The evolution of cheating in viruses

Leeks, Asher; West, Stuart A.; Ghoul, Melanie

doi:10.1038/s41467-021-27293-6

Cited by 33 publications

(45 citation statements)

References 157 publications

(270 reference statements)

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“…Our main qualitative result is that stable coexistence of all players is possible in extended regions of parameter space, thus paving the way to the emergence of highly diverse viral ecologies, where multiple interactions between viruses may take place. Though biological and epidemiological outcomes of interactions among co-infecting viruses seem to be hardly predictable (32), long-lived loose interactions as those arising between the agents in our model create favorable circumstances for the emergence of a viral social life (58,59) and the concomitant appearance of game-like strategies (60), for evolution towards more permanent associations, or to promote recombination between dissimilar viral and subviral particles (27,61). Recombination, for example, has led to the emergence of new species, both in DNA viruses as begomoviruses (62), and in RNA viruses, as is the case of Watermelon mosaic virus, which arose through recombination of two legume-infecting viruses (63).…”

Section: Discussionmentioning

confidence: 96%

Defective Subviral Particles Modify Ecological Equilibria and Enhance Viral Coexistence

Lucía-Sanz

Aguirre²,

Fraile³

et al. 2022

Front. Virol.

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Cooperation is a main driver of biological complexity at all levels. In the viral world, gene sharing among viral genomes, complementation between genomes or interactions within quasispecies are frequently observed. In this contribution, we explore the effects of flexible associations between fully fledged viruses and subviral entities, such as virus satellites, in viral dynamics and, in particular, in stable viral coexistence. We devise a mathematical model to compare different situations of competition between two viruses and to quantify how the association with a satellite qualitatively modifies dynamical equilibria. The relevant parameter is the invasion fitness of each virus or of the virus-satellite tandem, which in the model depends on the transmission rate of viruses and on their effect on host survival. In a virus-virus competition, one of the viruses becomes eventually extinct, recasting the competitive exclusion law of ecology. However, an association with a satellite might change the outcome of the competition in two ways, either to favor the less competitive virus (regardless of whether it is the helper virus or not) or to allow for the stable coexistence of the two viruses and the satellite. The virus-satellite association differs from other mechanisms proposed in ecology to date to enhance species coexistence. We hypothesize that such an association constitutes a parsimonious evolutionary pathway towards more stable cooperative associations, such as bipartite viral forms, a collaborative association unique to viruses.

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Section: Discussionmentioning

confidence: 96%

Defective Subviral Particles Modify Ecological Equilibria and Enhance Viral Coexistence

Lucía-Sanz

Aguirre²,

Fraile³

et al. 2022

Front. Virol.

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“…Furthermore, this can lead to evolutionary arms races between attempts to manipulate and to suppress that manipulation. A major task for the future is to determine the extent to which more complex forms of cheating occur in the natural world ( Pollak et al, 2016 ; Meir et al, 2020 ; Leeks et al, 2021 ). In many cases, this would require elucidation of the underlying mechanisms, which could be completely different across different species.…”

Section: Discussionmentioning

confidence: 99%

The evolution of manipulative cheating

Liu

West

Wild

2022

eLife

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A social cheat is typically assumed to be an individual that does not perform a cooperative behaviour, or performs less of it, but can still exploit the cooperative behaviour of others. However, empirical data suggests that cheating can be more subtle, involving evolutionary arms races over the ability to both exploit and resist exploitation. These complications have not been captured by evolutionary theory, which lags behind empirical studies in this area. We bridge this gap with a mixture of game-theoretical models and individual-based simulations, examining what conditions favour more elaborate patterns of cheating. We found that as well as adjusting their own behaviour, individuals can be selected to manipulate the behaviour of others, which we term 'manipulative cheating'. Further, we found that manipulative cheating can lead to dynamic oscillations (arms races), between selfishness, manipulation, and suppression of manipulation. Our results can help explain both variation in the level of cheating, and genetic variation in the extent to which individuals can be exploited by cheats.

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“…However, the pig gut virome had a higher number of quorum sensing receptors (n=20,627), with histidine kinase, stage 0 sporulation protein A homologue (Spo0A), LuxR, and a two-component system response regulator being the dominant receptors. These receptors may be crucial for maintaining the balance of the gut microbiota ecosystem through communication between viruses and hosts (Butala & Dragoš, 2022;Leeks et al, 2021). Nevertheless, further research is needed to investigate quorum sensing systems and establish a dedicated database for pig gut microbiota.…”

Section: Functional Capacity Of the Gut Viromementioning

confidence: 99%

Massive expansion of the pig gut virome based on global metagenomic mining

Jing

et al. 2023

Preprint

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The pig gut virome plays a crucial role in the gut microbial ecosystem of pigs, yet a comprehensive reference database is still lacking. To address this gap, we established the Pig Virome Database (PVD) of the gut that comprises 5,566,804 viral contig sequences from 4,650 publicly available gut metagenomic samples using a pipeline named metav developed in this study. The majority of viral operational taxonomic units (vOTUs) were identified as Caudoviricetes (65.36%). By clustering sequences, we identified 48,299 vOTU genomes, of which 92.83% were not found in existing major databases. The PVD database contains a total of 18,161,503 protein-coding genes that can be used to explore the functional potential of the pig gut virome. Our study showed that the PVD can improve the detection of viruses that carry antibiotic/metal resistance genes, mobile genetic elements, virulence factor genes, and quorum sensing systems. These findings highlight the extensive diversity of viruses in the pig gut and provide detailed insight into host-virus interactions.

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The evolution of cheating in viruses

Cited by 33 publications

References 157 publications

Defective Subviral Particles Modify Ecological Equilibria and Enhance Viral Coexistence

Defective Subviral Particles Modify Ecological Equilibria and Enhance Viral Coexistence

The evolution of manipulative cheating

Massive expansion of the pig gut virome based on global metagenomic mining

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