Understanding the spatial spread of viruses within wildlife populations is often a key component of disease management efforts. Viral spread is likely constrained by host ecology, but inter-virus differences in infection strategy might allow some viruses to overcome these constraints, leading to divergent population structures within a common host environment. We studied the phylogeographic structure of six virus taxa (dependoparvovirus, deltavirus, mastadenovirus, betaherpesvirus and two lineages of rabies virus) circulating in common vampire bats (Desmodus rotundus) in Peru, finding that viral population structure is inconsistently constrained by host ecology. Specifically, while bat travel distance structured the genetic diversity of betaherpesvirus and two lineages of rabies virus, other viruses were instead constrained by anthropogenic factors (dependoparvovirus), or had weakly defined population structure (mastadenovirus). The genetic structure of all viruses was affected by a measure of human travel difficulty between sites, but effects varied in size and direction. Distinct drivers of viral population structure within the same host species imply that virus infection strategy can outweigh host ecological connectivity, acting as a key determinant of geographic spread. Because barriers to gene flow generalise poorly between viruses, whether a tractable virus can illuminate host population structure or predict the spread of high-impact viruses depends on individual virus biology.

Identifying the drivers of wildlife immunity is critical for assessing stressor impacts and zoonotic risks. However, such studies are limited by logistical challenges of wildlife research and lack of species-specific reagents. We adapt flow cytometry, typically confined to laboratory settings, to field settings to profile cellular immunity with small blood volumes and extended sample holding times. We apply these methods to analyze immune cell seasonality in migratory Mexican free-tailed bats (Tadarida brasiliensis). We confirmed four antibodies recognizing CD3, CD79a, MHCII, and CD11b that were originally validated in Egyptian fruit bats (Rousettus aegyptiacus), allowing us to quantify T and B cells, macrophages, and neutrophils, respectively. Flow cytometry outperformed hematology in quantifying leukocyte profiles and revealed pronounced immune cell seasonality. Adaptive cells steadily increased between spring and fall migration. Neutrophils were most abundant during the reproductive period and decreased during migrations, whereas B cells were most abundant after reproduction and before fall migration; granulocytes as a whole, macrophages, and T cells had no seasonality. Females had more B cells than males but did not differ in other cells. Our findings lay the groundwork for applying flow cytometry to field studies of wildlife and provide important insights into the seasonality of bat immunity.

Emerging zoonoses remain a global public health concern. Surveillance of infectious and vector-borne diseases is vital for predicting and mitigating detrimental effects of zoonotic spillover events. Beyond assessing what microorganisms are circulating in specific environments, it is important to understand how potential reservoir hosts, especially animals such as bats, participate in pathogen transmission. Bats can host and potentially spread infections caused by bacteria, viruses, fungi, and protozoa. However, bats can also act as sentinels that test positive for pathogenic microorganisms without necessarily contributing to the pathogen replication cycle. Metagenomic next-generation sequencing (mNGS) provides an efficient means to broadly screen for pathogens, although microorganism selectivity can sometimes be lower than targeted approaches. Pairing mNGS results with higher-sensitivity tests such as quantitative PCR (qPCR) can validate results and together these tools provide a relatively fast and reliable method for conducting surveillance. To test this approach, we conducted an exploratory study surveying the types of microorganisms circulating in Belize by collecting 263 blood samples from 20 different bat species captured in the Orange Walk District in 2019, 2022, and 2023. We used mNGS to initially characterize the microbial communities and qPCR to confirm presence and intensity of human pathogens of interest. We detected 1,430 different microorganisms with some relevance to human or animal health, including the protozoan Trypanosoma cruzi, which was detected in the phyllostomid bats Desmodus rotundus and Artibeus jamaicensis . qPCR confirmed the presence and intensity of Trypanosoma cruzi in mNGS-positive bat samples. We documented the types of pathogenic microorganisms circulating throughout the bat community in northern Belize to demonstrate the capacity for bats to serve as sentinels.

Bats have been increasingly recognized to host relapsing fever borreliae as well as borreliae that form novel clades adjacent to the Lyme borreliosis group. However, the genetic diversity and zoonotic potential of bat-borne borreliae remain poorly understood, in part because most work to date has focused on bats in the tropics. Fewer bat-borne Borrelia surveys have been conducted in temperate zones, where many bats undertake seasonal migrations that may facilitate pathogen dispersal. We surveyed blood from nearly 400 Mexican free-tailed bats (Tadarida brasiliensis) during their seasonal occupancy in Oklahoma, USA, during 2022 and 2023, for Borrelia spp. Targeted PCR of the 16S rRNA and flaB genes revealed high nucleotide identity to Borrelia puertoricensis, and shotgun metagenomics further demonstrated high amino acid identity to strains isolated from argasid ticks and human blood. This represents the first detection of Borrelia puertoricensis in bats and only the second detection within wild vertebrate hosts. Infection prevalence was low but comparable to that of other borreliae in bats. Our findings suggest that Mexican free-tailed bats may contribute to the dispersal of this emerging tick-borne bacterial pathogen in North America. IMPORTANCE:Bacteria in the genus Borrelia are primarily spread by ticks and cause either Lyme borreliosis or relapsing fever. Substantial work has demonstrated the degree to which rodents and songbirds can contribute to the enzootic cycles and dispersal of these human diseases, but comparatively less attention has been paid to the role of wild bats, particularly in temperate regions. We here report human-relevant findings from a two-year, seasonal survey of migratory Mexican free-tailed bats (Tadarida brasiliensis) in Oklahoma, USA. We tested nearly 400 bats and identified Borrelia puertoricensis, a relapsing fever species that could infect humans. Importantly, this represents the first detection of Borrelia puertoricensis in bats and only the second detection in wild vertebrate hosts, expanding the known host range of this emerging tick-borne pathogen. Given the known migratory routes of Mexican free-tailed bats, our results have implications for the role that bats may play in tick-borne pathogen dispersal in North America.

Wild small mammals represent critical sources of zoonotic infections due to their high diversity, global distribution, and proximity to humans. Nevertheless, significant knowledge gaps persist in characterizing pan-taxonomic microbial richness and sharing dynamics, particularly regarding ecologically critical yet understudied Eulipotyphla (true insectivores). Here, we take a macroecological approach to compare how microbial hosting and sharing dynamics differ across insectivores, rodents, and bats, and what ecological factors drive such disparities. We find that insectivores host comparable microbial richness to rodents and bats while exhibiting superior connectivity in microbe-sharing networks, suggesting a higher potential for intra- and cross-order microbial transmission. Urban adaptation, geographic range area, and longevity are shared drivers of microbial richness and sharing across these host orders, while greater body mass and shorter gestation time specifically are positive predictors of these outcomes within insectivores. Climate change projections identify insectivores as primary transmission hosts in new high-latitude hotspots by 2035, including parts of the US, Canada, and Russia, posing greater zoonotic threats than rodents or bats. Our findings challenge the prevailing paradigm that prioritizes rodents and bats as special zoonotic reservoirs, establishing insectivores as critical but overlooked players in disease ecology. Collective proactive surveillance of insectivores, rodents, and bats is imperative for forecasting emerging zoonotic threats and informing global risk assessment frameworks.

Habitat fragmentation can negatively impact wildlife, including increasing infectious disease risk. We assessed spatiotemporal changes in pathogen dynamics in vampire bats (Desmodus rotundus) in response to habitat fragmentation using general linear mixed models to investigate the influence of site, year, and tree cover on Bartonella spp. and hemotropic Mycoplasma spp. (hemoplasmas) infection risk in bats in one large and one small forest fragment in Belize across seven years. While Bartonella infections were more likely in the final years of the study regardless of site, hemoplasma infection likelihood was not significantly different across years or sites. Bartonella infections were associated with increased forest loss in the large fragment only, whereas hemoplasma infections were not associated with forest loss. The effects of site, year, and forest loss on infection likelihood varied by pathogen genotype despite low model explanatory power. Neither site nor year was associated with bartonellae, but one genotype was positively associated with tree cover. Two hemoplasmas were influenced by year with differing trends: one genotype was negatively associated with tree loss across sites, while another was positively associated with forest loss at the small fragment only. Both pathogens were similarly influenced by bat demographics and showed instances of infection status and genotype switching. Our work suggests that the effects of habitat fragmentation on infection risk depend on both the pathogen and specific genotype, complicating expectations of how environmental change affects wildlife disease dynamics. Efforts to mitigate infectious disease impacts in fragmented systems should be tailored to specific pathogens of concern.

Abstract Desmodus rotundus Betaherpesvirus (DrBHV) is a candidate vector for a transmissible vaccine targeting the circulation of rabies virus within its vampire bat reservoir. Studies assessing the potential for DrBHV as a vector have not considered its geographic range, potential for transboundary spread or how the diversity of wildtype DrBHV in natural bat populations might impede the spread of a modified vaccine strain. Here, by sequencing DrBHVs from vampire bats spanning 15 regions across 7 rabies-affected countries in Latin America and the Caribbean, we characterise the continent-scale distribution of DrBHV diversity and demonstrate widespread and apparently unconstrained co-infection. DrBHV occurred in all regions, forming a monophyletic clade consistent with a single introduction to vampire bats or host–virus co-speciation rather than frequent host switching. Phylogeographic analyses revealed cross-boundary spread that was predicted by geographic proximity. We identified 50 putative DrBHV strains and 79% of DrBHV-infected bats harboured multiple strains. No strains were over- or under-represented in co-infection and co-infections occurred proportionately to local strain prevalence. Whether strains circulated in given populations was predominantly driven by the geographic proximity of other populations containing that strain. The evolutionary relatedness of strains constrained neither rates of co-infection within individuals nor whether strains co-circulated within regions, suggesting vaccine vectors might be locally sourced rather than requiring imported, divergent strains to ameliorate interference. These results support the viability of DrBHV-vectored vaccines for mitigating rabies virus across Latin America and the Caribbean, despite widespread circulation of wildtype viruses.

A central unsolved problem in RNA virus evolution is understanding why some viral reassortants establish and persist while others do not. To answer this question, we reconstructed reassortant histories across 553 viral genomes from seven orthohantavirus species between 1983 and 2024 using phylogenetic reconciliation and molecular dating. We found that the frequency of retained reassortants varied among orthohantaviruses. For example, reassortment ranged from absent in Andes virus to frequent in Dobrava-Belgrade, Sin Nombre, Seoul, Puumala, and Tula viruses, showing that effective reassortment is not a genus-wide constant. Our Bayesian hierarchical models identified local host overlap as the strongest ecological factor associated with viral reassortment, while cross-segment linkage and terminal RNA structure serve as a molecular filter. We found that the probability of reassortment establishment is highest when ecological opportunity is paired with molecular permissiveness, with their interaction term inferred as the strongest signal in our establishment models (posterior probability = 0.97). These results suggest that reassortment in orthohantaviruses is a sequentially filtered evolutionary process in which divergent lineages must first meet in a host through ecological overlap, exchange segments that are molecularly compatible, and do so within a lineage background permissive to establishment in the host population.

When you think of bats, you might picture mysterious creatures flying around inside caves and drinking blood in the night, but bats are much more than that! Did you know that bats are the only mammals that can fly? Not all bats are nocturnal—some are active during the day; some live in trees instead of caves; and they might eat fruit or insects. Bats also protect the health of the environment. They pollinate plants, spread seeds, and eat pest insects that can spread pathogens to crops. Even more fascinating, bats can carry viruses that make people sick, yet they rarely get sick themselves. Could it be that bats do not ever get sick, or do they have special ways of handling infection? In this article, you will explore the fascinating world of bats, their relationship with viruses, and their extraordinary immune systems!

We detected Borrelia puertoricensis in migratory Mexican free-tailed bats sampled in Oklahoma during 2022 and 2023, representing only the second detection of this relapsing fever species in wild vertebrates. Although prevalence was low (0.79%), our findings suggest migratory bats could contribute to dispersal of tick-borne pathogens in North America.

BackgroundBat flies are ubiquitous ectoparasites of bats, recognised as potential vectors for viral and bacterial transmission between individual bats within a roost. Despite this, little is known about the seasonal dynamics of bat flies. Here, we present the results of a longitudinal study that compares seasonal prevalence and host risk factors for bat fly (Diptera: Nycteribiidae) parasitism with that of Bartonella and Borrelia spp. detected in Pteropus alecto and P. poliocephalus in eastern Australia.MethodsFlying foxes were sampled at nine different roosts in south-east Queensland and northern New South Wales between February 2018 and September 2022 using mist nets. Host and ectoparasite data were recorded, and bat fly specimens were collected for identification. Blood samples collected from the flying foxes were screened for the presence of Bartonella and Borrelia DNA using polymerase chain reaction (PCR).ResultsEctoparasite data were recorded from 2235 flying foxes and 840 had blood samples screened for Bartonella and Borrelia DNA. Cyclopodia albertisii was the predominate nycteribiid species identified, with few detections of C. australis. Nycteribiid prevalence had a consistent annual cycle (ranging from 8.6% to 100%) that depended on local climatic factors, increasing with increased temperature and humidity during summer and decreasing in winter. Bartonella spp. prevalence exhibited less variation seasonally (ranging from 50% to 100%) with a peak in winter that was driven by host age, with juvenile bats having a reduced probability of infection compared with subadults and adults. Borrelia spp. were rare and showed no clear seasonality.ConclusionsThis study reports the longitudinal occurrence of the blood-borne bacteria Bartonella spp. and their likely ectoparasite vectors in Australian flying foxes. The findings contribute to knowledge of nycteribiid ecology critical for understanding their vector potential within flying fox roosts and provide direction for future research into nycteribiid-mediated transmission dynamics.

Abstract Identifying and characterizing zoonotic pathogens in wildlife is essential for understanding disease risk to humans. In Sub-Saharan Africa, many people live with bats in their houses and are exposed to their pathogens, yet little is known about the bacterial pathogens in Afrotropical bat species. Globally, Bartonella spp. (bartonellae) and hemotropic Mycoplasma spp. (hemoplasmas) are common bacterial pathogens in bats, and some lineages are known to spill over and cause infections in humans. To evaluate this disease risk, we screened three common synanthropic bat species in Kenya, and their ectoparasites, for hemoplasmas and bartonellae and assessed their relatedness to known human pathogens. Of 767 bats across 21 sites, 17.9% of bats were Bartonella spp. positive and 19.3% were hemoplasma positive. Bat ectoparasites had similar Bartonella prevalence (13.5–25.0%) and, for most bat species, ectoparasite loads were not associated with increased likelihood of Bartonella infection. We found that Bartonella lineages displayed phylogenetic overlap between different bat species and ectoparasites, suggesting pathogen sharing between species, while hemoplasma lineages corresponded strictly to host taxonomy. Finally, we found that 16S rRNA sequences from one heart-nosed bat ( Cardioderma cor ) were 97.85% similar to a human-associated hemoplasma found previously in Schreiber’s bats ( Miniopterus schreibersii ) in Spain. We show that synanthropic bats host bacteria of potential public health concern, highlighting the need to investigate the emerging impacts of these pathogens on human health in Kenya and elsewhere in Sub-Saharan Africa.

Understanding the drivers of seasonal disease outbreaks remains a fundamental challenge in disease ecology. Periodic outbreaks can be driven by several seasonally varying factors, including pulses of susceptible individuals through births, changes in host behaviour and social aggregation and variation in host immunity. However, when these potential drivers overlap temporally, isolating their relative contributions to outbreak patterns becomes challenging. We studied Hendra virus, a zoonotic pathogen with seasonal spillovers from bats to horses and humans. Multiple seasonal factors have been hypothesized to drive Hendra virus transmission, including food shortages, birth pulses and changes in host aggregation, but their temporal overlap has made identifying primary drivers difficult. We conducted a 4-year longitudinal study of Pteropus bats to test whether seasonal birth pulses and the resulting influx of susceptible juveniles drive Hendra virus transmission. Using a Bayesian ageing model, we aged sexually immature bats and placed them into birth cohorts. We used our age predictions to model how viral shedding and antibody responses changed as bats aged. We tracked Bartonella spp. Infection-a bacterial pathogen requiring close contact for transmission-as an indicator of transmission opportunities within each cohort for comparison. We found no evidence that seasonal birth pulses of immunologically naïve juveniles drove Hendra virus transmission. Two out of three cohorts showed substantially reduced maternal antibody transfer compared to the 2018 cohort, with seroprevalence near zero at our earliest sampling timepoints and showed no clear evidence of synchronized seroconversion. Furthermore, Bartonella infection rates were consistent across cohorts, indicating that opportunities for pathogen transmission remained consistent across cohorts despite varying viral shedding patterns. Our findings demonstrate that birth pulses alone cannot explain observed patterns of Hendra virus outbreaks. These results highlight the importance of using multiple lines of evidence to evaluate competing mechanisms underlying seasonal disease dynamics, particularly when potential drivers coincide temporally.

Cross-species transmission of pathogens can be facilitated by frequent contact among wildlife. Cross-species transmission is often driven by phylogenetic similarity between host species, but the role this plays when multiple host species co-roost is unknown. We developed a generalizable framework for understanding how cross-species transmission is driven by contact among co-roosting species spanning evolutionary similarities and the net impact on roost-level infection prevalence. We developed ordinary differential equation models describing population and infection dynamics between two and three co-roosting species. We derived conditions for pathogen invasion and parameterized models using co-roosting Neotropical bat systems, with interspecific transmission exponentially declining with phylogenetic distance. To assess the relative contribution of contact rates and phylogenetic similarity, we co-varied intraspecific transmission rates and phylogenetic distances while considering sensitivity to epidemiological structure and pathogen traits. For both susceptible-infected-recovered-susceptible and susceptible-infected-latent-infected models, we show that relatedness between co-roosting hosts facilitates pathogen invasion, particularly for poorly transmissible pathogens with short durations of infection and immunity or latency. These models converged on similar equilibria, and roost-level prevalence was greatest when hosts were most closely related. However, we also identified regions of parameter space where roost-level prevalence increased when hosts were distantly related. Our generalizable models are adaptable to other co-roosting systems with low-virulence pathogens that are directly transmitted and inform our understanding of pathogen spillover.

The repeated emergence of pandemic viruses underscores the linkages between land-use change and wildlife disease, and urban-adapted wildlife are of special interest due to their close proximity to humans. However, viral diversity within urban-adapted species and their zoonotic potential remain largely unexplored. Here we compiled a dataset of documented records spanning from 1574 to 2023 on red foxes, raccoons, raccoon dogs, masked palm civets, European hedgehogs, European shrews, wild boars and their viruses, covering 116 countries. These urban-adapted mammals host 286 virus species spanning 24 orders and 38 families, 14 of which are potentially high risk for human infection. Raccoon dogs had increased viral positivity in urban habitats compared to raccoons, wild boars and red foxes. Many viruses in urban-adapted species were phylogenetically related to those found in humans, and our data suggest possible viral spillback. These results highlight zoonotic risks associated with urban-adapted species and suggest enhanced surveillance to mitigate future outbreaks.

The Eulipotyphla (true insectivores) is the third largest mammalian order, comprising over 500 species, and could be an important source of human infectious diseases. However, relatively little is known about the microbial diversity in insectivores and their contribution to virus transmission among wild hosts. In this study, we compile a comprehensive dataset containing over 400,000 records of insectivores and their associated microbes from 1903 to 2023 from multiple public databases. Meta-analyses show that insectivores host 941 unique microbes, 60% of which are viruses; these are predominantly found in shrews and hedgehogs. Human-associated viruses harbored by shrews and hedgehogs are phylogenetically closely related to those in humans, suggesting potential bidirectional transmission between insectivores and humans. Moreover, virus-sharing networks reveal that insectivores hold the second-most central position for virus sharing, second to bats, among all mammalian orders. Insectivores have a high proportion of cross-order transmitted viruses, including many human-associated viruses. Dietary diversity, habitat diversity, and distributional traits emerge as the key ecological factors contributing to cross-species virus transmission. Our findings highlight the microbial diversity in insectivores, indicating this order may serve as potential incubators for viruses capable of infecting mammals and spreading viruses of public health concern. Here, using a meta-analysis approach the authors compile a database of microbes hosted by insectivores, showing that a majority of them are viruses, that shrews and hedgehogs particularly contribute to the global virus sharing networks and that insectivores may spread of viruses of potential public health concern.

Wildlife face a number of extrinsic stressors, such as habitat loss, pathogen infections, and contaminant exposure, which can increase the energy needed to maintain optimal health and survival. These multiple extrinsic stressors can also occur simultaneously during intrinsically stressful life stages such as reproduction, migration, or hibernation. To fully understand how to support healthy wildlife populations, we must quantify physiological and immunological phenotypes across a variety of stressors. We pose a framework for conducting field studies to collect individual-level samples that can be used for measuring physiological and immunological phenotypes as well as the potentially stressful intrinsic and extrinsic drivers of those phenotypes. We suggest that collaborative efforts should then be made to create broader, spatially coordinated hypotheses for determining patterns of wildlife health under intrinsically stressful time periods and across extrinsically stressful landscapes. We provide an example and preliminary findings for this multi-stressor, collaborative, and spatially coordinated approach with an ongoing study of North American bat health. Quantifying direct and critical measures of wildlife health and identifying key intrinsic and extrinsic stressors that drive physiological and immunological phenotypes will provide broad targets for conservation strategies and where and when those strategies should be prioritized in the future.

Food availability determines where and how animals use space across a landscape and, therefore, affects the risk of encounters leading to zoonotic spillover. This relationship is evident in Australian flying foxes (Pteropus spp.; fruit bats), where acute food shortages precede clusters of Hendra virus spillovers. Using machine learning, we predicted months of food shortages from climatological and ecological covariates (1996–2022) in subtropical Australia. Overall accuracy in predicting months of low food availability on a test set from 2018 up to 2022 reached 93.33 and 92.59% based on climatological and bat-level features, respectively. Seasonality and the Oceanic El Niño Index were the most important environmental features, while the number of bats in rescue centres and their body weights were the most important bat-level features. These models support predictive signals up to nine months in advance, facilitating action to mitigate spillover risk.

Climate change threatens organismal health and ecological stability in myriad ways, the impacts of which are often difficult to characterize given their complex and interacting nature. To facilitate comparisons across taxa and ecosystems, we discuss the importance of a cross-scale approach to better characterize the ways in which climate change processes threaten wildlife immunity. Centering available examples from the vertebrate wildlife literature, we supplement with examples from the livestock literature to illustrate ways in which abiotic stress impacts immunity from molecular to community scales of biological organization. To highlight opportunities for cross-scale integration, we present a series of vignettes-drought, temperature extremes, storms and flooding, and habitat alterations and shifts-prior to discussing the complexities inherent to studying multiple interacting threats using heavy metal contamination as an example. Finally, we outline mechanisms by which collaborations across disciplines and sectors can continue strengthening capacity for studying the drivers of climate change-associated threats to wildlife immunology.