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Zhang Y, Chen H, Lian C, Cao L, Guo Y, Wang M, Zhong Z, Li M, Zhang H, Li C. Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses. Sci Rep 2024; 14:10540. [PMID: 38719945 PMCID: PMC11078923 DOI: 10.1038/s41598-024-61272-3] [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: 12/11/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.
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Affiliation(s)
- Yan Zhang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Lian
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lei Cao
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yang Guo
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Minxiao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Zhaoshan Zhong
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Mengna Li
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National Deep Sea Center, Qingdao, 266071, China
| | - Huan Zhang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National Deep Sea Center, Qingdao, 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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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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3
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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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Lin CH, Chen B, Chao DY, Hsieh FC, Lai CC, Wang WC, Kuo CY, Yang CC, Hsu HW, Tam HMH, Wu HY. Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo. Virol J 2023; 20:232. [PMID: 37828527 PMCID: PMC10571414 DOI: 10.1186/s12985-023-02201-0] [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: 06/30/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND In addition to the well-known coronavirus genomes and subgenomic mRNAs, the existence of other coronavirus RNA species, which are collectively referred to as noncanonical transcripts, has been suggested; however, their biological characteristics have not yet been experimentally validated in vitro and in vivo. METHODS To comprehensively determine the amounts, species and structures of noncanonical transcripts for bovine coronavirus in HRT-18 cells and mouse hepatitis virus A59, a mouse coronavirus, in mouse L cells and mice, nanopore direct RNA sequencing was employed. To experimentally validate the synthesis of noncanonical transcripts under regular infection, Northern blotting was performed. Both Northern blotting and nanopore direct RNA sequencing were also applied to examine the reproducibility of noncanonical transcripts. In addition, Northern blotting was also employed to determine the regulatory features of noncanonical transcripts under different infection conditions, including different cells, multiplicities of infection (MOIs) and coronavirus strains. RESULTS In the current study, we (i) experimentally determined that coronavirus noncanonical transcripts were abundantly synthesized, (ii) classified the noncanonical transcripts into seven populations based on their structures and potential synthesis mechanisms, (iii) showed that the species and amounts of the noncanonical transcripts were reproducible during regular infection but regulated in altered infection environments, (iv) revealed that coronaviruses may employ various mechanisms to synthesize noncanonical transcripts, and (v) found that the biological characteristics of coronavirus noncanonical transcripts were similar between in vitro and in vivo conditions. CONCLUSIONS The biological characteristics of noncanonical coronavirus transcripts were experimentally validated for the first time. The identified features of noncanonical transcripts in terms of abundance, reproducibility and variety extend the current model for coronavirus gene expression. The capability of coronaviruses to regulate the species and amounts of noncanonical transcripts may contribute to the pathogenesis of coronaviruses during infection, posing potential challenges in disease control. Thus, the biology of noncanonical transcripts both in vitro and in vivo revealed here can provide a database for biological research, contributing to the development of antiviral strategies.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - BoJia Chen
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, 40227, Taiwan
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, 40227, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Feng-Cheng Hsieh
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Cheng-Yu Kuo
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chun-Chun Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsuan-Wei Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hon-Man-Herman Tam
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
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5
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Lin CH, Chen B, Chao DY, Hsieh FC, Yang CC, Hsu HW, Tam HMH, Wu HY. Unveiling the biology of defective viral genomes in vitro and in vivo: implications for gene expression and pathogenesis of coronavirus. Virol J 2023; 20:225. [PMID: 37803357 PMCID: PMC10559480 DOI: 10.1186/s12985-023-02189-7] [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: 07/13/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Defective viral genome (DVG) is a truncated version of the full-length virus genome identified in most RNA viruses during infection. The synthesis of DVGs in coronavirus has been suggested; however, the fundamental characteristics of coronavirus DVGs in gene expression and pathogenesis have not been systematically analyzed. METHODS Nanopore direct RNA sequencing was used to investigate the characteristics of coronavirus DVGs in gene expression including reproducibility, abundance, species and genome structures for bovine coronavirus in cells, and for mouse hepatitis virus (MHV)-A59 (a mouse coronavirus) in cells and in mice. The MHV-A59 full-length genomic cDNAs (~ 31 kilobases) were in vitro constructed to experimentally validate the origin of coronavirus DVG. The synthesis of DVGs was also experimentally identified by RT-PCR followed by sequencing. In addition, the alterations of DVGs in amounts and species under different infection environments and selection pressures including the treatment of antiviral remdesivir and interferon were evaluated based on the banding patterns by RT-PCR. RESULTS The results are as follows: (i) the structures of DVGs are with diversity, (ii) DVGs are overall synthesized with moderate (MHV-A59 in cells) to high (BCoV in cells and MHV-A59 in mice) reproducibility under regular infection with the same virus inoculum, (iii) DVGs can be synthesized from the full-length coronavirus genome, (iv) the sequences flanking the recombination point of DVGs are AU-rich and thus may contribute to the recombination events during gene expression, (v) the species and amounts of DVG are altered under different infection environments, and (vi) the biological nature of DVGs between in vitro and in vivo is similar. CONCLUSIONS The identified biological characteristics of coronavirus DVGs in terms of abundance, reproducibility, and variety extend the current model for coronavirus gene expression. In addition, the biological features of alterations in amounts and species of coronavirus DVGs under different infection environments may assist the coronavirus to adapt to the altered environments for virus fitness and may contribute to the coronavirus pathogenesis. Consequently, the unveiled biological features may assist the community to study the gene expression mechanisms of DVGs and their roles in pathogenesis, contributing to the development of antiviral strategy and public health.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - BoJia Chen
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, 40227, Taiwan
| | - Day-Yu Chao
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, 40227, Taiwan
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Feng-Cheng Hsieh
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chun-Chun Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsuan-Wei Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hon-Man-Herman Tam
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
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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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7
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Franco EJ, Cella E, Tao X, Hanrahan KC, Azarian T, Brown AN. Favipiravir Suppresses Zika Virus (ZIKV) through Activity as a Mutagen. Microorganisms 2023; 11:1342. [PMID: 37317316 DOI: 10.3390/microorganisms11051342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
In a companion paper, we demonstrated that the nucleoside analogue favipiravir (FAV) suppressed Zika virus (ZIKV) replication in three human-derived cell lines-HeLa, SK-N-MC, and HUH-7. Our results revealed that FAV's effect was most pronounced in HeLa cells. In this work, we aimed to explain variation in FAV activity, investigating its mechanism of action and characterizing host cell factors relevant to tissue-specific differences in drug effect. Using viral genome sequencing, we show that FAV therapy was associated with an increase in the number of mutations and promoted the production of defective viral particles in all three cell lines. Our findings demonstrate that defective viral particles made up a larger portion of the viral population released from HeLa cells both at increasing FAV concentrations and at increasing exposure times. Taken together, our companion papers show that FAV acts via lethal mutagenesis against ZIKV and highlight the host cell's influence on the activation and antiviral activity of nucleoside analogues. Furthermore, the information gleaned from these companion papers can be applied to gain a more comprehensive understanding of the activity of nucleoside analogues and the impact of host cell factors against other viral infections for which we currently have no approved antiviral therapies.
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Affiliation(s)
- Evelyn J Franco
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, FL 32827, USA
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA
| | - Xun Tao
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, FL 32827, USA
| | - Kaley C Hanrahan
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA
| | - Ashley N Brown
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, FL 32827, USA
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8
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Leeks A, Young PG, Turner PE, Wild G, West SA. Cheating leads to the evolution of multipartite viruses. PLoS Biol 2023; 21:e3002092. [PMID: 37093882 PMCID: PMC10159356 DOI: 10.1371/journal.pbio.3002092] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 05/04/2023] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
In multipartite viruses, the genome is split into multiple segments, each of which is transmitted via a separate capsid. The existence of multipartite viruses poses a problem, because replication is only possible when all segments are present within the same host. Given this clear cost, why is multipartitism so common in viruses? Most previous hypotheses try to explain how multipartitism could provide an advantage. In so doing, they require scenarios that are unrealistic and that cannot explain viruses with more than 2 multipartite segments. We show theoretically that selection for cheats, which avoid producing a shared gene product, but still benefit from gene products produced by other genomes, can drive the evolution of both multipartite and segmented viruses. We find that multipartitism can evolve via cheating under realistic conditions and does not require unreasonably high coinfection rates or any group-level benefit. Furthermore, the cheating hypothesis is consistent with empirical patterns of cheating and multipartitism across viruses. More broadly, our results show how evolutionary conflict can drive new patterns of genome organisation in viruses and elsewhere.
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Affiliation(s)
- Asher Leeks
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | | | - Paul Eugene Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Quantitative Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Geoff Wild
- Department of Mathematics, The University of Western Ontario, London, Canada
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9
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Franco EJ, Hanrahan KC, Brown AN. Favipiravir Inhibits Zika Virus (ZIKV) Replication in HeLa Cells by Altering Viral Infectivity. Microorganisms 2023; 11:1097. [PMID: 37317071 DOI: 10.3390/microorganisms11051097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 06/16/2023] Open
Abstract
This study aims to evaluate the antiviral potential of the nucleoside analogue favipiravir (FAV) against ZIKV, an arbovirus for which there are no approved antiviral therapies, in three human-derived cell lines. HeLa (cervical), SK-N-MC (neuronal), and HUH-7 (liver) cells were infected with ZIKV and exposed to different concentrations of FAV. Viral supernatant was sampled daily, and infectious viral burden was quantified by plaque assay. Changes in ZIKV infectivity were quantified by calculating specific infectivity. FAV-related toxicities were also assessed for each cell line in both infected and uninfected cells. Our results demonstrate that FAV activity was most pronounced in HeLa cells, as substantial declines in infectious titers and viral infectivity were observed in this cell type. The decline in infectious virus occurred in an exposure-dependent manner and was more pronounced as FAV exposure times increased. Additionally, toxicity studies showed that FAV was not toxic to any of the three cell lines and, surprisingly, caused substantial improvements in the viability of infected HeLa cells. Although SK-N-MC and HUH-7 cells were susceptible to FAV's anti-ZIKV activity, similar effects on viral infectivity and improvements in cell viability with therapy were not observed. These results indicate that FAV's ability to substantially alter viral infectivity is host cell specific and suggest that the robust antiviral effect observed in HeLa cells is mediated through drug-induced losses of viral infectivity.
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Affiliation(s)
- Evelyn J Franco
- Institute for Therapeutic Innovation, Department of Medicine, University of Florida College of Medicine, Orlando, FL 32827, USA
- Department of Pharmaceutics, University of Florida College of Pharmacy, Orlando, FL 32827, USA
| | - Kaley C Hanrahan
- Institute for Therapeutic Innovation, Department of Medicine, University of Florida College of Medicine, Orlando, FL 32827, USA
| | - Ashley N Brown
- Institute for Therapeutic Innovation, Department of Medicine, University of Florida College of Medicine, Orlando, FL 32827, USA
- Department of Pharmaceutics, University of Florida College of Pharmacy, Orlando, FL 32827, USA
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10
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Girgis S, Xu Z, Oikonomopoulos S, Fedorova AD, Tchesnokov EP, Gordon CJ, Schmeing TM, Götte M, Sonenberg N, Baranov PV, Ragoussis J, Hobman TC, Pelletier J. Evolution of naturally arising SARS-CoV-2 defective interfering particles. Commun Biol 2022; 5:1140. [PMID: 36302891 PMCID: PMC9610340 DOI: 10.1038/s42003-022-04058-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Defective interfering (DI) particles arise during virus propagation, are conditional on parental virus for replication and packaging, and interfere with viral expansion. There is much interest in developing DIs as anti-viral agents. Here we characterize DI particles that arose following serial passaging of SARS-CoV-2 at high multiplicity of infection. The prominent DIs identified have lost ~84% of the SARS-CoV-2 genome and are capable of attenuating parental viral titers. Synthetic variants of the DI genomes also interfere with infection and can be used as conditional, gene delivery vehicles. In addition, the DI genomes encode an Nsp1-10 fusion protein capable of attenuating viral replication. These results identify naturally selected defective viral genomes that emerged and stably propagated in the presence of parental virus. Genomes from defective interfering (DI) particles following serial passaging of SARS-CoV-2 reveal a fusion protein that attenuates viral replication. Synthetic, recombinant DI genomes are designed to interfere with SARS-CoV-2 replication.
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Affiliation(s)
- Samer Girgis
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Zaikun Xu
- Department of Cell Biology, U Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Spyros Oikonomopoulos
- McGill Genome Centre, Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Alla D Fedorova
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.,Rosalind and Morris Goodman Cancer Institute, Montreal, QC, H3A 1A3, Canada
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, McGill University, Montreal, QC, Canada.,Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Tom C Hobman
- Department of Cell Biology, U Alberta, Edmonton, AB, T6G 2H7, Canada. .,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,Li Ka Shing Institute of Virology, U Alberta, Edmonton, AB, T6G 2E1, Canada. .,Women & Children's Health Research Institute, U Alberta, Edmonton, AB, T6G 1C9, Canada.
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada. .,Rosalind and Morris Goodman Cancer Institute, Montreal, QC, H3A 1A3, Canada. .,Department of Oncology, McGill University, Montreal, QC, H3A 1G5, Canada.
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11
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Chung H, Bui-Marinos MP, Rahmani W, Corcoran JA, Chun J. Infecting kidney organoids with a cDNA reporter clone of SARS-CoV-2. STAR Protoc 2022; 3:101617. [PMID: 35990736 PMCID: PMC9300580 DOI: 10.1016/j.xpro.2022.101617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Induced pluripotent stem cell (iPSC)-derived kidney organoids can be used for disease modeling and drug testing. Here, we describe a protocol to prepare stocks of an infectious clone of SARS-CoV-2 expressing a stable mNeonGreen reporter (icSARS-CoV-2-mNG). We demonstrate the infection of kidney organoids, primarily at the proximal tubular cells, with icSARS-CoV-2-mNG. Using a TCID50 (tissue culture infectious dose 50) assay and confocal microscopy, we show the quantification of SARS-CoV-2-mNG signal in proximal tubular cells of the kidney organoids. For complete details on the use and execution of this protocol, please refer to Rahmani et al. (2022). Detailed procedure for the production and titration of SARS-CoV-2-mNG Efficient SARS-CoV-2-mNG infection of kidney organoid of varying sizes Quantitative analysis of SARS-CoV-2 in kidney organoids by mNG expression
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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12
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Göbel S, Kortum F, Chavez KJ, Jordan I, Sandig V, Reichl U, Altomonte J, Genzel Y. Cell-line screening and process development for a fusogenic oncolytic virus in small-scale suspension cultures. Appl Microbiol Biotechnol 2022; 106:4945-4961. [PMID: 35767011 PMCID: PMC9329169 DOI: 10.1007/s00253-022-12027-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/09/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022]
Abstract
Abstract
Oncolytic viruses (OVs) represent a novel class of immunotherapeutics under development for the treatment of cancers. OVs that express a cognate or transgenic fusion protein is particularly promising as their enhanced intratumoral spread via syncytia formation can be a potent mechanism for tumor lysis and induction of antitumor immune responses. Rapid and efficient fusion of infected cells results in cell death before high titers are reached. Although this is an attractive safety feature, it also presents unique challenges for large-scale clinical-grade manufacture of OVs. Here we evaluate the use of four different suspension cell lines for the production of a novel fusogenic hybrid of vesicular stomatitis virus and Newcastle disease virus (rVSV-NDV). The candidate cell lines were screened for growth, metabolism, and virus productivity. Permissivity was evaluated based on extracellular infectious virus titers and cell-specific virus yields (CSVYs). For additional process optimizations, virus adaptation and multiplicity of infection (MOI) screenings were performed and confirmed in a 1 L bioreactor. BHK-21 and HEK293SF cells infected at concentrations of 2 × 106 cells/mL were identified as promising candidates for rVSV-NDV production, leading to infectious titers of 3.0 × 108 TCID50/mL and 7.5 × 107 TCID50/mL, and CSVYs of 153 and 9, respectively. Compared to the AGE1.CR.pIX reference produced in adherent cultures, oncolytic potency was not affected by production in suspension cultures and possibly even increased in cultures of HEK293SF and AGE1.CR.pIX. Our study describes promising suspension cell-based processes for efficient large-scale manufacturing of rVSV-NDV. Key points • Cell contact-dependent oncolytic virus (OV) replicates in suspension cells. • Oncolytic potency is not encompassed during suspension cultivation. • Media composition, cell line, and MOI are critical process parameters for OV production. • The designed process is scalable and shows great promise for manufacturing clinical-grade material. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12027-5.
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Affiliation(s)
- Sven Göbel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Fabian Kortum
- Department of Internal Medicine II, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Karim Jaén Chavez
- Department of Internal Medicine II, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Ingo Jordan
- ProBioGen AG, Herbert-Bayer-Str. 8, 13086, Berlin, Germany
| | - Volker Sandig
- ProBioGen AG, Herbert-Bayer-Str. 8, 13086, Berlin, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106, Magdeburg, Germany
- Chair for Bioprocess Engineering, Otto-Von-Guericke-University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Jennifer Altomonte
- Department of Internal Medicine II, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106, Magdeburg, Germany.
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13
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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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14
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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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15
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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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16
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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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17
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Pelz L, Rüdiger D, Dogra T, Alnaji FG, Genzel Y, Brooke CB, Kupke SY, Reichl U. Semi-continuous Propagation of Influenza A Virus and Its Defective Interfering Particles: Analyzing the Dynamic Competition To Select Candidates for Antiviral Therapy. J Virol 2021; 95:e0117421. [PMID: 34550771 PMCID: PMC8610589 DOI: 10.1128/jvi.01174-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/19/2021] [Indexed: 12/26/2022] Open
Abstract
Defective interfering particles (DIPs) of influenza A virus (IAV) are naturally occurring mutants that have an internal deletion in one of their eight viral RNA (vRNA) segments, rendering them propagation-incompetent. Upon coinfection with infectious standard virus (STV), DIPs interfere with STV replication through competitive inhibition. Thus, DIPs are proposed as potent antivirals for treatment of the influenza disease. To select corresponding candidates, we studied de novo generation of DIPs and propagation competition between different defective interfering (DI) vRNAs in an STV coinfection scenario in cell culture. A small-scale two-stage cultivation system that allows long-term semi-continuous propagation of IAV and its DIPs was used. Strong periodic oscillations in virus titers were observed due to the dynamic interaction of DIPs and STVs. Using next-generation sequencing, we detected a predominant formation and accumulation of DI vRNAs on the polymerase-encoding segments. Short DI vRNAs accumulated to higher fractions than longer ones, indicating a replication advantage, yet an optimum fragment length was observed. Some DI vRNAs showed breaking points in a specific part of their bundling signal (belonging to the packaging signal), suggesting its dispensability for DI vRNA propagation. Over a total cultivation time of 21 days, several individual DI vRNAs accumulated to high fractions, while others decreased. Using reverse genetics for IAV, purely clonal DIPs derived from highly replicating DI vRNAs were generated. We confirm that these DIPs exhibit a superior in vitro interfering efficacy compared to DIPs derived from lowly accumulated DI vRNAs and suggest promising candidates for efficacious antiviral treatment. IMPORTANCE Defective interfering particles (DIPs) emerge naturally during viral infection and typically show an internal deletion in the viral genome. Thus, DIPs are propagation-incompetent. Previous research suggests DIPs as potent antiviral compounds for many different virus families due to their ability to interfere with virus replication by competitive inhibition. For instance, the administration of influenza A virus (IAV) DIPs resulted in a rescue of mice from an otherwise lethal IAV dose. Moreover, no apparent toxic effects were observed when only DIPs were administered to mice and ferrets. IAV DIPs show antiviral activity against many different IAV strains, including pandemic and highly pathogenic avian strains, and even against nonhomologous viruses, such as SARS-CoV-2, by stimulation of innate immunity. Here, we used a cultivation/infection system, which exerted selection pressure toward accumulation of highly competitive IAV DIPs. These DIPs showed a superior interfering efficacy in vitro, and we suggest them for effective antiviral therapy.
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Affiliation(s)
- Lars Pelz
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Daniel Rüdiger
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Tanya Dogra
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Fadi G. Alnaji
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, Illinois, USA
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Christopher B. Brooke
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, Illinois, USA
| | - 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
- Otto-von-Guericke-University Magdeburg, Bioprocess Engineering, Magdeburg, Germany
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18
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Blahove MR, Carter JR. Flavivirus Persistence in Wildlife Populations. Viruses 2021; 13:v13102099. [PMID: 34696529 PMCID: PMC8541186 DOI: 10.3390/v13102099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
A substantial number of humans are at risk for infection by vector-borne flaviviruses, resulting in considerable morbidity and mortality worldwide. These viruses also infect wildlife at a considerable rate, persistently cycling between ticks/mosquitoes and small mammals and reptiles and non-human primates and humans. Substantially increasing evidence of viral persistence in wildlife continues to be reported. In addition to in humans, viral persistence has been shown to establish in mammalian, reptile, arachnid, and mosquito systems, as well as insect cell lines. Although a considerable amount of research has centered on the potential roles of defective virus particles, autophagy and/or apoptosis-induced evasion of the immune response, and the precise mechanism of these features in flavivirus persistence have yet to be elucidated. In this review, we present findings that aid in understanding how vector-borne flavivirus persistence is established in wildlife. Research studies to be discussed include determining the critical roles universal flavivirus non-structural proteins played in flaviviral persistence, the advancement of animal models of viral persistence, and studying host factors that allow vector-borne flavivirus replication without destructive effects on infected cells. These findings underscore the viral–host relationships in wildlife animals and could be used to elucidate the underlying mechanisms responsible for the establishment of viral persistence in these animals.
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19
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Evidence that two instead of one defective interfering RNA in influenza A virus-derived defective interfering particles (DIPs) does not enhance antiviral activity. Sci Rep 2021; 11:20477. [PMID: 34650149 PMCID: PMC8516915 DOI: 10.1038/s41598-021-99691-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/23/2021] [Indexed: 11/08/2022] Open
Abstract
Influenza A virus (IAV) infection constitutes a significant health threat. Defective interfering particles (DIPs) can arise during IAV infection and inhibit spread of wild type (WT) IAV. DIPs harbor defective RNA segments, termed DI RNAs, that usually contain internal deletions and interfere with replication of WT viral RNA segments. Here, we asked whether DIPs harboring two instead of one DI RNA exert increased antiviral activity. For this, we focused on DI RNAs derived from segments 1 and 3, which encode the polymerase subunits PB2 and PA, respectively. We demonstrate the successful production of DIPs harboring deletions in segments 1 and/or 3, using cell lines that co-express PB2 and PA. Further, we demonstrate that DIPs harboring two instead of one DI RNA do not exhibit increased ability to inhibit replication of a WT RNA segment. Similarly, the presence of two DI RNAs did not augment the induction of the interferon-stimulated gene MxA and the inhibition of IAV infection. Collectively, our findings suggest that the presence of multiple DI RNAs derived from genomic segments encoding polymerase subunits might not result in increased antiviral activity.
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20
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Rüdiger D, Pelz L, Hein MD, Kupke SY, Reichl U. Multiscale model of defective interfering particle replication for influenza A virus infection in animal cell culture. PLoS Comput Biol 2021; 17:e1009357. [PMID: 34491996 PMCID: PMC8448327 DOI: 10.1371/journal.pcbi.1009357] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/17/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Cell culture-derived defective interfering particles (DIPs) are considered for antiviral therapy due to their ability to inhibit influenza A virus (IAV) production. DIPs contain a large internal deletion in one of their eight viral RNAs (vRNAs) rendering them replication-incompetent. However, they can propagate alongside their homologous standard virus (STV) during infection in a competition for cellular and viral resources. So far, experimental and modeling studies for IAV have focused on either the intracellular or the cell population level when investigating the interaction of STVs and DIPs. To examine these levels simultaneously, we conducted a series of experiments using highly different multiplicities of infections for STVs and DIPs to characterize virus replication in Madin-Darby Canine Kidney suspension cells. At several time points post infection, we quantified virus titers, viable cell concentration, virus-induced apoptosis using imaging flow cytometry, and intracellular levels of vRNA and viral mRNA using real-time reverse transcription qPCR. Based on the obtained data, we developed a mathematical multiscale model of STV and DIP co-infection that describes dynamics closely for all scenarios with a single set of parameters. We show that applying high DIP concentrations can shut down STV propagation completely and prevent virus-induced apoptosis. Interestingly, the three observed viral mRNAs (full-length segment 1 and 5, defective interfering segment 1) accumulated to vastly different levels suggesting the interplay between an internal regulation mechanism and a growth advantage for shorter viral RNAs. Furthermore, model simulations predict that the concentration of DIPs should be at least 10000 times higher than that of STVs to prevent the spread of IAV. Ultimately, the model presented here supports a comprehensive understanding of the interactions between STVs and DIPs during co-infection providing an ideal platform for the prediction and optimization of vaccine manufacturing as well as DIP production for therapeutic use.
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Affiliation(s)
- Daniel Rüdiger
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Lars Pelz
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marc D. Hein
- Chair of Bioprocess Engineering, Institute of Process Engineering, Faculty of Process & Systems Engineering, Otto-von-Guericke University, Magdeburg, Germany
| | - Sascha Y. Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Chair of Bioprocess Engineering, Institute of Process Engineering, Faculty of Process & Systems Engineering, Otto-von-Guericke University, Magdeburg, Germany
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21
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Zhao Y, Sun J, Li Y, Li Z, Xie Y, Feng R, Zhao J, Hu Y. The strand-biased transcription of SARS-CoV-2 and unbalanced inhibition by remdesivir. iScience 2021; 24:102857. [PMID: 34278249 PMCID: PMC8277956 DOI: 10.1016/j.isci.2021.102857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/13/2021] [Accepted: 07/12/2021] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, causes the coronavirus disease 19 pandemic. During the viral replication and transcription, the RNA-dependent RNA polymerase "jumps" along the genome template, resulting in discontinuous negative-stranded transcripts. Although the sense-mRNA architectures of SARS-CoV-2 were reported, its negative strand was unexplored. Here, we deeply sequenced both strands of RNA and found SARS-CoV-2 transcription is strongly biased to form the sense strand with variable transcription efficiency for different genes. During negative strand synthesis, numerous non-canonical fusion transcripts are also formed, driven by 3-15 nt sequence homology scattered along the genome but more prone to be inhibited by SARS-CoV-2 RNA polymerase inhibitor remdesivir. The drug also represses more of the negative than the positive strand synthesis as supported by a mathematic simulation model and experimental quantifications. Overall, this study opens new sights into SARS-CoV-2 biogenesis and may facilitate the antiviral vaccine development and drug design.
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Affiliation(s)
- Yan Zhao
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China.,Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany.,Department of Mathematics and Computer Science, Free University Berlin, Berlin 14195, Germany
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Yunfei Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China
| | - Zhengxuan Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China
| | - Yu Xie
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China
| | - Ruoqing Feng
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
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22
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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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23
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Abstract
Despite their simplicity, viruses exhibit certain types of social interactions. Situations in which a given virus achieves higher fitness in combination with other members of the viral population have been described at the level of transmission, replication, suppression of host immune responses, and host killing, enabling the evolution of viral cooperation. Although cellular coinfection with multiple viral particles is the typical playground for these interactions, cooperation between viruses infecting different cells is also established through cellular and viral-encoded communication systems. In general, the stability of cooperation is compromised by cheater genotypes, as best exemplified by defective interfering particles. As predicted by social evolution theory, cheater invasion can be avoided when cooperators interact preferentially with other cooperators, a situation that is promoted in spatially structured populations. Processes such as transmission bottlenecks, organ compartmentalization, localized spread of infection foci, superinfection exclusion, and even discrete intracellular replication centers promote multilevel spatial structuring in viruses. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas and Universitat de València, 46980 Paterna, València, Spain;
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24
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Li D, Lin MH, Rawle DJ, Jin H, Wu Z, Wang L, Lor M, Hussain M, Aaskov J, Harrich D. Dengue virus-free defective interfering particles have potent and broad anti-dengue virus activity. Commun Biol 2021; 4:557. [PMID: 33976375 PMCID: PMC8113447 DOI: 10.1038/s42003-021-02064-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/23/2021] [Indexed: 02/03/2023] Open
Abstract
Dengue virus (DENV) is spread from human to human through the bite of the female Aedes aegypti mosquito and leads to about 100 million clinical infections yearly. Treatment options and vaccine availability for DENV are limited. Defective interfering particles (DIPs) are considered a promising antiviral approach but infectious virus contamination has limited their development. Here, a DENV-derived DIP production cell line was developed that continuously produced DENV-free DIPs. The DIPs contained and could deliver to cells a DENV serotype 2 subgenomic defective-interfering RNA, which was originally discovered in DENV infected patients. The DIPs released into cell culture supernatant were purified and could potently inhibit replication of all DENV serotypes in cells. Antiviral therapeutics are limited for many viral infection. The DIP system described could be re-purposed to make antiviral DIPs for many other RNA viruses such as SARS-CoV-2, yellow fever, West Nile and Zika viruses.
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Affiliation(s)
- Dongsheng Li
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Min-Hsuan Lin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Daniel J Rawle
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Hongping Jin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Zhonglan Wu
- Ningxia Center for Disease Control and Prevention, Ningxia, China
| | - Lu Wang
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Mary Lor
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Mazhar Hussain
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - John Aaskov
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - David Harrich
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
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25
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Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive, heritable immunity against their viruses (bacteriophages and phages) and other parasitic genetic elements. CRISPR-Cas systems are highly diverse, and we are only beginning to understand their relative importance in phage defense. In this review, we will discuss when and why CRISPR-Cas immunity against phages evolves, and how this, in turn, selects for the evolution of immune evasion by phages. Finally, we will discuss our current understanding of if, and when, we observe coevolution between CRISPR-Cas systems and phages, and how this may be influenced by the mechanism of CRISPR-Cas immunity.
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26
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Linder A, Bothe V, Linder N, Schwarzlmueller P, Dahlström F, Bartenhagen C, Dugas M, Pandey D, Thorn-Seshold J, Boehmer DFR, Koenig LM, Kobold S, Schnurr M, Raedler J, Spielmann G, Karimzadeh H, Schmidt A, Endres S, Rothenfusser S. Defective Interfering Genomes and the Full-Length Viral Genome Trigger RIG-I After Infection With Vesicular Stomatitis Virus in a Replication Dependent Manner. Front Immunol 2021; 12:595390. [PMID: 33995343 PMCID: PMC8119886 DOI: 10.3389/fimmu.2021.595390] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 03/30/2021] [Indexed: 12/25/2022] Open
Abstract
Replication competent vesicular stomatitis virus (VSV) is the basis of a vaccine against Ebola and VSV strains are developed as oncolytic viruses. Both functions depend on the ability of VSV to induce adequate amounts of interferon-α/β. It is therefore important to understand how VSV triggers interferon responses. VSV activates innate immunity via retinoic acid-inducible gene I (RIG-I), a sensor for viral RNA. Our results show that VSV needs to replicate for a robust interferon response. Analysis of RIG-I-associated RNA identified a copy-back defective-interfering (DI) genome and full-length viral genomes as main trigger of RIG-I. VSV stocks depleted of DI genomes lost most of their interferon-stimulating activity. The remaining full-length genome and leader-N-read-through sequences, however, still triggered RIG-I. Awareness for DI genomes as trigger of innate immune responses will help to standardize DI genome content and to purposefully deplete or use DI genomes as natural adjuvants in VSV-based therapeutics.
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Affiliation(s)
- Andreas Linder
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Viktoria Bothe
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Nicolas Linder
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Paul Schwarzlmueller
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Frank Dahlström
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | | | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Dharmendra Pandey
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Julia Thorn-Seshold
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Daniel F. R. Boehmer
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Lars M. Koenig
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- German Center for Translational Cancer Research (DKTK), Partner Site Munich, Munich, Germany
| | - Max Schnurr
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Johannes Raedler
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Giulia Spielmann
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Hadi Karimzadeh
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Andreas Schmidt
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Stefan Endres
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Simon Rothenfusser
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
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27
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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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28
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Johnson KEE, Noval MG, Rangel MV, De Jesus E, Geber A, Schuster S, Cadwell K, Ghedin E, Stapleford KA. Mapping the evolutionary landscape of Zika virus infection in immunocompromised mice. Virus Evol 2020; 6:veaa092. [PMID: 33408879 PMCID: PMC7772475 DOI: 10.1093/ve/veaa092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The fundamental basis of how arboviruses evolve in nature and what regulates the adaptive process remain unclear. To address this problem, we established a Zika virus (ZIKV) vector-borne transmission system in immunocompromised mice to study the evolutionary characteristics of ZIKV infection. Using this system, we defined factors that influence the evolutionary landscape of ZIKV infection and show that transmission route and specific organ microenvironments impact viral diversity and defective viral genome production. In addition, we identified in mice the emergence of ZIKV mutants previously seen in natural infections, including variants present in currently circulating Asian and American strains, as well as mutations unique to the mouse infections. With these studies, we have established an insect-to-mouse transmission model to study ZIKV evolution in vivo. We also defined how organ microenvironments and infection route impact the ZIKV evolutionary landscape, providing a deeper understanding of the factors that regulate arbovirus evolution and emergence.
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Affiliation(s)
| | | | | | - Elfie De Jesus
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Adam Geber
- Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY, USA
| | - Samantha Schuster
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Ken Cadwell
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Elodie Ghedin
- Present address: National Institutes of Health/NIAID,
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29
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Zheng B, Xu Y, Huang M, Li X, Wang T, Ming D. Bio-Inorganic Hybrid Nongenetically Modified Viruses as an Immune Agonist for Systemic Elimination of Cancer Cells. ACS APPLIED MATERIALS & INTERFACES 2020; 12:53691-53704. [PMID: 33206505 DOI: 10.1021/acsami.0c16978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial-based cancer therapy is nowadays considered as an interesting approach, especially with viruses which are attracting more attention owing to their simple structure and nanoscale. However, because of the need for cumbersome genetic modification and poor biosafety, its application is seriously limited. Here, nonpathogenic natural Sendai viruses (SEVs) are used as an alternative immune agonist after being mineralized by calcium ions. Both in vitro and in vivo studies indicated that virus-inorganic hybrids can effectively excite antigen-presenting cells (APCs). Then, the tumor antigens were released in large amounts by photothermal damage. Meanwhile, these released antigens were presented to lymph nodes to mature antitumor T lymphocytes via the peritumoral APCs previously recruited by the SEV. Our results demonstrated that even after administration at one point, the nanohybrids could still effectively stimulate systemic antitumor immune response to suppress the potential cancer metastatic spread. The bio-inorganic hybrid nongenetically modified virus-inorganic nanocomposites might serve as an alternative strategy for synergistic immune therapy.
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Affiliation(s)
- Bin Zheng
- Academy of Medical Engineering and Translational Medicine, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Yanan Xu
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Mengqian Huang
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Xianhuang Li
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Tao Wang
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Dong Ming
- Academy of Medical Engineering and Translational Medicine, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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30
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Das A, Dutta S, Sen M, Saxena A, Kumar J, Giri L, Murhammer DW, Chakraborty J. A detailed model and Monte Carlo simulation for predicting DIP genome length distribution in baculovirus infection of insect cells. Biotechnol Bioeng 2020; 118:238-252. [PMID: 32936454 DOI: 10.1002/bit.27566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/04/2020] [Accepted: 09/09/2020] [Indexed: 01/14/2023]
Abstract
Baculoviruses have enormous potential for use as biopesticides to control insect pest populations without the adverse environmental effects posed by the widespread use of chemical pesticides. However, continuous baculovirus production is susceptible to DNA mutation and the subsequent production of defective interfering particles (DIPs). The amount of DIPs produced and their genome length distribution are of great interest not only for baculoviruses but for many other DNA and RNA viruses. In this study, we elucidate this aspect of virus replication using baculovirus as an example system and both experimental and modeling studies. The existing mathematical models for the virus replication process consider DIPs as a lumped quantity and do not consider the genome length distribution of the DIPs. In this study, a detailed population balance model for the cell-virus culture is presented, which predicts the genome length distribution of the DIP population along with their relative proportion. The model is simulated using the kinetic Monte Carlo algorithm, and the results agree well with the experimental results. Using this model, a practical strategy to maintain the DIP fraction to near to its maximum and minimum limits has been demonstrated.
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Affiliation(s)
- Ashok Das
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Soumajit Dutta
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | | | - Abha Saxena
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, Telangana, India
| | - Jitendra Kumar
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, Telangana, India
| | - David W Murhammer
- Department of Chemical and Biochemical Engineering, The University of Iowa, Iowa City, California, USA
| | - Jayanta Chakraborty
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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31
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Brisse M, Vrba SM, Kirk N, Liang Y, Ly H. Emerging Concepts and Technologies in Vaccine Development. Front Immunol 2020; 11:583077. [PMID: 33101309 PMCID: PMC7554600 DOI: 10.3389/fimmu.2020.583077] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/14/2020] [Indexed: 01/05/2023] Open
Abstract
Despite the success of vaccination to greatly mitigate or eliminate threat of diseases caused by pathogens, there are still known diseases and emerging pathogens for which the development of successful vaccines against them is inherently difficult. In addition, vaccine development for people with compromised immunity and other pre-existing medical conditions has remained a major challenge. Besides the traditional inactivated or live attenuated, virus-vectored and subunit vaccines, emerging non-viral vaccine technologies, such as viral-like particle and nanoparticle vaccines, DNA/RNA vaccines, and rational vaccine design, offer innovative approaches to address existing challenges of vaccine development. They have also significantly advanced our understanding of vaccine immunology and can guide future vaccine development for many diseases, including rapidly emerging infectious diseases, such as COVID-19, and diseases that have not traditionally been addressed by vaccination, such as cancers and substance abuse. This review provides an integrative discussion of new non-viral vaccine development technologies and their use to address the most fundamental and ongoing challenges of vaccine development.
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Affiliation(s)
- Morgan Brisse
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota Twin Cities, St. Paul, MN, United States
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Sophia M. Vrba
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Natalie Kirk
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
- Comparative Molecular Biosciences Graduate Program, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Yuying Liang
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
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32
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Birzer A, Krawczyk A, Draßner C, Kuhnt C, Mühl-Zürbes P, Heilingloh CS, Steinkasserer A, Popella L. HSV-1 Modulates IL-6 Receptor Expression on Human Dendritic Cells. Front Immunol 2020; 11:1970. [PMID: 32983130 PMCID: PMC7479228 DOI: 10.3389/fimmu.2020.01970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Dendritic cells (DCs) are the guardians of the immune system since they are located in the majority of peripheral tissues. In addition, they are crucial for the induction of an effective immune response based on their unique capacity to stimulate naive T cells. During co-evolution, the human pathogen herpes simplex virus type 1 (HSV-1) has evolved several immune evasion mechanisms in order to subvert the host's immune system especially by targeting DC biology and function. Here we demonstrate that HSV-1 infection influences the IL-6 receptor (IL6R) expression both on protein and mRNA levels in/on human monocyte-derived mature DCs (mDCs). Surprisingly, reduced IL6R expression levels were also observed on uninfected bystander mDCs. Mechanistically, we clearly show that HSV-1-derived non-infectious light (L-) particles are sufficient to trigger IL6R regulation on uninfected bystander mDCs. These L-particles lack the viral DNA-loaded capsid and are predominantly produced during infection of mDCs. Our results show that the deletion of the HSV-1 tegument protein vhs partially rescued the reduced IL6R surface expression levels on/in bystander mDCs. Using a neutralizing antibody, which perturbs the transfer of L-particles to bystander mDCs, was sufficient to rescue the modulation of IL6R surface expression on uninfected bystander mDCs. This study provides evidence that L-particles transfer specific viral proteins to uninfected bystander mDCs, thereby negatively interfering with their IL6R expression levels, however, to a lesser extend compared to H-particles. Due to their immune-modulatory capacity, L-particles represent an elaborated approach of HSV-1-mediated immune evasion.
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Affiliation(s)
- Alexandra Birzer
- Department of Immune Modulation, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Adalbert Krawczyk
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christina Draßner
- Department of Immune Modulation, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christine Kuhnt
- Department of Immune Modulation, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Petra Mühl-Zürbes
- Department of Immune Modulation, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christiane Silke Heilingloh
- Department of Immune Modulation, Universitätsklinikum Erlangen, Erlangen, Germany
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Linda Popella
- Department of Immune Modulation, Universitätsklinikum Erlangen, Erlangen, Germany
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33
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Yang Y, Xiao Z, Ye K, He X, Sun B, Qin Z, Yu J, Yao J, Wu Q, Bao Z, Zhao W. SARS-CoV-2: characteristics and current advances in research. Virol J 2020; 17:117. [PMID: 32727485 PMCID: PMC7387805 DOI: 10.1186/s12985-020-01369-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection has spread rapidly across the world and become an international public health emergency. Both SARS-CoV-2 and SARS-CoV belong to subfamily Coronavirinae in the family Coronaviridae of the order Nidovirales and they are classified as the SARS-like species while belong to different cluster. Besides, viral structure, epidemiology characteristics and pathological characteristics are also different. We present a comprehensive survey of the latest coronavirus-SARS-CoV-2-from investigating its origin and evolution alongside SARS-CoV. Meanwhile, pathogenesis, cardiovascular disease in COVID-19 patients, myocardial injury and venous thromboembolism induced by SARS-CoV-2 as well as the treatment methods are summarized in this review.
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Affiliation(s)
- Yicheng Yang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Zhiqiang Xiao
- Department of clinical medicine, Zhengzhou university, 100 Science Avenue, Zhengzhou, 450001, China
| | - Kaiyan Ye
- Second Clinical Medical College, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoen He
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Bo Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Zhiran Qin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jianghai Yu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jinxiu Yao
- Yang Jiang Hospital, Yangjiang, 510515, Guangdong Province, China
| | - Qinghua Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Zhang Bao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Wei Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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34
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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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35
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Coinfections and their molecular consequences in the porcine respiratory tract. Vet Res 2020; 51:80. [PMID: 32546263 PMCID: PMC7296899 DOI: 10.1186/s13567-020-00807-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/02/2020] [Indexed: 01/15/2023] Open
Abstract
Understudied, coinfections are more frequent in pig farms than single infections. In pigs, the term “Porcine Respiratory Disease Complex” (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The clinical outcome of the various coinfection or superinfection situations is usually assessed in the studies while in most of cases there is no clear elucidation of the fine mechanisms shaping the complex interactions occurring between microorganisms. In this comprehensive review, we aimed at identifying the studies dealing with coinfections or superinfections in the pig respiratory tract and at presenting the interactions between pathogens and, when possible, the mechanisms controlling them. Coinfections and superinfections involving viruses and bacteria were considered while research articles including protozoan and fungi were excluded. We discuss the main limitations complicating the interpretation of coinfection/superinfection studies, and the high potential perspectives in this fascinating research field, which is expecting to gain more and more interest in the next years for the obvious benefit of animal health.
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Protein Kinase C subtype δ interacts with Venezuelan equine encephalitis virus capsid protein and regulates viral RNA binding through modulation of capsid phosphorylation. PLoS Pathog 2020; 16:e1008282. [PMID: 32150585 PMCID: PMC7082041 DOI: 10.1371/journal.ppat.1008282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 03/19/2020] [Accepted: 12/13/2019] [Indexed: 12/31/2022] Open
Abstract
Protein phosphorylation plays an important role during the life cycle of many viruses. Venezuelan equine encephalitis virus (VEEV) capsid protein has recently been shown to be phosphorylated at four residues. Here those studies are extended to determine the kinase responsible for phosphorylation and the importance of capsid phosphorylation during the viral life cycle. Phosphorylation site prediction software suggests that Protein Kinase C (PKC) is responsible for phosphorylation of VEEV capsid. VEEV capsid co-immunoprecipitated with PKCδ, but not other PKC isoforms and siRNA knockdown of PKCδ caused a decrease in viral replication. Furthermore, knockdown of PKCδ by siRNA decreased capsid phosphorylation. A virus with capsid phosphorylation sites mutated to alanine (VEEV CPD) displayed a lower genomic copy to pfu ratio than the parental virus; suggesting more efficient viral assembly and more infectious particles being released. RNA:capsid binding was significantly increased in the mutant virus, confirming these results. Finally, VEEV CPD is attenuated in a mouse model of infection, with mice showing increased survival and decreased clinical signs as compared to mice infected with the parental virus. Collectively our data support a model in which PKCδ mediated capsid phosphorylation regulates viral RNA binding and assembly, significantly impacting viral pathogenesis.
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Intact Viral Particle Counts Measured by Flow Virometry Provide Insight into the Infectivity and Genome Packaging Efficiency of Moloney Murine Leukemia Virus. J Virol 2020; 94:JVI.01600-19. [PMID: 31694951 DOI: 10.1128/jvi.01600-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Murine leukemia viruses (MLVs) have long been used as a research model to further our understanding of retroviruses. These simple gammaretroviruses have been studied extensively in various facets of science for nearly half a century, yet we have surprisingly little quantitative information about some of the basic features of these viral particles. These include parameters such as the genome packaging efficiency and the number of particles required for a productive infection. The reason for this knowledge gap relies primarily on the technical challenge of accurately measuring intact viral particles from infected cell supernatants. Virus-infected cells are well known to release soluble viral proteins, defective viruses, and extracellular vesicles (EVs) harboring viral proteins that may mimic viruses, all of which can skew virus titer quantifications. Flow virometry, also known as nanoscale flow cytometry or simply small-particle flow cytometry, is an emerging analytical method enabling high-throughput single-virus phenotypic characterizations. By utilizing the viral envelope glycoprotein (Env) and monodisperse light scattering characteristics as discerning parameters of intact virus particles, here, we analyzed the basic properties of Moloney MLV (M-MLV). We show that <24% of the total p30 capsid protein measured in infected cell supernatants is associated with intact viruses. We calculate that about one in five M-MLV particles contains a viral RNA genome pair and that individual intact particle infectivity is about 0.4%. These findings provide new insights into the characteristics of an extensively studied prototypical retrovirus while highlighting the benefits of flow virometry for the field of virology.IMPORTANCE Gammaretroviruses, or, more specifically, murine leukemia viruses (MLVs), have been a longstanding model for studying retroviruses. Although being extensively analyzed and dissected for decades, several facets of MLV biology are still poorly understood. One of the primary challenges has been enumerating total intact virus particles in a sample. While several analytical methods can precisely measure virus protein amounts, MLVs are known to induce the secretion of soluble and vesicle-associated viral proteins that can skew these measurements. With recent technological advances in flow cytometry, it is now possible to analyze viruses down to 90 nm in diameter with an approach called flow virometry. The technique has the added benefit of being able to discriminate viruses from extracellular vesicles and free viral proteins in order to confidently provide an intact viral particle count. Here, we used flow virometry to provide new insights into the basic characteristics of Moloney MLV.
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