RNA virus genetic robustness: possible causes and some consequences

[EN] In general terms, robustness is the capacity of biological systems to function in spite of genetic or environmental perturbations. The small and compacted genomes and high mutation rates of RNA viruses, as well as the ever-changing environments wherein they replicate, create the conditions for robustness to be advantageous. In this review, I will enumerate possible mechanisms by which viral populations may acquire robustness, distinguishing between mechanisms that are inherent to virus replication and population dynamics and those that result from the interaction with host factors. Then, I will move to review some evidences that RNA virus populations are robust indeed. Finally, I will comment on the implications of robustness for virus evolvability, the emergence of new viruses and the efficiency of lethal mutagenesis as an antiviral strategyThis work was supported by the Spanish MICINN grant BFU2009-06993 and by the Santa Fe Institute. I thank Mark P. Zwart for critical reading of the manuscript.Elena Fito, SF. (2012). RNA virus genetic robustness: possible causes and some consequences. Current Opinion in Virology. 2(5):525-530. https://doi.org/10.1016/j.coviro.2012.06.008S5255302

Nonlinear trade-offs allow the cooperation game to evolve from prisoner's dilemma to snowdrift

[EN] The existence of cooperation, or the production of public goods, is an evolutionary problem. Cooperation is not favoured because the Prisoner s Dilemma (PD) game drives cooperators to extinction. We have re-analysed this problem by using RNA viruses to motivate a model for the evolution of cooperation. Gene products are the public goods and group size is the number of virions co-infecting the same host cell. Our results show that if the trade-off between replication and production of gene products is linear, PD is observed. However, if the trade-off is nonlinear, the viruses evolve into separate lineages of ultra-defectors and ultra-cooperators as group size is increased. The nonlinearity was justified by the existence of real viral ultra-defectors, known as defective interfering particles, which gain a nonlinear advantage by being smaller. The evolution of ultra-defectors and ultra-cooperators creates the Snowdrift game, which promotes high-level production of public goods.Work was supported by grants to L.C. from the National Science Foundation (DEB-1354253) and to S.F.E. from Spain's Ministries of Education, Culture and Sport (Salvador de Madariaga Programme PRX15/00149) and Economy, Industry and Competitiveness (BFU2015-65037-P), Generalitat Valenciana (PROMETEOII/2014/021) and the European Commission 7th Framework Programme EvoEvo Project (grant ICT-610427)Chao, L.; Elena Fito, SF. (2017). Nonlinear trade-offs allow the cooperation game to evolve from prisoner's dilemma to snowdrift. Proceedings of The Royal Society B Biological Sciences. 284(1854):1-9. https://doi.org/10.1098/rspb.2017.0228S192841854Whitaker-Dowling, P., Ungner, J. S., Widnell, C. C., & Wilcox, D. K. (1983). Superinfect on exclusion by vesicular stomatitis virus. Virology, 131(1), 137-143. doi:10.1016/0042-6822(83)90540-8Doebeli, M. (2004). 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Proceedings of the National Academy of Sciences, 91(18), 8685-8689. doi:10.1073/pnas.91.18.8685Bangham, C. (1990). Defective interfering particles: Effects in modulating virus growth and persistence. Virology, 179(2), 821-826. doi:10.1016/0042-6822(90)90150-pCole, C. N., & Baltimore, D. (1973). Defective interfering particles of poliovirus. Journal of Molecular Biology, 76(3), 345-361. doi:10.1016/0022-2836(73)90509-3Giachetti, C., & Holland, J. J. (1988). Altered replicase specificity is responsible for resistance to defective interfering particle interference of an Sdi- mutant of vesicular stomatitis virus. Journal of Virology, 62(10), 3614-3621. doi:10.1128/jvi.62.10.3614-3621.1988Giachetti, C., & Holland, J. J. (1989). Vesicular stomatitis virus and its defective interfering particles exhibit in vitro transcriptional and replicative competition for purified L-NS polymerase molecules. Virology, 170(1), 264-267. doi:10.1016/0042-6822(89)90375-9Horodyski, F. M., & Holland, J. J. (1984). Reconstruction Experiments Demonstrating Selective Effects of Defective Interfering Particles on Mixed Populations of Vesicular Stomatitis Virus. Journal of General Virology, 65(4), 819-823. doi:10.1099/0022-1317-65-4-819Kolakofsky, D. (1976). Isolation and characterization of Sendai virus DI-RNAs. Cell, 8(4), 547-555. doi:10.1016/0092-8674(76)90223-3Nayak, D. P., Sivasubramanian, N., Davis, A. R., Cortini, R., & Sung, J. (1982). Complete sequence analyses show that two defective interfering influenza viral RNAs contain a single internal deletion of a polymerase gene. Proceedings of the National Academy of Sciences, 79(7), 2216-2220. doi:10.1073/pnas.79.7.2216Nonoyama, M., & Graham, A. F. (1970). Appearance of Defective Virions in Clones of Reovirus. Journal of Virology, 6(5), 693-694. doi:10.1128/jvi.6.5.693-694.1970Weiss, B., Goran, D., Cancedda, R., & Schlesinger, S. (1974). Defective Interfering Passages of Sindbis Virus: Nature of the Intracellular Defective Viral RNA. 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Spatially-induced nestedness in a neutral model of phage-bacteria networks

[EN] Ecological networks, both displaying mutualistic or antagonistic interactions, seem to share common structural traits: the presence of nestedness and modularity. A variety of model approaches and hypothesis have been formulated concerning the significance and implications of these properties. In phage-bacteria bipartite infection networks, nestedness seems to be the rule in many different contexts. Modeling the coevolution of a diverse virus¿host ensemble is a difficult task, given the dimensionality and multi parametric nature of a standard continuous approximation. Here, we take a different approach, by using a neutral, toy model of host¿phage interactions on a spatial lattice. Each individual is represented by a bit string (a digital genome) but all strings in each class (i.e. hosts or phages) share the same sets of parameters. A matching allele model of phage-virus recognition rule is enough to generate a complex, diverse ecosystem with heterogeneous patterns of interaction and nestedness, provided that interactions take place under a spatially constrained setting. It is found that nestedness seems to be an emergent property of the co-evolutionary dynamics. Our results indicate that the enhanced diversity resulting from localized interactions strongly promotes the presence of nested infection matrices.The authors would like to thank the members of the Complex Systems Lab and our colleagues at the Santa Fe Institute for fruitful discussions. This work has been supported by the Botin Foundation by Banco Santander through its Santander Universities Global Division. This work was supported by the grants BFU2015-65037-P (S.F.E.) and FIS2016-77447-R (S.V.) from Spain Ministerio de Economia, Industria y Competitividad, AEI/MINEICO/FEDER and UE. The authors also thank the Santa Fe Institute, wheremost of this work was doneValverde, S.; Elena Fito, SF.; Solé, R. (2017). Spatially-induced nestedness in a neutral model of phage-bacteria networks. Virus Evolution. 3(2):1-7. https://doi.org/10.1093/ve/vex021S1732Ashby, B., & Boots, M. (2017). Multi-mode fluctuating selection in host-parasite coevolution. Ecology Letters, 20(3), 357-365. doi:10.1111/ele.12734Atmar, W., & Patterson, B. D. (1993). The measure of order and disorder in the distribution of species in fragmented habitat. Oecologia, 96(3), 373-382. doi:10.1007/bf00317508Bangham, J., Obbard, D. J., Kim, K.-W., Haddrill, P. R., & Jiggins, F. M. (2007). The age and evolution of an antiviral resistance mutation in Drosophila melanogaster. Proceedings of the Royal Society B: Biological Sciences, 274(1621), 2027-2034. doi:10.1098/rspb.2007.0611Bastolla, U., Fortuna, M. A., Pascual-García, A., Ferrera, A., Luque, B., & Bascompte, J. (2009). 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Evolution and emergence of plant viruses

[EN] Viruses are common agents of plant infectious diseases. During last decades, worldwide agriculture production has been compromised by a series of epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that show new pathogenic and epidemiological properties. Virus emergence has been generally associated with ecological change or with intensive agronomical practices. However, the complete picture is much more complex since the viral populations constantly evolve and adapt to their new hosts and vectors. This chapter puts emergence of plant viruses into the framework of evolutionary ecology, genetics, and epidemiology. We will stress that viral emergence begins with the stochastic transmission of preexisting genetic variants from the reservoir to the new host, whose fate depends on their fitness on each hosts, followed by adaptation to new hosts or vectors, and finalizes with an efficient epidemiological spread.We acknowledge the financial support from the Spanish Dirección General de Investigación Científica y Técnica grants BFU2012-30805 (S. F. E.) and AGL2008-02458 (F. G. A.)Elena Fito, SF.; Fraile, A.; García-Arena, F. (2014). Evolution and emergence of plant viruses. Advances in Virus Research. (88):161-191. https://doi.org/10.1016/B978-0-12-800098-4.00003-9S1611918

Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections

[EN] The molecular mechanisms underlying viral pathogenesis are yet poorly understood owed to the large number of factors involved and the complexity of their interactions. Could we identify a minimal set of host transcription factors (TF) whose misregulation would result in the transcriptional profile characteristic of infected cells in absence of the virus? How many of such sets exist? Are all orthogonal or share critical TFs involved in specific biological functions? We have developed a computational methodology that uses a quantitative model of the transcriptional regulatory network (TRN) of Arabidopsis thaliana to explore the landscape of all possible re-engineered TRNs whose transcriptomic profiles mimic those observed in infected plants. We found core sets containing between six and 34 TFs, depending on the virus, whose in silico knockout or overexpression in the TRN resulted in transcriptional profiles that minimally deviate from those observed in infected plants.We thank J.A. Daros, M. A. Fares and G. Rodrigo for fruitful comments and suggestions and O. Voinnet and C. Llave for sharing with us the TCV and TRV transcriptomic data, respectively. This research was supported by grant BFU2009-06993 by the Spanish Secretaria de Estado de Investigacion, Desarrollo e Innovacion to S.F.E.Carrera Montesinos, J.; Elena Fito, SF. (2012). Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections. Scientific Reports. 2:1-10. https://doi.org/10.1038/srep01006S1102Dodds, P. N. & Rathjen, J. P. Plant immunity: towards an integrated view of plant-pathogen interactions. Nat Rev Genet 11, 539–48 (2010).Jenner, R. G. & Young, R. A. Insights into host responses against pathoghens from transcriptional profiling. Nat Rev Microbiol 3, 281–94 (2005).Andeweg, A. C., Haagmans, B. L. & Osterhaus, A. D. Virogenomics: the virus-host interaction revisited. Curr Opin Microbiol 11, 461–6 (2008).Elena, S. 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J. & Halkier, B. A. A complex interplay of three R2R3 MYB transcription factors determines the profile of aliphatic glucosinolates in Arabidopsis. Plant Physiol 153, 348–63 (2010).Sønderby, I. E., Geu-Flores, F. & Halkier, B. A. Biosynthesis of glucosinolates – gene discovery and beyond. Trends Plant Sci 15, 283–90 (2010).Burow, M., Halkier, B. A. & Kliebenstein, D. J. Regulatory networks of glucosinolates shape Arabidopsis thaliana fitness. Curr Opin Plant Biol 13, 347–52 (2010)

Diminishing returns of inoculum size on the rate of a plant RNA virus evolution

[EN] Understanding how genetic drift, mutation and selection interplay in determining the evolutionary fate of populations is one of the central themes of Evolutionary Biology. Theory predicts that by increasing the number of coexisting beneficial alleles in a population beyond some point does not necessarily translates into an acceleration in the rate of evolution. This diminishing-returns effect of beneficial genetic variability in microbial asexual populations is known as clonal interference. Clonal interference has been shown to operate in experimental populations of animal RNA viruses replicating in cell cultures. Here we carried out experiments to test whether a similar diminishing-returns of population size on the rate of adaptation exists for a plant RNA virus infecting real multicellular hosts. We have performed evolution experiments with tobacco etch potyvirus in two hosts, the natural and a novel one, at different inoculation sizes and estimated the rates of evolution for two phenotypic fitness-related traits. Firstly, we found that evolution proceeds faster in the novel than in the original host. Secondly, results were compatible with a diminishing-returns effect of inoculum size on the rate of evolution for one of the fitness traits, but not for the other, which suggests that selection operates differently on each trait.We thank F. DE LA IGLESIA and P. AGUDO for excellent technical support and J. A. CUESTA for critical reading and insightful suggestions. This work was supported by grant BFU2015-65037-P from Spain's Ministry of Economy, Industry and Competitiveness and by the Santa Fe Institute.Navarro, R.; Ambros Palaguerri, S.; Martinez, F.; Elena Fito, SF. (2017). Diminishing returns of inoculum size on the rate of a plant RNA virus evolution. EPL (Europhysics Letters). 120(38001):1-6. https://doi.org/10.1209/0295-5075/120/38001S161203800

Genotypic but not phenotypic historical contingency revealed by viral experimental evolution

[EN] Background: The importance of historical contingency in determining the potential of viral populations to evolve has been largely unappreciated. Identifying the constraints imposed by past adaptations is, however, of importance for understanding many questions in evolutionary biology, such as the evolution of host usage dynamics by multi-host viruses or the emergence of escape mutants that persist in the absence of antiviral treatments. To address this issue, we undertook an experimental approach in which sixty lineages of Tobacco etch potyvirus that differ in their past evolutionary history and degree of adaptation to Nicotiana tabacum were allowed to adapt to this host for 15 rounds of within host multiplication and transfer. We thereafter evaluated the degree of adaptation to the new host as well as to the original ones and characterized the consensus sequence of each lineage. Results: We found that past evolutionary history did not determine the phenotypic outcome of this common host evolution phase, and that the signal of local adaptation to past hosts had largely disappeared. By contrast, evolutionary history left footprints at the genotypic level, since the majority of host-specific mutations present at the beginning of this experiment were retained in the end-point populations and may have affected which new mutations were consequently fixed. This resulted in further divergence between the sequences despite a shared selective environment. Conclusions: The present experiment reinforces the idea that the answer to the question "How important is historical contingency in evolution?" strongly depends on the level of integration of the traits studied. A strong historical contingency was found for TEV genotype, whereas a weak effect of on phenotypic evolution was revealed. In an applied context, our results imply that viruses are not easily trapped into suboptimal phenotypes and that (re) emergence is not evolutionarily constrained.We thank Francisca de la Iglesia and Angels Prosper for excellent technical assistance and Mario A. Fares and anonymous reviewers for valuable comments. This research was supported by the Spanish Direccion General de Investigacion Cientifica y Tecnica grants BFU2009-06993 and BFU2012-30805 to SFE. SB was supported by the JAE-doc program from CSIC.Bedhomme, S.; Lafforgue, G.; Elena Fito, SF. (2013). Genotypic but not phenotypic historical contingency revealed by viral experimental evolution. BMC Evolutionary Biology. 13(46):1-13. https://doi.org/10.1186/1471-2148-13-46S1131346Travisano, M., Mongold, J., Bennett, A., & Lenski, R. (1995). Experimental tests of the roles of adaptation, chance, and history in evolution. Science, 267(5194), 87-90. doi:10.1126/science.7809610Blount, Z. D., Borland, C. Z., & Lenski, R. E. (2008). 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N., HELLGREN, O., Bensch, S., & SVENSSON, E. I. (2009). Parallelism and historical contingency during rapid ecotype divergence in an isopod. Journal of Evolutionary Biology, 22(5), 1098-1110. doi:10.1111/j.1420-9101.2009.01723.xBurch, C. L., & Chao, L. (2000). Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature, 406(6796), 625-628. doi:10.1038/35020564Blount, Z. D., Barrick, J. E., Davidson, C. J., & Lenski, R. E. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature, 489(7417), 513-518. doi:10.1038/nature11514Kolbe, J. J., Leal, M., Schoener, T. W., Spiller, D. A., & Losos, J. B. (2012). Founder Effects Persist Despite Adaptive Differentiation: A Field Experiment with Lizards. Science, 335(6072), 1086-1089. doi:10.1126/science.1209566Joshi, A., Castillo, R. B., & Mueller, L. D. (2003). The contribution of ancestry, chance, and past and ongoing selection to adaptive evolution. 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Virus-host interactome: Putting the accent on how it changes

[EN] Viral infections are extremely complex processes that could only be well understood by precisely characterizing the interaction networks between the virus and the host components. In recent years, much effort has gone in this directionwith the aimof unveiling themolecular basis of viral pathology. These networks are mostly formed by viral and host proteins, and are expected to be dynamic bothwith time and space (i.e., with the progression of infection, as well as with the virus and host genotypes; what we call plastodynamic). This largely overlooked spatio-temporal evolution urgently calls for a change both in the conceptual paradigms and experimental techniques used so far to characterize virus-host interactions. More generally, molecular plasticity and temporal dynamics are unavoidable components of themechanisms that underlie any complex disease; components whose understandingwill eventually enhance our ability to modulate those networkswith the aimof improving disease treatments.This work is supported by the grants BFU2015-66894-P (to G.R.), BI02014-54269-R (to J-A.D.) and BFU2015-65037-P (to S.F.E.) from the Ministerio de Economia, Industria y Competitividad, and by the grant PROMETEOII/2014/021 from the Generalitat Valenciana (to S.F.E. and J-A.D.).Rodrigo Tarrega, G.; Daros Arnau, JA.; Elena Fito, SF. (2017). Virus-host interactome: Putting the accent on how it changes. Journal of Proteomics. 156:1-4. https://doi.org/10.1016/j.jprot.2016.12.007S1415