Experimental Evolution Studies in Φ6 Cystovirus

Experimental evolution studies, in which biological populations are evolved in a specific environment over time, can address questions about the nature of spontaneous mutations, responses to selection, and the origins and maintenance of novel traits. Here, we review more than 30 years of experimental evolution studies using the bacteriophage (phage) Φ6 cystovirus. Similar to many lab-studied bacteriophages, Φ6 has a high mutation rate, large population size, fast generation time, and can be genetically engineered or cryogenically frozen, which facilitates its rapid evolution in the laboratory and the subsequent characterization of the effects of its mutations. Moreover, its segmented RNA genome, outer membrane, and capacity for multiple phages to coinfect a single host cell make Φ6 a good non-pathogenic model for investigating the evolution of RNA viruses that infect humans. We describe experiments that used Φ6 to address the fitness effects of spontaneous mutations, the consequences of evolution in the presence of coinfection, the evolution of host ranges, and mechanisms and consequences of the evolution of thermostability. We highlight open areas of inquiry where further experimentation on Φ6 could inform predictions for pathogenic viruses.

Superinfection exclusion: A viral strategy with short-term benefits and long-term drawbacks

Viral superinfection occurs when multiple viral particles subsequently infect the same host. In nature, several viral species are found to have evolved diverse mechanisms to prevent superinfection (superinfection exclusion) but how this strategic choice impacts the fate of mutations in the viral population remains unclear. Using stochastic simulations, we find that genetic drift is suppressed when superinfection occurs, thus facilitating the fixation of beneficial mutations and the removal of deleterious ones. Interestingly, we also find that the competitive (dis)advantage associated with variations in life history parameters is not necessarily captured by the viral growth rate for either infection strategy. Putting these together, we then show that a mutant with superinfection exclusion will easily overtake a superinfecting population even if the latter has a much higher growth rate. Our findings suggest that while superinfection exclusion can negatively impact the long-term adaptation of a viral population, in the short-term it is ultimately a winning strategy.

A genome-wide association study identifies Arabidopsis thaliana genes that contribute to differences in the outcome of infection with two Turnip mosaic potyvirus strains that differ in their evolutionary history and degree of host specialization

Viruses lie in a continuum between generalism and specialism depending on their ability to infect more or less hosts. While generalists are able to successfully infect a wide variety of hosts, specialists are limited to one or a few. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a pleiotropic fitness cost within each host. On the contrary, a specialist has maximal fitness within its own host. A relevant yet poorly explored question is whether viruses differ in the way they interact with their hosts' gene expression depending on their degree of specialization. Using a genome-wide association study approach, we have identified host genes whose expression depends on whether hosts were infected with more or less specialized viral strains. Four hundred fifty natural accessions of Arabidopsis thaliana were inoculated with Turnip mosaic potyvirus strains with different past evolutionary histories and that shown different degrees of specialization. Three disease-related traits were measured and associated with different sets of host genes for each strain. The genetic architectures of these traits differed among viral strains and, in the case of the more specialized virus, also varied along the duration of infection. While most of the mapped loci were strain specific, one shared locus was mapped for both strains, a disease-resistance TIR-NBS-LRR class protein. Likewise, only putative cysteine-rich receptor-like protein kinases were involved in all three traits. The impact on disease progress of 10 selected genes was validated by studying the infection phenotypes of loss-of-function mutant plants. Nine of these mutants have altered the disease progress and/or symptoms intensity between both strains. Compared to wild-type plants six had an effect on both viral strains, three had an effect only on the more specialized, and two were significant during infection with the less specialized.

Effects of historical co-infection on host shift abilities of exploitative and competitive viruses

Rapid evolution contributes to frequent emergence of RNA viral pathogens on novel hosts. However, accurately predicting which viral genotypes will emerge has been elusive. Prior work with lytic RNA bacteriophage ɸ6 (family Cystoviridae) suggested that evolution under low multiplicity of infection (MOI; proportion of viruses to susceptible cells) selected for greater host exploitation, while evolution under high MOI selected for better intracellular competition against co-infecting viruses. We predicted that phage genotypes that had experienced 300 generations of low MOI ecological history would be relatively advantaged in initial growth on two novel hosts. We inferred viral growth through changes in host population density, specifically by analyzing five attributes of growth curves of infected bacteria. Despite equivalent growth of evolved viruses on the original host, low MOI evolved clones were generally advantaged relative to high MOI clones in exploiting novel hosts. However, the specific attributes of growth curves that supported their advantage differed by host, indicating interactions between both viral and host genotype. Although there will be host specificity in viral growth, we suggest based on infectivity differences of viruses from high versus low MOI histories that prior MOI selection can later affect emergence potential.

Increasing temperature alters the within-host competition of viral strains and influences virus genetic variability

Environmental conditions can affect viral accumulation, virulence and adaptation, which have implications in the disease outcomes and efficiency of control measures. Concurrently, mixed viral infections are relevant in plants, being their epidemiology shaped by within-host virus–virus interactions. However, the extent in which the combined effect of variations in abiotic components of the plant ecological niche and the prevalence of mixed infections affect the evolutionary dynamics of viral populations is not well understood. Here, we explore the interplay between ecological and evolutionary factors during viral infections and show that isolates of two strains of Pepino mosaic potexvirus coexisted in tomato plants in a temperature-dependent continuum between neutral and antagonistic interactions. After a long-term infection, the mutational analysis of the evolved viral genomes revealed strain-specific single-nucleotide polymorphisms that were modulated by the interaction between the type of infection and temperature. These results suggest that the temperature is an ecological driver of virus-virus interactions, with an effect on the genetic diversity of individual viruses that are co-infecting an individual host. This research provides insights into the effect that changes in host growth temperatures might have on the evolutionary dynamics of viral populations in mixed infections.

Implications of mixed viral infections on plant disease ecology and evolution

Mixed viral infections occur more commonly than would be expected by chance in nature. Virus-virus interactions may affect viral traits and leave a genetic signature in the population, and thus influence the prevalence and emergence of viral diseases. Understanding about how the interactions between viruses within a host shape the evolutionary dynamics of the viral populations is needed for viral disease prevention and management. Here, we first synthesize concepts implied in the occurrence of virus-virus interactions. Second, we consider the role of the within-host interactions of virus-virus and virus-other pathogenic microbes, on the composition and structure of viral populations. Third, we contemplate whether mixed viral infections can create opportunities for the generation and maintenance of viral genetic diversity. Fourth, we attempt to summarize the evolutionary response of viral populations to mixed infections to understand how they shape the spatio-temporal dynamics of viral populations at the individual plant and field scales. Finally, we anticipate the future research under the reconciliation of molecular epidemiology and evolutionary ecology, drawing attention to the need of adding more complexity to future research in order to gain a better understanding about the mechanisms operating in nature.

Gauging genetic diversity of generalists: A test of genetic and ecological generalism with RNA virus experimental evolution

Generalist viruses, those with a comparatively larger host range, are considered more likely to emerge on new hosts. The potential to emerge in new hosts has been linked to viral genetic diversity, a measure of evolvability. However, there is no consensus on whether infecting a larger number of hosts leads to higher genetic diversity, or whether diversity is better maintained in a homogeneous environment, similar to the lifestyle of a specialist virus. Using experimental evolution with the RNA bacteriophage phi6, we directly tested whether genetic generalism (carrying an expanded host range mutation) or environmental generalism (growing on heterogeneous hosts) leads to viral populations with more genetic variation. Sixteen evolved viral lineages were deep sequenced to provide genetic evidence for population diversity. When evolved on a single host, specialist and generalist genotypes both maintained the same level of diversity (measured by the number of single nucleotide polymorphisms (SNPs) above 1%, P = 0.81). However, the generalist genotype evolved on a single host had higher SNP levels than generalist lineages under two heterogeneous host passaging schemes (P = 0.001, P < 0.001). RNA viruses’ response to selection in alternating hosts reduces standing genetic diversity compared to those evolving in a single host to which the virus is already well-adapted.

Multiple infection of cells changes the dynamics of basic viral evolutionary processes

The infection of cells by multiple copies of a given virus can impact viral evolution in a variety of ways, yet some of the most basic evolutionary dynamics remain underexplored. Using computational models, we investigate how infection multiplicity affects the fixation probability of mutants, the rate of mutant generation, and the timing of mutant invasion. An important insight from these models is that for neutral and disadvantageous phenotypes, rare mutants initially enjoy a fitness advantage in the presence of multiple infection of cells. This arises because multiple infection allows the rare mutant to enter more target cells and to spread faster, while it does not accelerate the spread of the resident wild-type virus. The rare mutant population can increase by entry into both uninfected and wild-type-infected cells, while the established wild-type population can initially only grow through entry into uninfected cells. Following this initial advantageous phase, the dynamics are governed by drift or negative selection, respectively, and a higher multiplicity reduces the chances that mutants fix in the population. Hence, while increased infection multiplicity promotes the presence of neutral and disadvantageous mutants in the short-term, it makes it less likely in the longer term. We show how these theoretical insights can be useful for the interpretation of experimental data on virus evolution at low and high multiplicities. The dynamics explored here provide a basis for the investigation of more complex viral evolutionary processes, including recombination, reassortment, as well as complementary/inhibitory interactions.

Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution

RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution. Here, we review some of the emerging viral and host mechanisms that underlie the evolution of RNA viruses. We also discuss new studies that demonstrate that the relationship between evolutionary dynamics and virus biology spans many spatial and temporal scales, affecting transmission dynamics within and between hosts as well as pathogenesis.

The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico

Current declines in biodiversity put at risk ecosystem services that are fundamental for human welfare. Increasing evidence indicates that one such service is the ability to reduce virus emergence. It has been proposed that the reduction of virus emergence occurs at two levels: through a reduction of virus prevalence/transmission and, as a result of these epidemiological changes, through a limitation of virus genetic diversity. Although the former mechanism has been studied in a few host-virus interactions, very little is known about the association between ecosystem biodiversity and virus genetic diversity. To address this subject, we estimated genetic diversity, synonymous and non-synonymous nucleotide substitution rates, selection pressures, and frequency of recombinants and re-assortants in populations of Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV) that infect chiltepin plants in Mexico. We then analyzed how these parameters varied according to the level of habitat anthropization, which is the major cause of biodiversity loss. Our results indicated that genetic diversity of PepGMV (but not of PHYVV) populations increased with the loss of biodiversity at higher levels of habitat anthropization. This was mostly the consequence of higher rates of synonymous nucleotide substitutions, rather than of adaptive selection. The frequency of recombinants and re-assortants was higher in PepGMV populations infecting wild chiltepin than in those infecting cultivated ones, suggesting that genetic exchange is not the main mechanism for generating genetic diversity in PepGMV populations. These findings provide evidence that biodiversity may modulate the genetic diversity of plant viruses, but it may differentially affect even two closely related viruses. Our analyses may contribute to understanding the factors involved in virus emergence.

Evolvability and robustness in populations of RNA virus Φ6

Microbes can respond quickly to environmental disturbances through adaptation. However, processes determining the constraints on this adaptation are not well understood. One process that could affect the rate of adaptation to environmental perturbations is genetic robustness, the ability to maintain phenotype despite mutation. Genetic robustness has been theoretically linked to evolvability but rarely tested empirically using evolving populations. We used populations of the RNA bacteriophage ϕ6 previously characterized as differing in robustness, and passaged them through a repeated environmental disturbance: periodic 45°C heat shock. The robust populations evolved faster to withstand the disturbance, relative to the less robust (brittle) populations. The robust populations also achieved relatively greater thermotolerance by the end of the experimental evolution. Sequencing revealed that thermotolerance occurred via a key mutation in gene P5 (viral lysis protein), previously shown to be associated with heat shock survival in the virus. Whereas this identical mutation fixed in all of the independently evolving robust populations, it was absent in some brittle populations, which instead fixed a less beneficial mutation. We concluded that robust populations adapted faster to the environmental change, and more easily accessed mutations of large benefit. Our study shows that genetic robustness can play a role in determining the relative ability for microbes to adapt to changing environments.