Interfering Viral Particle Treatment Reduces Clinical Signs and Protects Hamsters from Lethal Nipah Virus Disease. mBio 2022; 13:e0329421. [PMID: 35297677 PMCID: PMC9040845 DOI: 10.1128/mbio.03294-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Defective interfering particles (DIs) contain a considerably smaller genome than the parental virus but retain replication competency. As DIs can directly or indirectly alter propagation kinetics of the parental virus, they offer a novel approach to antiviral therapy, capitalizing on knowledge from natural infection. However, efforts to translate in vitro inhibition to in vivo screening models remain limited. We investigated the efficacy of virus-like particles containing DI genomes (therapeutic infectious particles [TIPs]) in the Syrian hamster model of lethal Nipah virus (NiV) disease. We found that coadministering a high dose of TIPs intraperitoneally with virus challenge improved clinical course and reduced lethality. To mimic natural exposure, we also evaluated lower-dose TIP delivery and virus challenge intranasally, finding equally efficacious reduction in disease severity and overall lethality. Eliminating TIP replicative capacity decreased efficacy, suggesting protection via direct inhibition. These data provide evidence that TIP-mediated treatment can confer protection against disease and lethal outcome in a robust animal NiV model, supporting further development of TIP treatment for NiV and other high-consequence pathogens. IMPORTANCE Here, we demonstrate that treatment with defective interfering particles (DIs), a natural by-product of viral infection, can significantly improve the clinical course and outcome of viral disease. When present with their parental virus, DIs can directly or indirectly alter viral propagation kinetics and exert potent inhibitory properties in cell culture. We evaluated the efficacy of a selection of virus-like particles containing DI genomes (TIPs) delivered intranasally in a lethal hamster model of Nipah virus disease. We demonstrate significantly improved clinical outcomes, including reduction in both lethality and the appearance of clinical signs. This work provides key efficacy data in a robust model of Nipah virus disease to support further development of TIP-mediated treatment against high-consequence viral pathogens.
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21
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Chen YG, Hur S. Cellular origins of dsRNA, their recognition and consequences. Nat Rev Mol Cell Biol 2021; 23:286-301. [PMID: 34815573 DOI: 10.1038/s41580-021-00430-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2021] [Indexed: 01/02/2023]
Abstract
Double-stranded RNA (dsRNA) is associated with most viral infections - it either constitutes the viral genome (in the case of dsRNA viruses) or is generated in host cells during viral replication. Hence, nearly all organisms have the capability of recognizing dsRNA and mounting a response, the primary aim of which is to mitigate the potential infection. In vertebrates, a set of innate immune receptors for dsRNA induce a multitude of cell-intrinsic and cell-extrinsic immune responses upon dsRNA recognition. Notably, recent studies showed that vertebrate cells can accumulate self-derived dsRNAs or dsRNA-like species upon dysregulation of several cellular processes, activating the very same immune pathways as in infected cells. On the one hand, such aberrant immune activation in the absence of infection can lead to pathogenesis of immune disorders, such as Aicardi-Goutières syndrome. On the other hand, the same innate immune reaction can be induced in a controlled setting for a therapeutic benefit, as occurs in immunotherapies. In this Review, we describe mechanisms by which immunostimulatory dsRNAs are generated in mammalian cells, either by viruses or by the host cells, and how cells respond to them, with the focus on recent developments regarding the role of cellular dsRNAs in immune modulation.
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Affiliation(s)
- Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Sun Hur
- Harvard Medical School & Boston Children's Hospital, Boston, MA, USA.
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22
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Effect of NV gene deletion in the genome of hirame rhabdovirus (HIRRV) on viral replication and the type I interferon response of the host cell. Arch Virol 2021; 167:77-84. [PMID: 34709467 DOI: 10.1007/s00705-021-05286-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Hirame rhabdovirus (HIRRV), a member of the genus Novirhabdovirus, causes morbidity and mortality in farmed olive flounder (Paralichthys olivaceus). As no information is available on the role of the NV gene of HIRRV, we produced a recombinant HIRRV with the NV gene deleted (rHIRRV-ΔNV) using reverse genetic technology and investigated whether the NV gene knockout affected HIRRV replication and the type I interferon response of the host cell. The rescue of rHIRRV-ΔNV was successful only when IRF9-gene-knockout Epithelioma papulosum cyprini (ΔIRF9-EPC) cells were used, suggesting that the NV protein of HIRRV might be involved in inhibition of the type I interferon response of the host cell. This conclusion was also supported by the significantly higher level of Mx gene induction in EPC cells infected with rHIRRV-ΔNV than in cells infected with recombinant HIRRV without the deletion. When cells were coinfected with rHIRRV-ΔNV and either wild-type HIRRV or wild-type viral hemorrhagic septicemia virus (VHSV), there was a decrease in the growth rate of not only wild-type HIRRV but also wild-type VHSV in a concentration-dependent manner. Further studies are required to investigate the role of HIRRV NV in virulence and its possible importance for the development of attenuated vaccines.
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23
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Greninger AL, Rybkina K, Lin MJ, Drew-Bear J, Marcink TC, Shean RC, Makhsous N, Boeckh M, Harder O, Bovier F, Burstein SR, Niewiesk S, Rima BK, Porotto M, Moscona A. Human parainfluenza virus evolution during lung infection of immunocompromised humans promotes viral persistence. J Clin Invest 2021; 131:150506. [PMID: 34609969 DOI: 10.1172/jci150506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
The capacity of respiratory viruses to undergo evolution within the respiratory tract raises the possibility of evolution under the selective pressure of the host environment or drug treatment. Long-term infections in immunocompromised hosts are potential drivers of viral evolution and development of infectious variants. We show that intra-host evolution in chronic human parainfluenza virus 3 (HPIV3) infection in immunocompromised individuals elicited mutations that favor viral entry and persistence, suggesting that similar processes may operate across enveloped respiratory viruses. We profiled longitudinal HPIV3 infections from two immunocompromised individuals that persisted for 278 and 98 days. Mutations accrued in the HPIV3 attachment protein hemagglutinin-neuraminidase (HN), including the first in vivo mutation in HN's receptor binding site responsible for activating the viral fusion process. Fixation of this mutation was associated with exposure to a drug that cleaves host cell sialic acid moieties. Longitudinal adaptation of HN was associated with features that promote viral entry and persistence in cells, including greater avidity for sialic acid and more active fusion activity in vitro, but not with antibody escape. Long term infection thus led to mutations promoting viral persistence, suggesting that host-directed therapeutics may support the evolution of viruses that alter their biophysical characteristics to persist in the face of these agents in vivo.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Ksenia Rybkina
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Jennifer Drew-Bear
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Tara C Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Ryan C Shean
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Negar Makhsous
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Olivia Harder
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, United States of America
| | - Francesca Bovier
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Shana R Burstein
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Stefan Niewiesk
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, United States of America
| | - Bert K Rima
- School of Medicine Dentistry and Biomedical Sceinces, Queen's University of Belfast, Belfast, United Kingdom
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Anne Moscona
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
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24
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Suomalainen M, Greber UF. Virus Infection Variability by Single-Cell Profiling. Viruses 2021; 13:1568. [PMID: 34452433 PMCID: PMC8402812 DOI: 10.3390/v13081568] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/05/2021] [Indexed: 12/15/2022] Open
Abstract
Cell-to-cell variability of infection has long been known, yet it has remained one of the least understood phenomena in infection research. It impacts on disease onset and development, yet only recently underlying mechanisms have been studied in clonal cell cultures by single-virion immunofluorescence microscopy and flow cytometry. In this review, we showcase how single-cell RNA sequencing (scRNA-seq), single-molecule RNA-fluorescence in situ hybridization (FISH), and copper(I)-catalyzed azide-alkyne cycloaddition (click) with alkynyl-tagged viral genomes dissect infection variability in human and mouse cells. We show how the combined use of scRNA-FISH and click-chemistry reveals highly variable onsets of adenoviral gene expression, and how single live cell plaques reveal lytic and nonlytic adenovirus transmissions. The review highlights how scRNA-seq profiling and scRNA-FISH of coxsackie, influenza, dengue, zika, and herpes simplex virus infections uncover transcriptional variability, and how the host interferon response tunes influenza and sendai virus infections. We introduce the concept of "cell state" in infection variability, and conclude with advances by single-cell simultaneous measurements of chromatin accessibility and mRNA counts at high-throughput. Such technology will further dissect the sequence of events in virus infection and pathology, and better characterize the genetic and genomic stability of viruses, cell autonomous innate immune responses, and mechanisms of tissue injury.
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Affiliation(s)
- Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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25
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Rand U, Kupke SY, Shkarlet H, Hein MD, Hirsch T, Marichal-Gallardo P, Cicin-Sain L, Reichl U, Bruder D. Antiviral Activity of Influenza A Virus Defective Interfering Particles against SARS-CoV-2 Replication In Vitro through Stimulation of Innate Immunity. Cells 2021; 10:1756. [PMID: 34359926 PMCID: PMC8303422 DOI: 10.3390/cells10071756] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) emerged in late 2019 and resulted in a devastating pandemic. Although the first approved vaccines were already administered by the end of 2020, worldwide vaccine availability is still limited. Moreover, immune escape variants of the virus are emerging against which the current vaccines may confer only limited protection. Further, existing antivirals and treatment options against COVID-19 show only limited efficacy. Influenza A virus (IAV) defective interfering particles (DIPs) were previously proposed not only for antiviral treatment of the influenza disease but also for pan-specific treatment of interferon (IFN)-sensitive respiratory virus infections. To investigate the applicability of IAV DIPs as an antiviral for the treatment of COVID-19, we conducted in vitro co-infection experiments with cell culture-derived DIPs and the IFN-sensitive SARS-CoV-2 in human lung cells. We show that treatment with IAV DIPs leads to complete abrogation of SARS-CoV-2 replication. Moreover, this inhibitory effect was dependent on janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling. Further, our results suggest boosting of IFN-induced antiviral activity by IAV DIPs as a major contributor in suppressing SARS-CoV-2 replication. Thus, we propose IAV DIPs as an effective antiviral agent for treatment of COVID-19, and potentially also for suppressing the replication of new variants of SARS-CoV-2.
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Affiliation(s)
- Ulfert Rand
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (U.R.); (L.C.-S.)
| | - Sascha Young Kupke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; (P.M.-G.); (U.R.)
| | - Hanna Shkarlet
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (H.S.); (T.H.); (D.B.)
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Marc Dominique Hein
- Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany;
| | - Tatjana Hirsch
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (H.S.); (T.H.); (D.B.)
| | - Pavel Marichal-Gallardo
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; (P.M.-G.); (U.R.)
| | - Luka Cicin-Sain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (U.R.); (L.C.-S.)
- German Centre for Infection Research, Hannover-Braunschweig Site, 38124 Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of Helmholtz Centre for Infection Research and Medical School Hannover, 38124 Braunschweig, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; (P.M.-G.); (U.R.)
- Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany;
| | - Dunja Bruder
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (H.S.); (T.H.); (D.B.)
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany
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26
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In Vivo Generation of BK and JC Polyomavirus Defective Viral Genomes in Human Urine Samples Associated with Higher Viral Loads. J Virol 2021; 95:JVI.00250-21. [PMID: 33827948 PMCID: PMC8316075 DOI: 10.1128/jvi.00250-21] [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] [Received: 02/11/2021] [Accepted: 03/25/2021] [Indexed: 12/22/2022] Open
Abstract
Defective viral genomes (DVGs) are parasitic viral sequences containing point mutations, deletions, or duplications that might interfere with replication. DVGs are often associated with viral passage at high multiplicities of infection in culture systems but have been increasingly reported in clinical specimens. To date however, only RNA viruses have been shown to contain DVGs in clinical specimens. Here, using direct deep sequencing with multiple library preparation strategies and confirmatory digital droplet PCR (ddPCR) of urine samples taken from immunosuppressed individuals, we show that clinical BK polyomavirus (BKPyV) and JC polyomavirus (JCPyV) strains contain widespread genomic rearrangements across multiple loci that likely interfere with viral replication. BKPyV DVGs were derived from BKPyV genotypes Ia, Ib-1, and Ic. The presence of DVGs was associated with specimens containing higher viral loads but never reached clonality, consistent with a model of parasitized replication. These DVGs persisted during clinical infection as evidenced in two separate pairs of samples containing BK virus collected from the same individual up to 302 days apart. In a separate individual, we observed the generation of DVGs after a 57.5-fold increase in viral load. In summary, by extending the presence of DVGs in clinical specimens to DNA viruses, we demonstrate the ubiquity of DVGs in clinical virology. IMPORTANCE Defective viral genomes (DVGs) can have a significant impact on the production of infectious virus particles. DVGs have only been identified in cultured viruses passaged at high multiplicities of infection and RNA viruses collected from clinical specimens; no DNA virus in the wild has been shown to contain DVGs. Here, we identified BK and JC polyomavirus DVGs in clinical urine specimens and demonstrated that these DVGs are more frequently identified in samples with higher viral loads. The strains containing DVGs had rearrangements throughout their genomes, with the majority affecting genes required for viral replication. Longitudinal analysis showed that these DVGs can persist during an infection but do not reach clonality within the chronically infected host. Our identification of polyomavirus DVGs suggests that these parasitic sequences exist across the many classes of viruses capable of causing human disease.
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27
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Kiesslich S, Kim GN, Shen CF, Kang CY, Kamen AA. Bioreactor production of rVSV-based vectors in Vero cell suspension cultures. Biotechnol Bioeng 2021; 118:2649-2659. [PMID: 33837958 PMCID: PMC8252067 DOI: 10.1002/bit.27785] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/16/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022]
Abstract
The Vero cell line is the most used continuous cell line in viral vaccine manufacturing. This adherent cell culture platform requires the use of surfaces to support cell growth, typically roller bottles, or microcarriers. We have recently compared the production of rVSV‐ZEBOV on Vero cells between microcarrier and fixed‐bed bioreactors. However, suspension cultures are considered superior with regard to process scalability. Therefore, we further explore the Vero suspension system for recombinant vesicular stomatitis virus (rVSV)‐vectored vaccine production. Previously, this suspension cell line was only able to be cultivated in a proprietary medium. Here, we expand the adaptation and bioreactor cultivation to a serum‐free commercial medium. Following small‐scale optimization and screening studies, we demonstrate bioreactor productions of highly relevant vaccines and vaccine candidates against Ebola virus disease, HIV, and coronavirus disease 2019 in the Vero suspension system. rVSV‐ZEBOV, rVSV‐HIV, and rVSVInd‐msp‐SF‐Gtc can replicate to high titers in the bioreactor, reaching 3.87 × 107 TCID50/ml, 2.12 × 107 TCID50/ml, and 3.59 × 109 TCID50/ml, respectively. Furthermore, we compare cell‐specific productivities, and the quality of the produced viruses by determining the ratio of total viral particles to infectious viral particles.
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Affiliation(s)
- Sascha Kiesslich
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Gyoung N Kim
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Chun F Shen
- Human Health Therapeutics Research Center, National Research Council of Canada, Quebec, Canada
| | - C Yong Kang
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Amine A Kamen
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
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28
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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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