Flying-fox species density--a spatial risk factor for Hendra virus infection in horses in eastern Australia

Horse populations are severely underestimated in a region at risk of Hendra virus spillover

OBJECTIVE

To identify the size and distribution of the horse population in the Northern Rivers Region of NSW, including changes from 2007 to 2021, to better understand populations at risk of Hendra virus transmission.

METHODS

Census data from the 2007 Equine Influenza (EI) outbreak were compared with data collected annually by New South Wales Local Land Services (LLS) (2011-2021), and with field observations via road line transects (2021).

RESULTS

The horse populations reported to LLS in 2011 (3000 horses; 0.77 horses/km2) was 145% larger than that reported during the EI outbreak in 2007 (1225 horses; 0.32 horses/km2). This was inconsistent with the 6% increase in horses recorded from 2011 to 2020 within the longitudinal LLS dataset. Linear modelling suggested the true horse population of this region in 2007 was at least double that reported at the time. Distance sampling in 2021 estimated the region's population at 10,185 horses (3.89 per km2; 95% CI = 4854-21,372). Field sampling and modelling identified higher horse densities in rural cropland, with the percentage of conservation land, modified grazing, and rural residential land identified as the best predictors of horse densities.

CONCLUSIONS

Data from the 2007 EI outbreak no longer correlates to the current horse population in size or distribution and was likely not a true representation at the time. Current LLS data also likely underestimates horse populations. Ongoing efforts to further quantify and map horse populations in Australia are important for estimating and managing the risk of equine zoonoses.

Habitat loss for black flying foxes and implications for Hendra virus

Context

Environmental change impacts natural ecosystems and wildlife populations. In Australia, native forests have been heavily cleared and the local emergence of Hendra virus (HeV) has been linked to land-use change, winter habitat loss, and changing bat behavior.

Objectives

We quantified changes in landscape factors for black flying foxes (Pteropus alecto), a reservoir host of HeV, in sub-tropical Queensland, Australia from 2000-2020. We hypothesized that native winter habitat loss and native remnant forest loss were greatest in areas with the most human population growth.

Methods

We measured the spatiotemporal change in human population size and native 'remnant' woody vegetation extent. We assessed changes in the observed P. alecto population and native winter habitats in bioregions where P. alecto are observed roosting in winter. We assessed changes in the amount of remnant vegetation across bioregions and within 50 km foraging buffers around roosts.

Results

Human populations in these bioregions grew by 1.18 M people, mostly within 50 km foraging areas around roosts. Remnant forest extent decreased overall, but regrowth was observed when policy restricted vegetation clearing. Winter habitats were continuously lost across all spatial scales. Observed roost counts of P. alecto declined.

Conclusion

Native remnant forest loss and winter habitat loss were not directly linked to spatial human population growth. Rather, most remnant vegetation was cleared for indirect human use. We observed forest loss and regrowth in response to state land clearing policies. Expanded flying fox population surveys will help better understand how land-use change has impacted P. alecto distribution and Hendra virus spillover.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10980-023-01642-w.

Ecological conditions predict the intensity of Hendra virus excretion over space and time from bat reservoir hosts

The ecological conditions experienced by wildlife reservoirs affect infection dynamics and thus the distribution of pathogen excreted into the environment. This spatial and temporal distribution of shed pathogen has been hypothesised to shape risks of zoonotic spillover. However, few systems have data on both long-term ecological conditions and pathogen excretion to advance mechanistic understanding and test environmental drivers of spillover risk. We here analyse three years of Hendra virus data from nine Australian flying fox roosts with covariates derived from long-term studies of bat ecology. We show that the magnitude of winter pulses of viral excretion, previously considered idiosyncratic, are most pronounced after recent food shortages and in bat populations displaced to novel habitats. We further show that cumulative pathogen excretion over time is shaped by bat ecology and positively predicts spillover frequency. Our work emphasises the role of reservoir host ecology in shaping pathogen excretion and provides a new approach to estimate spillover risk.

Novel variant Hendra virus genotype 2 infection in a horse in the greater Newcastle region, New South Wales, Australia

In October 2021, the first contemporary detection of Hendra virus genotype 2 (HeV-g2) was made by veterinary priority disease investigation in a horse near Newcastle, New South Wales, Australia, as part of routine veterinary priority disease surveillance.

This discovery followed an update of Hendra virus diagnostic assays following retrospective identification of this variant from 2015 via sentinel emerging infectious disease research, enabling timely detection of this case. The sole infected horse was euthanized in moribund condition. As the southernmost recognised HeV spill-over detection to date, it extends the southern limit of known cases by approximately 95 km. The event occurred near a large urban centre, characterised by equine populations of diverse type, husbandry, and purpose, with low HeV vaccination rates.

Urgent multi-agency outbreak response involved risk assessment and monitoring of 11 exposed people and biosecurity management of at-risk animals. No human or additional animal cases were recognised.

This One Health investigation highlights need for research on risk perception and strategic engagement to support owners confronted with the death of companion animals and potential human exposure to a high consequence virus. The location and timing of this spill-over event diverging from that established for prototype HeV (HeV-g1), highlight benefit in proactive One Health surveillance and research activities that improve understanding of dynamic transmission and spill-over risks of both HeV genotypic lineages and related but divergent emerging pathogens.

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In October 2021 an equine case of Hendra virus genotype 2 (HeV-g2) was detected near Newcastle, Australia

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Detection was facilitated through recent adoption by animal health of an updated PCR assay able to detect HeV-g2

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The case occurred outside of the southern winter season typical for HeV and marks the southernmost equine detection to date

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This event highlights the expanded geographical risk of spillover from flying-foxes to horses that is presented by HeV-g2

A new Hendra virus genotype found in Australian flying foxes

BACKGROUND

Hendra virus (HeV) has caused lethal disease outbreaks in humans and horses in Australia. Flying foxes are the wildlife reservoir from which the virus was first isolated in 1996. Following a heat stress mortality event in Australian flying foxes in 2013, a novel HeV variant was discovered. This study describes the subsequent surveillance of Australian flying foxes for this novel virus over a nine year period using qRT-PCR testing of tissues from flying foxes submitted primarily for Australian bat lyssavirus diagnosis. Genome sequencing and characterisation of the novel HeV variant was also undertaken.

METHODS

Spleen and kidney samples harvested from flying fox carcasses were initially screened with two real-time qRT-PCR assays specific for the prototype HeV. Two additional qRT-PCR assays were developed specific for the HeV variant first detected in samples from a flying fox in 2013. Next-generation sequencing and virus isolation was attempted from selected samples to further characterise the new virus.

RESULTS

Since 2013, 98 flying foxes were tested and 11 were positive for the new HeV variant. No samples were positive for the original HeV. Ten of the positive samples were from grey-headed flying foxes (GHFF, Pteropus poliocephalus), however this species was over-represented in the opportunistic sampling (83% of bats tested were GHFF). The positive GHFF samples were collected from Victoria and South Australia and one positive Little red flying fox (LRFF, Pteropus scapulatus) was collected from Western Australia. Immunohistochemistry confirmed the presence of henipavirus antigen, associated with an inflammatory lesion in cardiac blood vessels of one GHFF. Positive samples were sequenced and the complete genome was obtained from three samples. When compared to published HeV genomes, there was 84% sequence identity at the nucleotide level. Based on phylogenetic analyses, the newly detected HeV belongs to the HeV species but occupies a distinct lineage. We have therefore designated this virus HeV genotype 2 (HeV-g2). Attempts to isolate virus from PCR positive samples have not been successful.

CONCLUSIONS

A novel HeV genotype (HeV-g2) has been identified in two flying fox species submitted from three states in Australia, indicating that the level of genetic diversity for HeV is broader than first recognised. Given its high genetic relatedness to HeV, HeV-g2 is a zoonotic pathogen.

Using Stochastic Modeling to Predict the Effect of Culling and Colony Dispersal of Bats on Zoonotic Viral Epidemics

Frequent outbreaks of emerging infectious diseases originating from wild animals have highlighted the necessity of managing wildlife populations to prevent zoonotic spillover, and the appropriate development of management protocols required attention on gaining a better understanding of viral dynamics in wild animal populations. In east Australia, there have been outbreaks of Hendra virus (HeV) infection in horses and humans following spillover from the virus's reservoir hosts, flying foxes (family Pteropodidae), and bat culling and colony dispersal have been proposed as appropriate management strategies. A key factor relating to flying fox population structure that influences HeV dynamics is that these bats form metapopulations, and consequently, to assess this factor, we designed an epidemic dynamics model of HeV transmission, focusing on bat metapopulation dynamics. Specifically, using flying fox movement data, we stochastically simulated models for a hypothetical metapopulation of flying foxes to examine the impact of metapopulation-related parameters, and subsequently simulated probable scenarios of culling and colony dispersal to estimate their effects on the probability of epidemic occurrence. Modeling of the hypothetical metapopulation revealed that a reduction in the number of large-sized colonies would lead to an increase in the probability of epidemic occurrence within the bat population, whereas the strong spatial coupling among colonies was found to dilute the effects of altering the number of colonies and the number of bats in each colony through culling or colony dispersal of bats on the probability that an epidemic within the bat population would occur. Culling and colony dispersal scenarios showed no significantly beneficial effect with respect to reducing the probability of an HeV epidemic occurring in flying foxes, and may indeed prove counterproductive. In conclusion, the modeling results indicate that bat culling and colony dispersal may not be an effective strategy to control HeV epidemics.

Hendra virus: Epidemiology dynamics in relation to climate change, diagnostic tests and control measures

Hendra virus (HeV) continues to pose a serious public health concern as spillover events occur sporadically. Terminally ill horses can exhibit a range of clinical signs including frothy nasal discharge, ataxia or forebrain signs. Early signs, if detected, can include depression, inappetence, colic or mild respiratory signs. All unvaccinated ill horses in areas where flying foxes exist, may potentially be infected with HeV, posing a significant risk to the veterinary community. Equivac® HeV vaccine has been fully registered in Australia since 2015 (and under an Australian Pesticides and Veterinary Medicines Authority special permit since 2012) for immunization of horses against HeV and is the most effective and direct solution to prevent disease transmission to horses and protect humans. No HeV vaccinated horse has tested positive for HeV infection. There is no registered vaccine to prevent, or therapeutics to treat, HeV infection in humans. Previous equine HeV outbreaks tended to cluster in winter overlapping with the foaling season (August to December), when veterinarians and horse owners have frequent close contact with horses and their bodily fluids, increasing the chance of zoonotic disease transmission. The most southerly case was detected in 2019 in the Upper Hunter region in New South Wales, which is Australia's Thoroughbred horse breeding capital. Future spillover events are predicted to move further south and inland in Queensland and New South Wales, aligning with the moving distribution of the main reservoir hosts. Here we (1) review HeV epidemiology and climate change predicted infection dynamics, (2) present a biosecurity protocol for veterinary clinics and hospitals to adopt, and (3) describe diagnostic tests currently available and those under development. Major knowledge and research gaps have been identified, including evaluation of vaccine efficacy in foals to assess current vaccination protocol recommendations.

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Hendra virus (HeV) continues to pose a serious public health threat to the equine and veterinary industries.

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HeV cases are likely to expand further south and inland due to climate change.

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Strict HeV specific biosecurity protocols should be implemented to protect veterinary staff.

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Research into HeV vaccination protocols in foals is required for evidence-based recommendations.

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Point-of-care and other diagnostic tests for HeV are currently under development.

Relationship between Land Use/Land-Use Change and Human Health in Australia: A Scoping Study

We undertook a scoping study to map the relevant evidence, summarise the findings, and to help identify gaps in the knowledge base on the relationship between land use/land-use change and human health in Australia. Our systematic search of the scientific literature for relevant articles up to August 2020 identified 37 articles. All 37 articles meeting our inclusion criteria were published after 2003. Zoonotic or vector-borne disease constituted the most common health outcome type studied. Agriculture/grazing was the land use/land-use change type most frequently represented in the literature, followed by coal seam gas extraction and open cut coal mining. The relationship between land use/land use change and human health in Australia, is not conclusive from the existing evidence. This is because of (1) a lack of comprehensive coverage of the topic, (2) a lack of coverage of the geography, (3) a lack of coverage of study types, and (4) conflicting results in the research already undertaken. If we are to protect human health and the ecosystems which support life, more high-quality, specific, end-user driven research is needed to support land management decisions in Australia. Until the health effects of further land use change are better known and understood, caution ought to be practiced in land management and land conversion.

Spatiotemporal analysis and hotspots detection of COVID-19 using geographic information system (March and April, 2020)

Understanding the spatial distribution of coronavirus disease 2019 (COVID-19) cases can provide valuable information to anticipate the world outbreaks and in turn improve public health policies. In this study, the cumulative incidence rate (CIR) and cumulative mortality rate (CMR) of all countries affected by the new corona outbreak were calculated at the end of March and April, 2020. Prior to the implementation of hot spot analysis, the spatial autocorrelation results of CIR were obtained. Hot spot analysis and Anselin Local Moran's I indices were then applied to accurately locate high and low-risk clusters of COVID-19 globally. San Marino and Italy revealed the highest CMR by the end of March, though Belgium took the place of Italy as of 30th April. At the end of the research period (by 30th April), the CIR showed obvious spatial clustering. Accordingly, southern, northern and western Europe were detected in the high-high clusters demonstrating an increased risk of COVID-19 in these regions and also the surrounding areas. Countries of northern Africa exhibited a clustering of hot spots, with a confidence level above 95%, even though these areas assigned low CIR values. The hot spots accounted for nearly 70% of CIR. Furthermore, analysis of clusters and outliers demonstrated that these countries are situated in the low-high outlier pattern. Most of the surveyed countries that exhibited clustering of high values (hot spot) with a confidence level of 99% (by 31st March) and 95% (by 30th April) were dedicated higher CIR values. In conclusion, hot spot analysis coupled with Anselin local Moran's I provides a scrupulous and objective approach to determine the locations of statistically significant clusters of COVID-19 cases shedding light on the high-risk districts.

Extreme mobility of the world's largest flying mammals creates key challenges for management and conservation

BACKGROUND

Effective conservation management of highly mobile species depends upon detailed knowledge of movements of individuals across their range; yet, data are rarely available at appropriate spatiotemporal scales. Flying-foxes (Pteropus spp.) are large bats that forage by night on floral resources and rest by day in arboreal roosts that may contain colonies of many thousands of individuals. They are the largest mammals capable of powered flight, and are highly mobile, which makes them key seed and pollen dispersers in forest ecosystems. However, their mobility also facilitates transmission of zoonotic diseases and brings them in conflict with humans, and so they require a precarious balancing of conservation and management concerns throughout their Old World range. Here, we analyze the Australia-wide movements of 201 satellite-tracked individuals, providing unprecedented detail on the inter-roost movements of three flying-fox species: Pteropus alecto, P. poliocephalus, and P. scapulatus across jurisdictions over up to 5 years.

RESULTS

Individuals were estimated to travel long distances annually among a network of 755 roosts (P. alecto, 1427-1887 km; P. poliocephalus, 2268-2564 km; and P. scapulatus, 3782-6073 km), but with little uniformity among their directions of travel. This indicates that flying-fox populations are composed of extremely mobile individuals that move nomadically and at species-specific rates. Individuals of all three species exhibited very low fidelity to roosts locally, resulting in very high estimated daily colony turnover rates (P. alecto, 11.9 ± 1.3%; P. poliocephalus, 17.5 ± 1.3%; and P. scapulatus, 36.4 ± 6.5%). This indicates that flying-fox roosts form nodes in a vast continental network of highly dynamic "staging posts" through which extremely mobile individuals travel far and wide across their species ranges.

CONCLUSIONS

The extreme inter-roost mobility reported here demonstrates the extent of the ecological linkages that nomadic flying-foxes provide across Australia's contemporary fragmented landscape, with profound implications for the ecosystem services and zoonotic dynamics of flying-fox populations. In addition, the extreme mobility means that impacts from local management actions can readily reverberate across jurisdictions throughout the species ranges; therefore, local management actions need to be assessed with reference to actions elsewhere and hence require national coordination. These findings underscore the need for sound understanding of animal movement dynamics to support evidence-based, transboundary conservation and management policy, tailored to the unique movement ecologies of species.

An Ecosystems Perspective on Virus Evolution and Emergence

Understanding the emergence of pathogenic viruses has dominated studies of virus evolution. However, new metagenomic studies imply that relatively few of an immense number of viruses may lead to overt disease. This suggests a change in emphasis, from viruses as habitual pathogens to integral components of ecosystems. Here we show how viruses alter interactions between host individuals, populations, and ecosystems, impacting ecosystem health, resilience, and function, and how host ecology in turn impacts viral abundance and diversity. Moving to an ecosystems perspective will put virus evolution and disease emergence in its true context, and enhance our understanding of ecological processes.

Global Epidemiology of Bat Coronaviruses

Bats are a unique group of mammals of the order Chiroptera. They are highly diversified and are the group of mammals with the second largest number of species. Such highly diversified cell types and receptors facilitate them to be potential hosts of a large variety of viruses. Bats are the only group of mammals capable of sustained flight, which enables them to disseminate the viruses they harbor and enhance the chance of interspecies transmission. This article aims at reviewing the various aspects of the global epidemiology of bat coronaviruses (CoVs). Before the SARS epidemic, bats were not known to be hosts for CoVs. In the last 15 years, bats have been found to be hosts of >30 CoVs with complete genomes sequenced, and many more if those without genome sequences are included. Among the four CoV genera, only alphaCoVs and betaCoVs have been found in bats. As a whole, both alphaCoVs and betaCoVs have been detected from bats in Asia, Europe, Africa, North and South America and Australasia; but alphaCoVs seem to be more widespread than betaCoVs, and their detection rate is also higher. For betaCoVs, only those from subgenera Sarbecovirus, Merbecovirus, Nobecovirus and Hibecovirus have been detected in bats. Most notably, horseshoe bats are the reservoir of SARS-CoV, and several betaCoVs from subgenus Merbecovirus are closely related to MERS-CoV. In addition to the interactions among various bat species themselves, bat⁻animal and bat⁻human interactions, such as the presence of live bats in wildlife wet markets and restaurants in Southern China, are important for interspecies transmission of CoVs and may lead to devastating global outbreaks.

Optimal foraging in seasonal environments: implications for residency of Australian flying foxes in food-subsidized urban landscapes

Bats provide important ecosystem services such as pollination of native forests; they are also a source of zoonotic pathogens for humans and domestic animals. Human-induced changes to native habitats may have created more opportunities for bats to reside in urban settings, thus decreasing pollination services to native forests and increasing opportunities for zoonotic transmission. In Australia, fruit bats (Pteropus spp. flying foxes) are increasingly inhabiting urban areas where they feed on anthropogenic food sources with nutritional characteristics and phenology that differ from native habitats. We use optimal foraging theory to investigate the relationship between bat residence time in a patch, the time it takes to search for a new patch (simulating loss of native habitat) and seasonal resource production. We show that it can be beneficial to reside in a patch, even when food productivity is low, as long as foraging intensity is low and the expected searching time is high. A small increase in the expected patch searching time greatly increases the residence time, suggesting nonlinear associations between patch residence and loss of seasonal native resources. We also found that sudden increases in resource consumption due to an influx of new bats has complex effects on patch departure times that again depend on expected searching times and seasonality. Our results suggest that the increased use of urban landscapes by bats may be a response to new spatial and temporal configurations of foraging opportunities. Given that bats are reservoir hosts of zoonotic diseases, our results provide a framework to study the effects of foraging ecology on disease dynamics.One contribution of 14 to a theme isssue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'.

Time of year, age class and body condition predict Hendra virus infection in Australian black flying foxes (Pteropus alecto)

Hendra virus (HeV) continues to cause fatal infection in horses and threaten infection in close-contact humans in eastern Australia. Species of Pteropus bats (flying-foxes) are the natural reservoir of the virus. We caught and sampled flying-foxes from a multispecies roost in southeast Queensland, Australia on eight occasions between June 2013 and June 2014. The effects of sample date, species, sex, age class, body condition score (BCS), pregnancy and lactation on HeV antibody prevalence, log-transformed median fluorescent intensity (lnMFI) values and HeV RNA status were assessed using unbalanced generalised linear models. A total of 1968 flying-foxes were sampled, comprising 1012 Pteropus alecto, 742 P. poliocephalus and 214 P. scapulatus. Sample date, species and age class were each statistically associated with HeV RNA status, antibody status and lnMFI values; BCS was statistically associated with HeV RNA status and antibody status. The findings support immunologically naïve sub-adult P. alecto playing an important role in maintaining HeV infection at a population level. The biological significance of the association between BCS and HeV RNA status, and BCS and HeV antibody status, is less clear and warrants further investigation. Contrary to previous studies, we found no direct association between HeV infection and pregnancy or lactation. The findings in P. poliocephalus suggest that HeV exposure in this species may not result in systemic infection and virus excretion, or alternatively, may reflect assay cross-reactivity with another (unidentified) henipavirus.

Hendra Virus Spillover is a Bimodal System Driven by Climatic Factors

Understanding environmental factors driving spatiotemporal patterns of disease can improve risk mitigation strategies. Hendra virus (HeV), discovered in Australia in 1994, spills over from bats (Pteropus sp.) to horses and thence to humans. Below latitude - 22°, almost all spillover events to horses occur during winter, and above this latitude spillover is aseasonal. We generated a statistical model of environmental drivers of HeV spillover per month. The model reproduced the spatiotemporal pattern of spillover risk between 1994 and 2015. The model was generated with an ensemble of methods for presence-absence data (boosted regression trees, random forests and logistic regression). Presences were the locations of horse cases, and absences per spatial unit (2.7 × 2.7 km pixels without spillover) were sampled with the horse census of Queensland and New South Wales. The most influential factors indicate that spillover is associated with both cold-dry and wet conditions. Bimodal responses to several variables suggest spillover involves two systems: one above and one below a latitudinal area close to - 22°. Northern spillovers are associated with cold-dry and wet conditions, and southern with cold-dry conditions. Biologically, these patterns could be driven by immune or behavioural changes in response to food shortage in bats and horse husbandry. Future research should look for differences in these traits between seasons in the two latitudinal regions. Based on the predicted risk patterns by latitude, we recommend enhanced preventive management for horses from March to November below latitude 22° south.

Climate Change Could Increase the Geographic Extent of Hendra Virus Spillover Risk

Disease risk mapping is important for predicting and mitigating impacts of bat-borne viruses, including Hendra virus (Paramyxoviridae:Henipavirus), that can spillover to domestic animals and thence to humans. We produced two models to estimate areas at potential risk of HeV spillover explained by the climatic suitability for its flying fox reservoir hosts, Pteropus alecto and P. conspicillatus. We included additional climatic variables that might affect spillover risk through other biological processes (such as bat or horse behaviour, plant phenology and bat foraging habitat). Models were fit with a Poisson point process model and a log-Gaussian Cox process. In response to climate change, risk expanded southwards due to an expansion of P. alecto suitable habitat, which increased the number of horses at risk by 175-260% (110,000-165,000). In the northern limits of the current distribution, spillover risk was highly uncertain because of model extrapolation to novel climatic conditions. The extent of areas at risk of spillover from P. conspicillatus was predicted shrink. Due to a likely expansion of P. alecto into these areas, it could replace P. conspicillatus as the main HeV reservoir. We recommend: (1) HeV monitoring in bats, (2) enhancing HeV prevention in horses in areas predicted to be at risk, (3) investigate and develop mitigation strategies for areas that could experience reservoir host replacements.

Changing resource landscapes and spillover of henipaviruses

Old World fruit bats (Chiroptera: Pteropodidae) provide critical pollination and seed dispersal services to forest ecosystems across Africa, Asia, and Australia. In each of these regions, pteropodids have been identified as natural reservoir hosts for henipaviruses. The genus Henipavirus includes Hendra virus and Nipah virus, which regularly spill over from bats to domestic animals and humans in Australia and Asia, and a suite of largely uncharacterized African henipaviruses. Rapid change in fruit bat habitat and associated shifts in their ecology and behavior are well documented, with evidence suggesting that altered diet, roosting habitat, and movement behaviors are increasing spillover risk of bat-borne viruses. We review the ways that changing resource landscapes affect the processes that culminate in cross-species transmission of henipaviruses, from reservoir host density and distribution to within-host immunity and recipient host exposure. We evaluate existing evidence and highlight gaps in knowledge that are limiting our understanding of the ecological drivers of henipavirus spillover. When considering spillover in the context of land-use change, we emphasize that it is especially important to disentangle the effects of habitat loss and resource provisioning on these processes, and to jointly consider changes in resource abundance, quality, and composition.

Environmental drivers of spatiotemporal foraging intensity in fruit bats and implications for Hendra virus ecology

In the Australian subtropics, flying-foxes (family Pteropididae) play a fundamental ecological role as forest pollinators. Flying-foxes are also reservoirs of the fatal zoonosis, Hendra virus. Understanding flying fox foraging ecology, particularly in agricultural areas during winter, is critical to determine their role in transmitting Hendra virus to horses and humans. We developed a spatiotemporal model of flying-fox foraging intensity based on foraging patterns of 37 grey-headed flying-foxes (Pteropus poliocephalus) using GPS tracking devices and boosted regression trees. We validated the model with independent population counts and summarized temporal patterns in terms of spatial resource concentration. We found that spatial resource concentration was highest in late-summer and lowest in winter, with lowest values in winter 2011, the same year an unprecedented cluster of spillover events occurred in Queensland and New South Wales. Spatial resource concentration was positively correlated with El Niño Southern Oscillation at 3–8 month time lags. Based on shared foraging traits with the primary reservoir of Hendra virus (Pteropus alecto), we used our results to develop hypotheses on how regional climatic history, eucalypt phenology, and foraging behaviour may contribute to the predominance of winter spillovers, and how these phenomena connote foraging habitat conservation as a public health intervention.

Unmasking the complexity of species identification in Australasian flying-foxes

Pteropus (flying-foxes) are a speciose group of non-echolocating large bats, with five extant Australian species and 24 additional species distributed amongst the Pacific Islands. In 2015, an injured flying-fox with unusual facial markings was found in Sydney, Australia, following severe and widespread storms. Based on an initial assessment, the individual belonged to Pteropus but could not be readily identified to species. As a consequence, four hypotheses for its identification/origin were posited: the specimen represented (1) an undescribed Australian species; or (2) a morphological variant of a recognised Australian species; or (3) a hybrid individual; or (4) a vagrant from the nearby Southwest Pacific Islands. We used a combination of morphological and both mitochondrial- and nuclear DNA-based identification methods to assess these hypotheses. Based on the results, we propose that this morphologically unique Pteropus most likely represents an unusual P. alecto (black flying-fox) potentially resulting from introgression from another Pteropus species. Unexpectedly, this individual, and the addition of reference sequence data from newly vouchered specimens, revealed a previously unreported P. alecto mitochondrial DNA lineage. This lineage was distinct from currently available haplotypes. It also suggests long-term hybridisation commonly occurs between P. alecto and P. conspicillatus (spectacled flying-fox). This highlights the importance of extensive reference data, and the inclusion of multiple vouchered specimens for each species to encompass both intraspecific and interspecific variation to provide accurate and robust species identification. Moreover, our additional reference data further demonstrates the complexity of Pteropus species relationships, including hybridisation, and potential intraspecific biogeographical structure that may impact on their management and conservation.

What's the risk? Identifying potential human pathogens within grey-headed flying foxes faeces

Pteropus poliocephalus (grey-headed flying foxes) are recognised vectors for a range of potentially fatal human pathogens. However, to date research has primarily focused on viral disease carriage, overlooking bacterial pathogens, which also represent a significant human disease risk. The current study applied 16S rRNA amplicon sequencing, community analysis and a multi-tiered database OTU picking approach to identify faecal-derived zoonotic bacteria within two colonies of P. poliocephalus from Victoria, Australia. Our data show that sequences associated with Enterobacteriaceae (62.8% ± 24.7%), Pasteurellaceae (19.9% ± 25.7%) and Moraxellaceae (9.4% ± 11.8%) dominate flying fox faeces. Further colony specific differences in bacterial faecal colonisation patterns were also identified. In total, 34 potential pathogens, representing 15 genera, were identified. However, species level definition was only possible for Clostridium perfringens, which likely represents a low infectious risk due to the low proportion observed within the faeces and high infectious dose required for transmission. In contrast, sequences associated with other pathogenic species clusters such as Haemophilus haemolyticus-H. influenzae and Salmonella bongori-S. enterica, were present at high proportions in the faeces, and due to their relatively low infectious doses and modes of transmissions, represent a greater potential human disease risk. These analyses of the microbial community composition of Pteropus poliocephalus have significantly advanced our understanding of the potential bacterial disease risk associated with flying foxes and should direct future epidemiological and quantitative microbial risk assessments to further define the health risks presented by these animals.

Conditions affecting the timing and magnitude of Hendra virus shedding across pteropodid bat populations in Australia

Understanding infection dynamics in animal hosts is fundamental to managing spillover and emergence of zoonotic infections. Hendra virus is endemic in Australian pteropodid bat populations and can be lethal to horses and humans. However, we know little about the factors driving Hendra virus prevalence in resevoir bat populations, making spillover difficult to predict. We use Hendra virus prevalence data collected from 13 000 pooled bat urine samples across space and time to determine if pulses of prevalence are periodic and synchronized across sites. We also test whether site-specific precipitation and temperature affect the amplitude of the largest annual prevalence pulses. We found little evidence for a periodic signal in Hendra virus prevalence. Although the largest amplitude pulses tended to occur over winter, pulses could also occur in other seasons. We found that Hendra virus prevalence was weakly synchronized across sites over short distances, suggesting that prevalence is driven by local-scale effects. Finally, we found that drier conditions in previous seasons and the abundance of Pteropus alecto were positively correlated with the peak annual values of Hendra virus prevalence. Our results suggest that in addition to seasonal effects, bat density and local climatic conditions interact to drive Hendra virus infection dynamics.

The impact of human population pressure on flying fox niches and the potential consequences for Hendra virus spillover

Hendra virus (HeV) is an emerging pathogen of concern in Australia given its ability to spillover from its reservoir host, pteropid bats, to horses and further on to humans, and the severe clinical presentation typical in these latter incidental hosts. Specific human pressures over recent decades, such as expanding human populations, urbanization, and forest fragmentation, may have altered the ecological niche of Pteropus species acting as natural HeV reservoirs and may modulate spillover risk. This study explored the influence of inter-decadal net human local migration between 1970 and 2000 on changes in the habitat suitability to P. alecto and P. conspicillatus from 1980 to 2015 in eastern Australia. These ecological niches were modeled using boosted regression trees and subsequently fitted, along with additional landscape factors, to HeV spillovers to explore the spatial dependency of this zoonosis. The spatial model showed that the ecological niche of these two flying fox species, the human footprint, and proximity to woody savanna were each strongly associated with HeV spillover and together explained most of the spatial dependency exhibited by this zoonosis. These findings reinforce the potential for anthropogenic pressures to shape the landscape epidemiology of HeV spillover.

Physiological stress and Hendra virus in flying-foxes (Pteropus spp.), Australia

Pteropid bats (flying-foxes) are the natural reservoir of Hendra virus, an emergent paramyxovirus responsible for fatal infection in horses and humans in Australia. Pteropus alecto (the Black flying-fox) and the paraphyletic P. conspicillatus (the Spectacled flying-fox) appear to be the primary reservoir hosts. Previous studies have suggested that physiological and ecological factors may underpin infection dynamics in flying-foxes, and subsequent spillover to horses and in turn humans. We sought to examine temporal trends in urinary cortisol concentration in wild Australian flying-fox populations, to elucidate the putative relationship between Hendra virus infection and physiological stress. Pooled and individual urine samples were non-invasively collected from under roosting flying-foxes at two latitudinally disparate regions in the eastern Australian state of Queensland. Hendra virus detection, and (in individual urine samples) sex and species determination were PCR-based. Urinary cortisol measurement used a validated enzyme immunoassay. We found no direct correlation between increased urinary cortisol and Hendra virus excretion, but our findings do suggest a biologically plausible association between low winter temperatures and elevated cortisol levels in P. alecto in the lower latitude Southeast Queensland roosts. We hypothesize an indirect association between low winter temperatures and increased Hendra virus infection and excretion, mediated by the physiological cost of thermoregulation. Our findings and our approach are directly relevant to elaboration of the disease ecology of Nipah virus and other emerging henipaviruses in bats. More broadly, they inform investigation of emerging disease infection dynamics across the wildlife/livestock/human interface.

Microclimates Might Limit Indirect Spillover of the Bat Borne Zoonotic Hendra Virus

Infectious diseases are transmitted when susceptible hosts are exposed to pathogen particles that can replicate within them. Among factors that limit transmission, the environment is particularly important for indirectly transmitted parasites. To try and assess a pathogens' ability to be transmitted through the environment and mitigate risk, we need to quantify its decay where transmission occurs in space such as the microclimate harbouring the pathogen. Hendra virus, a Henipavirus from Australian Pteropid bats, spills-over to horses and humans, causing high mortality. While a vaccine is available, its limited uptake has reduced opportunities for adequate risk management to humans, hence the need to develop synergistic preventive measures, like disrupting its transmission pathways. Transmission likely occurs shortly after virus excretion in paddocks; however, no survival estimates to date have used real environmental conditions. Here, we recorded microclimate conditions and fitted models that predict temperatures and potential evaporation, which we used to simulate virus survival with a temperature-survival model and modification based on evaporation. Predicted survival was lower than previously estimated and likely to be even lower according to potential evaporation. Our results indicate that transmission should occur shortly after the virus is excreted, in a relatively direct way. When potential evaporation is low, and survival is more similar to temperature dependent estimates, transmission might be indirect because the virus can wait several hours until contact is made. We recommend restricting horses' access to trees during night time and reducing grass under trees to reduce virus survival.

"Why won't they just vaccinate?" Horse owner risk perception and uptake of the Hendra virus vaccine

BACKGROUND

Hendra virus is a paramyxovirus that causes periodic serious disease and fatalities in horses and humans in Australia first identified in 1994. Pteropid bats (commonly known as flying-foxes) are the natural host of the virus, and the putative route of infection in horses is by ingestion or inhalation of material contaminated by flying-fox urine or other bodily fluids. Humans become infected after close contact with infected horses. Horse owners in Australia are encouraged to vaccinate their horses against Hendra virus to reduce the risk of Hendra virus infection, and to prevent potential transmission to humans. After the vaccine was released in 2012, uptake by horse owners was slow, with some estimated 11-17% of horses in Australia vaccinated. This study was commissioned to examine barriers to vaccine uptake and potential drivers to future adoption of vaccination by horse owners.

METHODS

This study examined qualitative comments from respondents to an on-line survey, reporting reasons for not vaccinating their horses. The study also investigated scenarios in which respondents felt they might consider vaccinating their horses.

RESULTS

Self-reported barriers to uptake of the Hendra virus vaccine by horse owners (N = 150) included concerns about vaccine safety, cost, and effectiveness. Reduction in vaccination costs and perception of immediacy of Hendra virus risk were reported as being likely to change future behaviour. However, the data also indicated that horse owners generally would not reconsider vaccinating their horses if advised by their veterinarian.

CONCLUSION

While changes to vaccine costs and the availability data supporting vaccine safety and efficacy may encourage more horse owners to vaccinate, this study highlights the importance of protecting the relationship between veterinarians and horse owners within the risk management strategies around Hendra virus. Interactions and trust between veterinarians and animal owners has important implications for management of and communication around Hendra virus and other zoonotic disease outbreaks.

"We've learned to live with it"-A qualitative study of Australian horse owners' attitudes, perceptions and practices in response to Hendra virus

Hendra virus causes sporadic zoonotic disease in Australia following spill over from flying foxes to horses and from horses to people. Prevention and risk mitigation strategies such as vaccination of horses or biosecurity and property management measures are widely publicised, but hinge on initiative and action taken by horse owners as they mediate management, care and treatment of their animals. Hence, underlying beliefs, values and attitudes of horse owners influence their uptake of recommended risk mitigation measures. We used a qualitative approach to investigate attitudes, perceptions and self-reported practices of horse owners in response to Hendra virus to gain a deeper understanding of their decision-making around prevention measures. Data presented here derive from a series of in-depth interviews with 27 horse owners from Hendra virus 'hot spot' areas in New South Wales and Queensland. Interviews explored previous experience, perceptions and resulting behaviour as well as communication around Hendra virus. All interviews were recorded, transcribed verbatim and analysed in NVivo using thematic analysis. Analysis revealed four major themes: perception of Hendra virus as a risk and factors influencing this perception, Hendra virus risk mitigation strategies implemented by horse owners, perceived motivators and barriers of these strategies, and interaction of perceived risk, motivators and barriers in the decision-making process. Although Hendra virus disease was perceived as a serious threat to the health of horses and humans, individual risk perception diverged among horse owners. Perceived severity, likelihood and unpredictability as well as awareness and knowledge of Hendra virus, trust in information obtained and information pathways, demographic characteristics and personal experience were the main factors influencing Hendra virus risk perceptions. Other key determinants of horse owners' decision-making process were attitudes towards Hendra virus risk mitigation measures as well as perceived motivators and barriers thereof. Horse owners' awareness of the necessity to consider individual Hendra virus risk and adequate risk management strategies was described as a learning process, which changed over time. However, different perceptions of risk, barriers and motivators in combination with a weighing up of advantages and disadvantages resulted in different behaviours. These findings demonstrate the multifactorial determinants of cognitive mediating processes and facilitate a better understanding of horse owners' perspectives on preventive horse health measures. Furthermore, they provide valuable feedback to industry and government stakeholders on how to improve effective risk communication and encourage uptake of recommended risk mitigation measures.

No Evidence of Hendra Virus Infection in the Australian Flying-fox Ectoparasite Genus Cyclopodia

Hendra virus (HeV) causes potentially fatal respiratory and/or neurological disease in both horses and humans. Although Australian flying-foxes of the genus Pteropus have been identified as reservoir hosts, the precise mechanism of HeV transmission has yet to be elucidated. To date, there has been limited investigation into the role of haematophagous insects as vectors of HeV. This mode of transmission is particularly relevant because Australian flying-foxes host the bat-specific blood-feeding ectoparasites of the genus Cyclopodia (Diptera: Nycteribiidae), also known as bat flies. Using molecular detection methods, we screened for HeV RNA in 183 bat flies collected from flying-foxes inhabiting a roost in Boonah, Queensland, Australia. It was subsequently demonstrated that during the study period, Pteropus alecto in this roost had a HeV RNA prevalence between 2 and 15% (95% CI [1, 6] to [8, 26], respectively). We found no evidence of HeV in any bat flies tested, including 10 bat flies collected from P. alecto in which we detected HeV RNA. Our negative findings are consistent with previous findings and provide additional evidence that bat flies do not play a primary role in HeV transmission.

Models of Eucalypt phenology predict bat population flux

Fruit bats (Pteropodidae) have received increased attention after the recent emergence of notable viral pathogens of bat origin. Their vagility hinders data collection on abundance and distribution, which constrains modeling efforts and our understanding of bat ecology, viral dynamics, and spillover. We addressed this knowledge gap with models and data on the occurrence and abundance of nectarivorous fruit bat populations at 3 day roosts in southeast Queensland. We used environmental drivers of nectar production as predictors and explored relationships between bat abundance and virus spillover. Specifically, we developed several novel modeling tools motivated by complexities of fruit bat foraging ecology, including: (1) a dataset of spatial variables comprising Eucalypt-focused vegetation indices, cumulative precipitation, and temperature anomaly; (2) an algorithm that associated bat population response with spatial covariates in a spatially and temporally relevant way given our current understanding of bat foraging behavior; and (3) a thorough statistical learning approach to finding optimal covariate combinations. We identified covariates that classify fruit bat occupancy at each of our three study roosts with 86-93% accuracy. Negative binomial models explained 43-53% of the variation in observed abundance across roosts. Our models suggest that spatiotemporal heterogeneity in Eucalypt-based food resources could drive at least 50% of bat population behavior at the landscape scale. We found that 13 spillover events were observed within the foraging range of our study roosts, and they occurred during times when models predicted low population abundance. Our results suggest that, in southeast Queensland, spillover may not be driven by large aggregations of fruit bats attracted by nectar-based resources, but rather by behavior of smaller resident subpopulations. Our models and data integrated remote sensing and statistical learning to make inferences on bat ecology and disease dynamics. This work provides a foundation for further studies on landscape-scale population movement and spatiotemporal disease dynamics.

Climatic suitability influences species specific abundance patterns of Australian flying foxes and risk of Hendra virus spillover

Hendra virus is a paramyxovirus of Australian flying fox bats. It was first detected in August 1994, after the death of 20 horses and one human. Since then it has occurred regularly within a portion of the geographical distribution of all Australian flying fox (fruit bat) species. There is, however, little understanding about which species are most likely responsible for spillover, or why spillover does not occur in other areas occupied by reservoir and spillover hosts. Using ecological niche models of the four flying fox species we were able to identify which species are most likely linked to spillover events using the concept of distance to the niche centroid of each species. With this novel approach we found that 20 out of 27 events occur disproportionately closer to the niche centroid of two species (P. alecto and P. conspicillatus). With linear regressions we found a negative relationship between distance to the niche centroid and abundance of these two species. Thus, we suggest that the bioclimatic niche of these two species is likely driving the spatial pattern of spillover of Hendra virus into horses and ultimately humans.

Hendra Virus Infection Dynamics in the Grey-Headed Flying Fox (Pteropus poliocephalus) at the Southern-Most Extent of Its Range: Further Evidence This Species Does Not Readily Transmit the Virus to Horses

Hendra virus (HeV) is an important emergent virus in Australia known to infect horses and humans in certain regions of the east coast. Whilst pteropid bats (“flying foxes”) are considered the natural reservoir of HeV, which of the four mainland species is the principal reservoir has been a source of ongoing debate, particularly as shared roosting is common. To help resolve this, we sampled a colony consisting of just one of these species, the grey-headed flying fox, (Pteropus poliocephalus), at the southernmost extent of its range. Using the pooled urine sampling technique at approximately weekly intervals over a two year period, we determined the prevalence of HeV and related paramyxoviruses using a novel multiplex (Luminex) platform. Whilst all the pooled urine samples were negative for HeV nucleic acid, we successfully identified four other paramyxoviruses, including Cedar virus; a henipavirus closely related to HeV. Collection of serum from individually caught bats from the colony showed that antibodies to HeV, as estimated by a serological Luminex assay, were present in between 14.6% and 44.5% of animals. The wide range of the estimate reflects uncertainties in interpreting intermediate results. Interpreting the study in the context of HeV studies from states to the north, we add support for an arising consensus that it is the black flying fox and not the grey-headed flying fox that is the principal source of HeV in spillover events to horses.

Landscape Utilisation, Animal Behaviour and Hendra Virus Risk

Hendra virus causes sporadic fatal disease in horses and humans in eastern Australia. Pteropid bats (flying-foxes) are the natural host of the virus. The mode of flying-fox to horse transmission remains unclear, but oro-nasal contact with flying-fox urine, faeces or saliva is the most plausible. We used GPS data logger technology to explore the landscape utilisation of black flying-foxes and horses to gain new insight into equine exposure risk. Flying-fox foraging was repetitious, with individuals returning night after night to the same location. There was a preference for fragmented arboreal landscape and non-native plant species, resulting in increased flying-fox activity around rural infrastructure. Our preliminary equine data logger study identified significant variation between diurnal and nocturnal grazing behaviour that, combined with the observed flying-fox foraging behaviour, could contribute to Hendra virus exposure risk. While we found no significant risk-exposing difference in individual horse movement behaviour in this study, the prospect warrants further investigation, as does the broader role of animal behaviour and landscape utilisation on the transmission dynamics of Hendra virus.

Temporal Variation in Physiological Biomarkers in Black Flying-Foxes (Pteropus alecto), Australia

Bats of the genus Pteropus (Pteropodidae) are recognised as the natural host of multiple emerging pathogenic viruses of animal and human health significance, including henipaviruses, lyssaviruses and ebolaviruses. Some studies have suggested that physiological and ecological factors may be associated with Hendra virus infection in flying-foxes in Australia; however, it is essential to understand the normal range and seasonal variability of physiological biomarkers before seeking physiological associations with infection status. We aimed to measure a suite of physiological biomarkers in P. alecto over time to identify any seasonal fluctuations and to examine possible associations with life-cycle and environmental stressors. We sampled 839 adult P. alecto in the Australian state of Queensland over a 12-month period. The adjusted population means of every assessed hematologic and biochemical parameter were within the reported reference range on every sampling occasion. However, within this range, we identified significant temporal variation in these parameters, in urinary parameters and body condition, which primarily reflected the normal annual life cycle. We found no evident effect of remarkable physiological demands or nutritional stress, and no indication of clinical disease driving any parameter values outside the normal species reference range. Our findings identify underlying temporal physiological changes at the population level that inform epidemiological studies and assessment of putative physiological risk factors driving Hendra virus infection in P. alecto. More broadly, the findings add to the knowledge of Pteropus populations in terms of their relative resistance and resilience to emerging infectious disease.

The Role of Bats as Reservoir Hosts of Emerging Neuroviruses

Recent studies have clearly shown that bats are the reservoir hosts of a wide diversity of novel viruses with representatives from most of the known animal virus families. In many respects bats make ideal reservoir hosts for viruses: they are the only mammals that fly, thus assisting in virus dispersal; they roost in large numbers, thus aiding transmission cycles; some bats hibernate over winter, thus providing a mechanism for viruses to persist between seasons; and genetic factors may play a role in the ability of bats to host viruses without resulting in clinical disease. Within the broad diversity of viruses found in bats are some important neurological pathogens, including rabies and other lyssaviruses, and Hendra and Nipah viruses, two recently described viruses that have been placed in a new genus, Henipaviruses in the family Paramyxoviridae. In addition, bats can also act as alternative hosts for the flaviviruses Japanese encephalitis and St Louis encephalitis viruses, two important mosquito-borne encephalitogenic viruses, and bats can assist in the dispersal and over-wintering of these viruses. Bats are also the reservoir hosts of progenitors of SARS and MERS coronaviruses, although other animals act as spillover hosts. This chapter presents the physiological and ecological factors affecting the ability of bats to act as reservoirs of neurotropic viruses, and describes the major transmission cycles leading to human infection.

Spatiotemporal Aspects of Hendra Virus Infection in Pteropid Bats (Flying-Foxes) in Eastern Australia

Hendra virus (HeV) causes highly lethal disease in horses and humans in the eastern Australian states of Queensland (QLD) and New South Wales (NSW), with multiple equine cases now reported on an annual basis. Infection and excretion dynamics in pteropid bats (flying-foxes), the recognised natural reservoir, are incompletely understood. We sought to identify key spatial and temporal factors associated with excretion in flying-foxes over a 2300 km latitudinal gradient from northern QLD to southern NSW which encompassed all known equine case locations. The aim was to strengthen knowledge of Hendra virus ecology in flying-foxes to improve spillover risk prediction and exposure risk mitigation strategies, and thus better protect horses and humans. Monthly pooled urine samples were collected from under roosting flying-foxes over a three-year period and screened for HeV RNA by quantitative RT-PCR. A generalised linear model was employed to investigate spatiotemporal associations with HeV detection in 13,968 samples from 27 roosts. There was a non-linear relationship between mean HeV excretion prevalence and five latitudinal regions, with excretion moderate in northern and central QLD, highest in southern QLD/northern NSW, moderate in central NSW, and negligible in southern NSW. Highest HeV positivity occurred where black or spectacled flying-foxes were present; nil or very low positivity rates occurred in exclusive grey-headed flying-fox roosts. Similarly, little red flying-foxes are evidently not a significant source of virus, as their periodic extreme increase in numbers at some roosts was not associated with any concurrent increase in HeV detection. There was a consistent, strong winter seasonality to excretion in the southern QLD/northern NSW and central NSW regions. This new information allows risk management strategies to be refined and targeted, mindful of the potential for spatial risk profiles to shift over time with changes in flying-fox species distribution.

Routes of Hendra Virus Excretion in Naturally-Infected Flying-Foxes: Implications for Viral Transmission and Spillover Risk

Pteropid bats or flying-foxes (Chiroptera: Pteropodidae) are the natural host of Hendra virus (HeV) which sporadically causes fatal disease in horses and humans in eastern Australia. While there is strong evidence that urine is an important infectious medium that likely drives bat to bat transmission and bat to horse transmission, there is uncertainty about the relative importance of alternative routes of excretion such as nasal and oral secretions, and faeces. Identifying the potential routes of HeV excretion in flying-foxes is important to effectively mitigate equine exposure risk at the bat-horse interface, and in determining transmission rates in host-pathogen models. The aim of this study was to identify the major routes of HeV excretion in naturally infected flying-foxes, and secondarily, to identify between-species variation in excretion prevalence. A total of 2840 flying-foxes from three of the four Australian mainland species (Pteropus alecto, P. poliocephalus and P. scapulatus) were captured and sampled at multiple roost locations in the eastern states of Queensland and New South Wales between 2012 and 2014. A range of biological samples (urine and serum, and urogenital, nasal, oral and rectal swabs) were collected from anaesthetized bats, and tested for HeV RNA using a qRT-PCR assay targeting the M gene. Forty-two P. alecto (n = 1410) had HeV RNA detected in at least one sample, and yielded a total of 78 positive samples, at an overall detection rate of 1.76% across all samples tested in this species (78/4436). The rate of detection, and the amount of viral RNA, was highest in urine samples (>serum, packed haemocytes >faecal >nasal >oral), identifying urine as the most plausible source of infection for flying-foxes and for horses. Detection in a urine sample was more efficient than detection in urogenital swabs, identifying the former as the preferred diagnostic sample. The detection of HeV RNA in serum is consistent with haematogenous spread, and with hypothesised latency and recrudesence in flying-foxes. There were no detections in P. poliocephalus (n = 1168 animals; n = 2958 samples) or P. scapulatus (n = 262 animals; n = 985 samples), suggesting (consistent with other recent studies) that these species are epidemiologically less important than P. alecto in HeV infection dynamics. The study is unprecedented in terms of the individual animal approach, the large sample size, and the use of a molecular assay to directly determine infection status. These features provide a high level of confidence in the veracity of our findings, and a sound basis from which to more precisely target equine risk mitigation strategies.

Zoonotic Viruses and Conservation of Bats

Many of the recently emerging highly virulent zoonotic diseases have a likely bat origin, for example Hendra, Nipah, Ebola and diseases caused by coronaviruses. Presumably because of their long history of coevolution, most of these viruses remain subclinical in bats, but have the potential to cause severe illnesses in domestic and wildlife animals and also humans. Spillovers from bats to humans either happen directly (via contact with infected bats) or indirectly (via intermediate hosts such as domestic or wildlife animals, by consuming food items contaminated by saliva, faeces or urine of bats, or via other environmental sources). Increasing numbers of breakouts of zoonotic viral diseases among humans and livestock have mainly been accounted to human encroachment into natural habitat, as well as agricultural intensification, deforestation and bushmeat consumption. Persecution of bats, including the destruction of their roosts and culling of whole colonies, has led not only to declines of protected bat species, but also to an increase in virus prevalence in some of these populations. Educational efforts are needed in order to prevent future spillovers of bat-borne viruses to humans and livestock, and to further protect bats from unnecessary and counterproductive culling.

Ecological dynamics of emerging bat virus spillover

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.

Natural Hendra Virus Infection in Flying-Foxes - Tissue Tropism and Risk Factors

Hendra virus (HeV) is a lethal zoonotic agent that emerged in 1994 in Australia. Pteropid bats (flying-foxes) are the natural reservoir. To date, HeV has spilled over from flying-foxes to horses on 51 known occasions, and from infected horses to close-contact humans on seven occasions. We undertook screening of archived bat tissues for HeV by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Tissues were tested from 310 bats including 295 Pteropodiformes and 15 Vespertilioniformes. HeV was detected in 20 individual flying-foxes (6.4%) from various tissues including spleen, kidney, liver, lung, placenta and blood components. Detection was significantly higher in Pteropus Alecto and P. conspicillatus, identifying species as a risk factor for infection. Further, our findings indicate that HeV has a predilection for the spleen, suggesting this organ plays an important role in HeV infection. The lack of detections in the foetal tissues of HeV-positive females suggests that vertical transmission is not a regular mode of transmission in naturally infected flying-foxes, and that placental and foetal tissues are not a major source of infection for horses. A better understanding of HeV tissue tropism will strengthen management of the risk of spillover from flying-foxes to horses and ultimately humans.

Flying-fox roost disturbance and Hendra virus spillover risk

Bats of the genus Pteropus (flying-foxes) are the natural host of Hendra virus (HeV) which periodically causes fatal disease in horses and humans in Australia. The increased urban presence of flying-foxes often provokes negative community sentiments because of reduced social amenity and concerns of HeV exposure risk, and has resulted in calls for the dispersal of urban flying-fox roosts. However, it has been hypothesised that disturbance of urban roosts may result in a stress-mediated increase in HeV infection in flying-foxes, and an increased spillover risk. We sought to examine the impact of roost modification and dispersal on HeV infection dynamics and cortisol concentration dynamics in flying-foxes. The data were analysed in generalised linear mixed models using restricted maximum likelihood (REML). The difference in mean HeV prevalence in samples collected before (4.9%), during (4.7%) and after (3.4%) roost disturbance was small and non-significant (P = 0.440). Similarly, the difference in mean urine specific gravity-corrected urinary cortisol concentrations was small and non-significant (before = 22.71 ng/mL, during = 27.17, after = 18.39) (P= 0.550). We did find an underlying association between cortisol concentration and season, and cortisol concentration and region, suggesting that other (plausibly biological or environmental) variables play a role in cortisol concentration dynamics. The effect of roost disturbance on cortisol concentration approached statistical significance for region, suggesting that the relationship is not fixed, and plausibly reflecting the nature and timing of disturbance. We also found a small positive statistical association between HeV excretion status and urinary cortisol concentration. Finally, we found that the level of flying-fox distress associated with roost disturbance reflected the nature and timing of the activity, highlighting the need for a ‘best practice’ approach to dispersal or roost modification activities. The findings usefully inform public discussion and policy development in relation to Hendra virus and flying-fox management.

Novel paramyxoviruses in Australian flying-fox populations support host-virus co-evolution

Understanding the diversity of henipaviruses and related viruses is important in determining the viral ecology within flying-fox populations and assessing the potential threat posed by these agents. This study sought to identify the abundance and diversity of previously unknown paramyxoviruses (UPVs) in Australian flying-fox species (Pteropus alecto, Pteropus scapulatus, Pteropus poliocephalus and Pteropus conspicillatus) and in the Christmas Island species Pteropus melanotus natalis. Using a degenerative reverse transcription-PCR specific for the L gene of known species of the genus Henipavirus and two closely related paramyxovirus genera Respirovirus and Morbillivirus, we identified an abundance and diversity of previously UPVs, with a representative 31 UPVs clustering in eight distinct groups (100 UPVs/495 samples). No new henipaviruses were identified. The findings were consistent with a hypothesis of co-evolution of paramyxoviruses and their flying-fox hosts. Quantification of the degree of co-speciation between host and virus (beyond the scope of this study) would strengthen this hypothesis.

Hendra virus survival does not explain spillover patterns and implicates relatively direct transmission routes from flying foxes to horses

Hendra virus (HeV) is lethal to humans and horses, and little is known about its epidemiology. Biosecurity restrictions impede advances, particularly on understanding pathways of transmission. Quantifying the environmental survival of HeV can be used for making decisions and to infer transmission pathways. We estimated HeV survival with a Weibull distribution and calculated parameters from data generated in laboratory experiments. HeV survival rates based on air temperatures 24 h after excretion ranged from 2 to 10 % in summer and from 12 to 33 % in winter. Simulated survival across the distribution of the black flying fox (Pteropus alecto), a key reservoir host, did not predict spillover events. Based on our analyses we concluded that the most likely pathways of transmission did not require long periods of virus survival and were likely to involve relatively direct contact with flying fox excreta shortly after excretion.