Are disease reservoirs special? Taxonomic and life history characteristics

Emerging patterns in rodent-borne zoonotic diseases

Rodents are ubiquitous and typically unwelcome dwellers in human habitats worldwide, infesting homes, farm fields, and agricultural stores and potentially shedding disease-causing microbes into the most human-occupied of spaces. Of the vertebrate animal taxa that share pathogens with us, rodents are the most abundant and diverse, with hundreds of species of confirmed zoonotic hosts, some of which have nearly global distributions. However, only 12% of rodent species are known to be sources of pathogens that also infect people, and those rodents that do are now recognized as tending to share a suite of predictable traits. Here, we characterize those traits and explore them in the context of three emerging or reemerging rodent-borne zoonotic diseases of people: Lassa fever, Lyme disease, and plague.

Novel Rickettsia and host records for argasid ticks, including Alveonasus cooleyi, on wild mammals in Baja California, Mexico

We conducted surveillance of mammals to investigate their associations with argasid ticks and tick-borne pathogens. During 2021, a total of 20 wild carnivores and 57 lagomorphs were sampled, and 39 argasid ticks belonging to two species were collected. All mammals and ticks were tested by molecular assays to detect Borrelia and Rickettsia infections. Nine ticks identified as Otobius megnini were collected from two coyotes (Canis latrans) and 30 Alveonasus cooleyi (McIvor 1941) were collected from six bobcats (Lynx rufus) and one rabbit (Sylvilagus auduboni). We detected Rickettsia spp. DNA in 21 of the 27 (77.8%) tested Av. cooleyi and none of the O. megnini. No ticks were PCR-positive for borreliae and all mammals were PCR-negative for both pathogen genera. Phylogenetic analysis based on gltA, htrA, and 16 S rRNA targets revealed that all rickettsiae from Av. cooleyi clustered with ancestral group rickettsiae, likely representing a novel species of possibly endosymbiotic Rickettsia. The significance of Av. cooleyi and the newly identified Rickettsia sp. to the health of wildlife is unknown, and further work is indicated to determine whether they may be relevant to public health or carnivore conservation.

Identifying life-history patterns along the fast-slow continuum of mammalian viral carriers

Life-history traits have been identified as major indicators of mammals' susceptibility and exposure to viruses due to evolutionary constraints that link life-history speed with species' ecology and immunity. Nonetheless, it is unclear where along the fast-slow continuum of mammalian life-history lies the greatest diversity of host species. Consequently, life-history patterns that govern host-virus associations remain largely unknown. Here we analyse the virome of 1350 wild mammals and detect the characteristics that drive species' compatibility with different groups of viruses. We highlight that mammals with larger body size and either very rapid or very slow life histories are more likely to carry different groups of viruses, particularly zoonotic ones. While some common life-history patterns emerge across carriers, eco-evolutionary characteristics of viral groups appear to determine association with certain carrier species. Our findings underline the importance of incorporating both mammals' life-history information and viruses' ecological diversity into surveillance strategies to identify potential zoonotic carriers in wildlife.

Early-stage loss of ecological integrity drives the risk of zoonotic disease emergence

Anthropogenic pressures have increasingly disrupted the integrity of ecosystems worldwide, jeopardizing their capacity to provide essential contributions to human well-being. Recently, the role of natural ecosystems in reducing disease emergence risk has gained prominence in decision-making processes, as scientific evidence indicates that human-driven pressure, such as habitat destruction and deforestation, can trigger the emergence of zoonotic infectious diseases. However, the intricate relationship between biodiversity and emerging infectious diseases (EIDs) remains only partially understood. Here, we updated the most comprehensive zoonotic EID event database with the latest reported events to analyse the relationship between EIDs of wildlife origin (zoonoses) and various facets of ecological integrity. We found EID risk was strongly predicted by structural integrity metrics such as human footprint and ecoregion intactness, in addition to environmental variables such as tropical rainforest density and mammal species richness. EID events were more likely to occur in areas with intermediate levels of compositional and structural integrity, underscoring the risk posed by human encroachment into pristine, undisturbed lands. Our study highlights the need to identify novel indicators and targets that can effectively address EID risk alongside other pressing global challenges in sustainable development, ultimately informing strategies for preserving both human and environmental health.

Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance

The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.

Association between anthropization and rodent reservoirs of zoonotic pathogens in Northwestern Mexico

The world is facing a major pulse of ecological and social changes that may favor the risk of zoonotic outbreaks. Such risk facilitation may occur through the modification of the host's community diversity and structure, leading to an increase in pathogen reservoirs and the contact rate between these reservoirs and humans. Here, we examined whether anthropization alters the relative abundance and richness of zoonotic reservoir and non-reservoir rodents in three Socio-Ecological Systems. We hypothesized that anthropization increases the relative abundance and richness of rodent reservoirs while decreasing non-reservoir species. We first developed an Anthropization index based on 15 quantitative socio-ecological variables classified into five groups: 1) Vegetation type, 2) Urbanization degree, 3) Water quality, 4) Potential contaminant sources, and 5) Others. We then monitored rodent communities in three regions of Northwestern Mexico (Baja California, Chihuahua, and Sonora). A total of 683 rodents of 14 genera and 27 species were captured, nine of which have been identified as reservoirs of zoonotic pathogens (359 individuals, 53%). In all regions, we found that as anthropization increased, the relative abundance of reservoir rodents increased; in contrast, the relative abundance of non-reservoir rodents decreased. In Sonora, reservoir richness increased with increasing anthropization, while in Baja California and Chihuahua non-reservoir richness decreased as anthropization increased. We also found a significant positive relationship between the anthropization degree and the abundance of house mice (Mus musculus) and deer mice (Peromyscus maniculatus), the most abundant reservoir species in the study. These findings support the hypothesis that reservoir species of zoonotic pathogens increase their abundance in disturbed environments, which may increase the risk of pathogen exposure to humans, while anthropization creates an environmental filtering that promotes the local extinction of non-reservoir species.

Range area and the fast-slow continuum of life history traits predict pathogen richness in wild mammals

Surveillance of pathogen richness in wildlife is needed to identify host species with a high risk of zoonotic disease spillover. While several predictors of pathogen richness in wildlife hosts have been proposed, their relative importance has not been formally examined. This hampers our ability to identify potential disease reservoirs, particularly in remote areas with limited surveillance efforts. Here we analyzed 14 proposed predictors of pathogen richness using ensemble modeling and a dataset of 1040 host species to identify the most important predictors of pathogen richness in wild mammal species. After controlling for research effort, larger species geographic range area was identified to be associated with higher pathogen richness. We found evidence of duality in the relationship between the fast-slow continuum of life-history traits and pathogen richness, where pathogen richness increases near the extremities. Taxonomic orders Carnivora, Proboscidea, Artiodactyla, and Perissodactyla were predicted to host high pathogen richness. The top three species with the highest pathogen richness predicted by our ensemble model were Canis lupus, Sus scrofa, and Alces alces. Our results can help support evidence-informed pathogen surveillance and disease reservoir management to prevent the emergence of future zoonotic diseases.

Vector-Borne Disease in Wild Mammals Impacted by Urban Expansion and Climate Change

Ecologies of zoonotic vector-borne diseases may shift with climate and land use change. As many urban-adapted mammals can host ectoparasites and pathogens of human and animal health concern, our goal was to compare patterns of arthropod-borne disease among medium-sized mammals across gradients of rural to urban landscapes in multiple regions of California. DNA of Anaplasma phagocytophilum was found in 1-5% of raccoons, coyotes, and San Joaquin kit foxes; Borrelia burgdorferi in one coyote, rickettsiae in two desert kit foxes, and Yersinia pestis in two coyotes. There was serological evidence of rickettsiae in 14-37% of coyotes, Virginia opossums, and foxes; and A. phagocytophilum in 6-40% of coyotes, raccoons, Virginia opossums, and foxes. Of six flea species, one Ctenocephalides felis from a raccoon was positive for Y. pestis, and Ct. felis and Pulex simulans fleas tested positive for Rickettsia felis and R. senegalensis. A Dermacentor similis tick off a San Joaquin kit fox was PCR-positive for A. phagocytophilum. There were three statistically significant risk factors: risk of A. phagocytophilum PCR-positivity was threefold greater in fall vs the other three seasons; hosts adjacent to urban areas had sevenfold increased A. phagocytophilum seropositivity compared with urban and rural areas; and there was a significant spatial cluster of rickettsiae within greater Los Angeles. Animals in areas where urban and rural habitats interconnect can serve as sentinels during times of change in disease risk.

Bitesize Epidemiology for General Awareness of All Students - I

This is the first part of a two-part series article. Recently, we have been in the middle of a difficult time due to the Covid-19 pandemic. Pandemics or global epidemics are not new to humankind; they have occurred many times in history. The discourse of epidemiology describes mainly the causal factors which need to be mitigated to prevent or combat the effects of epidemics. In epidemiology, we are not concerned for a person, but rather every individual globally, to make life healthier for all. In this article, we will discuss the basics of epidemiological practice that scientists have used for centuries to prevent epidemics with great results. Overall, we plan for better global health aided by epidemiology.

The one health perspective to improve environmental surveillance of zoonotic viruses: lessons from COVID-19 and outlook beyond

The human population has doubled in the last 50 years from about 3.7 billion to approximately 7.8 billion. With this rapid expansion, more people live in close contact with wildlife, livestock, and pets, which in turn creates increasing opportunities for zoonotic diseases to pass between animals and people. At present an estimated 75% of all emerging virus-associated infectious diseases possess a zoonotic origin, and outbreaks of Zika, Ebola and COVID-19 in the past decade showed their huge disruptive potential on the global economy. Here, we describe how One Health inspired environmental surveillance campaigns have emerged as the preferred tools to monitor human-adjacent environments for known and yet to be discovered infectious diseases, and how they can complement classical clinical diagnostics. We highlight the importance of environmental factors concerning interactions between animals, pathogens and/or humans that drive the emergence of zoonoses, and the methodologies currently proposed to monitor them-the surveillance of wastewater, for example, was identified as one of the main tools to assess the spread of SARS-CoV-2 by public health professionals and policy makers during the COVID-19 pandemic. One-Health driven approaches that facilitate surveillance, thus harbour the potential of preparing humanity for future pandemics caused by aetiological agents with environmental reservoirs. Via the example of COVID-19 and other viral diseases, we propose that wastewater surveillance is a useful complement to clinical diagnosis as it is centralized, robust, cost-effective, and relatively easy to implement.

Passive epidemiological surveillance in wildlife in Costa Rica identifies pathogens of zoonotic and conservation importance

Epidemiological surveillance systems for pathogens in wild species have been proposed as a preventive measure for epidemic events. These systems can minimize the detrimental effects of an outbreak, but most importantly, passive surveillance systems are the best adapted to countries with limited resources. Therefore, this research aimed to evaluate the technical and infrastructural feasibility of establishing this type of scheme in Costa Rica by implementing a pilot program targeting the detection of pathogens of zoonotic and conservation importance in wildlife. Between 2018 and 2020, 85 carcasses of free-ranging vertebrates were admitted for post-mortem and microbiology analysis. However, we encountered obstacles mainly related to the initial identification of cases and limited local logistics capacity. Nevertheless, this epidemiological surveillance scheme allowed us to estimate the general state of health of the country’s wildlife by establishing the causes of death according to pathological findings. For instance, 60% (51/85) of the deaths were not directly associated with an infectious agent. Though in 37.6% (32/85) of these cases an infectious agent associated or not with disease was detected. In 27.1% (23/85) of the cases, death was directly related to infectious agents. Furthermore, 12.9% (11/85), the cause of death was not determined. Likewise, this wildlife health monitoring program allowed the detection of relevant pathogens such as Canine Distemper Virus, Klebsiella pneumoniae, Angiostrongylus spp., Baylisascaris spp., among others. Our research demonstrated that this passive surveillance scheme is cost-effective and feasible in countries with limited resources. This passive surveillance can be adapted to the infrastructure dedicated to monitoring diseases in productive animals according to the scope and objectives of monitoring wildlife specific to each region. The information generated from the experience of the initial establishment of a WHMP is critical to meeting the challenges involved in developing this type of scheme in regions with limited resources and established as hotspots for emerging infectious diseases.

Zoonotic Disease Risk and Life-History Traits: Are Reservoirs Fast Life Species?

The relationship between humans, wildlife and disease transmission can be complex and context-dependent, and disease dynamics may be determined by idiosyncratic species. Therefore, an outstanding question is how general is the finding that species with faster life histories are more probable hosts of zoonoses. Ecological knowledge on species, jointly with public health data, can provide relevant information on species that should be targeted for epidemiological surveillance or management. We investigated whether mammal species traits can be good indicators of zoonotic reservoir status in an intensified agricultural region of Argentina. We find support for a relationship between reservoir status and the pace of life syndrome, confirming that fast life histories can be a factor of zoonotic risk. Nonetheless, we observed that for certain zoonosis, reservoirs may display a slow pace of life, suggesting that idiosyncratic interactions can occur. We conclude that applying knowledge from the life history-disease relationship can contribute significantly to disease risk assessment. Such an approach may be especially valuable in the current context of environmental change and agricultural intensification.

Long-term unsustainable patterns of development rather than recent deforestation caused the emergence of Orthocoronavirinae species

We investigated whether a set of phylogeographical tracked emergent events of Orthocoronavirinae were related to developed, urban and polluted environments worldwide. We explored coronavirus records in response to climate (rainfall parameters), population density, CO₂ emission, Human Developmental Index (HDI) and deforestation. We contrasted environmental characteristics from regions with spillovers or encounters of wild Orthocoronavirinae against adjacent areas having best-preserved conditions. We used all complete sequenced CoVs genomes deposited in NCBI and GISAID databases until January 2021. Except for Deltacoronavirus, concentrated in Hong Kong and in birds, the other three genera were scattered all over the planet, beyond the original distribution of the subfamily, and found in humans, mammals, fishes and birds, wild or domestic. Spillovers and presence in wild animals were only reported in developed/densely populated places. We found significantly more occurrences reported in places with higher HDI, CO₂ emission, or population density, along with more rainfall and more accentuated seasonality. Orthocoronavirinae occurred in areas with significantly higher human populations, CO₂ emissions and deforestation rates than in adjacent locations. Intermediately disturbed ecosystems seemed more vulnerable for Orthocoronavirinae emergence than forested regions in frontiers of deforestation. Sadly, people experiencing poverty in an intensely consumerist society are the most vulnerable.

A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What's New?

In the last decades, wildlife diseases and the health status of animal populations have gained increasing attention from the scientific community as part of a One Health framework. Furthermore, the need for non-invasive sampling methods with a minimal impact on wildlife has become paramount in complying with modern ethical standards and regulations, and to collect high-quality and unbiased data. We analysed the publication trends on non-invasive sampling in wildlife health and disease research and offer a comprehensive review on the different samples that can be collected non-invasively. We retrieved 272 articles spanning from 1998 to 2021, with a rapid increase in number from 2010. Thirty-nine percent of the papers were focussed on diseases, 58% on other health-related topics, and 3% on both. Stress and other physiological parameters were the most addressed research topics, followed by viruses, helminths, and bacterial infections. Terrestrial mammals accounted for 75% of all publications, and faeces were the most widely used sample. Our review of the sampling materials and collection methods highlights that, although the use of some types of samples for specific applications is now consolidated, others are perhaps still underutilised and new technologies may offer future opportunities for an even wider use of non-invasively collected samples.

Assessing the risk of human-to-wildlife pathogen transmission for conservation and public health

The SARS-CoV-2 pandemic has led to increased concern over transmission of pathogens from humans to animals, and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of human-to-wildlife transmission events, with a focus on how such events could threaten animal and human health. We identified 97 verified examples, involving a wide range of pathogens; however, reported hosts were mostly non-human primates or large, long-lived captive animals. Relatively few documented examples resulted in morbidity and mortality, and very few led to maintenance of a human pathogen in a new reservoir or subsequent "secondary spillover" back into humans. We discuss limitations in the literature surrounding these phenomena, including strong evidence of sampling bias towards non-human primates and human-proximate mammals and the possibility of systematic bias against reporting human parasites in wildlife, both of which limit our ability to assess the risk of human-to-wildlife pathogen transmission. We outline how researchers can collect experimental and observational evidence that will expand our capacity for risk assessment for human-to-wildlife pathogen transmission.

Urban-adapted mammal species have more known pathogens

The world is rapidly urbanizing, inviting mounting concern that urban environments will experience increased zoonotic disease risk. Urban animals could have more frequent contact with humans, therefore transmitting more zoonotic parasites; however, this relationship is complicated by sampling bias and phenotypic confounders. Here we test whether urban mammal species host more zoonotic parasites, investigating the underlying drivers alongside a suite of phenotypic, taxonomic and geographic predictors. We found that urban-adapted mammals have more documented parasites and more zoonotic parasites: despite comprising only 6% of investigated species, urban mammals provided 39% of known host-parasite combinations. However, contrary to predictions, much of the observed effect was attributable to parasite discovery and research effort rather than to urban adaptation status, and urban-adapted species in fact hosted fewer zoonotic parasites than expected on the basis of their total parasite richness. We conclude that extended historical contact with humans has had a limited impact on zoonotic parasite richness in urban-adapted mammals; instead, their greater observed zoonotic richness probably reflects sampling bias arising from proximity to humans, supporting a near-universal conflation between zoonotic risk, research effort and synanthropy. These findings underscore the need to resolve the mechanisms linking anthropogenic change, sampling bias and observed wildlife disease dynamics.

Toxocara cati and Toxoplasma gondii in French Birds of Prey

Parasites have developed many strategies to ensure their development, multiplication, and dissemination, including the use of reservoir hosts that are often nondomesticated species. Despite drastic reductions in their populations, wild birds remain widespread worldwide and could constitute some of these reservoirs. We focused on the identification of wild bird species harboring parasite stages in their muscles. Breast muscles of 327 birds of 27 different species were collected at three different sites in France. After artificial digestion, isolated nematode larvae were identified by PCR sequencing or restriction fragment length polymorphism (PCR-RFLP). Toxocara cati was identified mainly in birds of prey. The presence of anti-Toxoplasma antibodies was investigated by modified agglutination test on muscle fluids. Anti-Toxoplasma antibodies were detected in 65 out of 166 samples from various bird species. Avifauna, particularly birds of prey, could help on the surveillance of parasite circulation and play a role as sentinel species.

Biogeography of rodents in Iran: species richness, elevational distribution and their environmental correlates

Rodent biogeographic studies are disproportionately scarce in Iran, however, they are an ideal system to understand drivers of biodiversity distributions in the country. The aims of the present research are to determine (i) the pattern of rodent richness across the country, (ii) quantify their elevational distribution patterns, and (iii) explore the underlying mechanisms. To reach these goals, an updated species list was compiled based on the latest taxonomic revisions, published until December 2021. We mapped all 76 rodent species distributions to develop the first map of rodent richness in Iran. We furthermore investigated their elevational distribution patterns in the following four geographic regions based on 100 m intervals; the Zagros Mountains, north of Alborz Mountains, south of Alborz and Kopet-Dagh mountains, and central and east mountains. North-east of Iran, Zagros Mountains, Alborz Mountains, and northwestern of Iran showed the highest richness and were identified as biodiversity hotspots of rodents in the country. This study highlights the importance of past climate change as the key driver of rodent richness in Iran. We showed that rodents’ elevational distribution patterns differ among geographic regions. Areas and elevational zones with the highest species richness should be prioritized for the conservation planning of rodents in Iran.

The science of the host-virus network

Better methods to predict and prevent the emergence of zoonotic viruses could support future efforts to reduce the risk of epidemics. We propose a network science framework for understanding and predicting human and animal susceptibility to viral infections. Related approaches have so far helped to identify basic biological rules that govern cross-species transmission and structure the global virome. We highlight ways to make modelling both accurate and actionable, and discuss the barriers that prevent researchers from translating viral ecology into public health policies that could prevent future pandemics.

Land-use change and rodent-borne diseases: hazards on the shared socioeconomic pathways

Land-use change has a direct impact on species survival and reproduction, altering their spatio-temporal distributions. It acts as a selective force that favours the abundance and diversity of reservoir hosts and affects host-pathogen dynamics and prevalence. This has led to land-use change being a significant driver of infectious diseases emergence. Here, we predict the presence of rodent taxa and map the zoonotic hazard (potential sources of harm) from rodent-borne diseases in the short and long term (2025 and 2050). The study considers three different land-use scenarios based on the shared socioeconomic pathways narratives (SSPs): sustainable (SSP1-Representative Concentration Pathway (RCP) 2.6), fossil-fuelled development (SSP5-RCP 8.5) and deepening inequality (SSP4-RCP 6.0). We found that cropland expansion into forest and pasture may increase zoonotic hazards in areas with high rodent-species diversity. Nevertheless, a future sustainable scenario may not always reduce hazards. All scenarios presented high heterogeneity in zoonotic hazard, with high-income countries having the lowest hazard range. The SSPs narratives suggest that opening borders and reducing cropland expansion are critical to mitigate current and future zoonotic hazards globally, particularly in middle- and low-income economies. Our study advances previous efforts to anticipate the emergence of zoonotic diseases by integrating past, present and future information to guide surveillance and mitigation of zoonotic hazards at the regional and local scale. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Plague reservoir species throughout the world

Plague has been known since ancient times as a re-emerging infectious disease, causing considerable socioeconomic burden in regional hotspots. To better understand the epidemiological cycle of the causative agent of the plague, its potential occurrence, and possible future dispersion, one must carefully consider the taxonomy, distribution, and ecological requirements of reservoir-species in relation either to natural or human-driven changes (e.g. climate change or urbanization). In recent years, the depth of knowledge on species taxonomy and species composition in different landscapes has undergone a dramatic expansion, driven by modern taxonomic methods such as synthetic surveys that take into consideration morphology, genetics, and the ecological setting of captured animals to establish their species identities. Here, we consider the recent taxonomic changes of the rodent species in known plague reservoirs and detail their distribution across the world, with a particular focus on those rodents considered to be keystone host species. A complete checklist of all known plague-infectable vertebrates living in plague foci is provided as a Supporting Information table.

Inherent virus characteristics and host range drive the zoonotic and emerging potential of viruses

Understanding the zoonotic and emerging potential of viruses is critical to prevent and control spread that can cause disease epidemics or pandemics. We developed a database using the most up-to-date information from the International Committee on Taxonomy of Viruses (4958 virus species) and identified 1479 vertebrate virus species and their host ranges. Viral traits and host ranges were then used as predictors in generalized linear mixed models for three host-associated outcomes - confirmed zoonotic, potential zoonotic and disease emergence. We identified significant interactions between host range and viral characteristics, not previously reported, that influence the zoonotic and emergence potential of viruses. Bat- and livestock-adapted viruses posed high risk, and the risk increased substantially if these viruses were also present in other vertebrates or were not reported from invertebrates. Our model predicted 39 viruses of interest that have never been reported to have zoonotic potential (27) or to potentially become emerging human viruses (12). We conclude that nucleic acid type is important in identifying the zoonotic and emerging potential of viruses. We recommend enhanced surveillance and monitoring of these virus species identified with a zoonotic and emerging potential to mitigate disease outbreaks and future epidemics.

Dilution effects in disease ecology

For decades, people have reduced the transmission of pathogens by adding low‐quality hosts to managed environments like agricultural fields. More recently, there has been interest in whether similar ‘dilution effects’ occur in natural disease systems, and whether these effects are eroded as diversity declines. For some pathogens of plants, humans and other animals, the highest‐quality hosts persist when diversity is lost, so that high‐quality hosts dominate low‐diversity communities, resulting in greater pathogen transmission. Meta‐analyses reveal that these natural dilution effects are common. However, studying them remains challenging due to limitations on the ability of researchers to manipulate many disease systems experimentally, difficulties of acquiring data on host quality and confusion about what should and should not be considered a dilution effect. Because dilution effects are widely used in managed disease systems and have been documented in a variety of natural disease systems, their existence should not be considered controversial. Important questions remain about how frequently they occur and under what conditions to expect them. There is also ongoing confusion about their relationships to both pathogen spillover and general biogeographical correlations between diversity and disease, which has resulted in an inconsistent and confusing literature. Progress will require rigorous and creative research.

Impacts of biodiversity and biodiversity loss on zoonotic diseases

Zoonotic diseases are infectious diseases of humans caused by pathogens that are shared between humans and other vertebrate animals. Previously, pristine natural areas with high biodiversity were seen as likely sources of new zoonotic pathogens, suggesting that biodiversity could have negative impacts on human health. At the same time, biodiversity has been recognized as potentially benefiting human health by reducing the transmission of some pathogens that have already established themselves in human populations. These apparently opposing effects of biodiversity in human health may now be reconcilable. Recent research demonstrates that some taxa are much more likely to be zoonotic hosts than others are, and that these animals often proliferate in human-dominated landscapes, increasing the likelihood of spillover. In less-disturbed areas, however, these zoonotic reservoir hosts are less abundant and nonreservoirs predominate. Thus, biodiversity loss appears to increase the risk of human exposure to both new and established zoonotic pathogens. This new synthesis of the effects of biodiversity on zoonotic diseases presents an opportunity to articulate the next generation of research questions that can inform management and policy. Future studies should focus on collecting and analyzing data on the diversity, abundance, and capacity to transmit of the taxa that actually share zoonotic pathogens with us. To predict and prevent future epidemics, researchers should also focus on how these metrics change in response to human impacts on the environment, and how human behaviors can mitigate these effects. Restoration of biodiversity is an important frontier in the management of zoonotic disease risk.

COVID-19, a critical juncture in China's wildlife protection?

The COVID-19 crisis has called into question the utilitarianism-oriented human-wildlife relations and the legitimacy of wildlife protection regime in China. The pandemic has triggered significant, swift, and encompassing changes in policies. Drawing on insights from historical institutionalism, we argue that COVID-19 constitutes a critical juncture in China's wildlife protection policy.

Tackling zoonoses in a crowded world: Lessons to be learned from the COVID-19 pandemic

The COVID-19 zoonosis is bringing about a number of lessons to humanity. One is that of transforming our links with nature and, particularly, wildlife given the likely COVID-19 origin from illegal wildlife trading. Similar to vector borne diseases (VBD, diseases transmitted by vectors), the COVID-19 pandemic follows related patterns (e.g. no effective or available vaccines, difficult to diagnose, highly localized infection geographical foci, non-human reservoirs) for which we urgently need preventive measures. Towards this aim, governments worldwide must strive to prevent further devastation of natural environments that serve as buffer areas to humans against zoonotic agents (among other health risks), protecting biodiversity and its concomitant causes (e.g. global change), and banning use of wildlife of illegal origin. We herein state that some VBD prevention strategies could also be applied to zoonotic disease prevention, including COVID-19 or any type likely to be related to environmental conditions. The occurrence of future pandemic occurrence will depend on whether governments embrace these aims now.

Why disease ecology needs life-history theory: a host perspective

When facing an emerging infectious disease of conservation concern, we often have little information on the nature of the host-parasite interaction to inform management decisions. However, it is becoming increasingly clear that the life-history strategies of host species can be predictive of individual- and population-level responses to infectious disease, even without detailed knowledge on the specifics of the host-parasite interaction. Here, we argue that a deeper integration of life-history theory into disease ecology is timely and necessary to improve our capacity to understand, predict and mitigate the impact of endemic and emerging infectious diseases in wild populations. Using wild vertebrates as an example, we show that host life-history characteristics influence host responses to parasitism at different levels of organisation, from individuals to communities. We also highlight knowledge gaps and future directions for the study of life-history and host responses to parasitism. We conclude by illustrating how this theoretical insight can inform the monitoring and control of infectious diseases in wildlife.

Using host traits to predict reservoir host species of rabies virus

Wildlife are important reservoirs for many pathogens, yet the role that different species play in pathogen maintenance frequently remains unknown. This is the case for rabies, a viral disease of mammals. While Carnivora (carnivores) and Chiroptera (bats) are the canonical mammalian orders known to be responsible for the maintenance and onward transmission of rabies Lyssavirus (RABV), the role of most species within these orders remains unknown and is continually changing as a result of contemporary host shifting. We combined a trait-based analytical approach with gradient boosting machine learning models to identify physiological and ecological host features associated with being a reservoir for RABV. We then used a cooperative game theory approach to determine species-specific traits associated with known RABV reservoirs. Being a carnivore reservoir for RABV was associated with phylogenetic similarity to known RABV reservoirs, along with other traits such as having larger litters and earlier sexual maturity. For bats, location in the Americas and geographic range were the most important predictors of RABV reservoir status, along with having a large litter. Our models identified 44 carnivore and 34 bat species that are currently not recognized as RABV reservoirs, but that have trait profiles suggesting their capacity to be or become reservoirs. Further, our findings suggest that potential reservoir species among bats and carnivores occur both within and outside of areas with current RABV circulation. These results show the ability of a trait-based approach to detect potential reservoirs of infection and could inform rabies control programs and surveillance efforts by identifying the types of species and traits that facilitate RABV maintenance and transmission.

Fast-lived Hosts and Zoonotic Risk

Because most emerging human pathogens originate in mammals, many studies aim to identify host traits that determine the risk of sourcing zoonotic outbreaks. Studies regularly assert that 'fast-lived' mammal species exhibiting greater fecundity and shorter lifespans tend to host more zoonoses; however, the causes of this association remain poorly understood and they cover a range of immune and nonimmune mechanisms. We discuss these drivers in the context of evolutionary ecology and wildlife-human interactions. Ultimately, differentiating these mechanisms will require linking interspecific variation in life history with immunity, pathogen diversity, transmissibility, and zoonotic risk, and critical data gaps currently limit our ability to do so. We highlight sampling and analytical frameworks to address this gap and to better inform zoonotic reservoir prediction.

Population structure and diet generalism define a preliminary ecological profile of zoonotic virus hosts in the Western Ghats, India

The rainforests of the Western Ghats exhibit some of the highest biodiversity on the planet, and yet are undergoing rapid land use change due to the expansion of agriculture and other industries. As the landscape of the region is transformed, more people are coming into conflict with wildlife and becoming exposed to pathogens that previously circulated beyond the boundaries of human incursion. Despite an ecological knowledge imperative, this emerging landscape is ill-defined with respect to the ecology of zoonotic viruses and their mammalian wildlife hosts. Without a better understanding of the underlying infection ecology, the epidemiology of viral spillover will remain elusive and unsuited to the task of predicting and preventing outbreaks. The current investigation explored the association between mammalian zoonotic virus richness and species-level landscape, life-history, and dietary traits to describe an initial ecological profile of zoonotic virus hosts in the Western Ghats. Social group composition and dietary forage were both non-linearly associated with greater zoonotic viral richness among these species, whereby species active in smaller social groups, albeit in higher population densities, and exhibiting a tendency toward a generalist diet hosted more zoonotic viruses. While these findings provide no definitive ecological demarcation of zoonotic virus hosts or their contribution to viral maintenance or amplification, it is expected that this preliminary profile can help to develop targeted wildlife pathogen surveillance programs and to expand the current approach to epidemiological modelling of emerging zoonoses in the region, which typically do not account for the macroecological parameters of infection transmission.

Predicting the global mammalian viral sharing network using phylogeography

Understanding interspecific viral transmission is key to understanding viral ecology and evolution, disease spillover into humans, and the consequences of global change. Prior studies have uncovered macroecological drivers of viral sharing, but analyses have never attempted to predict viral sharing in a pan-mammalian context. Using a conservative modelling framework, we confirm that host phylogenetic similarity and geographic range overlap are strong, nonlinear predictors of viral sharing among species across the entire mammal class. Using these traits, we predict global viral sharing patterns of 4196 mammal species and show that our simulated network successfully predicts viral sharing and reservoir host status using internal validation and an external dataset. We predict high rates of mammalian viral sharing in the tropics, particularly among rodents and bats, and within- and between-order sharing differed geographically and taxonomically. Our results emphasize the importance of ecological and phylogenetic factors in shaping mammalian viral communities, and provide a robust, general model to predict viral host range and guide pathogen surveillance and conservation efforts.

Prior studies have investigated macroecological patterns of host sharing among viruses, although certain mammal clades have not been represented in these analyses, and the findings have not been used to predict the true network. Here the authors model the species level traits that predict viral sharing across all mammal clades and validate their predictions using an independent dataset.

A preliminary ecological profile of Kyasanur Forest disease virus hosts among the mammalian wildlife of the Western Ghats, India

Kyasanur Forest disease (KFD) virus is one of India's severe arboviruses capable of causing prolonged debilitating disease. It has been expanding beyond its historical endemic locus at an alarming rate over the last two decades. The natural nidus of this zoonosis is located in the monsoon rainforest of the Western Ghats, India, which is one of the world's most important biodiversity hotspots. Definitive reservoir hosts for KFD virus (KFDV) have yet to be delineated, and thus much of the infection ecology of this virus, and its consequent transmission dynamics, remains uncertain. Given its unique biogeographical context, identifying ecological parameters of KFDV relevant to the virus' epidemiology has been complex and challenging. The challenge has been exacerbated by diminished research efforts in wildlife surveillance over the last two decades, coinciding with the expansion of the range of KFD across the region. The current investigation sought to define a preliminary ecological profile of KFDV hosts based on their life history and feeding traits to aid in re-establishing targeted wildlife surveillance and to discern those ecological traits of wildlife hosts that may improve our understanding of KFD epidemiology. The importance of fast-living among KFDV hosts was of special interest with respect to the latter aim. We compared mammalian traits between host and non-host species using general additive models and phylogenetic generalised linear models. This study found that both body mass and forest forage were strongly associated with mammalian host infection status, but that reproductive life history traits were not. These findings will help in structuring ecologically based wildlife surveillance and field investigations, while also helping to parameterise novel epidemiological models of zoonotic infection risk that incorporate species functional traits in a region where biogeography, landscape ecology, and community ecology manifest extraordinary complexity, particularly under growing anthropogenic pressure.

Detection and complete genome characterization of a novel RNA virus related to members of the Hepe-Virga clade in bird species, hoopoe (Upupa epops)

Using viral metagenomics, next-generation sequencing and RT-PCR techniques a genetically divergent hepevirus-like RNA virus was identified and characterized from a faecal sample of wild bird species, hoopoe (Upupa epops) in Hungary. The complete viral genome sequence of hoopoe/BBanka01/2015/HUN (GenBank accession number MN852439) is 7052 nt long including a 54-nt 5' and an 18-nt 3' non-coding region without poly(A)-tail. Sequence analysis indicated that the hoopoe/BBanka01/2015/HUN genome has potentially three overlapping open reading frames (ORFs). The ORF1 (6558 nt/2185aa) encodes a long, non-structural polyprotein (replicase) including putative functional domains and conserved aa motifs of methyltransferase with domain Y, RNA helicase and RdRp and has <33% aa identity to the known hepe- and hepe-like viruses. The ORF2 (1446 nt/481aa) encodes a putative structural (capsid) protein overlapping with ORF1 but translated in different coding frame. The functions of the short ORF3 (426 nt/141aa) were not predictable. Similar virus sequences were not detected from samples from 21 further bird species. The taxonomic position of this novel virus is presently unknown.

Insights into the Host Specificity of Mosquito-Borne Flaviviruses Infecting Wild Mammals

Mosquito-borne flaviviruses (MBFVs) are of public and animal health concern because they cause millions of human deaths annually and impact domestic animals and wildlife globally. MBFVs are phylogenetically divided into two clades, one is transmitted by Aedes mosquitoes (Ae-MBFVs) associated with mammals and the other by Culex mosquitoes (Cx-MBFVs) associated with birds. However, this assumption has not been evaluated. Here, we synthesized 79 published reports of MBFVs from wild mammals, estimating their host. Then, we tested whether the host specificity was biased to sampling and investigation efforts or to phylogenetic relationships using a viral phylogenetic tree drawn from analyzing whole flavivirus genomes obtained in GenBank. We found in total 18 flaviviruses, nine related to Aedes spp. and nine to Culex spp. infecting 129 mammal species. Thus, this supports that vectors are transmitting MBFV across available host clades and that ornithophilic mosquitoes are readily infecting mammals. Although most of the mosquito species are generalists in their host-feeding preferences, we also found a certain degree of MBFV's specificity, as most of them infect closely related mammal species. The present study integrates knowledge regarding MBFVs, and it may help to understand their transmission dynamics between viruses, vectors, and mammal hosts.

The problem of scale in the prediction and management of pathogen spillover

Disease emergence events, epidemics and pandemics all underscore the need to predict zoonotic pathogen spillover. Because cross-species transmission is inherently hierarchical, involving processes that occur at varying levels of biological organization, such predictive efforts can be complicated by the many scales and vastness of data potentially required for forecasting. A wide range of approaches are currently used to forecast spillover risk (e.g. macroecology, pathogen discovery, surveillance of human populations, among others), each of which is bound within particular phylogenetic, spatial and temporal scales of prediction. Here, we contextualize these diverse approaches within their forecasting goals and resulting scales of prediction to illustrate critical areas of conceptual and pragmatic overlap. Specifically, we focus on an ecological perspective to envision a research pipeline that connects these different scales of data and predictions from the aims of discovery to intervention. Pathogen discovery and predictions focused at the phylogenetic scale can first provide coarse and pattern-based guidance for which reservoirs, vectors and pathogens are likely to be involved in spillover, thereby narrowing surveillance targets and where such efforts should be conducted. Next, these predictions can be followed with ecologically driven spatio-temporal studies of reservoirs and vectors to quantify spatio-temporal fluctuations in infection and to mechanistically understand how pathogens circulate and are transmitted to humans. This approach can also help identify general regions and periods for which spillover is most likely. We illustrate this point by highlighting several case studies where long-term, ecologically focused studies (e.g. Lyme disease in the northeast USA, Hendra virus in eastern Australia, Plasmodium knowlesi in Southeast Asia) have facilitated predicting spillover in space and time and facilitated the design of possible intervention strategies. Such studies can in turn help narrow human surveillance efforts and help refine and improve future large-scale, phylogenetic predictions. We conclude by discussing how greater integration and exchange between data and predictions generated across these varying scales could ultimately help generate more actionable forecasts and interventions. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.

Ecological and life history traits are associated with Ross River virus infection among sylvatic mammals in Australia

Background

Ross River virus (RRV) is Australia’s most important arbovirus given its annual burden of disease and the relatively large number of Australians at risk for infection. This mosquito-borne arbovirus is also a zoonosis, making its epidemiology and infection ecology complex and cryptic. Our grasp of enzootic, epizootic, and zoonotic RRV transmission dynamics is imprecise largely due to a poor understanding of the role of wild mammalian hosts in the RRV system.

Methods

The current study applied a piecewise structural equation model (PSEM) toward an interspecific comparison of sylvatic Australian mammals to characterize the ecological and life history profile of species with a history of RRV infection relative to those species with no such history among all wild mammalian species surveyed for RRV infection. The effects of species traits were assessed through multiple causal pathways within the PSEM framework.

Results

Sylvatic mammalian species with a history of RRV infection tended to express dietary specialization and smaller population density. These species were also characterized by a longer gestation length.

Conclusions

This study provides the first interspecific comparison of wild mammals for RRV infection and identifies some potential targets for future wildlife surveys into the infection ecology of this important arbovirus. An applied RRV macroecology may prove invaluable to the epidemiological modeling of RRV epidemics across diverse sylvatic landscapes, as well as to the development of human and animal health surveillance systems.

Electronic supplementary material

The online version of this article (10.1186/s12898-019-0220-5) contains supplementary material, which is available to authorized users.

Taxonomic patterns in the zoonotic potential of mammalian viruses

Predicting and simplifying which pathogens may spill over from animals to humans is a major priority in infectious disease biology. Many efforts to determine which viruses are at risk of spillover use a subset of viral traits to find trait-based associations with spillover. We adapt a new method-phylofactorization-to identify not traits but lineages of viruses at risk of spilling over. Phylofactorization is used to partition the International Committee on Taxonomy of Viruses viral taxonomy based on non-human host range of viruses and whether there exists evidence the viruses have infected humans. We identify clades on a range of taxonomic levels with high or low propensities to spillover, thereby simplifying the classification of zoonotic potential of mammalian viruses. Phylofactorization by whether a virus is zoonotic yields many disjoint clades of viruses containing few to no representatives that have spilled over to humans. Phylofactorization by non-human host breadth yields several clades with significantly higher host breadth. We connect the phylogenetic factors above with life-histories of clades, revisit trait-based analyses, and illustrate how cladistic coarse-graining of zoonotic potential can refine trait-based analyses by illuminating clade-specific determinants of spillover risk.

Going to Bat(s) for Studies of Disease Tolerance

A majority of viruses that have caused recent epidemics with high lethality rates in people, are zoonoses originating from wildlife. Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. Intriguingly, these viruses also all originate from bat reservoirs. Bats have been shown to have a greater mean viral richness than predicted by their phylogenetic distance from humans, their geographic range, or their presence in urban areas, suggesting other traits must explain why bats harbor a greater number of zoonotic viruses than other mammals. Bats are highly unusual among mammals in other ways as well. Not only are they the only mammals capable of powered flight, they have extraordinarily long life spans, with little detectable increases in mortality or senescence until high ages. Their physiology likely impacted their history of pathogen exposure and necessitated adaptations that may have also affected immune signaling pathways. Do our life history traits make us susceptible to generating damaging immune responses to RNA viruses or does the physiology of bats make them particularly tolerant or resistant? Understanding what immune mechanisms enable bats to coexist with RNA viruses may provide critical fundamental insights into how to achieve greater resilience in humans.

Interspecific network centrality, host range and early-life development are associated with wildlife hosts of Rift Valley fever virus

Rift Valley fever virus (RVFV) is responsible for a substantive disease burden in pastoralist communities and the agricultural sector in the African continent and Arabian Peninsula. Enzootic, epizootic and zoonotic RVFV transmission dynamics remain ill-defined, particularly due to a poor understanding of the role of mammalian hosts in the epidemiology and infection ecology of this arbovirus. Using a piecewise structural equation model, this study sought to identify associations between biological and ecological characteristics of mammalian species and documented RVFV infection to highlight species-level traits that may influence wildlife host status. Interspecific network centrality, size of species home range and reproductive life-history traits were all associated with being an RVFV host. The identification of these species-level characteristics may help to provide ecological context for the role of wildlife amplification hosts in the epidemiology of spillover to livestock and humans and may also help to identify specific points of vulnerability at the wildlife-livestock interface.

Experimental Cowpox Virus (CPXV) Infections of Bank Voles: Exceptional Clinical Resistance and Variable Reservoir Competence

Cowpox virus (CPXV) is a zoonotic virus and endemic in wild rodent populations in Eurasia. Serological surveys in Europe have reported high prevalence in different vole and mouse species. Here, we report on experimental CPXV infections of bank voles (Myodes glareolus) from different evolutionary lineages with a spectrum of CPXV strains. All bank voles, independently of lineage, sex and age, were resistant to clinical signs following CPXV inoculation, and no virus shedding was detected in nasal or buccal swabs. In-contact control animals became only rarely infected. However, depending on the CPXV strain used, inoculated animals seroconverted and viral DNA could be detected preferentially in the upper respiratory tract. The highest antibody titers and virus DNA loads in the lungs were detected after inoculation with two strains from Britain and Finland. We conclude from our experiments that the role of bank voles as an efficient and exclusive CPXV reservoir seems questionable, and that CPXV may be maintained in most regions by other hosts, including other vole species. Further investigations are needed to identify factors that allow and modulate CPXV maintenance in bank voles and other potential reservoirs, which may also influence spill-over infections to accidental hosts.