Defective viral genomes are key drivers of the virus–host interaction

Article metrics


Viruses survive often harsh host environments, yet we know little about the strategies they utilize to adapt and subsist given their limited genomic resources. We are beginning to appreciate the surprising versatility of viral genomes and how replication-competent and -defective virus variants can provide means for adaptation, immune escape and virus perpetuation. This Review summarizes current knowledge of the types of defective viral genomes generated during the replication of RNA viruses and the functions that they carry out. We highlight the universality and diversity of defective viral genomes during infections and discuss their predicted role in maintaining a fit virus population, their impact on human and animal health, and their potential to be harnessed as antiviral tools.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Classes of DVGs.
Fig. 2: Mechanisms of DVG generation.
Fig. 3: Functions and modes of actions of DVGs.


  1. 1.

    Poirier, E. Z. & Vignuzzi, M. Virus population dynamics during infection. Curr. Opin. Virol. 23, 82–87 (2017).

  2. 2.

    Von Magnus, P. & Gard, S. Studies on interference in experimental influenza. Ark. Kemi. Mineral. Geol. 24, 4 (1947).

  3. 3.

    Huang, A. S. & Baltimore, D. Defective viral particles and viral disease processes. Nature 226, 325–327 (1970).

  4. 4.

    Barrett, A. D. & Dimmock, N. J. Modulation of Semliki Forest virus-induced infection of mice by defective-interfering virus. J. Infect. Dis. 150, 98–104 (1984).

  5. 5.

    Rabinowitz, S. G. & Huprikar, J. The influence of defective-interfering particles of the PR-8 strain of influenza A virus on the pathogenesis of pulmonary infection in mice. J. Infect. Dis. 140, 305–315 (1979).

  6. 6.

    Fuller, F. J. & Marcus, P. I. Interferon induction by viruses. IV. Sindbis virus: early passage defective-interfering particles induce interferon. J. Gen. Virol. 48, 63–73 (1980).

  7. 7.

    Johnston, M. D. The characteristics required for a Sendai virus preparation to induce high levels of interferon in human lymphoblastoid cells. J. Gen. Virol. 56, 175–184 (1981).

  8. 8.

    Marcus, P. I. & Sekellick, M. J. Defective interfering particles with covalently linked [±]RNA induce interferon. Nature 266, 815–819 (1977).

  9. 9.

    Andzhaparidze, O. G., Bogomolova, N. N., Boriskin Yu, S. & Drynov, I. D. Chronic non-cytopathic infection of human continuous cell lines with mumps virus. Acta Virol. 27, 318–328 (1983).

  10. 10.

    De, B. K. & Nayak, D. P. Defective interfering influenza viruses and host cells: establishment and maintenance of persistent influenza virus infection in MDBK and HeLa cells. J. Virol. 36, 847–859 (1980).

  11. 11.

    Kawai, A., Matsumoto, S. & Tanabe, K. Characterization of rabies viruses recovered from persistently infected BHK cells. Virology 67, 520–533 (1975).

  12. 12.

    Kennedy, J. C. & Macdonald, R. D. Persistent infection with infectious pancreatic necrosis virus mediated by defective-interfering (DI) virus particles in a cell line showing strong interference but little DI replication. J. Gen. Virol. 58, 361–371 (1982).

  13. 13.

    Lehmann-Grube, F., Slenczka, W. & Tees, R. A persistent and inapparent infection of L cells with the virus of lymphocytic choriomeningitis. J. Gen. Virol. 5, 63–81 (1969).

  14. 14.

    Roux, L. & Waldvogel, F. A. Establishment of Sendai virus persistent infection: biochemical analysis of the early phase of a standard plus defective interfering virus infection of BHK cells. Virology 112, 400–410 (1981).

  15. 15.

    Schmaljohn, C. & Blair, C. D. Persistent infection of cultured mammalian cells by Japanese encephalitis virus. J. Virol. 24, 580–589 (1977).

  16. 16.

    Sekellick, M. J. & Marcus, P. I. Persistent infection. I Interferon-inducing defective-interfering particles as mediators of cell sparing: possible role in persistent infection by vesicular stomatitis virus. Virology 85, 175–186 (1978).

  17. 17.

    Baczko, K. et al. Expression of defective measles virus genes in brain tissues of patients with subacute sclerosing panencephalitis. J. Virol. 59, 472–478 (1986).

  18. 18.

    Popescu, M. & Lehmann-Grube, F. Defective interfering particles in mice infected with lymphocytic choriomeningitis virus. Virology 77, 78–83 (1977).

  19. 19.

    Mims, C. A. Rift Valley Fever virus in mice. IV. Incomplete virus; its production and properties. Brit. J. Exp. Pathol. 37, 129–143 (1956).

  20. 20.

    Viola, M. V., Scott, C. & Duffy, P. D. Persistent measles virus infection in vitro and in man. Arthritis Rheum. 21, S47–51 (1978).

  21. 21.

    Huang, A. S., Greenawalt, J. W. & Wagner, R. R. Defective T particles of vesicular stomatitis virus. I. Preparation, morphology, and some biologic properties. Virology 30, 161–172 (1966).

  22. 22.

    Duesberg, P. H. The RNA of influenza virus. Proc. Natl Acad. Sci. USA 59, 930–937 (1968).

  23. 23.

    Kingsbury, D. W., Portner, A. & Darlington, R. W. Properties of incomplete Sendai virions and subgenomic viral RNAs. Virology 42, 857–871 (1970).

  24. 24.

    Cole, C. N., Smoler, D., Wimmer, E. & Baltimore, D. Defective interfering particles of poliovirus. I. Isolation and physical properties. J. Virol. 7, 478–485 (1971).

  25. 25.

    Repik, P. & Bishop, D. H. Determination of the molecular weight of animal RNA viral genomes by nuclease digestions. I. Vesicular stomatitis virus and its defective T particle. J. Virol. 12, 969–983 (1973).

  26. 26.

    Sanjuan, R., Moya, A. & Elena, S. F. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc. Natl Acad. Sci. USA 101, 8396–8401 (2004).

  27. 27.

    Acevedo, A., Brodsky, L. & Andino, R. Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 505, 686–690 (2014).

  28. 28.

    Thyagarajan, B. & Bloom, J. D. The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. eLife 3, e03300 (2014).

  29. 29.

    Perales, C., Mateo, R., Mateu, M. G. & Domingo, E. Insights into RNA virus mutant spectrum and lethal mutagenesis events: replicative interference and complementation by multiple point mutants. J. Mol. Biol. 369, 985–1000 (2007).

  30. 30.

    Grande-Perez, A., Lazaro, E., Lowenstein, P., Domingo, E. & Manrubia, S. C. Suppression of viral infectivity through lethal defection. Proc. Natl Acad. Sci. USA 102, 4448–4452 (2005).

  31. 31.

    Cattaneo, R. et al. Biased hypermutation and other genetic changes in defective measles viruses in human brain infections. Cell 55, 255–265 (1988).

  32. 32.

    Yu, Q. et al. Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat. Struct. Mol. Biol. 11, 435–442 (2004).

  33. 33.

    Imamichi, H. et al. Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy. Proc. Natl Acad. Sci. USA 113, 8783–8788 (2016).

  34. 34.

    Ho, Y. C. et al. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 155, 540–551 (2013).

  35. 35.

    Nomoto, A., Jacobson, A., Lee, Y. F., Dunn, J. & Wimmer, E. Defective interfering particles of poliovirus: mapping of the deletion and evidence that the deletions in the genomes of DI(1), (2) and (3) are located in the same region. J. Mol. Biol. 128, 179–196 (1979).

  36. 36.

    Perrault, J. & Semler, B. L. Internal genome deletions in two distinct classes of defective interfering particles of vesicular stomatitis virus. Proc. Natl Acad. Sci. USA 76, 6191–6195 (1979).

  37. 37.

    Davis, A. R., Hiti, A. L. & Nayak, D. P. Influenza defective interfering viral RNA is formed by internal deletion of genomic RNA. Proc. Natl Acad. Sci. USA 77, 215–219 (1980).

  38. 38.

    O’Hara, P. J., Nichol, S. T., Horodyski, F. M. & Holland, J. J. Vesicular stomatitis virus defective interfering particles can contain extensive genomic sequence rearrangements and base substitutions. Cell 36, 915–924 (1984).

  39. 39.

    Hillman, B. I., Carrington, J. C. & Morris, T. J. A defective interfering RNA that contains a mosaic of a plant virus genome. Cell 51, 427–433 (1987).

  40. 40.

    Molenkamp, R., Rozier, B. C., Greve, S., Spaan, W. J. & Snijder, E. J. Isolation and characterization of an arterivirus defective interfering RNA genome. J. Virol. 74, 3156–3165 (2000).

  41. 41.

    Kolakofsky, D. Isolation and characterization of Sendai virus DI-RNAs. Cell 8, 547–555 (1976).

  42. 42.

    Lazzarini, R. A., Keene, J. D. & Schubert, M. The origins of defective interfering particles of the negative-strand RNA viruses. Cell 26, 145–154 (1981).

  43. 43.

    Nichol, S. T., O’Hara, P. J., Holland, J. J. & Perrault, J. Structure and origin of a novel class of defective interfering particle of vesicular stomatitis virus. Nucleic Acids Res. 12, 2775–2790 (1984).

  44. 44.

    Perrault, J. & Leavitt, R. W. Inverted complementary terminal sequences in single-stranded RNAs and snap-back RNAs from vesicular stomatitis defective interfering particles. J. Gen. Virol. 38, 35–50 (1978).

  45. 45.

    Re, G. G., Gupta, K. C. & Kingsbury, D. W. Genomic and copy-back 3′ termini in Sendai virus defective interfering RNA species. J. Virol. 45, 659–664 (1983).

  46. 46.

    Perrault, J. Origin and replication of defective interfering particles. Curr. Top. Microbiol. 93, 151–207 (1981).

  47. 47.

    Barrett, A. D., Crouch, C. F. & Dimmock, N. J. Defective interfering Semliki Forest virus populations are biologically and physically heterogeneous. J. Gen. Virol. 65, 1273–1283 (1984).

  48. 48.

    Jaworski, E. & Routh, A. Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus. PLoS Pathog. 13, e1006365 (2017).

  49. 49.

    Beauclair, G. et al. DI-tector: defective interfering viral genomes detector for next generation sequencing data. RNA 24, 1285–1296 (2018).

  50. 50.

    Sun, Y. et al. A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes. PLoS Pathog. 15, e1007707 (2019).

  51. 51.

    Saira, K. et al. Sequence analysis of in vivo defective interfering-like RNA of influenza A H1N1 pandemic virus. J. Virol. 87, 8064–8074 (2013).

  52. 52.

    van den Hoogen, B. G. et al. Excessive production and extreme editing of human metapneumovirus defective interfering RNA is associated with type I IFN induction. J. Gen. Virol. 95, 1625–1633 (2014).

  53. 53.

    Pfaller, C. K. et al. Measles virus defective interfering RNAs are generated frequently and early in the absence of C protein and pan be destabilized by adenosine deaminase acting on RNA-1-like hypermutations. J. Virol. 89, 7735–7747 (2015).

  54. 54.

    Tapia, K. et al. Defective viral genomes arising in vivo provide critical danger signals for the triggering of lung antiviral immunity. PLoS Pathog. 9, e1003703 (2013).

  55. 55.

    Sun, Y. et al. Immunostimulatory defective viral genomes from respiratory syncytial virus promote a strong innate antiviral response during Infection in mice and humans. PLoS Pathog. 11, e1005122 (2015).

  56. 56.

    Sanchez-Aparicio, M. T. et al. Loss of Sendai virus C protein leads to accumulation of RIG-I immunostimulatory defective interfering RNA. J. Gen. Virol. 98, 1282–1293 (2017).

  57. 57.

    Killip, M. J. et al. Deep sequencing analysis of defective genomes of parainfluenza virus 5 and their role in interferon induction. J. Virol. 87, 4798–4807 (2013).

  58. 58.

    Timm, C., Akpinar, F. & Yin, J. Quantitative characterization of defective virus emergence by deep sequencing. J. Virol. 88, 2623–2632 (2014).

  59. 59.

    Jennings, P. A., Finch, J. T., Winter, G. & Robertson, J. S. Does the higher order structure of the influenza virus ribonucleoprotein guide sequence rearrangements in influenza viral RNA? Cell 34, 619–627 (1983).

  60. 60.

    Van Slyke, G. A. et al. Sequence-specific fidelity alterations associated with West Nile virus attenuation in mosquitoes. PLoS Pathog. 11, e1005009 (2015).

  61. 61.

    Rozen-Gagnon, K. et al. Alphavirus mutator variants present host-specific defects and attenuation in mammalian and insect models. PLoS Pathog. 10, e1003877 (2014).

  62. 62.

    Vasilijevic, J. et al. Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. PLoS Pathog. 13, e1006650 (2017).

  63. 63.

    Poirier, E. Z. et al. Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles. J. Virol. 90, 2446–2454 (2015).

  64. 64.

    Fodor, E., Mingay, L. J., Crow, M., Deng, T. & Brownlee, G. G. A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase promotes the generation of defective interfering RNAs. J. Virol. 77, 5017–5020 (2003).

  65. 65.

    Panaviene, Z. & Nagy, P. D. Mutations in the RNA-binding domains of tombusvirus replicase proteins affect RNA recombination in vivo. Virology 317, 359–372 (2003).

  66. 66.

    Odagiri, T. & Tobita, K. Mutation in NS2, a nonstructural protein of influenza A virus, extragenically causes aberrant replication and expression of the PA gene and leads to generation of defective interfering particles. Proc. Natl Acad. Sci. USA 87, 5988–5992 (1990).

  67. 67.

    Yoshida, A. et al. A single amino acid substitution within the paramyxovirus Sendai virus nucleoprotein is a critical determinant for production of interferon-beta-inducing copyback-type defective interfering genomes. J. Virol. 92, e02094-17 (2018).

  68. 68.

    Ziegler, C. M. et al. The lymphocytic choriomeningitis virus matrix protein PPXY late domain drives the production of defective interfering particles. PLoS Pathog. 12, e1005501 (2016).

  69. 69.

    White, K. A., Morris, T. J. & Nonhomologous, R. N. A. recombination in tombusviruses: generation and evolution of defective interfering RNAs by stepwise deletions. J. Virol. 68, 14–24 (1994).

  70. 70.

    Kim, M. J. & Kao, C. Factors regulating template switch in vitro by viral RNA-dependent RNA polymerases: implications for RNA-RNA recombination. Proc. Natl Acad. Sci. USA 98, 4972–4977 (2001).

  71. 71.

    Wierzchoslawski, R. & Bujarski, J. J. Efficient in vitro system of homologous recombination in brome mosaic bromovirus. J. Virol. 80, 6182–6187 (2006).

  72. 72.

    Jaag, H. M. & Nagy, P. D. Silencing of Nicotiana benthamiana Xrn4p exoribonuclease promotes tombusvirus RNA accumulation and recombination. Virology 386, 344–352 (2009).

  73. 73.

    Ward, S. V., Sternsdorf, T. & Woods, N. B. Targeting expression of the leukemogenic PML-RARalpha fusion protein by lentiviral vector-mediated small interfering RNA results in leukemic cell differentiation and apoptosis. Hum. Gene Ther. 22, 1593–1598 (2011).

  74. 74.

    Calain, P., Monroe, M. C. & Nichol, S. T. Ebola virus defective interfering particles and persistent infection. Virology 262, 114–128 (1999).

  75. 75.

    Li, D. et al. Defective interfering viral particles in acute dengue infections. PLoS ONE 6, e19447 (2011).

  76. 76.

    Calain, P. & Roux, L. Generation of measles virus defective interfering particles and their presence in a preparation of attenuated live-virus vaccine. J. Virol. 62, 2859–2866 (1988).

  77. 77.

    Roux, L., Simon, A. E. & Holland, J. J. Effects of defective interfering viruses on virus replication and pathogenesis in vitro and in vivo. Adv. Virus Res. 40, 181–211 (1991).

  78. 78.

    Treuhaft, M. W. & Beem, M. O. Defective interfering particles of respiratory syncytial virus. Infect. Immun. 37, 439–444 (1982).

  79. 79.

    Wiktor, T. J., Dietzschold, B., Leamnson, R. N. & Koprowski, H. Induction and biological properties of defective interfering particles of rabies virus. J. Virol. 21, 626–635 (1977).

  80. 80.

    Huang, A. S. & Wagner, R. R. Defective T particles of vesicular stomatitis virus. II. Biologic role in homologous interference. Virology 30, 173–181 (1966).

  81. 81.

    Sekellick, M. J. & Marcus, P. I. Viral interference by defective particles of vesicular stomatitis virus measured in individual cells. Virology 104, 247–252 (1980).

  82. 82.

    Brinton, M. A. Analysis of extracellular West Nile virus particles produced by cell cultures from genetically resistant and susceptible mice indicates enhanced amplification of defective interfering particles by resistant cultures. J. Virol. 46, 860–870 (1983).

  83. 83.

    Li, T. & Pattnaik, A. K. Replication signals in the genome of vesicular stomatitis virus and its defective interfering particles: identification of a sequence element that enhances DI RNA replication. Virology 232, 248–259 (1997).

  84. 84.

    Calain, P. & Roux, L. Functional characterisation of the genomic and antigenomic promoters of Sendai virus. Virology 212, 163–173 (1995).

  85. 85.

    Portner, A. & Kingsbury, D. W. Homologous interference by incomplete Sendai virus particles: changes in virus-specific ribonucleic acid synthesis. J. Virol. 8, 388–394 (1971).

  86. 86.

    Genoyer, E. & Lopez, C. B. Defective viral genomes alter how Sendai virus interacts with cellular trafficking machinery leading to heterogeneity in the production of viral particles among infected cells. J. Virol. 93, e01579-18 (2018).

  87. 87.

    Xu, J. et al. Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence. Nat. Commun. 8, 7996 (2017).

  88. 88.

    Yount, J. S., Gitlin, L., Moran, T. M. & Lopez, C. B. 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. 180, 4910–4918 (2008).

  89. 89.

    Strahle, L., Garcin, D. & Kolakofsky, D. Sendai virus defective-interfering genomes and the activation of interferon-beta. Virology 351, 101–111 (2006).

  90. 90.

    Shivakoti, R., Siwek, M., Hauer, D., Schultz, K. L. & Griffin, D. E. 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. 87, 7816–7827 (2013).

  91. 91.

    Mercado-Lopez, X. et al. Highly immunostimulatory RNA derived from a Sendai virus defective viral genome. Vaccine 31, 5713–5721 (2013).

  92. 92.

    Yount, J. S., Kraus, T. A., Horvath, C. M., Moran, T. M. & Lopez, C. B. A novel role for viral-defective interfering particles in enhancing dendritic cell maturation. J. Immunol. 177, 4503–4513 (2006).

  93. 93.

    Barrett, A. D. & Dimmock, N. J. Modulation of a systemic Semliki Forest virus infection in mice by defective interfering virus. J. Gen. Virol. 65, 1827–1831 (1984).

  94. 94.

    Xu, J. et al. Identification of a natural viral RNA motif that optimizes sensing of viral RNA by RIG.-I. mBio 6, e01265-15 (2015).

  95. 95.

    Strahle, L. et al. Activation of the beta interferon promoter by unnatural Sendai virus infection requires RIG-I and is inhibited by viral C proteins. J. Virol. 81, 12227–12237 (2007).

  96. 96.

    Ho, T. H. et al. PACT- and RIG-I-dependent activation of Type I interferon production by a defective interfering RNA derived from measles virus vaccine. J. Virol. 90, 1557–1568 (2015).

  97. 97.

    Baum, A., Sachidanandam, R. & Garcia-Sastre, A. Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing. Proc. Natl Acad. Sci. USA 107, 16303–16308 (2010).

  98. 98.

    Lopez, C. B. et al. TLR-independent induction of dendritic cell maturation and adaptive immunity by negative-strand RNA viruses. J. Immunol. 173, 6882–6889 (2004).

  99. 99.

    Runge, S. et al. In vivo ligands of MDA5 and RIG-I in measles virus-infected cells. PLoS Pathog. 10, e1004081 (2014).

  100. 100.

    Mura, M. et al. Nonencapsidated 5′ Copy-Back Defective Interfering Genomes Produced by Recombinant Measles Viruses Are Recognized by RIG-I and LGP2 but Not MDA5. J. Virol. 91, e00643-17 (2017).

  101. 101.

    Patel, J. R. et al. ATPase-driven oligomerization of RIG-I on RNA allows optimal activation of type-I interferon. EMBO Rep. 14, 780–787 (2013).

  102. 102.

    Weber, F., Wagner, V., Rasmussen, S. B., Hartmann, R. & Paludan, S. R. Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses. J. Virol. 80, 5059–5064 (2006).

  103. 103.

    Poirier, E. Z. et al. Dicer-2-dependent generation of viral DNA from defective genomes of RNA viruses modulates antiviral immunity in insects. Cell Host Microbe 23, 353–365 (2018).

  104. 104.

    Roux, L. & Holland, J. J. Role of defective interfering particles of Sendai virus in persistent infections. Virology 93, 91–103 (1979).

  105. 105.

    Andzhaparidze, O. G., Bogomolova, N. N., Boriskin, Y. S., Bektemirova, M. S. & Drynov, I. D. Comparative study of rabies virus persistence in human and hamster cell lines. J. Virol. 37, 1–6 (1981).

  106. 106.

    Barrett, A. D. et al. Subclinical infections in mice resulting from the modulation of a lethal dose of Semliki Forest virus with defective interfering viruses: neurochemical abnormalities in the central nervous system. J. Gen. Virol. 67, 1727–1732 (1986).

  107. 107.

    Bangham, C. R. & Kirkwood, T. B. Defective interfering particles: effects in modulating virus growth and persistence. Virology 179, 821–826 (1990).

  108. 108.

    Atkinson, T., Barrett, A. D., Mackenzie, A. & Dimmock, N. J. Persistence of virulent Semliki Forest virus in mouse brain following co-inoculation with defective interfering particles. J. Gen. Virol. 67, 1189–1194 (1986).

  109. 109.

    Cave, D. R., Hendrickson, F. M. & Huang, A. S. Defective interfering virus particles modulate virulence. J. Virol. 55, 366–373 (1985).

  110. 110.

    Frensing, T. et al. Continuous influenza virus production in cell culture shows a periodic accumulation of defective interfering particles. PLoS ONE 8, e72288 (2013).

  111. 111.

    Stauffer Thompson, K. A., Rempala, G. A. & Yin, J. Multiple-hit inhibition of infection by defective interfering particles. J. Gen. Virol. 90, 888–899 (2009).

  112. 112.

    Moscona, A. Defective interfering particles of human parainfluenza virus type 3 are associated with persistent infection in cell culture. Virology 183, 821–824 (1991).

  113. 113.

    Dimmock, N. J. & Easton, A. J. Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad-spectrum antivirals? J. Virol. 88, 5217–5227 (2014).

  114. 114.

    Vasou, A., Sultanoglu, N., Goodbourn, S., Randall, R. E. & Kostrikis, L. G. Targeting pattern recognition receptors (PRR) for vaccine adjuvantation: from synthetic PRR agonists to the potential of defective interfering particles of viruses. Viruses 9, 186 (2017).

  115. 115.

    Santak, M. et al. Accumulation of defective interfering viral particles in only a few passages in Vero cells attenuates mumps virus neurovirulence. Microbes Infect. 17, 228–236 (2015).

  116. 116.

    Dimmock, N. J. & Marriott, A. C. In vivo antiviral activity: defective interfering virus protects better against virulent Influenza A virus than avirulent virus. J. Gen. Virol. 87, 1259–1265 (2006).

  117. 117.

    Mann, A. et al. Interfering vaccine (defective interfering influenza A virus) protects ferrets from influenza, and allows them to develop solid immunity to reinfection. Vaccine 24, 4290–4296 (2006).

  118. 118.

    Notton, T., Sardanyes, J., Weinberger, A. D. & Weinberger, L. S. The case for transmissible antivirals to control population-wide infectious disease. Trends Biotechnol. 32, 400–405 (2014).

  119. 119.

    Rast, L. I. et al. Conflicting selection pressures will constrain viral escape from interfering particles: principles for designing resistance-proof antivirals. PLoS Comput. Biol. 12, e1004799 (2016).

  120. 120.

    Martinez-Gil, L. et al. A Sendai virus-derived RNA agonist of RIG-I as a virus vaccine adjuvant. J. Virol. 87, 1290–1300 (2013).

  121. 121.

    Fisher, D. G., Coppock, G. M. & Lopez, C. B. Virus-derived immunostimulatory RNA induces type I IFN-dependent antibodies and T-cell responses during vaccination. Vaccine 36, 4039–4045 (2018).

  122. 122.

    Easton, A. J. et al. A novel broad-spectrum treatment for respiratory virus infections: influenza-based defective interfering virus provides protection against pneumovirus infection in vivo. Vaccine 29, 2777–2784 (2011).

  123. 123.

    Bellocq, C., Mottet, G. & Roux, L. Wide occurrence of measles virus subgenomic RNAs in attenuated live-virus vaccines. Biologicals 18, 337–343 (1990).

  124. 124.

    McLaren, L. C. & Holland, J. J. Defective interfering particles from poliovirus vaccine and vaccine reference strains. Virology 60, 579–583 (1974).

  125. 125.

    Xue, J., Chambers, B. S., Hensley, S. E. & Lopez, C. B. Propagation and characterization of influenza virus stocks that lack high levels of defective viral genomes and hemagglutinin mutations. Front. Microbiol. 7, 326 (2016).

  126. 126.

    Gould, P. S., Easton, A. J. & Dimmock, N. J. Live attenuated influenza vaccine contains substantial and unexpected amounts of defective viral genomic RNA. Viruses 9, 269 (2017).

  127. 127.

    McCrone, J. T. et al. Stochastic processes constrain the within and between host evolution of influenza virus. eLife 7, e35962 (2018).

  128. 128.

    Loney, C., Mottet-Osman, G., Roux, L. & Bhella, D. Paramyxovirus ultrastructure and genome packaging: cryo-electron tomography of sendai virus. J. Virol. 83, 8191–8197 (2009).

  129. 129.

    Cuevas, J. M., Duran-Moreno, M. & Sanjuan, R. Multi-virion infectious units arise from free viral particles in an enveloped virus. Nat. Microbiol. 2, 17078 (2017).

  130. 130.

    Aguilera, E. R., Erickson, A. K., Jesudhasan, P. R., Robinson, C. M. & Pfeiffer, J. K. Plaques formed by mutagenized viral populations have elevated coinfection frequencies. mBio 8, e02020-16 (2017).

  131. 131.

    Laske, T., Heldt, F. S., Hoffmann, H., Frensing, T. & Reichl, U. Modeling the intracellular replication of influenza A virus in the presence of defective interfering RNAs. Virus Res. 213, 90–99 (2016).

  132. 132.

    Rouzine, I. M. & Weinberger, L. S. Design requirements for interfering particles to maintain coadaptive stability with HIV-1. J. Virol. 87, 2081–2093 (2013).

  133. 133.

    Li, Q., Tong, Y., Xu, Y., Niu, J. & Zhong, J. Genetic analysis of serum-derived defective Hepatitis C virus genomes revealed novel viral cis elements for virus replication and assembly. J. Virol. 92, e02182-17 (2018).

  134. 134.

    Xiao, C. T. et al. Identification of new defective interfering RNA species associated with porcine reproductive and respiratory syndrome virus infection. Virus Res. 158, 33–36 (2011).

  135. 135.

    Mawassi, M. et al. Multiple species of defective RNAs in plants infected with citrus tristeza virus. Virology 214, 264–268 (1995).

  136. 136.

    Che, X., Mawassi, M. & Bar-Joseph, M. A novel class of large and infectious defective RNAs of Citrus tristeza virus. Virology 298, 133–145 (2002).

  137. 137.

    Snijder, E. J., den Boon, J. A., Horzinek, M. C. & Spaan, W. J. Characterization of defective interfering RNAs of Berne virus. J. Gen. Virol. 72, 1635–1643 (1991).

  138. 138.

    Hofmann, M. A., Sethna, P. B. & Brian, D. A. Bovine coronavirus mRNA replication continues throughout persistent infection in cell culture. J. Virol. 64, 4108–4114 (1990).

  139. 139.

    Penzes, Z., Wroe, C., Brown, T. D., Britton, P. & Cavanagh, D. Replication and packaging of coronavirus infectious bronchitis virus defective RNAs lacking a long open reading frame. J. Virol. 70, 8660–8668 (1996).

  140. 140.

    Makino, S., Yokomori, K. & Lai, M. M. Analysis of efficiently packaged defective interfering RNAs of murine coronavirus: localization of a possible RNA-packaging signal. J. Virol. 64, 6045–6053 (1990).

  141. 141.

    van der Most, R. G., Bredenbeek, P. J. & Spaan, W. J. A domain at the 3′ end of the polymerase gene is essential for encapsidation of coronavirus defective interfering RNAs. J. Virol. 65, 3219–3226 (1991).

  142. 142.

    Mendez, A., Smerdou, C., Izeta, A., Gebauer, F. & Enjuanes, L. Molecular characterization of transmissible gastroenteritis coronavirus defective interfering genomes: packaging and heterogeneity. Virology 217, 495–507 (1996).

  143. 143.

    Aaskov, J., Buzacott, K., Thu, H. M., Lowry, K. & Holmes, E. C. Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes. Science 311, 236–238 (2006).

  144. 144.

    Juarez-Martinez, A. B. et al. Detection and sequencing of defective viral genomes in C6/36 cells persistently infected with dengue virus 2. Arch. Virol. 158, 583–599 (2013).

  145. 145.

    Yoon, S. W. et al. Characterization of homologous defective interfering RNA during persistent infection of Vero cells with Japanese encephalitis virus. Mol. Cells 21, 112–120 (2006).

  146. 146.

    Noppornpanth, S. et al. Characterization of Hepatitis C virus deletion mutants circulating in chronically infected patients. J. Virol. 81, 7 (2007).

  147. 147.

    Pacini, L., Graziani, R., Bartholomew, L., De Francesco, R. & Paonessa, G. Naturally occurring Hepatitis C virus subgenomic deletion mutants replicate efficiently in huh-7 Cells and are trans-packaged in vitro to generate infectious defective particles. J. Virol. 83, 14 (2009).

  148. 148.

    Lancaster, M. U., Hodgetts, S. I., Mackenzie, J. S. & Urosevic, N. Characterization of defective viral RNA produced during persistent infection of Vero cells with Murray Valley encephalitis virus. J. Virol. 72, 2474–2482 (1998).

  149. 149.

    Mandl, C. W. et al. Spontaneous and engineered deletions in the 3′ noncoding region of tick-borne encephalitis virus: construction of highly attenuated mutants of a flavivirus. J. Virol. 72, 2132–2140 (1998).

  150. 150.

    Brinton, M. A. Characterization of West Nile virus persistent infections in genetically resistant and susceptible mouse cells. I. Generation of defective nonplaquing virus particles. Virology 116, 84–98 (1982).

  151. 151.

    Hasiow-Jaroszewska, B., Minicka, J., Zarzynska-Nowak, A., Budzynska, D. & Elena, S. F. Defective RNA particles derived from Tomato black ring virus genome interfere with the replication of parental virus. Virus Res. 250, 87–94 (2018).

  152. 152.

    Radloff, R. J. & Young, S. A. Defective interfering particles of encephalomyocarditis virus. J. Gen. Virol. 64, 1637–1641 (1983).

  153. 153.

    Garcia-Arriaza, J., Domingo, E. & Escarmis, C. A segmented form of foot-and-mouth disease virus interferes with standard virus: a link between interference and competitive fitness. Virology 335, 155–164 (2005).

  154. 154.

    McClure, M. A., Holland, J. J. & Perrault, J. Generation of defective interfering particles in picornaviruses. Virology 100, 408–418 (1980).

  155. 155.

    Lundquist, R. E., Sullivan, M. & Maizel, J. V. Jr. Characterization of a new isolate of poliovirus defective interfering particles. Cell 18, 759–769 (1979).

  156. 156.

    Derdeyn, C. A. & Frey, T. K. Characterization of defective-interfering RNAs of rubella virus generated during serial undiluted passage. Virology 206, 216–226 (1995).

  157. 157.

    Dimmock, N. J. & Kennedy, S. I. Prevention of death in Semliki Forest virus-infected mice by administration of defective-interfering Semliki Forest virus. J. Gen. Virol. 39, 231–242 (1978).

  158. 158.

    Barrett, A. D. & Dimmock, N. J. Properties of host and virus which influence defective interfering virus mediated-protection of mice against Semliki Forest virus lethal encephalitis. Brief report. Arch. Virol. 81, 185–188 (1984).

  159. 159.

    Fuller, F. J. & Marcus, P. I. Interferon induction by viruses. Sindbis virus: defective-interfering particles temperature-sensitive for interferon induction. J. Gen. Virol. 48, 391–394 (1980).

  160. 160.

    Finnen, R. L. & Rochon, D. M. Sequence and structure of defective interfering RNAs associated with cucumber necrosis virus infections. J. Gen. Virol. 74, 1715–1720 (1993).

  161. 161.

    Li, X. H., Heaton, L. A., Morris, T. J. & Simon, A. E. Turnip crinkle virus defective interfering RNAs intensify viral symptoms and are generated de novo. Proc. Natl Acad. Sci. USA 86, 9173–9177 (1989).

  162. 162.

    Welsh, R. M., O’Connell, C. M. & Pfau, C. J. Properties of defective lymphocytic choriomeningitis virus. J. Gen. Virol. 17, 355–359 (1972).

  163. 163.

    Meyer, B. J. & Southern, P. J. A novel type of defective viral genome suggests a unique strategy to establish and maintain persistent lymphocytic choriomeningitis virus infections. J. Virol. 71, 6757–6764 (1997).

  164. 164.

    Isaacs, A. & Edney, M. Interference between inactive and active influenza viruses in the chick embryo. II. The site of interference. Aust. J. Exp. Biol. Med. 28, 231–238 (1950).

  165. 165.

    Ada, G. L. & Perry, B. T. Influenza virus nucleic acid: relationship between biological characteristics of the virus particle and properties of the nucleic acid. J. Gen. Microbiol. 14, 623–633 (1956).

  166. 166.

    Chanda, P. K., Chambers, T. M. & Nayak, D. P. In vitro transcription of defective interfering particles of influenza virus produces polyadenylic acid-containing complementary RNAs. J. Virol. 45, 55–61 (1983).

  167. 167.

    Bean, W. J., Kawaoka, Y., Wood, J. M., Pearson, J. E. & Webster, R. G. Characterization of virulent and avirulent A/chicken/Pennsylvania/83 influenza A viruses: potential role of defective interfering RNAs in nature. J. Virol. 54, 151–160 (1985).

  168. 168.

    Chambers, T. M. & Webster, R. G. Defective interfering virus associated with A/Chicken/Pennsylvania/83 influenza virus. J. Virol. 61, 1517–1523 (1987).

  169. 169.

    Morgan, D. J. & Dimmock, N. J. Defective interfering influenza virus inhibits immunopathological effects of infectious virus in the mouse. J. Virol. 66, 1188–1192 (1992).

  170. 170.

    Scott, P. D., Meng, B., Marriott, A. C., Easton, A. J. & Dimmock, N. J. Defective interfering influenza virus confers only short-lived protection against influenza virus disease: evidence for a role for adaptive immunity in DI virus-mediated protection in vivo. Vaccine 29, 6584–6591 (2011).

  171. 171.

    Murphy, D. G., Dimock, K. & Kang, C. Y. Defective interfering particles of human parainfluenza virus 3. Virology 158, 439–443 (1987).

  172. 172.

    Sidhu, M. S. et al. Defective measles virus in human subacute sclerosing panencephalitis brain. Virology 202, 10 (1994).

  173. 173.

    Whistler, T., Bellini, W. J. & Rota, P. A. Generation of defective interfering particles by two vaccine strains of measles virus. Virology 220, 480–484 (1996).

  174. 174.

    Andzhaparidze, O. G., Boriskin, Yu,S., Bogomolova, N. N. & Drynov, I. D. Mumps virus-persistently infected cell cultures release defective interfering virus particles. J. Gen. Virol. 63, 499–503 (1982).

  175. 175.

    Portner, A. & Kingsbury, D. W. Identification of transcriptive and replicative intermediates in Sendai virus-infected cells. Virology 47, 711–725 (1972).

  176. 176.

    Calain, P., Curran, J., Kolakofsky, D. & Roux, L. Molecular cloning of natural paramyxovirus copy-back defective interfering RNAs and their expression from DNA. Virology 191, 62–71 (1992).

  177. 177.

    Patel, A. H. & Elliott, R. M. Characterization of Bunyamwera virus defective interfering particles. J. Gen. Virol. 73, 389–396 (1992).

  178. 178.

    Marchi, A., Nicoletti, L., Accardi, L., Di Bonito, P. & Giorgi, C. Characterization of Toscana virus-defective interfering particles generated in vivo. Virology 246, 125–133 (1998).

  179. 179.

    Sarmiento, R. E., Tirado, R. & Gomez, B. Characteristics of a respiratory syncytial virus persistently infected macrophage-like culture. Virus Res. 84, 45–58 (2002).

  180. 180.

    Cooper, P. D. & Bellett, A. J. A transmissible interfering component of vesicular stomatitis virus preparations. J. Gen. Microbiol. 21, 485–497 (1959).

  181. 181.

    Palma, E. L. & Huang, A. Cyclic production of vesicular stomatitis virus caused by defective interfering particles. J. Infect. Dis. 129, 402–410 (1974).

  182. 182.

    Schubert, M., Keene, J. D., Lazzarini, R. A. & Emerson, S. U. The complete sequence of a unique RNA species synthesized by a DI particle of VSV. Cell 15, 103–112 (1978).

  183. 183.

    Rao, D. D. & Huang, A. S. Interference among defective interfering particles of vesicular stomatitis virus. J. Virol. 41, 210–221 (1982).

  184. 184.

    DePolo, N. J. & Holland, J. J. Very rapid generation/amplification of defective interfering particles by vesicular stomatitis virus variants isolated from persistent infection. J. Gen. Virol. 67, 1195–1198 (1986).

  185. 185.

    Marcus, P. I. & Gaccione, C. Interferon induction by viruses. XIX. Vesicular stomatitis virus—New Jersey: high multiplicity passages generate interferon-inducing, defective-interfering particles. Virology 171, 630–633 (1989).

  186. 186.

    Resende Rde, O. et al. Generation of envelope and defective interfering RNA mutants of tomato spotted wilt virus by mechanical passage. J. Gen. Virol. 72, 2375–2383 (1991).

  187. 187.

    Chiba, S., Lin, Y. H., Kondo, H., Kanematsu, S. & Suzuki, N. A novel betapartitivirus RnPV6 from Rosellinia necatrix tolerates host RNA silencing but is interfered by its defective RNAs. Virus Res. 219, 62–72 (2016).

  188. 188.

    Nonoyama, M., Watanabe, Y. & Graham, A. F. Defective virions of reovirus. J. Virol. 6, 226–236 (1970).

  189. 189.

    Anzola, J. V., Xu, Z. K., Asamizu, T. & Nuss, D. L. Segment-specific inverted repeats found adjacent to conserved terminal sequences in wound tumor virus genome and defective interfering RNAs. Proc. Natl Acad. Sci. USA 84, 8301–8305 (1987).

  190. 190.

    Bruner, K. M. et al. Defective proviruses rapidly accumulate during acute HIV-1 infection. Nat. Med. 22, 1043–1049 (2016).

  191. 191.

    Sanchez, G., Xu, X., Chermann, J. C. & Hirsch, I. Accumulation of defective viral genomes in peripheral blood mononuclear cells of human immunodeficiency virus type 1-infected individuals. J. Virol. 71, 2233–2240 (1997).

  192. 192.

    Palukaitis, P. Satellite RNAs and satellite viruses. Mol. Plant Microbe 29, 181–186 (2016).

  193. 193.

    Simon, A. E., Roossinck, M. J. & Havelda, Z. Plant virus satellite and defective interfering RNAs: new paradigms for a new century. Annu. Rev. Phytopathol. 42, 415–437 (2004).

  194. 194.

    Sivanandam, V., Mathews, D. & Rao, A. L. Properties of satellite tobacco mosaic virus phenotypes expressed in the presence and absence of helper virus. Virology 483, 163–173 (2015).

  195. 195.

    Krupovic, M., Kuhn, J. H. & Fischer, M. G. A classification system for virophages and satellite viruses. Arch. Virol. 161, 233–247 (2016).

  196. 196.

    Rao, A. L. & Kalantidis, K. Virus-associated small satellite RNAs and viroids display similarities in their replication strategies. Virology 479–480, 627–636 (2015).

  197. 197.

    Palukaitis, P. What has been happening with viroids? Virus Genes 49, 175–184 (2014).

  198. 198.

    Bekliz, M., Colson, P. & La Scola, B. The expanding family of virophages. Viruses 8, 317 (2016).

  199. 199.

    La Scola, B. et al. The virophage as a unique parasite of the giant mimivirus. Nature 455, 100–104 (2008).

  200. 200.

    Roux, S. et al. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nat. Commun. 8, 858 (2017).

  201. 201.

    Born, D. et al. Capsid protein structure, self-assembly, and processing reveal morphogenesis of the marine virophage mavirus. Proc. Natl Acad. Sci. USA 115, 7332–7337 (2018).

  202. 202.

    Gong, D. et al. Virus-Like Vesicles of Kaposi’s Sarcoma-Associated Herpesvirus Activate Lytic Replication by Triggering Differentiation Signaling. J. Virol. 91, e00362-17 (2017).

  203. 203.

    Gastaminza, P. et al. Ultrastructural and biophysical characterization of hepatitis C virus particles produced in cell culture. J. Virol. 84, 10999–11009 (2010).

  204. 204.

    Deschamps, T. & Kalamvoki, M. Extracellular vesicles released by herpes simplex virus 1 infected cells block virus replication in recipient cells in a STING-dependent manner. J. Virol. 92, e01102-18 (2018).

Download references


This work was supported by the US National Institutes of Health National Institute of Allergy and Infectious Diseases (grants nos. NIH AI083284, AI137062 and AI134862 to C.B.L.) and the DARPA INTERCEPT program (to M.V.) managed by J. Gimlett and administered though DARPA Cooperative Agreement (grant no. HR0011-17-2-0023). In addition, this work was supported by a Fulbright US Scholar award to C.B.L. The views expressed in this article do not necessarily represent the position or the policy of the US government, and no official endorsement should be inferred.

Author information

Correspondence to Carolina B. López.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Vignuzzi, M., López, C.B. Defective viral genomes are key drivers of the virus–host interaction. Nat Microbiol 4, 1075–1087 (2019) doi:10.1038/s41564-019-0465-y

Download citation

Further reading