Invasion thresholds and the evolution of nonequilibrium virulence

Investigating and combatting the key drivers of viral zoonoses in Africa: an analysis of eight epidemics

Investigating the interplay of factors that result in a viral zoonotic outbreak is difficult, though it is increasingly important. As anthropogenic influences shift the delicate balance of ecosystems, new zoonoses emerge in humans. Sub-Saharan Africa is a notable hotspot for zoonotic disease due to abundant competent mammalian reservoir hosts. Furthermore, poverty, corruption, and an overreliance on natural resources play considerable roles in depleting biological resources, exacerbating the population's susceptibility. Unsurprisingly, viral zoonoses have emerged in Africa, including HIV/AIDS, Ebola, Avian influenza, Lassa fever, Zika, and Monkeypox. These diseases are among the principal causes of death in endemic areas. Though typically distinct in their manifestations, viral zoonoses are connected by underlying, definitive factors. This review summarises vital findings on viral zoonoses in Africa using nine notable case studies as a benchmark for future studies. We discuss the importance of ecological recuperation and protection as a central strategy to control zoonotic diseases. Emphasis was made on moderating key drivers of zoonotic diseases to forestall future pandemics. This is in conjunction with attempts to redirect efforts from reactive to pre-emptive through a multidisciplinary "one health" approach.

Homo medicus: The transition to meat eating increased pathogen pressure and the use of pharmacological plants in Homo

The human lineage transitioned to a more carnivorous niche 2.6 mya and evolved a large body size and slower life history, which likely increased zoonotic pathogen pressure. Evidence for this increase includes increased zoonotic infections in modern hunter-gatherers and bushmeat hunters, exceptionally low stomach pH compared to other primates, and divergence in immune-related genes. These all point to change, and probably intensification, in the infectious disease environment of Homo compared to earlier hominins and other apes. At the same time, the brain, an organ in which immune responses are constrained, began to triple in size. We propose that the combination of increased zoonotic pathogen pressure and the challenges of defending a large brain and body from pathogens in a long-lived mammal, selected for intensification of the plant-based self-medication strategies already in place in apes and other primates. In support, there is evidence of medicinal plant use by hominins in the middle Paleolithic, and all cultures today have sophisticated, plant-based medical systems, add spices to food, and regularly consume psychoactive plant substances that are harmful to helminths and other pathogens. We propose that the computational challenges of discovering effective plant-based treatments, the consequent ability to consume more energy-rich animal foods, and the reduced reliance on energetically-costly immune responses helped select for increased cognitive abilities and unique exchange relationships in Homo. In the story of human evolution, which has long emphasized hunting skills, medical skills had an equal role to play.

Do pathogens always evolve to be less virulent? The virulence–transmission trade-off in light of the COVID-19 pandemic

The direction the evolution of virulence takes in connection with any pathogen is a long-standing question. Formerly, it was theorized that pathogens should always evolve to be less virulent. As observations were not in line with this theoretical outcome, new theories emerged, chief among them the transmission–virulence trade-off hypotheses, which predicts an intermediate level of virulence as the endpoint of evolution. At the moment, we are very much interested in the future evolution of COVID-19’s virulence. Here, we show that the disease does not fulfill all the assumptions of the hypothesis. In the case of COVID-19, a higher viral load does not mean a higher risk of death; immunity is not long-lasting; other hosts can act as reservoirs for the virus; and death as a consequence of viral infection does not shorten the infectious period. Consequently, we cannot predict the short- or long-term evolution of the virulence of COVID-19.

The future of evolutionary medicine: sparking innovation in biomedicine and public health

Evolutionary medicine - i.e. the application of insights from evolution and ecology to biomedicine - has tremendous untapped potential to spark transformational innovation in biomedical research, clinical care and public health. Fundamentally, a systematic mapping across the full diversity of life is required to identify animal model systems for disease vulnerability, resistance, and counter-resistance that could lead to novel clinical treatments. Evolutionary dynamics should guide novel therapeutic approaches that target the development of treatment resistance in cancers (e.g., via adaptive or extinction therapy) and antimicrobial resistance (e.g., via innovations in chemistry, antimicrobial usage, and phage therapy). With respect to public health, the insight that many modern human pathologies (e.g., obesity) result from mismatches between the ecologies in which we evolved and our modern environments has important implications for disease prevention. Life-history evolution can also shed important light on patterns of disease burden, for example in reproductive health. Experience during the COVID-19 (SARS-CoV-2) pandemic has underlined the critical role of evolutionary dynamics (e.g., with respect to virulence and transmissibility) in predicting and managing this and future pandemics, and in using evolutionary principles to understand and address aspects of human behavior that impede biomedical innovation and public health (e.g., unhealthy behaviors and vaccine hesitancy). In conclusion, greater interdisciplinary collaboration is vital to systematically leverage the insight-generating power of evolutionary medicine to better understand, prevent, and treat existing and emerging threats to human, animal, and planetary health.

Which 'imperfect vaccines' encourage the evolution of higher virulence?

Background and objectives

Theory suggests that some types of vaccines against infectious pathogens may lead to the evolution of variants that cause increased harm, particularly when they infect unvaccinated individuals. This theory was supported by the observation that the use of an imperfect vaccine to control Marek's disease virus in chickens resulted in the virus evolving to be more lethal to unvaccinated birds. This raises the concern that the use of some other vaccines may lead to similar pernicious outcomes. We examine that theory with a focus on considering the regimes in which such outcomes are expected.

Methodology

We evaluate the plausibility of assumptions in the original theory. The previous theory rested heavily on a particular form of transmission-mortality-recovery trade-off and invoked other assumptions about the pathways of evolution. We review alternatives to mortality in limiting transmission and consider evolutionary pathways that were omitted in the original theory.

Results

The regime where the pernicious evolutionary outcome occurs is narrowed by our analysis but remains possible in various scenarios. We propose a more nuanced consideration of alternative models for the within-host dynamics of infections and for factors that limit virulence. Our analysis suggests imperfect vaccines against many pathogens will not lead to the evolution of pathogens with increased virulence in unvaccinated individuals.

Conclusions and implications

Evolution of greater pathogen mortality driven by vaccination remains difficult to predict, but the scope for such outcomes appears limited. Incorporation of mechanistic details into the framework, especially regarding immunity, may be requisite for prediction accuracy.

Lay Summary

A virus of chickens appears to have evolved high mortality in response to a vaccine that merely prevented disease symptoms. Theory has predicted this type of evolution in response to a variety of vaccines and other interventions such as drug treatment. Under what circumstances is this pernicious result likely to occur? Analysis of the theory in light of recent changes in our understanding of viral biology raises doubts that medicine-driven, pernicious evolution is likely to be common. But we are far from a mechanistic understanding of the interaction between pathogen and host that can predict when vaccines and other medical interventions will lead to the unwanted evolution of more virulent pathogens. So, while the regime where a pernicious result obtains may be limited, caution remains warranted in designing many types of interventions.

Antigenic escape selects for the evolution of higher pathogen transmission and virulence

Despite the propensity for complex and non-equilibrium dynamics in nature, eco-evolutionary analytical theory typically assumes that populations are at equilibria. In particular, pathogens often show antigenic escape from host immune defences, leading to repeated epidemics, fluctuating selection and diversification, but we do not understand how this impacts the evolution of virulence. We model the impact of antigenic drift and escape on the evolution of virulence in a generalized pathogen and apply a recently introduced oligomorphic methodology that captures the dynamics of the mean and variance of traits, to show analytically that these non-equilibrium dynamics select for the long-term persistence of more acute pathogens with higher virulence. Our analysis predicts both the timings and outcomes of antigenic shifts leading to repeated epidemics and predicts the increase in variation in both antigenicity and virulence before antigenic escape. There is considerable variation in the degree of antigenic escape that occurs across pathogens and our results may help to explain the difference in virulence between related pathogens including, potentially, human influenzas. Furthermore, it follows that these pathogens will have a lower R₀, with clear implications for epidemic behaviour, endemic behaviour and control. More generally, our results show the importance of examining the evolutionary consequences of non-equilibrium dynamics.

The effect of human vaccination behaviour on strain competition in an infectious disease: An imitation dynamic approach

Strain competition plays an important role in shaping the dynamics of multiple pathogen outbreaks in a population. Competition may lead to exclusion of some pathogens, while it may influence the invasion of an emerging mutant in the population. However, little emphasis has been given to understand the influence of human vaccination choice on pathogen competition or strain invasion for vaccine-preventable infectious diseases. Coupling game dynamic framework of vaccination choice and compartmental disease transmission model of two strains, we explore invasion and persistence of a mutant in the population despite having a lower reproduction rate than the resident one. We illustrate that higher perceived strain severity and lower perceived vaccine efficacy are necessary conditions for the persistence of a mutant strain. The numerical simulation also extends these invasion and persistence analyses under asymmetric cross-protective immunity of these strains. We show that the dynamics of this cross-immunity model under human vaccination choices is determined by the interplay of parameters defining the cross-immune response function, perceived risk of infection, and vaccine efficacy, and it can exhibit invasion and persistence of mutant strain, even complete exclusion of resident strain in the regime of sufficiently high perceived risk. We conclude by discussing public health implications of the results, that proper risk communication in public about the severity of the disease is an important task to reduce the chance of mutant invasion. Thus, understanding pathogen competitions under social interactions and choices may be an important component for policymakers for strategic decision-making.

The three Ts of virulence evolution during zoonotic emergence

There is increasing interest in the role that evolution may play in current and future pandemics, but there is often also considerable confusion about the actual evolutionary predictions. This may be, in part, due to a historical separation of evolutionary and medical fields, but there is a large, somewhat nuanced body of evidence-supported theory on the evolution of infectious disease. In this review, we synthesize this evolutionary theory in order to provide a framework for clearer understanding of the key principles. Specifically, we discuss the selection acting on zoonotic pathogens' transmission rates and virulence at spillover and during emergence. We explain how the direction and strength of selection during epidemics of emerging zoonotic disease can be understood by a three Ts framework: trade-offs, transmission, and time scales. Virulence and transmission rate may trade-off, but transmission rate is likely to be favoured by selection early in emergence, particularly if maladapted zoonotic pathogens have 'no-cost' transmission rate improving mutations available to them. Additionally, the optimal virulence and transmission rates can shift with the time scale of the epidemic. Predicting pathogen evolution, therefore, depends on understanding both the trade-offs of transmission-improving mutations and the time scales of selection.

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

One year into the global COVID-19 pandemic, the focus of attention has shifted to the emergence and spread of SARS-CoV-2 variants of concern (VOCs). After nearly a year of the pandemic with little evolutionary change affecting human health, several variants have now been shown to have substantial detrimental effects on transmission and severity of the virus. Public health officials, medical practitioners, scientists, and the broader community have since been scrambling to understand what these variants mean for diagnosis, treatment, and the control of the pandemic through nonpharmaceutical interventions and vaccines. Here we explore the evolutionary processes that are involved in the emergence of new variants, what we can expect in terms of the future emergence of VOCs, and what we can do to minimise their impact.

Rapid adaptation of the Irish potato famine pathogen Phytophthora infestans to changing temperature

Temperature plays a multidimensional role in host-pathogen interactions. As an important element of climate change, elevated world temperature resulting from global warming presents new challenges to sustainable disease management. Knowledge of pathogen adaptation to global warming is needed to predict future disease epidemiology and formulate mitigating strategies. In this study, 21 Phytophthora infestans isolates originating from seven thermal environments were acclimated for 200 days under stepwise increase or decrease of experimental temperatures and evolutionary responses of the isolates to the thermal changes were evaluated. We found temperature acclimation significantly increased the fitness and genetic adaptation of P. infestans isolates at both low and high temperatures. Low-temperature acclimation enforced the countergradient adaptation of the pathogen to its past selection and enhanced the positive association between the pathogen's intrinsic growth rate and aggressiveness. At high temperatures, we found that pathogen growth collapsed near the maximum temperature for growth, suggesting a thermal niche boundary may exist in the evolutionary adaptation of P. infestans. These results indicate that pathogens can quickly adapt to temperature shifts in global warming. If this is associated with environmental conditions favoring pathogen spread, it will threaten future food security and human health and require the establishment of mitigating actions.

The Price equation and evolutionary epidemiology

The Price equation has found widespread application in many areas of evolutionary biology, including the evolutionary epidemiology of infectious diseases. In this paper, we illustrate the utility of this approach to modelling disease evolution by first deriving a version of Price's equation that can be applied in continuous time and to populations with overlapping generations. We then show how this version of Price's equation provides an alternative perspective on pathogen evolution by considering the epidemiological meaning of each of its terms. Finally, we extend these results to the case where population size is small and generates demographic stochasticity. We show that the particular partitioning of evolutionary change given by Price's equation is also a natural way to partition the evolutionary consequences of demographic stochasticity, and demonstrate how such stochasticity tends to weaken selection on birth rate (e.g. the transmission rate of an infectious disease) and enhance selection on mortality rate (e.g. factors, like virulence, that cause the end of an infection). In the long term, if there is a trade-off between virulence and transmission across parasite strains, the weaker selection on transmission and stronger selection on virulence that arises from demographic stochasticity will tend to drive the evolution of lower levels of virulence. This article is part of the theme issue 'Fifty years of the Price equation'.

Broad thermal tolerance is negatively correlated with virulence in an opportunistic bacterial pathogen

Predicting the effects of global increase in temperatures on disease virulence is challenging, especially for environmental opportunistic bacteria, because pathogen fitness may be differentially affected by temperature within and outside host environment. So far, there is very little empirical evidence on the connections between optimal temperature range and virulence in environmentally growing pathogens. Here, we explored whether the virulence of an environmentally growing opportunistic fish pathogen, Flavobacterium columnare, is malleable to evolutionary changes via correlated selection on thermal tolerance. To this end, we experimentally quantified the thermal performance curves (TPCs) for maximum biomass yield of 49 F. columnare isolates from eight different geographic locations in Finland over ten years (2003-2012). We also characterized virulence profiles of these strains in a zebra fish (Danio rerio) infection model. We show that virulence among the strains increased over the years, but thermal generalism, and in particular tolerance to higher temperatures, was negatively associated with virulence. Our data suggest that temperature has a strong effect on the pathogen genetic diversity and therefore presumably also on disease dynamics. However, the observed increase in frequency and severity of F. columnare epidemics over the last decade cannot be directly linked to bacterial evolution due to increased mean temperature, but is most likely associated with factors related to increased length of growing season, or other time-dependent change in environment. Our study demonstrates that complex interactions between the host, the pathogen and the environment influence disease virulence of an environmentally growing opportunistic pathogen.

Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context

An extensive body of theory addresses the topic of pathogen virulence evolution, yet few studies have empirically demonstrated the presence of fitness trade-offs that would select for intermediate virulence. Here we show the presence of transmission-clearance trade-offs in dengue virus using viremia measurements. By fitting a within-host model to these data, we further find that the interaction between dengue and the host immune response can account for the observed trade-offs. Finally, we consider dengue virulence evolution when selection acts on the virus’s production rate. By combining within-host model simulations with empirical findings on how host viral load affects human-to-mosquito transmission success, we show that the virus’s transmission potential is maximized at production rates associated with intermediate virulence and that the optimal production rate critically depends on dengue’s epidemiological context. These results indicate that long-term changes in dengue’s global distribution impact the invasion and spread of virulent dengue virus genotypes.

Theory predicts that pathogens will evolve towards intermediate virulence, yet the necessary trade-offs invoked by this theory have rarely been demonstrated empirically. Here, the authors show that dengue virus dynamics exhibit a trade-off between transmission and clearance rates.

Adaptation of a Chytrid Parasite to Its Cyanobacterial Host Is Hampered by Host Intraspecific Diversity

Experimental evolution can be used to test for and characterize parasite and pathogen adaptation. We undertook a serial-passage experiment in which a single parasite population of the obligate fungal (chytrid) parasite Rhizophydium megarrhizum was maintained over a period of 200 days under different mono- and multiclonal compositions of its phytoplankton host, the bloom-forming cyanobacterium Planktothrix. Despite initially inferior performance, parasite populations under sustained exposure to novel monoclonal hosts experienced rapid fitness increases evidenced by increased transmission rates. This demonstrates rapid adaptation of chytrids to novel hosts and highlights their high evolutionary potential. In contrast, increased fitness was not detected in parasites exposed to multiclonal host mixtures, indicating that cyanobacterial intraspecific diversity hampers parasites adaptation. Significant increases in intensity of infection were observed in monoclonal and multiclonal treatments, suggesting high evolvability of traits involved in parasite attachment onto hosts (i.e., encystment). A comparison of the performance of evolved and unevolved (control) parasite populations against their common ancestral host did not reveal parasite attenuation. Our results exemplify the ability of chytrid parasites to adapt rapidly to new hosts, while providing experimental evidence that genetic diversity in host populations grants increased resistance to disease by hindering parasite adaptation.

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

Evolutionary ecology of Chagas disease; what do we know and what do we need?

The aetiological agent of Chagas disease, Trypanosoma cruzi, is a key human pathogen afflicting most populations of Latin America. This vectorborne parasite is transmitted by haematophageous triatomines, whose control by large‐scale insecticide spraying has been the main strategy to limit the impact of the disease for over 25 years. While those international initiatives have been successful in highly endemic areas, this systematic approach is now challenged by the emergence of insecticide resistance and by its low efficacy in controlling species that are only partially adapted to human habitat. In this contribution, we review evidences that Chagas disease control shall now be entering a second stage that will rely on a better understanding of triatomines adaptive potential, which requires promoting microevolutionary studies and –omic approaches. Concomitantly, we show that our knowledge of the determinants of the evolution of T. cruzi high diversity and low virulence remains too limiting to design evolution‐proof strategies, while such attributes may be part of the future of Chagas disease control after the 2020 WHO's target of regional elimination of intradomiciliary transmission has been reached. We should then aim at developing a theory of T. cruzi virulence evolution that we anticipate to provide an interesting enrichment of the general theory according to the specificities of transmission of this very generalist stercorarian trypanosome. We stress that many ecological data required to better understand selective pressures acting on vector and parasite populations are already available as they have been meticulously accumulated in the last century of field research. Although more specific information will surely be needed, an effective research strategy would be to integrate data into the conceptual and theoretical framework of evolutionary ecology and life‐history evolution that provide the quantitative backgrounds necessary to understand and possibly anticipate adaptive responses to public health interventions.

Understanding Immunity through the Lens of Disease Ecology

As we describe the immune system in ever more exquisite detail, we might find that no matter how successful, this approach will not be sufficient to understand the spread of infectious agents, their susceptibility to vaccine therapy, and human disease resistance. Compared with the strict reductionism practiced as a means of characterizing most biological processes, I propose that the progression and outcome of disease-causing host-parasite interactions will be more clearly understood through a focus on disease ecology.

High virulence does not necessarily impede viral adaptation to a new host: a case study using a plant RNA virus

BACKGROUND

Theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels. Alternatively, highly virulent microparasites could also curtail host development, thereby limiting both the host resources available to them and their own within-host effective population size. In this case, high virulence might restrain the mutation supply rate and increase the strength with which genetic drift acts on microparasite populations. Thereby, this alternative explanation limits the microparasites' potential to adapt to the host and ultimately the ability to evolve lower virulence. As a first exploration of this hypothesis, we evolved Tobacco etch virus carrying an eGFP fluorescent marker in two semi-permissive host species, Nicotiana benthamiana and Datura stramonium, for which it has a large difference in virulence. We compared the results to those previously obtained in the natural host, Nicotiana tabacum, where we have shown that carriage of eGFP has a high fitness cost and its loss serves as a real-time indicator of adaptation.

RESULTS

After over half a year of evolution, we sequenced the genomes of the evolved lineages and measured their fitness. During the evolution experiment, marker loss leading to viable virus variants was only observed in one lineage of the host for which the virus has low virulence, D. stramonium. This result was consistent with the observation that there was a fitness cost of eGFP in this host, while surprisingly no fitness cost was observed in the host for which the virus has high virulence, N. benthamiana. Furthermore, in both hosts we observed increases in viral fitness in few lineages, and host-specific convergent evolution at the genomic level was only found in N. benthamiana.

CONCLUSIONS

The results of this study do not lend support to the hypothesis that high virulence impedes microparasites' evolution. Rather, they exemplify that jumps between host species can be game changers for evolutionary dynamics. When considering the evolution of genome architecture, host species jumps might play a very important role, by allowing evolutionary intermediates to be competitive.

Beyond Mortality: Sterility As a Neglected Component of Parasite Virulence

Virulence is generally defined as the reduction in host fitness following infection by a parasite (see Box 1 for glossary) [1]. In general, parasite exploitation of host resources may reduce host survival (mortality virulence), decrease host fecundity (sterility virulence), or even have sub-lethal effects that disturb the way individuals interact within a community (morbidity) [2,3]. In fact, the virulence of many parasites involves a combination of these various effects (Box 2). In practice, however, virulence is most often defined as disease-induced mortality [1, 4–6]. This is especially true in the theoretical literature, where the evolution of sterility virulence, morbidity, and mixed strategies of host exploitation have received relatively little attention. While the focus on mortality effects has allowed for easy comparison between models and, thus, rapid advancement of the field, we ask whether these theoretical simplifications have led us to inadvertently minimize the evolutionary importance of host sterilization and secondary virulence effects. As explicit theoretical work on morbidity is currently lacking (but see [7]), our aim in this Opinion piece is to discuss what is understood about sterility virulence evolution, its adaptive potential, and the implications for parasites that utilize a combination of host survival and reproductive resources.

Virulence evolution at the front line of spreading epidemics

Understanding and predicting the spatial spread of emerging pathogens is a major challenge for the public health management of infectious diseases. Theoretical epidemiology shows that the speed of an epidemic is governed by the life-history characteristics of the pathogen and its ability to disperse. Rapid evolution of these traits during the invasion may thus affect the speed of epidemics. Here we study the influence of virulence evolution on the spatial spread of an epidemic. At the edge of the invasion front, we show that more virulent and transmissible genotypes are expected to win the competition with other pathogens. Behind the front line, however, more prudent exploitation strategies outcompete virulent pathogens. Crucially, even when the presence of the virulent mutant is limited to the edge of the front, the invasion speed can be dramatically altered by pathogen evolution. We support our analysis with individual-based simulations and we discuss the additional effects of demographic stochasticity taking place at the front line on virulence evolution. We confirm that an increase of virulence can occur at the front, but only if the carrying capacity of the invading pathogen is large enough. These results are discussed in the light of recent empirical studies examining virulence evolution at the edge of spreading epidemics.

The adaptive evolution of virulence: a review of theoretical predictions and empirical tests

Why is it that some parasites cause high levels of host damage (i.e. virulence) whereas others are relatively benign? There are now numerous reviews of virulence evolution in the literature but it is nevertheless still difficult to find a comprehensive treatment of the theory and data on the subject that is easily accessible to non-specialists. Here we attempt to do so by distilling the vast theoretical literature on the topic into a set of relatively few robust predictions. We then provide a comprehensive assessment of the available empirical literature that tests these predictions. Our results show that there have been some notable successes in integrating theory and data but also that theory and empiricism in this field do not ‘speak’ to each other very well. We offer a few suggestions for how the connection between the two might be improved.

Within-host evolution decreases virulence in an opportunistic bacterial pathogen

Background

Pathogens evolve in a close antagonistic relationship with their hosts. The conventional theory proposes that evolution of virulence is highly dependent on the efficiency of direct host-to-host transmission. Many opportunistic pathogens, however, are not strictly dependent on the hosts due to their ability to reproduce in the free-living environment. Therefore it is likely that conflicting selection pressures for growth and survival outside versus within the host, rather than transmission potential, shape the evolution of virulence in opportunists. We tested the role of within-host selection in evolution of virulence by letting a pathogen Serratia marcescens db11 sequentially infect Drosophila melanogaster hosts and then compared the virulence to strains that evolved only in the outside-host environment.

Results

We found that the pathogen adapted to both Drosophila melanogaster host and novel outside-host environment, leading to rapid evolutionary changes in the bacterial life-history traits including motility, in vitro growth rate, biomass yield, and secretion of extracellular proteases. Most significantly, selection within the host led to decreased virulence without decreased bacterial load while the selection lines in the outside-host environment maintained the same level of virulence with ancestral bacteria.

Conclusions

This experimental evidence supports the idea that increased virulence is not an inevitable consequence of within-host adaptation even when the epidemiological restrictions are removed. Evolution of attenuated virulence could occur because of immune evasion within the host. Alternatively, rapid fluctuation between outside-host and within-host environments, which is typical for the life cycle of opportunistic bacterial pathogens, could lead to trade-offs that lower pathogen virulence.

Imperfect Vaccination Can Enhance the Transmission of Highly Virulent Pathogens

Could some vaccines drive the evolution of more virulent pathogens? Conventional wisdom is that natural selection will remove highly lethal pathogens if host death greatly reduces transmission. Vaccines that keep hosts alive but still allow transmission could thus allow very virulent strains to circulate in a population. Here we show experimentally that immunization of chickens against Marek's disease virus enhances the fitness of more virulent strains, making it possible for hyperpathogenic strains to transmit. Immunity elicited by direct vaccination or by maternal vaccination prolongs host survival but does not prevent infection, viral replication or transmission, thus extending the infectious periods of strains otherwise too lethal to persist. Our data show that anti-disease vaccines that do not prevent transmission can create conditions that promote the emergence of pathogen strains that cause more severe disease in unvaccinated hosts.

A study using Marek's disease virus in poultry shows that by reducing natural selection against highly virulent strains, imperfect vaccination enables the spread of viral strains that would otherwise be too lethal to persist.

There is a theoretical expectation that some types of vaccines could prompt the evolution of more virulent (“hotter”) pathogens. This idea follows from the notion that natural selection removes pathogen strains that are so “hot” that they kill their hosts and, therefore, themselves. Vaccines that let the hosts survive but do not prevent the spread of the pathogen relax this selection, allowing the evolution of hotter pathogens to occur. This type of vaccine is often called a leaky vaccine. When vaccines prevent transmission, as is the case for nearly all vaccines used in humans, this type of evolution towards increased virulence is blocked. But when vaccines leak, allowing at least some pathogen transmission, they could create the ecological conditions that would allow hot strains to emerge and persist. This theory proved highly controversial when it was first proposed over a decade ago, but here we report experiments with Marek’s disease virus in poultry that show that modern commercial leaky vaccines can have precisely this effect: they allow the onward transmission of strains otherwise too lethal to persist. Thus, the use of leaky vaccines can facilitate the evolution of pathogen strains that put unvaccinated hosts at greater risk of severe disease. The future challenge is to identify whether there are other types of vaccines used in animals and humans that might also generate these evolutionary risks.

Host-parasite interactions during a biological invasion: The fate of lungworms (Rhabdias spp.) inside native and novel anuran hosts

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Rhabdias hylae (frog) lungworms entered cane toads and migrated through the body but were not found in the target tissue, the lungs.

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Larvae of both lungworm species induced inflammation in both types of hosts.

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The immune response (relative numbers of different cell types) differed between hosts and between parasite species.

The cane toad invasion in Australia provides a robust opportunity to clarify the infection process in co-evolved versus de novo host–parasite interactions. We investigated these infection dynamics through histological examination following experimental infections of metamorphs of native frogs (Cyclorana australis) and cane toads (Rhinella marina) with Rhabdias hylae (the lungworm found in native frogs) and Rhabdias pseudosphaerocephala (the lungworm found in cane toads). Cane toads reared under continuous exposure to infective larvae of the frog lungworm were examined after periods of 2, 6, 10 and 15 days. Additionally, both toads and frogs were exposed for 24 h to larvae of either the toad or the frog lungworm, and examined 2, 5, 10 and 20 days post-treatment. R. hylae (frog) lungworms entered cane toads and migrated through the body but were not found in the target tissue, the lungs. Larvae of both lungworm species induced inflammation in both types of hosts, although the immune response (relative numbers of different cell types) differed between hosts and between parasite species. Co-evolution has modified the immune response elicited by infection and (perhaps for that reason) has enhanced the parasite's ability to survive and to reach the host's lungs.

War and peace: social interactions in infections

One of the most striking facts about parasites and microbial pathogens that has emerged in the fields of social evolution and disease ecology in the past few decades is that these simple organisms have complex social lives, indulging in a variety of cooperative, communicative and coordinated behaviours. These organisms have provided elegant experimental tests of the importance of relatedness, kin discrimination, cooperation and competition, in driving the evolution of social strategies. Here, we briefly review the social behaviours of parasites and microbial pathogens, including their contributions to virulence, and outline how inclusive fitness theory has helped to explain their evolution. We then take a mechanistically inspired ‘bottom-up’ approach, discussing how key aspects of the ways in which parasites and pathogens exploit hosts, namely public goods, mobile elements, phenotypic plasticity, spatial structure and multi-species interactions, contribute to the emergent properties of virulence and transmission. We argue that unravelling the complexities of within-host ecology is interesting in its own right, and also needs to be better incorporated into theoretical evolution studies if social behaviours are to be understood and used to control the spread and severity of infectious diseases.

Emergence of MD type infectious hematopoietic necrosis virus in Washington State coastal steelhead trout

Infectious hematopoietic necrosis virus (IHNV) occurs in North America as 3 major phylogenetic groups designated U, M, and L. In coastal Washington State, IHNV has historically consisted of U genogroup viruses found predominantly in sockeye salmon Oncorhynchus nerka. M genogroup IHNV, which has host-specific virulence for rainbow and steelhead trout O. mykiss, was detected only once in coastal Washington prior to 2007, in an epidemic among juvenile steelhead trout in 1997. Beginning in 2007 and continuing through 2011, there were 8 IHNV epidemics in juvenile steelhead trout, involving 7 different fish culture facilities in 4 separate watersheds. During the same time period, IHNV was also detected in asymptomatic adult steelhead trout from 6 coastal watersheds. Genetic typing of 283 recent virus isolates from coastal Washington revealed that the great majority were in the M genogroup of IHNV and that there were 2 distinct waves of viral emergence between the years 2007 and 2011. IHNV type mG110M was dominant in coastal steelhead trout during 2007 to 2009, and type mG139M was dominant between 2010 and 2011. Phylogenetic analysis of viral isolates indicated that all coastal M genogroup viruses detected in 1997 and 2007 to 2011 were part of the MD subgroup and that several novel genetic variants related to the dominant types arose in the coastal sites. Comparison of spatial and temporal incidence of coastal MD viruses with that of the rest of the Pacific Northwest indicated that the likely source of the emergent viruses was Columbia River Basin steelhead trout.

What limits the evolutionary emergence of pathogens?

The ability of a pathogen to cause an epidemic when introduced in a new host population often relies on its ability to adapt to this new environment. Here, we give a brief overview of recent theoretical and empirical studies of such evolutionary emergence of pathogens. We discuss the effects of several ecological and genetic factors that may affect the likelihood of emergence: migration, life history of the infectious agent, host heterogeneity, and the rate and effects of mutations. We contrast different modelling approaches and indicate how details in the way we model each step of a life cycle can have important consequences on the predicted probability of evolutionary emergence. These different theoretical perspectives yield important insights into optimal surveillance and intervention strategies, which should aim for a reduction in the emergence (and re-emergence) of infectious diseases.

Evolution of virulence in emerging epidemics

Theory predicts that selection for pathogen virulence and horizontal transmission is highest at the onset of an epidemic but decreases thereafter, as the epidemic depletes the pool of susceptible hosts. We tested this prediction by tracking the competition between the latent bacteriophage λ and its virulent mutant λcI857 throughout experimental epidemics taking place in continuous cultures of Escherichia coli. As expected, the virulent λcI857 is strongly favored in the early stage of the epidemic, but loses competition with the latent virus as prevalence increases. We show that the observed transient selection for virulence and horizontal transmission can be fully explained within the framework of evolutionary epidemiology theory. This experimental validation of our predictions is a key step towards a predictive theory for the evolution of virulence in emerging infectious diseases.

Disease emergence and invasions

Emerging infectious diseases (EIDs) are recognized as having significant social, economic and ecological costs, threatening human health, food security, wildlife conservation and biodiversity. We review the processes underlying the emergence of infectious disease, focusing on the similarities and differences between conceptual models of disease emergence and biological invasions in general.Study of the IUCN's list of the world's worst invaders reveals that disease is cited as a driver behind the conservation, medical or economic impact of nearly a quarter of the species on the data base.The emergence of novel diseases in new host species are, in essence, examples of invasions by parasites. Many of the ecological and anthropogenic drivers of disease emergence and classical invasions are also shared, with environmental change and global transport providing opportunities for the introduction and spread of invaders and novel parasites.The phases of disease emergence and biological invasions have many parallels; particularly the early and late phases, where demographic and anthropogenic factors are key drivers. However, there are also differences in the intermediate phases, where host-parasite co-evolution plays a crucial role in determining parasite establishment in novel hosts.Similar opportunities and constraints on control and management occur at the different phases of invasions and disease emergence. However, exploitation of host immune responses offers additional control opportunities through contact control and vaccination against EIDs. We propose that cross-fertilization between the disciplines of disease emergence and invasion biology may provide further insights into their prediction, control and management.

Vaccination and reduced cohort duration can drive virulence evolution: Marek's disease virus and industrialized agriculture

Marek's disease virus (MDV), a commercially important disease of poultry, has become substantially more virulent over the last 60 years. This evolution was presumably a consequence of changes in virus ecology associated with the intensification of the poultry industry. Here, we assess whether vaccination or reduced host life span could have generated natural selection, which favored more virulent strains. Using previously published experimental data, we estimated viral fitness under a range of cohort durations and vaccine treatments on broiler farms. We found that viral fitness maximized at intermediate virulence, as a result of a trade-off between virulence and transmission previously reported. Our results suggest that vaccination, acting on this trade-off, could have led to the evolution of increased virulence. By keeping the host alive, vaccination prolongs infectious periods of virulent strains. Improvements in host genetics and nutrition, which reduced broiler life spans below 50 days, could have also increased the virulence of the circulating MDV strains because shortened cohort duration reduces the impact of host death on viral fitness. These results illustrate the dramatic impact anthropogenic change can potentially have on pathogen virulence.

An experimental test of the transmission-virulence trade-off hypothesis in a plant virus

The transmission-virulence trade-off hypothesis is one of the few adaptive explanations of virulence evolution, and assumes that there is an overall positive correlation between parasite transmission and virulence. The shape of the transmission-virulence relationship predicts whether virulence should evolve toward either a maximum or to an intermediate optimum. A positive correlation between each of these traits and within-host growth is often suggested to underlie the relationship between virulence and transmission. There are few experimental tests of this hypothesis; this study reports on the first empirical test on a plant pathogen. We infected Brassica rapa plants with nine natural isolates of Cauliflower mosaic virus and then estimated three traits: transmission, virulence, and within-host viral accumulation. As predicted by the trade-off hypothesis, we observed a positive correlation between transmission and virulence, suggestive of the existence of an intermediate optimum. We discovered the unexpected existence of two groups of within-host accumulation, differing by at least an order of magnitude. When accumulation groups were not accounted for, within-host accumulation was correlated neither to virulence nor transmission, although our results suggest that within each group these correlations exist.

Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control

Standard virulence evolution theory assumes that virulence factors are maintained because they aid parasitic exploitation, increasing growth within and/or transmission between hosts. An increasing number of studies now demonstrate that many opportunistic pathogens (OPs) do not conform to these assumptions, with virulence factors maintained instead because of advantages in non-parasitic contexts. Here we review virulence evolution theory in the context of OPs and highlight the importance of incorporating environments outside a focal virulence site. We illustrate that virulence selection is constrained by correlations between these external and focal settings and pinpoint drivers of key environmental correlations, with a focus on generalist strategies and phenotypic plasticity. We end with a summary of key theoretical and empirical challenges to be met for a fuller understanding of OPs.

High host density favors greater virulence: a model of parasite-host dynamics based on multi-type branching processes

We use a multitype continuous time Markov branching process model to describe the dynamics of the spread of parasites of two types that can mutate into each other in a common host population. While most mathematical models for the virulence of infectious diseases focus on the interplay between the dynamics of host populations and the optimal characteristics for the success of the pathogen, our model focuses on how pathogen characteristics may change at the start of an epidemic, before the density of susceptible hosts decline. We envisage animal husbandry situations where hosts are at very high density and epidemics are curtailed before host densities are much reduced. The use of three pathogen characteristics: lethality, transmissibility and mutability allows us to investigate the interplay of these in relation to host density. We provide some numerical illustrations and discuss the effects of the size of the enclosure containing the host population on the encounter rate in our model that plays the key role in determining what pathogen type will eventually prevail. We also present a multistage extension of the model to situations where there are several populations and parasites can be transmitted from one of them to another. We conclude that animal husbandry situations with high stock densities will lead to very rapid increases in virulence, where virulent strains are either more transmissible or favoured by mutation. Further the process is affected by the nature of the farm enclosures.

Transient virulence of emerging pathogens

Should emerging pathogens be unusually virulent? If so, why? Existing theories of virulence evolution based on a tradeoff between high transmission rates and long infectious periods imply that epidemic growth conditions will select for higher virulence, possibly leading to a transient peak in virulence near the beginning of an epidemic. This transient selection could lead to high virulence in emerging pathogens. Using a simple model of the epidemiological and evolutionary dynamics of emerging pathogens, along with rough estimates of parameters for pathogens such as severe acute respiratory syndrome, West Nile virus and myxomatosis, we estimated the potential magnitude and timing of such transient virulence peaks. Pathogens that are moderately evolvable, highly transmissible, and highly virulent at equilibrium could briefly double their virulence during an epidemic; thus, epidemic-phase selection could contribute significantly to the virulence of emerging pathogens. In order to further assess the potential significance of this mechanism, we bring together data from the literature for the shapes of tradeoff curves for several pathogens (myxomatosis, HIV, and a parasite of Daphnia) and the level of genetic variation for virulence for one (myxomatosis). We discuss the need for better data on tradeoff curves and genetic variance in order to evaluate the plausibility of various scenarios of virulence evolution.

Measuring parasite fitness under genetic and thermal variation

Accurate measures of parasite fitness are essential to study host-parasite evolution. Parasite fitness depends on several traits involved in establishing infection, growth and transmission. Individually, these traits provide a reasonable approximation of fitness, but they may also be under the shared control of both host and parasite genetics (G(H) x G(P) interactions), or be differentially sensitive to environmental variation. Using the natural host-parasite system Daphnia magna-Pasteuria ramosa, we performed experimental infections that incorporated host and parasite genetic variation at three different temperatures, and compared the measures of parasite fitness based only on growth rate, or incorporating the ability to infect. We found that infectivity was most important for parasite fitness and depended mainly on the combination of host and parasite genotypes. Variation in post-infection parasite growth and killing time depended on the parasite genotype and its interaction with temperature. These results highlight the merits of studies that can incorporate natural infection routes and emphasize that accurate measures of parasite fitness require knowledge of the genetic control and environmental sensitivity of more than one trait. In addition, no G(H) x G(P) x E interactions were present, suggesting that the potential for genetic specificities to drive frequency-dependent coevolution in this system is robust to thermal variation.

Competition favours reduced cost of plasmids to host bacteria

Conjugative plasmids of Gram-negative bacteria have both vertical and horizontal modes of transmission: they are segregated to daughter cells during division, and transferred between hosts by plasmid-encoded conjugative machinery. Despite maintaining horizontal mobility, many plasmids carry fertility inhibition (fin) systems that repress their own conjugative transfer. To assess the ecological basis of self-transfer repression, we compared the invasion of bacterial populations by fin(+) and fin(-) variants of the plasmid R1 using a computational model and co-culture competitions. We observed that the fin(+) variant had a modest cost to the host (measured by reduction in growth rate), while the fin(-) variant incurred a larger cost. In simulations and empirical competitions the fin(-) plasmid invaded cultures quickly, but was subsequently displaced by the fin(+) plasmid. This indicated a competitive advantage to reducing horizontal transmission and allowing increased host replication. Computational simulations predicted that the advantage associated with reduced cost to the host would be maintained over a wide range of environmental conditions and plasmid costs. We infer that vertical transmission in concert with competitive exclusion favour decreased horizontal mobility of plasmids. Similar dynamics may exert evolutionary pressure on parasites, such as temperate bacteriophages and vertically transmitted animal viruses, to limit their rates of horizontal transfer.

The pig as a mixing vessel for influenza viruses: Human and veterinary implications

Influenza A viruses are highly infectious respiratory pathogens that can infect many species. Birds are the reservoir for all known influenza A subtypes; and novel influenza viruses can emerge from birds and infect mammalian species including humans. Because swine are susceptible to infection with both avian and human influenza viruses, novel reassortant influenza viruses can be generated in this mammalian species by reassortment of influenza viral segments leading to the "mixing vessel" theory. There is no direct evidence that the reassortment events culminating in the 1918, 1957 or 1968 pandemic influenza viruses originated from pigs. Genetic reassortment among avian, human and/or swine influenza virus gene segments has occurred in pigs and some novel reassortant swine viruses have been transmitted to humans. Notably, novel reassortant H2N3 influenza viruses isolated from the US pigs, most likely infected with avian influenza viruses through surface water collected in ponds for cleaning barns and watering animals, had a similar genetic make-up to early isolates (1957) of the H2N2 human pandemic. These novel H2N3 swine viruses were able to cause disease in swine and mice and were infectious and highly transmissible in swine and ferrets without prior adaptation. The preceding example shows that pigs could transmit novel viruses from an avian reservoir to other mammalian species. Importantly, H2 viruses pose a substantial risk to humans because they have been absent from mammalian species since 1968 and people born after 1968 have little preexisting immunity to the H2 subtype. It is difficult to predict which virus will cause the next human pandemic and when that pandemic might begin. Importantly, the establishment and spread of a reassorted mammalian-adapted virus from pigs to humans could happen anywhere in the world. Therefore, both human and veterinary research needs to give more attention to potential cross-species transmission capacity of influenza A viruses.