Investigating the emergence of a zoonotic virus: phylogenetic analysis of European bat lyssavirus 1 in the UK.

European bat lyssavirus 1 (EBLV-1, Lyssavirus hamburg) is predominantly detected in serotine bats (Eptesicus serotinus) and is responsible for the majority of bat rabies cases in mainland Europe. A passive bat rabies surveillance scheme detected the virus in a serotine bat in the UK for the first time in October 2018. As of May 2024, 34 cases have been reported, 20 of which involved contact with an animal and 5 reported human contact. We investigated the emergence of EBLV-1 by undertaking comprehensive sequence analysis and Bayesian phylogenetics, based on complete virus genomes of 33 UK sequences and 108 sequences covering six countries in mainland Europe (1968-2023), including 21 French EBLV-1-positive RNA samples sequenced for this study. Sequence analysis revealed extreme similarity among UK EBLV-1 sequences (99.9%-100%), implying a single source of introduction rather than multiple independent introductions. Bayesian analysis revealed that the UK EBLV-1 sequences shared their most recent common ancestor with an EBLV-1 sequence from a serotine bat detected in Brittany, France, in 2001, with an estimated date of divergence of 1997. Within the UK sequences, the earliest divergence was estimated to occur in 2007. This study provides valuable insights into the molecular epidemiology of an emerging zoonotic pathogen and improved understanding of the risks posed to public and animal health.

A multi-species, multi-pathogen avian viral disease outbreak event: Investigating potential for virus transmission at the wild bird - poultry interface.

A free-range organic broiler (Gallus gallus domesticus) premises in Staffordshire was infected by high pathogenicity avian influenza virus (HPAIV) H5N8 during the 2020-2021 epizootic in the United Kingdom (UK). Following initial confirmation of the infection in poultry, multiple wild bird species were seen scavenging on chicken carcasses. Detected dead wild birds were subsequently demonstrated to have been infected and succumbed to HPAIV H5N8. Initially, scavenging species, magpie (Pica pica) and raven (Corvus corax) were found dead on the premises but over the following days, buzzards (Buteo buteo) were also found dead within the local area with positive detection of HPAIV in submitted carcasses. The subacute nature of microscopic lesions within a buzzard was consistent with the timeframe of infection. Finally, a considerable number of free-living pheasants (Phasianus colchicus) were also found dead in the surrounding area, with carcasses having higher viral antigen loads compared to infected chickens. Limited virus dissemination was observed in the carcasses of the magpie, raven, and buzzard. Further, an avirulent avian paramyxovirus type 1 (APMV-1) was detected within poultry samples as well as in the viscera of a magpie infected with HPAIV. Immunohistochemistry did not reveal colocalization of avian paramyxovirus antigens with lesions, supporting an avirulent APMV-1 infection. Overall, this case highlights scenarios in which bi-directional transmission of avian viral diseases between commercial and wild bird species may occur. It also underlines the importance of bio separation and reduced access when infection pressure from HPAIV is high.

Genetic Analysis of H5N1 High-Pathogenicity Avian Influenza Virus following a Mass Mortality Event in Wild Geese on the Solway Firth.

The United Kingdom (UK) and Europe have seen successive outbreaks of H5N1 clade 2.3.4.4b high-pathogenicity avian influenza virus (HPAIV) since 2020 peaking in the autumn/winter periods. During the 2021/22 season, a mass die-off event of Svalbard Barnacle Geese (Branta leucopsis) was observed on the Solway Firth, a body of water on the west coast border between England and Scotland. This area is used annually by Barnacle Geese to over-winter, before returning to Svalbard to breed. Following initial identification of HPAIV in a Barnacle Goose on 8 November 2021, up to 32% of the total Barnacle Goose population may have succumbed to disease by the end of March 2022, along with other wild bird species in the area. Potential adaptation of the HPAIV to the Barnacle Goose population within this event was evaluated. Whole-genome sequencing of thirty-three HPAIV isolates from wild bird species demonstrated that there had been two distinct incursions of the virus, but the two viruses had remained genetically stable within the population, whilst viruses from infected wild birds were closely related to those from poultry cases occurring in the same region. Analysis of sera from the following year demonstrated that a high percentage (76%) of returning birds had developed antibodies to H5 AIV. This study demonstrates genetic stability of this strain of HPAIV in wild Anseriformes, and that, at the population scale, whilst there is a significant impact on survival, a high proportion of birds recover following infection.

Testing bats in rehabilitation for SARS-CoV-2 before release into the wild.

Several studies have suggested SARS-CoV-2 originated from a viral ancestor in bats, but whether transmission occurred directly or via an intermediary host to humans remains unknown. Concerns of spillover of SARS-CoV-2 into wild bat populations are hindering bat rehabilitation and conservation efforts in the United Kingdom and elsewhere. Current protocols state that animals cared for by individuals who have tested positive for SARS-CoV-2 cannot be released into the wild and must be isolated to reduce the risk of transmission to wild populations. Here, we propose a reverse transcription-quantitative polymerase chain reaction (RT-qPCR)-based protocol for detection of SARS-CoV-2 in bats, using fecal sampling. Bats from the United Kingdom were tested following suspected exposure to SARS-CoV-2 and tested negative for the virus. With current UK and international legislation, the identification of SARS-CoV-2 infection in wild animals is becoming increasingly important, and protocols such as the one developed here will help improve understanding and mitigation of SARS-CoV-2 in the future.

Investigations associated with the 2020/21 highly pathogenic avian influenza epizootic in wild birds in Great Britain.

This focus article has been prepared by Paul Duff, Paul Holmes, James Aegerter, Cat Man, Ed Fullick, Scott Reid, Fabian Lean, Alex Núñez, Rowena Hansen, Joanna Tye, Lévon Stephan and Ian Brown of the APHA and Caroline Robinson of SRUC.

Incursion of European Bat Lyssavirus 1 (EBLV-1) in Serotine Bats in the United Kingdom.

Lyssaviruses are an important genus of zoonotic viruses which cause the disease rabies. The United Kingdom is free of classical rabies (RABV). However, bat rabies due to European bat lyssavirus 2 (EBLV-2), has been detected in Daubenton's bats (Myotis daubentonii) in Great Britain since 1996, including a fatal human case in Scotland in 2002. Across Europe, European bat lyssavirus 1 (EBLV-1) is commonly associated with serotine bats (Eptesicus serotinus). Despite the presence of serotine bats across large parts of southern England, EBLV-1 had not previously been detected in this population. However, in 2018, EBLV-1 was detected through passive surveillance in a serotine bat from Dorset, England, using a combination of fluorescent antibody test, reverse transcription-PCR, Sanger sequencing and immunohistochemical analysis. Subsequent EBLV-1 positive serotine bats have been identified in South West England, again through passive surveillance, during 2018, 2019 and 2020. Here, we confirm details of seven cases of EBLV-1 and present similarities in genetic sequence indicating that emergence of EBLV-1 is likely to be recent, potentially associated with the natural movement of bats from the near continent.

Animal Research beyond the Laboratory: Report from a Workshop on Places Other than Licensed Establishments (POLEs) in the UK.

Research involving animals that occurs outside the laboratory raises an array of unique challenges. With regard to UK legislation, however, it receives only limited attention in terms of official guidelines, support, and statistics, which are unsurprisingly orientated towards the laboratory environment in which the majority of animal research takes place. In September 2019, four social scientists from the Animal Research Nexus program gathered together a group of 13 experts to discuss nonlaboratory research under the Animals (Scientific Procedures) Act (A(SP)A) of 1986 (mirroring European Union (EU) Directive 2010/63/EU), which is the primary mechanism for regulating animal research in the UK. Such nonlaboratory research under the A(SP)A often occurs at Places Other than Licensed Establishments (POLEs). The primary objective of the workshop was to assemble a diverse group with experience across a variety of POLEs (e.g., wildlife field sites, farms, fisheries, veterinary clinics, zoos) to explore the practical, ethical, and regulatory challenges of conducting research at POLEs. While consensus was not sought, nor reached on every point of discussion, we collectively identified five key areas that we propose require further discussion and attention. These relate to: (1) support and training; (2) ethical review; (3) cultures of care, particularly in nonregulated research outside of the laboratory; (4) the setting of boundaries; and (5) statistics and transparency. The workshop generated robust discussion and thereby highlighted the value of focusing on the unique challenges posed by POLEs, and the need for further opportunities for exchanging experiences and sharing best practice relating to research projects outside of the laboratory in the UK and elsewhere.

Modelling Spatial and Temporal Patterns of African Swine Fever in an Isolated Wild Boar Population to Support Decision-Making.

African swine fever (ASF) is a highly contagious disease affecting all suids including wild boar. As the disease can damage commercial pig production and its circulation can threaten international trade, understanding the risks produced by free-living wild boar (as a wildlife reservoir) is important to ensure proportionate policies to exclude the disease, as well as an effective contingency response. The recent spread of the virus into Western Europe has produced concerns in many stakeholders including pig producers and national governments. Unlike in mainland Europe, where wild boar are widespread, in Britain, free-living populations have only recently re-established, and whilst these are still relatively small and isolated, they may provide a sufficient reservoir capable of sustaining disease and may thus present a continual source of infection risk to domestic pigs. This study focuses on one component of the risk produced by wild boar, specifically the distribution and persistence of virus in a landscape produced by the natural circulation of disease within wild boar. We used a spatial individual-based model run across a representation of a real landscape to explore the epidemiological consequences of an introduction of ASF into the Forest of Dean, currently hosting the largest population of wild boar in England. We explore various scenarios including variations in the prophylactic management of boar, as well as variations in reactive management (contingency response) following the detection of disease to evaluate their value in reducing this specific risk (presence of ASF virus of wild boar origin in the landscape). The abundance and distribution of wild boar is predicted to increase across our study extent over the next 20 years. Outbreaks of ASF are not predicted to be self-sustaining, with the median time to disease "burn-out" (no new infections) being 14 weeks. Carcass removal, as a tool in a package of reactive management, was of limited value in reducing the duration of outbreaks in this study. We suggest that useful predictions of some of the risks produced by ASF might be possible using only the distribution of the boar, rather than more difficult abundance or density measures.

Between roost contact is essential for maintenance of European bat lyssavirus type-2 in Myotis daubentonii bat reservoir: 'The Swarming Hypothesis'.

Many high-consequence human and animal pathogens persist in wildlife reservoirs. An understanding of the dynamics of these pathogens in their reservoir hosts is crucial to inform the risk of spill-over events, yet our understanding of these dynamics is frequently insufficient. Viral persistence in a wild bat population was investigated by combining empirical data and in-silico analyses to test hypotheses on mechanisms for viral persistence. A fatal zoonotic virus, European Bat lyssavirus type 2 (EBLV-2), in Daubenton's bats (Myotis daubentonii) was used as a model system. A total of 1839 M. daubentonii were sampled for evidence of virus exposure and excretion during a prospective nine year serial cross-sectional survey. Multivariable statistical models demonstrated age-related differences in seroprevalence, with significant variation in seropositivity over time and among roosts. An Approximate Bayesian Computation approach was used to model the infection dynamics incorporating the known host ecology. The results demonstrate that EBLV-2 is endemic in the study population, and suggest that mixing between roosts during seasonal swarming events is necessary to maintain EBLV-2 in the population. These findings contribute to understanding how bat viruses can persist despite low prevalence of infection, and why infection is constrained to certain bat species in multispecies roosts and ecosystems.

Modeling current and potential distributions of mammal species using presence-only data: A case study on British deer.

AIM: Decisions on wildlife conservation, management, and epidemiological risk are best based on robust evidence. The continual improvement of species distributions, such that they can be relied upon in decision-making, is important. Here we seek to refine aspects of a generic modelling approach and improve the utility of species distribution maps. LOCATION: Great Britain (GB). METHODS: We applied a modeling framework based on hierarchical Bayesian species distribution models exploiting opportunistic occurrence records from citizen science datasets to predict both current and potential distributions for each of the six deer species known to be present in GB. Using the resulting maps, we performed a simple analysis of the overlap between species to illustrate possible contact, which we interpret as the relative risk of potential disease spread given an introduction. RESULTS: Predicted distribution maps showed good agreement with the broader scale occurrence reported by a recent national deer survey with an average True Skill Statistics and AUC of 0.69 and 0.89, respectively. Aggregation of the maps for all species highlighted regions of central and eastern England as well as parts of Scotland where extensive areas of range overlap could result in interspecific contact with consequences for risk assessments for diseases of deer. However, if populations are allowed to expand to their predicted potential, then areas of overlap, and therefore disease interspecific transmission risk, will become extensive and widespread across all of mainland Britain. MAIN CONCLUSIONS: The generic modeling approach outlined performed well across all of the deer species tested, offering a robust and reliable tool through which current and potential animal distributions can be estimated and presented. Our application, intended to inform quantitative risk assessments, demonstrates the practical use of such outputs to generate the valuable evidence required to inform policy decisions on issues such as management strategy.

The risk of foot-and-mouth disease becoming endemic in a wildlife host is driven by spatial extent rather than density.

In the past 20 years, free living populations of feral wild boar have re-established in several locations across the UK. One of the largest populations is in the Forest of Dean where numbers have been steadily increasing since monitoring began in 2008, with estimates from 2016 reporting a population of more than 1500. Feral wild boar have significant ecological and environmental impacts and may present a serious epidemiological risk to neighbouring livestock as they are a vector for a number of important livestock diseases. This includes foot-and-mouth disease (FMD) which is currently absent from the UK. We developed an individual-based spatially explicit modelling approach to simulate feral wild boar populations in the Forest of Dean (England, UK) and use it to explore whether current or future populations might be sufficient to produce long-lived outbreaks of FMD in this potential wildlife reservoir. Our findings suggest that if you exclude the spread from feral wild boar to other susceptible species, the current population of boar is insufficient to maintain FMD, with 95% of unmanaged simulations indicating disease burn-out within a year (not involving boar management specifically for disease). However, if boar are allowed to spread beyond their current range into the adjacent landscape, they might maintain a self-sustaining reservoir of infection for the disease.

Bats and Viruses: Emergence of Novel Lyssaviruses and Association of Bats with Viral Zoonoses in the EU.

: Bats in the EU have been associated with several zoonotic viral pathogens of significance to both human and animal health. Virus discovery continues to expand the existing understating of virus classification, and the increased interest in bats globally as reservoirs or carriers of zoonotic agents has fuelled the continued detection and characterisation of new lyssaviruses and other viral zoonoses. Although the transmission of lyssaviruses from bat species to humans or terrestrial species appears rare, interest in these viruses remains, through their ability to cause the invariably fatal encephalitis-rabies. The association of bats with other viral zoonoses is also of great interest. Much of the EU is free of terrestrial rabies, but several bat species harbor lyssaviruses that remain a risk to human and animal health. Whilst the rabies virus is the main cause of rabies globally, novel related viruses continue to be discovered, predominantly in bat populations, that are of interest purely through their classification within the lyssavirus genus alongside the rabies virus. Although the rabies virus is principally transmitted from the bite of infected dogs, these related lyssaviruses are primarily transmitted to humans and terrestrial carnivores by bats. Even though reports of zoonotic viruses from bats within the EU are rare, to protect human and animal health, it is important characterise novel bat viruses for several reasons, namely: (i) to investigate the mechanisms for the maintenance, potential routes of transmission, and resulting clinical signs, if any, in their natural hosts; (ii) to investigate the ability of existing vaccines, where available, to protect against these viruses; (iii) to evaluate the potential for spill over and onward transmission of viral pathogens in novel terrestrial hosts. This review is an update on the current situation regarding zoonotic virus discovery within bats in the EU, and provides details of potential future mechanisms to control the threat from these deadly pathogens.

A first estimate of the structure and density of the populations of pet cats and dogs across Great Britain.

Policy development, implementation, and effective contingency response rely on a strong evidence base to ensure success and cost-effectiveness. Where this includes preventing the establishment or spread of zoonotic or veterinary diseases infecting companion cats and dogs, descriptions of the structure and density of the populations of these pets are useful. Similarly, such descriptions may help in supporting diverse fields of study such as; evidence-based veterinary practice, veterinary epidemiology, public health and ecology. As well as maps of where pets are, estimates of how many may rarely, or never, be seen by veterinarians and might not be appropriately managed in the event of a disease outbreak are also important. Unfortunately both sources of evidence are absent from the scientific and regulatory literatures. We make this first estimate of the structure and density of pet populations by using the most recent national population estimates of cats and dogs across Great Britain and subdividing these spatially, and categorically across ownership classes. For the spatial model we used the location and size of veterinary practises across GB to predict the local density of pets, using client travel time to define catchments around practises, and combined this with residential address data to estimate the rate of ownership. For the estimates of pets which may provoke problems in managing a veterinary or zoonotic disease we reviewed the literature and defined a comprehensive suite of ownership classes for cats and dogs, collated estimates of the sub-populations for each ownership class as well as their rates of interaction and produced a coherent scaled description of the structure of the national population. The predicted density of pets varied substantially, with the lowest densities in rural areas, and the highest in the centres of large cities where each species could exceed 2500 animals.km-2. Conversely, the number of pets per household showed the opposite relationship. Both qualitative and quantitative validation support key assumptions in the model structure and suggest the model is useful at predicting the populations of cats at geographical scales important for decision-making, although it also indicates where further research may improve model performance. In the event of an animal health crisis, it appears that almost all dogs could be brought under control rapidly. For cats, a substantial and unknown number might never be bought under control and would be less likely to receive veterinary support to facilitate surveillance and disease management; we estimate this to be at least 1.5 million cats. In addition, the lack of spare capacity to care for unowned cats in welfare organisations suggests that any increase in their rate of acquisition of cats, or any decrease in the rate of re-homing might provoke problems during a period of crisis.

Interspecies variation in the risks of metals to bats.

A modeling framework was used to assess the risk of four metals to UK bat species. Eight species of bats were predicted to be "at risk" from one or more of the metals in over 5% of their ranges. Species differed significantly in their predicted risk. Contamination by Pb was found to pose the greatest risk, followed by Cu, Cd and Zn. A sensitivity analysis identified the proportion of invertebrates ingested as most important in determining the risk. We then compared the model predictions with a large dataset of metals concentrations in the tissues (liver, kidney) of Pipistrellus sp. from across England and Wales. Bats found in areas predicted to be the most "at risk" contained higher metal concentrations in their tissues than those found in areas predicted "not at risk" by the model. Our spatially explicit modeling framework provides a useful tool for further environmental risk assessment studies for wildlife species.

Demographic variation in the U.K. serotine bat: filling gaps in knowledge for management.

Species of conservation concern, or those in conflict with man, are most efficiently managed with an understanding of their population dynamics. European bats exemplify the need for successful and cost-effective management for both reasons, often simultaneously. Across Europe, bats are protected, and the concept of Favourable Conservation Status (FCS) is used as a key tool for the assessment and licensing of disruptive actions to populations. However, for efficient decision-making, this assessment requires knowledge on the demographic rates and long-term dynamics of populations. We used capture-mark-recapture to describe demographic rates for the Serotine bat (Eptesicus serotinus) at two sites in England and investigate the transition rates between three stages: juveniles, immatures, and breeders. We then use these rates in an individual-based population dynamics model to investigate the expected trajectories for both populations. Our results demonstrate for the first time the presence and scale of temporal variation in this species' demography. We describe the lengthy prereproductive period (3.5 years) that female Serotines experience. Finally, we show how site-specific variation in demographic rates can produce divergent population trajectories. Effective management of European bat populations can be achieved through the understanding of life histories, and local demographic rates and population dynamics, in order to anticipate the presence of source and sink sites in the landscape. Using the Serotine bat in England, we show that these can be obtained from rigorous and systematic studies of long-term demographic datasets.

Landscape as a model: the importance of geometry.

In all models, but especially in those used to predict uncertain processes (e.g., climate change and nonnative species establishment), it is important to identify and remove any sources of bias that may confound results. This is critical in models designed to help support decisionmaking. The geometry used to represent virtual landscapes in spatially explicit models is a potential source of bias. The majority of spatial models use regular square geometry, although regular hexagonal landscapes have also been used. However, there are other ways in which space can be represented in spatially explicit models. For the first time, we explicitly compare the range of alternative geometries available to the modeller, and present a mechanism by which uncertainty in the representation of landscapes can be incorporated. We test how geometry can affect cell-to-cell movement across homogeneous virtual landscapes and compare regular geometries with a suite of irregular mosaics. We show that regular geometries have the potential to systematically bias the direction and distance of movement, whereas even individual instances of landscapes with irregular geometry do not. We also examine how geometry can affect the gross representation of real-world landscapes, and again show that individual instances of regular geometries will always create qualitative and quantitative errors. These can be reduced by the use of multiple randomized instances, though this still creates scale-dependent biases. In contrast, virtual landscapes formed using irregular geometries can represent complex real-world landscapes without error. We found that the potential for bias caused by regular geometries can be effectively eliminated by subdividing virtual landscapes using irregular geometry. The use of irregular geometry appears to offer spatial modellers other potential advantages, which are as yet underdeveloped. We recommend their use in all spatially explicit models, but especially for predictive models that are used in decisionmaking.

European bat lyssavirus in Scottish bats.

We report the first seroprevalence study of the occurrence of specific antibodies to European bat lyssavirus type 2 (EBLV-2) in Daubenton's bats. Bats were captured from 19 sites across eastern and southern Scotland. Samples from 198 Daubenton's bats, 20 Natterer's bats, and 6 Pipistrelle's bats were tested for EBLV-2. Blood samples (N = 94) were subjected to a modified fluorescent antibody virus neutralization test to determine antibody titer. From 0.05% to 3.8% (95% confidence interval) of Daubenton's bats were seropositive. Antibodies to EBLV-2 were not detected in the 2 other species tested. Mouth swabs (N = 218) were obtained, and RNA was extracted for a reverse transcription-polymerase chain reaction (RT-PCR). The RT-PCR included pan lyssavirus-primers (N gene) and internal PCR control primers for ribosomal RNA. EBLV-2 RNA was not detected in any of the saliva samples tested, and live virus was not detected in virus isolation tests.