Defective viral genomes (DVGs) are truncated and/or rearranged viral genomes produced during virus replication. Described in many RNA virus families, some of them have interfering activity on their parental virus and/or strong immunostimulatory potential, and are being considered in antiviral approaches. Chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes spp. that infected millions of humans in the last 15 years. Here, we describe the DVGs arising during CHIKV infection in vitro in mammalian and mosquito cells, and in vivo in experimentally infected Aedes aegypti mosquitoes. We combined experimental and computational approaches to select DVG candidates most likely to have inhibitory activity and showed that, indeed, they strongly interfere with CHIKV replication both in mammalian and mosquito cells. We further demonstrated that some DVGs present broad-spectrum activity, inhibiting several CHIKV strains and other alphaviruses. Finally, we showed that pre-treating Aedes aegypti with DVGs prevented viral dissemination in vivo.

Department of Biomedical Sciences and Pathobiology Virginia Tech VA MD Regional College of Veterinary Medicine Blacksburg Virginia United States of America

Department of Biophysics and Physical Chemistry Faculty of Pharmacy Charles University Hradec Králové Czech Republic

École doctorale BioSPC Université Paris Diderot Sorbonne Paris Cité Paris France

École doctorale Frontières du vivant Université Paris Diderot Paris France

Institut Pasteur Viral Populations and Pathogenesis Unit CNRS UMR 3569 Paris France

Institut Pasteur Viruses and RNAi Unit CNRS UMR 3569 Paris France

Zobrazit více v PubMed

Chretien J-P, Anyamba A, Bedno S, Breiman R, Sang R, Sergon K, et al. Drought-associated chikungunya emergence along coastal East Africa.: 3. PubMed

Vignuzzi M, Higgs S. The Bridges and Blockades to Evolutionary Convergence on the Road to Predicting Chikungunya Virus Evolution. Annu Rev Virol. 2017;4: 181–200. 10.1146/annurev-virology-101416-041757 PubMed DOI

Levi L, Vignuzzi M. Arthritogenic Alphaviruses: A Worldwide Emerging Threat? Microorganisms. 2019;7: 133 10.3390/microorganisms7050133 PubMed DOI PMC

Von Magnus P. Incomplete forms of influenza virus. Advances in virus research. 1954. 10.1016/s0065-3527(08)60529-1 PubMed DOI

Rezelj V, Levi L, Vignuzzi M. The defective component of viral populations. Curr Opin Virol. 2018;33: 74–80. 10.1016/j.coviro.2018.07.014 PubMed DOI

Vignuzzi M, López C. Defective viral genomes are key drivers of the virus–host interaction. Nat Microbiol. 2019; 1 10.1038/s41564-018-0331-3 PubMed DOI PMC

Tapia K, Kim W-K, Sun Y, Mercado-López X, Dunay E, Wise M, et al. Defective viral genomes arising in vivo provide critical danger signals for the triggering of lung antiviral immunity. PLoS Pathog. 2013;9: e1003703 10.1371/journal.ppat.1003703 PubMed DOI PMC

Shirogane Y, Rousseau E, Voznica J, Rouzine I, Bianco S, Andino R. Experimental and mathematical insights on the competition between poliovirus and a defective interfering genome. bioRxiv. 2019; 519751 10.1101/519751 PubMed DOI PMC

Poirier E, Goic B, Tomé-Poderti L, Frangeul L, Boussier J, Gausson V, et al. Dicer-2-Dependent Generation of Viral DNA from Defective Genomes of RNA Viruses Modulates Antiviral Immunity in Insects. Cell Host Microbe. 2018;23: 353–365.e8. 10.1016/j.chom.2018.02.001 PubMed DOI PMC

Sun Y, Jain D, Koziol-White C, Genoyer E, Gilbert M, Tapia K, et al. Immunostimulatory Defective Viral Genomes from Respiratory Syncytial Virus Promote a Strong Innate Antiviral Response during Infection in Mice and Humans. Thomas PG, editor. PLOS Pathog. 2015;11: e1005122 10.1371/journal.ppat.1005122 PubMed DOI PMC

Mura M, Combredet C, Najburg V, Sanchez David R, Tangy F, Komarova A. Nonencapsidated 5’ Copy-Back Defective Interfering Genomes Produced by Recombinant Measles Viruses Are Recognized by RIG-I and LGP2 but Not MDA5. J Virol. 2017;91 10.1128/JVI.00643-17 PubMed DOI PMC

Li D, Lott W, Lowry K, Jones A, Thu H, Aaskov J. Defective interfering viral particles in acute dengue infections. PloS One. 2011;6: e19447 10.1371/journal.pone.0019447 PubMed DOI PMC

Vasilijevic J, Zamarreño N, Oliveros J, Rodriguez-Frandsen A, Gómez G, Rodriguez G, et al. Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Thomas PG, editor. PLOS Pathog. 2017;13: e1006650 10.1371/journal.ppat.1006650 PubMed DOI PMC

Dimmock N, Rainsford E, Scott P, Marriott A. Influenza Virus Protecting RNA: an Effective Prophylactic and Therapeutic Antiviral. J Virol. 2008;82: 8570–8578. 10.1128/JVI.00743-08 PubMed DOI PMC

Dimmock N, Easton A. Defective Interfering Influenza Virus RNAs: Time To Reevaluate Their Clinical Potential as Broad-Spectrum Antivirals? J Virol. 2014;88: 5217–5227. 10.1128/JVI.03193-13 PubMed DOI PMC

Poirier E, Mounce B, Rozen-Gagnon K, Hooikaas P, Stapleford K, Moratorio G, et al. Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles. J Virol. 2015;90: 2446–2454. 10.1128/JVI.02921-15 PubMed DOI PMC

Zhang X, Huang Y, Wang M, Yang F, Wu C, Huang D, et al. Differences in genome characters and cell tropisms between two chikungunya isolates of Asian lineage and Indian Ocean lineage. Virol J. 2018;15: 130 10.1186/s12985-018-1024-5 PubMed DOI PMC

Dimmock N. In vivo antiviral activity: defective interfering virus protects better against virulent Influenza A virus than avirulent virus. J Gen Virol. 2006;87: 1259–1265. 10.1099/vir.0.81678-0 PubMed DOI

Mann A, Marriott A, Balasingam S, Lambkin R, Oxford J, Dimmock N. Interfering vaccine (defective interfering influenza A virus) protects ferrets from influenza, and allows them to develop solid immunity to reinfection. Vaccine. 2006;24: 4290–4296. 10.1016/j.vaccine.2006.03.004 PubMed DOI

Mercado-López X, Cotter C, Kim W-K, Sun Y, Muñoz L, Tapia K, et al. Highly immunostimulatory RNA derived from a Sendai virus defective viral genome. Vaccine. 2013;31: 5713–5721. 10.1016/j.vaccine.2013.09.040 PubMed DOI PMC

Fisher D, Coppock G, López C. Virus-derived immunostimulatory RNA induces type I IFN-dependent antibodies and T-cell responses during vaccination. Vaccine. 2018;36: 4039–4045. 10.1016/j.vaccine.2018.05.100 PubMed DOI PMC

Martínez-Gil L, Goff P, Hai R, García-Sastre A, Shaw M, Palese P. A Sendai virus-derived RNA agonist of RIG-I as a virus vaccine adjuvant. J Virol. 2013;87: 1290–1300. 10.1128/JVI.02338-12 PubMed DOI PMC

Easton A, Scott P, Edworthy N, Meng B, Marriott A, Dimmock N. A novel broad-spectrum treatment for respiratory virus infections: influenza-based defective interfering virus provides protection against pneumovirus infection in vivo. Vaccine. 2011;29: 2777–2784. 10.1016/j.vaccine.2011.01.102 PubMed DOI

Fuller F, Marcus P. Interferon induction by viruses. IV. Sindbis virus: early passage defective-interfering particles induce interferon. J Gen Virol. 1980;48: 63–73. 10.1099/0022-1317-48-1-63 PubMed DOI

Johnston M. The characteristics required for a Sendai virus preparation to induce high levels of interferon in human lymphoblastoid cells. J Gen Virol. 1981;56: 175–184. 10.1099/0022-1317-56-1-175 PubMed DOI

Marcus P, Sekellick M. Defective interfering particles with covalently linked [+/-]RNA induce interferon. Nature. 1977;266: 815–819. 10.1038/266815a0 PubMed DOI

van den Hoogen B, van Boheemen S, de Rijck J, van Nieuwkoop S, Smith D, Laksono B, et al. Excessive production and extreme editing of human metapneumovirus defective interfering RNA is associated with type I IFN induction. J Gen Virol. 2014;95: 1625–1633. 10.1099/vir.0.066100-0 PubMed DOI PMC

Yount J, Gitlin L, Moran TM, Lopez C. MDA5 Participates in the Detection of Paramyxovirus Infection and Is Essential for the Early Activation of Dendritic Cells in Response to Sendai Virus Defective Interfering Particles. J Immunol. 2008;180: 4910–4918. 10.4049/jimmunol.180.7.4910 PubMed DOI

Shivakoti R, Siwek M, Hauer D, Schultz K, Griffin D. Induction of dendritic cell production of type I and type III interferons by wild-type and vaccine strains of measles virus: role of defective interfering RNAs. J Virol. 2013;87: 7816–7827. 10.1128/JVI.00261-13 PubMed DOI PMC

Meng B, Bentley K, Marriott A, Scott P, Dimmock N, Easton A. Unexpected complexity in the interference activity of a cloned influenza defective interfering RNA. Virol J. 2017;14: 138 10.1186/s12985-017-0805-6 PubMed DOI PMC

Matusali G, Colavita F, Bordi L, Lalle E, Ippolito G, Capobianchi M, et al. Tropism of the Chikungunya Virus. Viruses. 2019;11 10.3390/v11020175 PubMed DOI PMC

Forrester N, Coffey L, Weaver S. Arboviral Bottlenecks and Challenges to Maintaining Diversity and Fitness during Mosquito Transmission. Viruses. 2014;6: 3991–4004. 10.3390/v6103991 PubMed DOI PMC

Forrester N, Guerbois M, Seymour R, Spratt H, Weaver S. Vector-Borne Transmission Imposes a Severe Bottleneck on an RNA Virus Population. Vignuzzi M, editor. PLoS Pathog. 2012;8: e1002897 10.1371/journal.ppat.1002897 PubMed DOI PMC

Stapleford K, Coffey L, Lay S, Bordería A, Duong V, Isakov O, et al. Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential. Cell Host Microbe. 2014;15: 706–716. 10.1016/j.chom.2014.05.008 PubMed DOI

Weger-Lucarelli J, Garcia SM, Rückert C, Byas A, O’Connor SL, Aliota MT, et al. Using barcoded Zika virus to assess virus population structure in vitro and in Aedes aegypti mosquitoes. Virology. 2018;521: 138–148. 10.1016/j.virol.2018.06.004 PubMed DOI PMC

Cuevas J, Durán-Moreno M, Sanjuán R. Multi-virion infectious units arise from free viral particles in an enveloped virus. Nat Microbiol. 2017;2: 17078 10.1038/nmicrobiol.2017.78 PubMed DOI PMC

Sanjuán R. Collective Infectious Units in Viruses. Trends Microbiol. 2017;25: 402–412. 10.1016/j.tim.2017.02.003 PubMed DOI PMC

Leeks A, Sanjuán R, West S. The evolution of collective infectious units in viruses. Virus Res. 2019;265: 94–101. 10.1016/j.virusres.2019.03.013 PubMed DOI PMC

Acosta-Ampudia Y, Monsalve D, Rodríguez Y, Pacheco Y, Anaya J-M, Ramírez-Santana C. Mayaro: an emerging viral threat? Emerg Microbes Infect. 2018;7: 163 10.1038/s41426-018-0163-5 PubMed DOI PMC

Rezza G, Chen R, Weaver S. O’nyong-nyong fever: a neglected mosquito-borne viral disease. Pathog Glob Health. 2017;111: 271–275. 10.1080/20477724.2017.1355431 PubMed DOI PMC

Mackay I, Arden K. Mayaro virus: a forest virus primed for a trip to the city? Microbes Infect. 2016;18: 724–734. 10.1016/j.micinf.2016.10.007 PubMed DOI

Esposito D, Fonseca B da. Will Mayaro virus be responsible for the next outbreak of an arthropod-borne virus in Brazil? Braz J Infect Dis Off Publ Braz Soc Infect Dis. 2017;21: 540–544. 10.1016/j.bjid.2017.06.002 PubMed DOI PMC

Liu X, Tharmarajah K, Taylor A. Ross River virus disease clinical presentation, pathogenesis and current therapeutic strategies. Microbes Infect. 2017;19: 496–504. 10.1016/j.micinf.2017.07.001 PubMed DOI

Pilot R, Signorini R, Durante C, Orian L, Bhamidipati M, Fabris L. A Review on Surface-Enhanced Raman Scattering. Biosensors. 2019;9: 57 10.3390/bios9020057 PubMed DOI PMC

Erasmus J, Khandhar A, Guderian J, Granger B, Archer J, Archer M, et al. A Nanostructured Lipid Carrier for Delivery of a Replicating Viral RNA Provides Single, Low-Dose Protection against Zika. Mol Ther. 2018. [cited 8 Aug 2018]. 10.1016/j.ymthe.2018.07.010 PubMed DOI PMC

Couderc T, Khandoudi N, Grandadam M, Visse C, Gangneux N, Bagot S, et al. Prophylaxis and therapy for Chikungunya virus infection. J Infect Dis. 2009;200: 516–523. 10.1086/600381 PubMed DOI PMC

Haese N, Broeckel R, Hawman D, Heise M, Morrison T, Streblow D. Animal Models of Chikungunya Virus Infection and Disease. J Infect Dis. 2016;214: S482–S487. 10.1093/infdis/jiw284 PubMed DOI PMC

Ferguson N, Kien D, Clapham H, Aguas R, Trung V, Chau T, et al. Modeling the impact on virus transmission of Wolbachia-mediated blocking of dengue virus infection of Aedes aegypti. Sci Transl Med. 2015;7: 279ra37 10.1126/scitranslmed.3010370 PubMed DOI PMC

Ferguson N. Challenges and opportunities in controlling mosquito-borne infections. Nature. 2018;559: 490–497. 10.1038/s41586-018-0318-5 PubMed DOI

Coffey L, Vignuzzi M. Host alternation of chikungunya virus increases fitness while restricting population diversity and adaptability to novel selective pressures. J Virol. 2011;85: 1025–1035. 10.1128/JVI.01918-10 PubMed DOI PMC

Stapleford K, Moratorio G, Henningsson R, Chen R, Matheus S, Enfissi A, et al. Whole-Genome Sequencing Analysis from the Chikungunya Virus Caribbean Outbreak Reveals Novel Evolutionary Genomic Elements. PLoS Negl Trop Dis. 2016;10: e0004402 10.1371/journal.pntd.0004402 PubMed DOI PMC

García-Nafría J, Watson J, Greger I. IVA cloning: A single-tube universal cloning system exploiting bacterial In Vivo Assembly. Sci Rep. 2016;6 10.1038/s41598-016-0015-2 PubMed DOI PMC