1
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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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2
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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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3
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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: 0] [Impact Index Per Article: 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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4
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Atari N, Erster O, Shteinberg YH, Asraf H, Giat E, Mandelboim M, Goldstein I. Proof-of-concept for effective antiviral activity of an in silico designed decoy synthetic mRNA against SARS-CoV-2 in the Vero E6 cell-based infection model. Front Microbiol 2023; 14:1113697. [PMID: 37152730 PMCID: PMC10157240 DOI: 10.3389/fmicb.2023.1113697] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
The positive-sense single-stranded (ss) RNA viruses of the Betacoronavirus (beta-CoV) genus can spillover from mammals to humans and are an ongoing threat to global health and commerce, as demonstrated by the current zoonotic pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Current anti-viral strategies focus on vaccination or targeting key viral proteins with antibodies and drugs. However, the ongoing evolution of new variants that evade vaccination or may become drug-resistant is a major challenge. Thus, antiviral compounds that circumvent these obstacles are needed. Here we describe an innovative antiviral modality based on in silico designed fully synthetic mRNA that is replication incompetent in uninfected cells (termed herein PSCT: parasitic anti-SARS-CoV-2 transcript). The PSCT sequence was engineered to include key untranslated cis-acting regulatory RNA elements of the SARS-CoV-2 genome, so as to effectively compete for replication and packaging with the standard viral genome. Using the Vero E6 cell-culture based SARS-CoV-2 infection model, we determined that the intracellular delivery of liposome-encapsulated PSCT at 1 hour post infection significantly reduced intercellular SARS-CoV-2 replication and release into the extracellular milieu as compared to mock treatment. In summary, our findings are a proof-of-concept for the therapeutic feasibility of in silico designed mRNA compounds formulated to hinder the replication and packaging of ssRNA viruses sharing a comparable genomic-structure with beta-CoVs.
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Affiliation(s)
- Nofar Atari
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel HaShomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel HaShomer, Israel
| | | | - Hadar Asraf
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel HaShomer, Israel
| | - Eitan Giat
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Department of Medicine, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel HaShomer, Israel
- The Department of Medicine, Sheba Medical Center, Ramat Gan, Israel
| | - Itamar Goldstein
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Department of Medicine, Sheba Medical Center, Ramat Gan, Israel
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5
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Stincarelli MA, Rocca A, Antonelli A, Rossolini GM, Giannecchini S. Antiviral Activity of Oligonucleotides Targeting the SARS-CoV-2 Genomic RNA Stem-Loop Sequences within the 3'-End of the ORF1b. Pathogens 2022; 11:1286. [PMID: 36365037 PMCID: PMC9696570 DOI: 10.3390/pathogens11111286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/30/2023] Open
Abstract
Increased evidence shows vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited no long-term efficacy and limited worldwide availability, while existing antivirals and treatment options have only limited efficacy. In this study, the main objective was the development of antiviral strategies using nucleic acid-based molecules. To this purpose, partially overlapped 6-19-mer phosphorothioate deoxyoligonucleotides (S-ONs) designed on the SARS-CoV-2 genomic RNA stem-loop packaging sequences within the 3' end of the ORF1b were synthetized using the direct and complementary sequence. Among the S-ONs tested, several oligonucleotides exhibited a fifty percent inhibitory concentration antiviral activity ranging from 0.27 to 34 μM, in the absence of cytotoxicity. The S-ON with a scrambled sequence used in the same conditions was not active. Moreover, selected 10-mer S-ONs were tested using different infectious doses and against different SARS-CoV-2 variants, showing comparable antiviral activity that was abrogated when the central sequence was mutated. Experiments to evaluate the intracellular functional target localization of the S-ON inhibitory activity were also performed. Collectively the data indicate that the SARS-CoV-2 packaging region in the 3' end of the ORF1b may be a promising target candidate for further investigation to develop innovative nucleic-acid-based antiviral therapy.
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Affiliation(s)
| | - Arianna Rocca
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, I-50134 Florence, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
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6
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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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7
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A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters. Proc Natl Acad Sci U S A 2022; 119:e2204624119. [PMID: 36074824 PMCID: PMC9522362 DOI: 10.1073/pnas.2204624119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The high transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a primary driver of the COVID-19 pandemic. While existing interventions prevent severe disease, they exhibit mixed efficacy in preventing transmission, presumably due to their limited antiviral effects in the respiratory mucosa, whereas interventions targeting the sites of viral replication might more effectively limit respiratory virus transmission. Recently, intranasally administered RNA-based therapeutic interfering particles (TIPs) were reported to suppress SARS-CoV-2 replication, exhibit a high barrier to resistance, and prevent serious disease in hamsters. Since TIPs intrinsically target the tissues with the highest viral replication burden (i.e., respiratory tissues for SARS-CoV-2), we tested the potential of TIP intervention to reduce SARS-CoV-2 shedding. Here, we report that a single, postexposure TIP dose lowers SARS-CoV-2 nasal shedding, and at 5 days postinfection, infectious virus shed is below detection limits in 4 out of 5 infected animals. Furthermore, TIPs reduce shedding of Delta variant or WA-1 from infected to uninfected hamsters. Cohoused "contact" animals exposed to infected, TIP-treated animals exhibited significantly lower viral loads, reduced inflammatory cytokines, no severe lung pathology, and shortened shedding duration compared to animals cohoused with untreated infected animals. TIPs may represent an effective countermeasure to limit SARS-CoV-2 transmission.
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8
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A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35982679 DOI: 10.1101/2022.08.10.503534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The high transmissibility of SARS-CoV-2 is a primary driver of the COVID-19 pandemic. While existing interventions prevent severe disease, they exhibit mixed efficacy in preventing transmission, presumably due to their limited antiviral effects in the respiratory mucosa, whereas interventions targeting the sites of viral replication might more effectively limit respiratory virus transmission. Recently, intranasally administered RNA-based therapeutic interfering particles (TIPs) were reported to suppress SARS-CoV-2 replication, exhibit a high barrier to resistance, and prevent serious disease in hamsters. Since TIPs intrinsically target the tissues with the highest viral replication burden (i.e., respiratory tissues for SARS-CoV-2), we tested the potential of TIP intervention to reduce SARS-CoV-2 shedding. Here, we report that a single, post-exposure TIP dose lowers SARS-CoV-2 nasal shedding and at 5 days post-infection infectious virus shed is below detection limits in 4 out of 5 infected animals. Furthermore, TIPs reduce shedding of Delta variant or WA-1 from infected to uninfected hamsters. Co-housed 'contact' animals exposed to infected, TIP-treated, animals exhibited significantly lower viral loads, reduced inflammatory cytokines, no severe lung pathology, and shortened shedding duration compared to animals co-housed with untreated infected animals. TIPs may represent an effective countermeasure to limit SARS-CoV-2 transmission. Significance COVID-19 vaccines are exceptionally effective in preventing severe disease and death, but they have mixed efficacy in preventing virus transmission, consistent with established literature that parenteral vaccines for other viruses fail to prevent mucosal virus shedding or transmission. Likewise, small-molecule antivirals, while effective in reducing viral-disease pathogenesis, also appear to have inconsistent efficacy in preventing respiratory virus transmission including for SARS-CoV-2. Recently, we reported the discovery of a single-administration antiviral Therapeutic Interfering Particle (TIP) against SARS-CoV-2 that prevents severe disease in hamsters and exhibits a high genetic barrier to the evolution of resistance. Here, we report that TIP intervention also reduces SARS-CoV-2 transmission between hamsters.
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9
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Abstract
The term Gain-of-Function (GoF) describes the gain of new functions by organisms through genetic changes, which can naturally occur or by experimental genetic modifications. Gain-of-Function research on viruses is enhancing transmissibility, virus replication, virulence, host range, immune evasion or drug and vaccine resistance to get insights into the viral mechanisms, to create and analyze animal models, to accelerate drug and vaccine development and to improve pandemic preparedness. A subset is the GoF research of concern (GOFROC) on enhanced potentially pandemic pathogens (ePPPs) that could be harmful for humans. A related issue is the military use of research as dual-use research of concern (DURC). Influenza and coronaviruses are main research targets, because they cause pandemics by airborne infections. Two studies on avian influenza viruses initiated a global debate and a temporary GoF pause in the United States which ended with a new regulatory framework in 2017. In the European Union and China, GoF and DURC are mainly covered by the legislation for laboratory safety and genetically modified organisms. After the coronavirus outbreaks, the GoF research made significant advances, including analyses of modified MERS-like and SARS-like viruses and the creation of synthetic SARS-CoV-2 viruses as a platform to generate mutations. The GoF research on viruses will still play an important role in future, but the need to clarify the differences and overlaps between GoF research, GOFROC and DURC and the need for specialized oversight authorities are still debated.
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10
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Karki B, Bull JJ, Krone SM. Modeling the Therapeutic Potential of Defective Interfering Particles in the Presence of Immunity. Virus Evol 2022; 8:veac047. [PMID: 35799886 PMCID: PMC9255601 DOI: 10.1093/ve/veac047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/29/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Defective interfering particles (DIPs) are naturally occurring viruses that have evolved to parasitize other viruses. They suppress wild-type (WT) virus infections through their role as intracellular parasites. Because most encode few or no viral proteins, they have been entertained as possible safe antiviral therapies—something that might be given to patients infected with the WT virus. Adding to their safety, they cannot reproduce except when co-infecting the same cells as the WT, so they pose no danger of evolving into independent disease agents. But this dependence on the WT also limits their therapeutic utility by restricting the timing at which their administration can be effective. To develop a qualitative sense of these constraints for acute viral infections, we use ordinary differential equation models to study the mass-action dynamics of DIPs and WT virus in the presence of adaptive and innate immunity that will otherwise clear the infection. Our goal is to understand whether the therapeutic administration of DIPs will augment or interfere with the immune response and, in the former case, we seek to provide guidance on how virus suppression is affected by infection and clearance parameters, as well as by the timing of DIP introduction. Consistent with previous theoretical work, we find that DIPs can significantly suppress viral load. When immunity is present, the timing of DIP administration matters, with an intermediate optimum. When successful at viral suppression, DIPs even slow the immune response, but the combined effect of DIPs and immunity is still beneficial. Outcomes depend somewhat on whether immunity is elicited by and clears DIPs, but timing appears to have the greater effect.
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Affiliation(s)
- Bandita Karki
- Department of Mathematics and Statistical Science, University of Idaho , Moscow, ID 83844-1103 USA
| | - James J Bull
- Department of Biological Sciences, University of Idaho , Moscow, ID 83844-3051 USA
| | - Stephen M Krone
- Department of Mathematics and Statistical Science, University of Idaho , Moscow, ID 83844-1103 USA
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11
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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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12
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Galkin SO, Anisenko AN, Shadrina OA, Gottikh MB. Genetic Engineering Systems to Study Human Viral Pathogens from the Coronaviridae Family. Mol Biol 2022; 56:72-89. [PMID: 35194246 PMCID: PMC8853348 DOI: 10.1134/s0026893322010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 12/02/2022]
Abstract
The COVID-19 pandemic caused by the previously unknown SARS-CoV-2 Betacoronavirus made it extremely important to develop simple and safe cellular systems which allow manipulation of the viral genome and high-throughput screening of its potential inhibitors. In this review, we made an attempt at summarizing the currently existing data on genetic engineering systems used to study not only SARS-CoV-2, but also other viruses from the Coronaviridae family. In addition, the review covers the basic knowledge about the structure and the life cycle of coronaviruses.
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Affiliation(s)
- S. O. Galkin
- Bioengineering and Bioinformatics Department, Moscow State University, 119991 Moscow, Russia
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
| | - A. N. Anisenko
- Bioengineering and Bioinformatics Department, Moscow State University, 119991 Moscow, Russia
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
| | - O. A. Shadrina
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
| | - M. B. Gottikh
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
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Kalamvoki M, Norris V. A Defective Viral Particle Approach to COVID-19. Cells 2022; 11:302. [PMID: 35053418 PMCID: PMC8774189 DOI: 10.3390/cells11020302] [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: 09/14/2021] [Revised: 12/03/2021] [Accepted: 01/13/2022] [Indexed: 12/10/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 has caused a pandemic resulting in millions of deaths worldwide. While multiple vaccines have been developed, insufficient vaccination combined with adaptive mutations create uncertainty for the future. Here, we discuss novel strategies to control COVID-19 relying on Defective Interfering Particles (DIPs) and related particles that arise naturally during an infection. Our intention is to encourage and to provide the basis for the implementation of such strategies by multi-disciplinary teams. We therefore provide an overview of SARS-CoV-2 for a multi-disciplinary readership that is specifically tailored to these strategies, we identify potential targets based on the current knowledge of the properties and functions of coronaviruses, and we propose specific strategies to engineer DIPs and other interfering or therapeutic nanoparticles.
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Affiliation(s)
- Maria Kalamvoki
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, University of Rouen, 76821 Mont Saint Aignan, France;
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Fatehi F, Bingham RJ, Dechant PP, Stockley PG, Twarock R. Therapeutic interfering particles exploiting viral replication and assembly mechanisms show promising performance: a modelling study. Sci Rep 2021; 11:23847. [PMID: 34903795 PMCID: PMC8668974 DOI: 10.1038/s41598-021-03168-0] [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: 08/18/2021] [Accepted: 11/22/2021] [Indexed: 11/09/2022] Open
Abstract
Defective interfering particles arise spontaneously during a viral infection as mutants lacking essential parts of the viral genome. Their ability to replicate in the presence of the wild-type (WT) virus (at the expense of viable viral particles) is mimicked and exploited by therapeutic interfering particles. We propose a strategy for the design of therapeutic interfering RNAs (tiRNAs) against positive-sense single-stranded RNA viruses that assemble via packaging signal-mediated assembly. These tiRNAs contain both an optimised version of the virus assembly manual that is encoded by multiple dispersed RNA packaging signals and a replication signal for viral polymerase, but lack any protein coding information. We use an intracellular model for hepatitis C viral (HCV) infection that captures key aspects of the competition dynamics between tiRNAs and viral genomes for virally produced capsid protein and polymerase. We show that only a small increase in the assembly and replication efficiency of the tiRNAs compared with WT virus is required in order to achieve a treatment efficacy greater than 99%. This demonstrates that the proposed tiRNA design could be a promising treatment option for RNA viral infections.
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Affiliation(s)
- Farzad Fatehi
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
| | - Richard J Bingham
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Pierre-Philippe Dechant
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
- School of Science, Technology and Health, York St John University, York, YO31 7EX, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Reidun Twarock
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK.
- Department of Mathematics, University of York, York, YO10 5DD, UK.
- Department of Biology, University of York, York, YO10 5DD, UK.
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Abstract
The success of many viruses depends upon cooperative interactions between viral genomes. However, whenever cooperation occurs, there is the potential for 'cheats' to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, the evolutionary theory of cheating could help us understand and manipulate viral dynamics, while viruses also offer new opportunities to study the evolution of cheating.
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Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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