West, S. A., Griffin, A. S., Gardner, A. & Diggle, S. P. Social evolution theory for microorganisms. Nat. Rev. Microbiol. 4, 597–607 (2006).
Leeks, A., West, S. & Ghoul, M. The evolution of cheating in viruses. Nat. Commun. 12, 2916 (2021).
Brown, S. P., West, S. A., Diggle, S. P. & Griffin, A. S. Social evolution in micro-organisms and a Trojan horse approach to medical intervention strategies. Philos. Trans. R. Soc. B 364, 3157–3168 (2009).
Rumbaugh, K. P. et al. Quorum sensing and the social evolution of bacterial virulence. Curr. Biol. 19, 341–345 (2009).
Gurney, J., Simonet, C., Waldetoft, K. & Brown, S. Challenges and opportunities for cheat therapy in the control of bacterial infections. Nat. Prod. Rep. 39, 325–334 (2022).
Lissens, M., Joos, M., Lories, B. & Steenackers, H. Evolution-proof inhibitors of public good cooperation: a screening strategy inspired by social evolution theory. FEMS Microbiol. Rev. 46, fuac024 (2022).
Rezzoagli, C., Granato, E. & Kümmerli, R. Harnessing bacterial interactions to manage infections: a review on the opportunistic pathogen Pseudomonas aeruginosa as a case example. J. Med. Microbiol. 69, 147–161 (2020).
Andersen, S., Shapiro, B., Vandenbroucke-Grauls, C. & de Vos, M. Microbial evolutionary medicine: from theory to clinical practice. Lancet Infect. Dis. 19, e273–e283 (2019).
García-Contreras, R. & Loarca, D. The bright side of social cheaters: potential beneficial roles of ‘social cheaters’ in microbial communities. FEMS Microbiol. Ecol. 97, fiaa214 (2021).
Diggle, S. P., Griffin, A. S., Campbell, G. S. & West, S. A. Cooperation and conflict in quorum-sensing bacterial populations. Nature 450, 411–414 (2007).
Griffin, A., West, S. & Buckling, A. Cooperation and competition in pathogenic bacteria. Nature 430, 1024–1027 (2004).
André, J. & Godelle, B. Multicellular organization in bacteria as a target for drug therapy. Ecol. Lett. 8, 800–810 (2005).
Darch, S. E., West, S. A., Winzer, K. & Diggle, S. P. Density-dependent fitness benefits in quorum-sensing bacterial populations. Proc. Natl. Acad. Sci. USA 109, 8259–8263 (2012).
Rasko, D. A. & Sperandio, V. Anti-virulence strategies to combat bacteria-mediated disease. Nat. Rev. Drug Discov. 9, 117–128 (2010).
Martinez, O. F., Cardoso, M. H., Ribeiro, S. M. & Franco, O. L. Recent advances in anti-virulence therapeutic strategies. Front. Cell. Infect. Microbiol. 9, 34 (2019).
West, S. A., Diggle, S. P., Buckling, A., Gardner, A. & Griffin, A. S. The social lives of microbes. Annu. Rev. Ecol. Evol. Syst. 38, 53–77 (2007).
West, S. A., Griffin, A. S. & Gardner, A. Social semantics: altruism, cooperation, mutualism, strong reciprocity and group selection. J. Evol. Biol. 20, 415–432 (2007).
Sorg, R. A. et al. Collective resistance in microbial communities by intracellular antibiotic deactivation. PLoS Biol 14, e2000631 (2016).
Köhler, T., Buckling, A. & Van Delden, C. Cooperation and virulence of clinical Pseudomonas aeruginosa populations. Proc. Natl. Acad. Sci. USA 106, 6339–6344 (2009).
Andersen, S. B., Marvig, R. L., Molin, S., Johansen, H. K. & Griffin, A. S. Long-term social dynamics drive loss of function in pathogenic bacteria. Proc. Natl. Acad. Sci. USA 112, 10756–10761 (2015).
Wall, D. Kin recognition in bacteria. Annu. Rev. Microbiol. 70, 143–160 (2016).
Andersen, S. B. et al. Privatisation rescues function following loss of cooperation. eLife 7, e38594 (2018).
Kümmerli, R. et al. Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa. J. Evol. Biol 28, 2264–2274 (2015).
West, S. & Buckling, A. Cooperation, virulence and siderophore production in bacterial parasites. Proc. R. Soc. B 270, 37–44 (2003).
Dieltjens, L. et al. Inhibiting bacterial cooperation is an evolutionarily robust anti-biofilm strategy. Nat. Commun. 11, 1–10 (2020).
Harrison, F., Browning, L. E., Vos, M. & Buckling, A. Cooperation and virulence in acute Pseudomonas aeruginosa infections. BMC Biol 4, 21 (2006).
González, J. et al. Loss of a pyoverdine secondary receptor in Pseudomonas aeruginosa results in a fitter strain suitable for population invasion. ISME J. 15, 1330–1343 (2021).
Rezzoagli, C., Granato, E. T. & Kümmerli, R. In-vivo microscopy reveals the impact of Pseudomonas aeruginosa social interactions on host colonization. ISME J. 13, 2403–2414 (2019).
Waldetoft, K. W. & Brown, S. P. Alternative therapeutics for self-limiting infections – an indirect approach to the antibiotic resistance challenge. PLoS Biol. 15, e2001356 (2017).
Ross-Gillespie, A., Gardner, A., Buckling, A., West, S. A. & Griffin, A. S. Density dependence and cooperation: theory and a test with bacteria. Evolution 63, 2315–2325 (2009).
Ross-Gillespie, A., Gardner, A., West, S. A. & Griffin, A. S. Frequency dependence and cooperation: theory and a test with bacteria. Am. Nat. 170, 331–342 (2007).
Kümmerli, R., Griffin, A. S., West, S. A., Buckling, A. & Harrison, F. Viscous medium promotes cooperation in the pathogenic bacterium Pseudomonas aeruginosa. Proc. R. Soc. B 276, 3531–3538 (2009).
Kümmerli, R. & Brown, S. P. Molecular and regulatory properties of a public good shape the evolution of cooperation. Proc. Natl. Acad. Sci. USA 107, 18921–18926 (2010).
Jiricny, N. et al. Fitness correlates with the extent of cheating in a bacterium. J. Evol. Biol. 23, 738–747 (2010).
Ghoul, M. et al. Pyoverdin cheats fail to invade bacterial populations in stationary phase. J. Evol. Biol. 29, 1728–1736 (2016).
Harrison, F., McNally, A., da Silva, A., Heeb, S. & Diggle, S. Optimised chronic infection models demonstrate that siderophore ‘cheating’ in Pseudomonas aeruginosa is context specific. ISME J. 11, 2492–2509 (2017).
Mutlu, A., Vanderpool, E. J., Rumbaugh, K. P., Diggle, S. P. & Griffin, A. S. Exploiting cooperative pathogen behaviour for enhanced antibiotic potency: a Trojan horse approach. Microbiology 170, 1–9 (2024).
Granato, E. T., Ziegenhain, C., Marvig, R. L. & Kümmerli, R. Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa. Nat. Commun. 12, 2907–2918 (2018).
Edwards, R. & Harding, K. G. Bacteria and wound healing. Curr. Opin. Infect. Dis. 17, 91–99 (2004).
Friesen, M. L. Social evolution and cheating in plant pathogens. Annu. Rev. Phytopathol. 58, 55–75 (2020).
Huang, A. S. & Baltimore, D. Defective viral particles and viral disease processes. Nature 226, 325–337 (1970).
Ghoul, M., Griffin, A. S. & West, S. A. Toward an evolutionary definition of cheating. Evolution 68, 318–331 (2014).
Vignuzzi, M. & López, C. B. Defective viral genomes are key drivers of the virus–host interaction. Nat. Microbiol. 1, 1–9 (2019).
von Magnus, P. Studies on interference in experimental influenza. Almqvist Wiksell 1, 120 (1947).
Pitchai, F. N. N. et al. Engineered deletions of HIV replicate conditionally to reduce disease in nonhuman primates. Science 385, eadn5866 (2024).
Rezelj, V. V. et al. Defective viral genomes as therapeutic interfering particles against flavivirus infection in mammalian and mosquito hosts. Nat. Commun. 12, 2290 (2021).
Walter, M. et al. Viral gene drive spread during herpes simplex virus 1 infection in mice. Nat. Commun. 15, 8161 (2024).
Walter, M. & Verdin, E. Viral gene drive in herpesviruses. Nat. Commun. 11, 4884 (2020).
Tanner, E. J. et al. Dominant drug targets suppress the emergence of antiviral resistance. eLife 3, e03830 (2014).
Tanner, E. J., Kirkegaard, K. A. & Weinberger, L. S. Exploiting genetic interference for antiviral therapy. PLoS Genet. 12, e1005986 (2016).
Amato, K. A. et al. Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks. Nat. Commun. 13, 3416 (2022).
Gutiérrez, S. et al. The multiplicity of cellular infection changes depending on the route of cell infection in a plant virus. J. Virol. 89, 9665–9675 (2015).
Zwart, M. P. & Elena, S. F. Matters of size: genetic bottlenecks in virus infection and their potential impact on evolution. Annu. Rev. Virol. 2, 161–179 (2015).
Shirogane, Y. et al. Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome. PLoS Pathog. 17, e1009277 (2021).
Manzoni, T. B. & López, C. B. Defective (interfering) viral genomes re-explored: impact on antiviral immunity and virus persistence. Future Virol 13, 1–9 (2018).
Levi, L. I. et al. Defective viral genomes from chikungunya virus are broad-spectrum antivirals and prevent virus dissemination in mosquitoes. PLoS Pathog. 17, e1009110 (2021).
Kupke, S. Y., Riedel, D., Frensing, T., Zmora, P. & Reichl, U. A novel type of influenza A virus-derived defective interfering particle with nucleotide substitutions in its genome. J. Virol. 93, https://doi.org/10.1128/jvi.01786-18 (2019).
Leeks, A. et al. Open questions in the social lives of viruses. J. Evol. Biol. 36, 1551–1567 (2023).
DePolo, N., Giachetti & Holland, J. Continuing coevolution of virus and defective interfering particles and of viral genome sequences during undiluted passages: virus mutants exhibiting nearly complete resistance to formerly dominant defective interfering particles. J. Virol. 61, 454–464 (1987).
Horiuchi, K. Co-evolution of a filamentous bacteriophage and its defective interfering particles. J. Mol. Biol. 169, 389–407 (1983).
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.e8 (2018).
Metzger, V. T., Lloyd-Smith, J. O. & Weinberger, L. S. Autonomous targeting of infectious superspreaders using engineered transmissible therapies. PLoS Comput. Biol. 7, e1002015 (2011).
Ke, R. & Lloyd-Smith, J. O. Evolutionary analysis of human immunodeficiency virus type 1 therapies based on conditionally replicating vectors. PLoS Comput. Biol. 8, e1002744 (2012).
Rüdiger, D., Pelz, L., Hein, M. D., Kupke, S. Y. & Reichl, U. Multiscale model of defective interfering particle replication for influenza A virus infection in animal cell culture. PLoS Comput. Biol. 17, e1009357 (2021).
Rouzine, I. M. & Weinberger, L. S. Design requirements for interfering particles to maintain coadaptive stability with HIV-1. J. Virol. 87, 2081–2093 (2013).
Felt, S. A. et al. Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes. Nat. Microbiol. 6, 1–10 (2021).
Martin, M. A., Berg, N. & Koelle, K. Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks. Virus Evol. 10, veae042 (2024).
Vasilijevic, J. et al. Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. PLoS Pathog. 13, e1006650 (2017).
Welch, S. R. et al. Defective interfering viral particle treatment reduces clinical signs and protects hamsters from lethal Nipah virus disease. mBio 13, e03294-21 (2022).
Chaturvedi, S. et al. Identification of a therapeutic interfering particle – a single-administration SARS-CoV-2 antiviral intervention with a high barrier to resistance. Cell 0, 1–10 (2021).
Noble, S. & Dimmock, N. J. Defective interfering type A equine influenza virus (H3N8) protects mice from morbidity and mortality caused by homologous and heterologous subtypes of influenza A virus. J. Gen. Virol. 75, 3485–3491 (1994).
