Viral Co-Infections and Antiviral Immunity in Honey Bees

Over the past few decades, honey bees have been facing an increasing number of stressors. Beyond individual stress factors, the synergies between them have been identified as a key factor in the observed increase in colony mortality. However, these interactions are numerous and complex and call for further research. Here, in line with our need for a systemic understanding of the threats that they pose to bee health, we review the interactions between honey bee viruses. As viruses are obligate parasites, the interactions between them not only depend on the viruses themselves but also on the immune responses of honey bees. Thus, we first summarise our current knowledge of the antiviral immunity of honey bees. We then review the interactions between specific pathogenic viruses and their interactions with their host. Finally, we draw hypotheses from the current literature and suggest directions for future research.

Principles of seed banks and the emergence of complexity from dormancy

Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology.

Seasonal variation of Batrachochytrium dendrobatidis in a threatened anuran species from Uruguay

Chytridiomycosis, an emergent infectious disease caused by the fungus Batrachochytrium dendrobatidis (Bd), is considered one of the drivers of the current amphibian biodiversity loss. To inform endangered species conservation efforts, it is essential to improve our knowledge about the abiotic and biotic factors that influence Bd infection dynamics in the wild. Here, we analyzed variation of Bd infection in the redbelly toad Melanophryniscus montevidensis, a threatened bufonid from Uruguay. We tested the influence of temperature, precipitation, season, and host population size on Bd prevalence and intensity. Additionally, considering the sub-lethal effects of Bd, we tested if these variables, potentially through their effect on Bd, also explain the variation in host body condition. We determined a high Bd prevalence of 41% (100/241), and that population size influenced both Bd prevalence and infection intensity. We identified an effect of precipitation and season on Bd infection intensity and an effect of season on toad body condition. In addition, we found a negative effect of infection intensity on body condition; moreover, while some toads cleared the infection, their body condition did not improve, suggesting a long-term cost. This is the first report on host population size as an important factor in Bd infection dynamics in a threatened anuran species, and seasonal demographic changes appear to play an important role in the dynamics. Finally, we highlight the need for monitoring Bd in this and other endangered amphibian populations, especially those within the genus Melanophryniscus, which includes several Endangered and Data Deficient species in South America.

Rectal Swabs as an Alternative Sample Collection Method to Bulk Stool for the Real-Time PCR Detection of Giardia duodenalis

Though bulk stool remains the gold standard specimen type for enteropathogen diagnosis, rectal swabs may offer comparable sensitivity with greater ease of collection for select pathogens. This study sought to evaluate the validity and reproducibility of rectal swabs as a sample collection method for the molecular diagnosis of Giardia duodenalis. Paired rectal swab and bulk stool samples were collected from 86 children ages 0-4 years living in southwest Niger, with duplicate samples collected among a subset of 50 children. Infection was detected using a previously validated real-time PCR diagnostic targeting the small subunit ribosomal RNA gene. Giardia duodenalis was detected in 65.5% (55/84) of bulk stool samples and 44.0% (37/84) of swab samples. The kappa evaluating test agreement was 0.81 (95% CI: 0.54-1.00) among duplicate stool samples (N = 49) and 0.75 (95% CI: 0.47-1.00) among duplicate rectal swabs (N = 48). Diagnostic sensitivity was 93% (95% CI: 84-98) by bulk stool and 63% (95% CI: 49-75) by rectal swabs. When restricting to the lowest three quartiles of bulk stool quantitation cycle values (an indication of relatively high parasite load), sensitivity by rectal swabs increased to 78.0% (95% CI: 64-89, P < 0.0001). These findings suggest that rectal swabs provide less sensitive and reproducible results than bulk stool for the real-time PCR diagnosis of G. duodenalis. However, their fair sensitivity for higher parasite loads suggests that swabs may be a useful tool for detecting higher burden infections when stool collection is excessively expensive or logistically challenging.

Separate seasons of infection and reproduction can lead to multi-year population cycles

Many host-pathogen systems are characterized by a temporal order of disease transmission and host reproduction. For example, this can be due to pathogens infecting certain life cycle stages of insect hosts; transmission occurring during the aggregation of migratory birds; or plant diseases spreading between planting seasons. We develop a simple discrete-time epidemic model with density-dependent transmission and disease affecting host fecundity and survival. The model shows sustained multi-annual cycles in host population abundance and disease prevalence, both in the presence and absence of density dependence in host reproduction, for large horizontal transmissibility, imperfect vertical transmission, high virulence, and high reproductive capability. The multi-annual cycles emerge as invariant curves in a Neimark-Sacker bifurcation. They are caused by a carry-over effect, because the reproductive fitness of an individual can be reduced by virulent effects due to infection in an earlier season. As the infection process is density-dependent but shows an effect only in a later season, this produces delayed density dependence typical for second-order oscillations. The temporal separation between the infection and reproduction season is crucial in driving the cycles; if these processes occur simultaneously as in differential equation models, there are no sustained oscillations. Our model highlights the destabilizing effects of inter-seasonal feedbacks and is one of the simplest epidemic models that can generate population cycles.

LETHAL AND SUBLETHAL AMPHIBIAN HOST RESPONSES TO BATRACHOCHYTRIUM DENDROBATIDIS EXPOSURE ARE DETERMINED BY THE ADDITIVE INFLUENCE OF HOST RESOURCE AVAILABILITY

Host species may differ in their responses to pathogen exposures based on host energy reserves, which could be important for long-term trends in host population growth. Batrachochytrium dendrobatidis (BD) is a pathogen associated with amphibian population declines but also occurs without causing mass mortalities. The impact of BD in populations without associated declines is not well understood, and food abundance could play a role in determining the magnitude of its effects. We exposed American toad (Anaxyrus americanus), northern leopard frog (Lithobates pipiens), and cricket frog (Acris blanchardi) metamorphs to BD under low or high food treatments. Overall, anuran species responded differently to BD exposure and the combined effect of BD exposure and food abundance was additive. American toad survival was lowered by BD exposure and low food availability. Based on these results, we developed a population model for American toads to estimate how reductions in survival could influence population growth. We found that BD could reduce population growth by 14% with high food availability and 21% with low food availability. In contrast, survival of northern leopard frogs was high across all treatments, but their growth was negatively impacted by the additive effects of BD exposure and low food availability. Cricket frog growth and survival were unaffected by BD exposure, suggesting that this species is not sensitive to the effects of this pathogen in terms of growth and survival across environments of different quality in the time period examined. Our results showed that low food availability additively increased the species-specific lethal and sublethal impacts of BD on hosts, which could have implications for long-term host population dynamics.

Breaking beta: deconstructing the parasite transmission function

Transmission is a fundamental step in the life cycle of every parasite but it is also one of the most challenging processes to model and quantify. In most host–parasite models, the transmission process is encapsulated by a single parameter β. Many different biological processes and interactions, acting on both hosts and infectious organisms, are subsumed in this single term. There are, however, at least two undesirable consequences of this high level of abstraction. First, nonlinearities and heterogeneities that can be critical to the dynamic behaviour of infections are poorly represented; second, estimating the transmission coefficient β from field data is often very difficult. In this paper, we present a conceptual model, which breaks the transmission process into its component parts. This deconstruction enables us to identify circumstances that generate nonlinearities in transmission, with potential implications for emergent transmission behaviour at individual and population scales. Such behaviour cannot be explained by the traditional linear transmission frameworks. The deconstruction also provides a clearer link to the empirical estimation of key components of transmission and enables the construction of flexible models that produce a unified understanding of the spread of both micro- and macro-parasite infectious disease agents.

This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.

Disease Dynamics in Ants: A Critical Review of the Ecological Relevance of Using Generalist Fungi to Study Infections in Insect Societies

It is assumed that social life can lead to the rapid spread of infectious diseases and outbreaks. In ants, disease outbreaks are rare and the expression of collective behaviors is invoked to explain the absence of epidemics in natural populations. Here, we address the ecological approach employed by many studies that have notably focused (89% of the studies) on two genera of generalist fungal parasites (Beauveria and Metarhizium). We ask whether these are the most representative models to study the evolutionary ecology of ant-fungal parasite interactions. To assess this, we critically examine the literature on ants and their interactions with fungal parasites from the past 114years (1900-2014). We discuss how current evolutionary ecology approaches emerged from studies focused on the biological control of pest ants. We also analyzed the ecological relevance of the laboratory protocols used in evolutionary ecology studies employing generalist parasites, as well as the rare natural occurrence of these parasites on ants. After a detailed consideration of all the publications, we suggest that using generalist pathogens such as Beauveria and Metarhizium is not an optimal approach if the goal is to study the evolutionary ecology of disease in ants. We conclude by advocating for approaches that incorporate greater realism.

Development of a Real-Time qPCR Assay for Quantification of Covert Baculovirus Infections in a Major African Crop Pest

Many pathogens and parasites are present in host individuals and populations without any obvious signs of disease. This is particularly true for baculoviruses infecting lepidopteran hosts, where studies have shown that covert persistent viral infections are almost ubiquitous in many species. To date, the infection intensity of covert viruses has rarely been quantified. In this study, we investigated the dynamics of a covert baculovirus infection within the lepidopteran crop pest Spodoptera exempta. A real-time quantitative polymerase chain reaction (qPCR) procedure using a 5' nuclease hydrolysis (TaqMan) probe was developed for specific detection and quantification of Spodoptera exempta nucleopolyhedrovirus (SpexNPV). The qPCR assay indicated that covert baculovirus dynamics varied considerably over the course of the host life-cycle, with infection load peaking in early larval instars and being lowest in adults and final-instar larvae. Adult dissections indicated that, contrary to expectation, viral load aggregation was highest in the head, wings and legs, and lowest in the thorax and abdomen. The data presented here have broad implications relating to our understanding of transmission patterns of baculoviruses and the role of covert infections in host-pathogen dynamics.

Host species vary in infection probability, sub-lethal effects, and costs of immune response when exposed to an amphibian parasite

The amphibian parasite Batrachochytrium dendrobatidis (Bd) is regarded as an extreme generalist, infecting over 500 species, but amongst these hosts there exists a great deal of variation in the susceptibility to and the costs of parasite exposure. We use two infection experiments to determine whether inter-specific variation in the sublethal and lethal effects of parasite exposure exist in two host species. We then tested the relative roles of host density and diversity on infection probability of a focal susceptible host. Our results show significant heterogeneity in host species response to parasite exposure, and that both lethal and sub-lethal costs exist in individuals that are able to resist infection, indicating that successful immune response to infection comes at a cost. Further, we show that increasing host density significantly increased the likelihood of susceptible individuals becoming infected with Bd irrespective of host diversity and variation in host susceptibility. These results suggest that populations of resistant species are likely to suffer ill-effects of exposure to Bd regardless of their infection status, and that at the stage of initial infection there was no support for the dilution of transmission events, in contrast to other studies that focus on subsequent transmission of infection.

A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission

The globally distributed ectoparasite Varroa destructor is a vector for viral pathogens of the Western honeybee (Apis mellifera), in particular the Iflavirus Deformed Wing Virus (DWV). In the absence of Varroa low levels DWV occur, generally causing asymptomatic infections. Conversely, Varroa-infested colonies show markedly elevated virus levels, increased overwintering colony losses, with impairment of pupal development and symptomatic workers. To determine whether changes in the virus population were due Varroa amplifying and introducing virulent virus strains and/or suppressing the host immune responses, we exposed Varroa-naïve larvae to oral and Varroa-transmitted DWV. We monitored virus levels and diversity in developing pupae and associated Varroa, the resulting RNAi response and transcriptome changes in the host. Exposed pupae were stratified by Varroa association (presence/absence) and virus levels (low/high) into three groups. Varroa-free pupae all exhibited low levels of a highly diverse DWV population, with those exposed per os (group NV) exhibiting changes in the population composition. Varroa-associated pupae exhibited either low levels of a diverse DWV population (group VL) or high levels of a near-clonal virulent variant of DWV (group VH). These groups and unexposed controls (C) could be also discriminated by principal component analysis of the transcriptome changes observed, which included several genes involved in development and the immune response. All Varroa tested contained a diverse replicating DWV population implying the virulent variant present in group VH, and predominating in RNA-seq analysis of temporally and geographically separate Varroa-infested colonies, was selected upon transmission from Varroa, a conclusion supported by direct injection of pupae in vitro with mixed virus populations. Identification of a virulent variant of DWV, the role of Varroa in its transmission and the resulting host transcriptome changes furthers our understanding of this important viral pathogen of honeybees.

Honeybees are the most important managed pollinating insect, contributing billions of dollars to annual global agricultural production. Over the last century a parasitic mite, Varroa, has spread worldwide, with significant impacts on honeybee colony health as a consequence of its transmission of a cocktail of viruses while feeding on honeybee ‘blood’. The most important virus for colony health is deformed wing virus (DWV), high levels of which cause developmental deformities and premature ageing resulting in high overwintering colony losses. In experiments on individual Varroa-exposed pupae we demonstrate that a single type of virulent DWV is amplified 1,000–10,000 times in the recipient pupae, despite the mite containing a high diversity of replicating DWV strains. We could recapitulate this by direct injection of pupae with mixed virus populations, showing the virulent strain is advantaged by the route of transmission. In parallel, we detected changes in the immune response and developmental gene expression of the honeybee and propose that these contribute to the characteristic pathogenesis of DWV. Identification of a virulent strain of DWV has implications for therapeutic or prophylactic interventions to improve honeybee colony health, as well as contributing to our understanding of the biology of this important honeybee viral pathogen.

Viral Dynamics and Mathematical Models

Mathematical tools have been widely applied in understanding the dynamics and control of viral infections. Here we present some fundamental aspects of infection dynamics, starting with acute immunising infections as a case study for herd immunity and other important factors in the spread and control of infection. We then discuss the dynamics of infections with more complex life histories, including chronic infections, and those showing evolution for immune escape. We conclude with a discussion of important gaps in our current understanding of viral dynamics, along with future research needs.

Pathogen persistence in the environment and insect-baculovirus interactions: disease-density thresholds, epidemic burnout, and insect outbreaks

Classical epidemic theory focuses on directly transmitted pathogens, but many pathogens are instead transmitted when hosts encounter infectious particles. Theory has shown that for such diseases pathogen persistence time in the environment can strongly affect disease dynamics, but estimates of persistence time, and consequently tests of the theory, are extremely rare. We consider the consequences of persistence time for the dynamics of the gypsy moth baculovirus, a pathogen transmitted when larvae consume foliage contaminated with particles released from infectious cadavers. Using field-transmission experiments, we are able to estimate persistence time under natural conditions, and inserting our estimates into a standard epidemic model suggests that epidemics are often terminated by a combination of pupation and burnout rather than by burnout alone, as predicted by theory. Extending our models to allow for multiple generations, and including environmental transmission over the winter, suggests that the virus may survive over the long term even in the absence of complex persistence mechanisms, such as environmental reservoirs or covert infections. Our work suggests that estimates of persistence times can lead to a deeper understanding of environmentally transmitted pathogens and illustrates the usefulness of experiments that are closely tied to mathematical models.

Low cost antiviral activity of Plodia interpunctella haemolymph in vivo demonstrated by dose dependent infection

Given the ubiquity of infectious disease it is important to understand the way in which hosts defend themselves and any costs that they may pay for this defence. Despite this, we know relatively little about insect immune responses to viruses when compared to their well-characterized responses to other pathogens. In particular it is unclear whether there is significant haemocoelic response to viral infection. Here we directly examine this question by examining whether there is a dose-dependency in infection risk when a DNA virus is injected directly into the haemocoel. Infection from direct injection into the haemocoel showed a clear dose dependency that is indicative of an active intrahaemocoelic immune response to DNA viruses in insects. In contrast to the natural oral infection route, we found no measurable sublethal effects in the survivors from direct injection. This suggests that the immune responses in the haemocoel are less costly than those that occur earlier.

The evolution of covert, silent infection as a parasite strategy

Many parasites and pathogens cause silent/covert infections in addition to the more obvious infectious disease-causing pathology. Here, we consider how assumptions concerning superinfection, protection and seasonal host birth and transmission rates affect the evolution of such covert infections as a parasite strategy. Regardless of whether there is vertical infection or effects on sterility, overt infection is always disadvantageous in relatively constant host populations unless it provides protection from superinfection. If covert infections are protective, all individuals will enter the covert stage if there is enough vertical transmission, and revert to overt infections after a ‘latent’ period (susceptible, exposed, infected epidemiology). Seasonal variation in transmission rates selects for non-protective covert infections in relatively long-lived hosts with low birth rates typical of many mammals. Variable host population density caused by seasonal birth rates may also select for covert transmission, but in this case it is most likely in short-lived fecund hosts. The covert infections of some insects may therefore be explained by their outbreak population dynamics. However, our models consistently predict proportions of covert infection, which are lower than some of those observed in nature. Higher proportions of covert infection may occur if there is a direct link between covert infection and overt transmission success, the covert infection is protective or the covert state is the result of suppression by the host. Relatively low proportions of covert transmission may, however, be explained as a parasite strategy when transmission opportunities vary.

Family Iridoviridae: poor viral relations no longer

Members of the family Iridoviridae infect a diverse array of invertebrate and cold-blooded vertebrate hosts and are currently viewed as emerging pathogens of fish and amphibians. Iridovirid replication is unique and involves both nuclear and cytoplasmic compartments, a circularly permuted, terminally redundant genome that, in the case of vertebrate iridoviruses, is also highly methylated, and the efficient shutoff of host macromolecular synthesis. Although initially neglected largely due to the perceived lack of health, environmental, and economic concerns, members of the genus Ranavirus, and the newly recognized genus Megalocytivirus, are rapidly attracting growing interest due to their involvement in amphibian population declines and their adverse impacts on aquaculture. Herein we describe the molecular and genetic basis of viral replication, pathogenesis, and immunity, and discuss viral ecology with reference to members from each of the invertebrate and vertebrate genera.

Reduced parasite infestation in urban Eurasian blackbirds (Turdus merula): a factor favoring urbanization?

Humans nowadays dramatically alter environmental and ecological conditions worldwide. One of the most extreme forms of anthropogenic land-use alteration is urbanization. Animals thriving in urban areas are not only exposed to different environmental conditions compared with their nonurban conspecifics, but prevalence and impacts of wildlife diseases on urban populations may also be affected. In the present study, we tested whether blood-parasite prevalence differs between urban and forest habitats by comparing haematozoan infections of urban and forest-living Eurasian blackbirds ( Turdus merula L., 1758). In total, 76% of Eurasian blackbirds were infected with haematozoa and we detected five different blood parasite genera in both habitats. Blood-parasite prevalence varied both between years and between spring and summer in both urban and forest populations. Forest blackbirds had more parasite genera per individual than urban blackbirds, and in summer, forest blackbirds had higher blood-parasite prevalence than their urban conspecifics. These differences in blood-parasite prevalence between urban and forest blackbirds suggest a lower risk of haematozoan infections in urban than in forest habitats. The lower parasite prevalence could be one of the factors favoring the invasion of urban ecosystems.

Directly transmitted viral diseases: modeling the dynamics of transmission

A key hurdle in understanding the spread and control of infectious diseases is to capture appropriately the dynamics of pathogen transmission. As people and goods travel increasingly rapidly around the world, so do pathogens; we must be prepared to understand their spread, in terms of the contact network between hosts, viral life history and within-host dynamics. This will require collaborative work that takes into account viral life history, strategy and evolution, and host genetics, demographics and immunodynamics. Mathematical models are a useful tool for integrating the data and analyses from diverse fields that contribute to our understanding of viral transmission dynamics in heterogeneous host populations.

Interference and the persistence of vertically transmitted parasites

Given their ubiquity in nature, understanding the factors that allow the persistence of multiple enemies and in particular vertically transmitted parasites (VTPs) is of considerable importance. Here a model that allows a virulent VTP to be maintained in a system containing a host and a horizontally transmitted parasite (HTP) is analysed. The method of persistence relies on the VTP offering the host a level of protection from the HTP. The VTP is assumed to reduce the HTPs ability to transmit to the host through ecological interference. We show that VTPs are more likely to persist with HTPs that prevent host reproduction than with those that allow it. The VTP persists more easily in r-selected hosts and with highly transmittable HTPs. As the level of protection through interference increases the densities of the host also increase. We also show that VTPs when they do persist tend to stabilise the host population cycles produced by free-living HTPs. The study raised questions about persistence of diseases through interactions with others, and also the stabilising effects of VTPs on dynamical systems in a biological control context.

Transmission of freshwater myxozoans during the asexual propagation of invertebrate hosts

The phylum Myxozoa contains over 1350 species almost all of which are considered to be obligate parasites of aquatic animals. The phylum is composed of two classes, the Myxosporea and the Malacosporea, species of which are important pathogens responsible for severe economic losses in cultured fisheries. The life cycles of freshwater Myxozoa are believed to involve horizontal, indirect transmission, involving an invertebrate (oligochaetes or bryozoans) and a vertebrate host (fish or amphibians). Here, we describe myxozoan propagation through the fragmentation of invertebrate hosts to form new infected individuals. The two hosts examined are an oligochaete Lumbriculus variegatus infected with an unidentified myxosporean (Triactinomyxon sp.) and the bryozoan Fredericella sultana infected with the malacosporean Tetracapsuloides bryosalmonae which causes proliferative kidney disease, a major constraint of the European rainbow trout industry. Such intra-clonal propagation is a novel form of vertical transmission that is likely to be widespread within the Myxozoa and could form an important method by which some of these parasites maintain and proliferate within the aquatic environment.

Roles of parasites in animal invasions

Biological invasions are global threats to biodiversity and parasites might play a role in determining invasion outcomes. Transmission of parasites from invading to native species can occur, aiding the invasion process, whilst the 'release' of invaders from parasites can also facilitate invasions. Parasites might also have indirect effects on the outcomes of invasions by mediating a range of competitive and predatory interactions among native and invading species. Although pathogen outbreaks can cause catastrophic species loss with knock-on effects for community structure, it is less clear what impact persistent, sub-lethal parasitism has on native-invader interactions and community structure. Here, we show that the influence of parasitism on the outcomes of animal invasions is more subtle and wide ranging than has been previously realized.