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The populations of South Australian duck and wader species have recently decreased considerabl y , but their abundance at Bolivar W astewater T reatment Plant in metropolitan Adelaide is poorly known. T o help assess the importance of this site for ducks and waders, we made 25 trips to Bolivar between December 2018 and July 2020, during most of which time south-eastern Australia was experiencing a long dry period. On each trip, we observed between 1 1 and 26 species of ducks and waders, with a mean total of 9804 (range 2437–15,653) individuals per trip. At times, we observed several thousand Pink-eared Ducks Malacorhynchus membranaceus , Grey T eal Anas gracilis , and Australian Shelducks T adorna tadornoides , with occasionally up to 1200 Blue-billed Ducks Oxyura australis and 2000 Hardheads A ythya australis . Several wader species that largely breed in Australia ’ s semi-arid and arid zones were also observed, including occasionally >1000 Red-necked A vocets Recurvirostra novaehollandiae . Five species of waders that breed in the Northern Hemisphere were also recorded fairly regularly in the summer of both 2018–2019 and 2019–2020, including up to ~2000 Sharp-tailed Sandpipers Calidris acuminata , 2000 Red-necked Stints C. ruficollis and 150 Curlew Sandpipers C. ferruginea . These observations indicate that this wastewater treatment plant is a critically important refuge site for several species of ducks and waders. Every effort should thus be made to maintain this site for the conservation of these species in the future.

The transmission of pathogens across the interface between wildlife and livestock presents a challenge to the development of effective surveillance and control measures. Wild birds, especially waterbirds such as the Anseriformes and Charadriiformes are considered to be the natural hosts of Avian Influenza (AI), and are presumed to pose one of the most likely vectors for incursion of AI into European poultry flocks. We have developed a generic quantitative risk map, derived from the classical epidemiological risk equation, to describe the relative, spatial risk of disease incursion into poultry flocks via wild birds. We then assessed the risk for AI incursion into British flocks. The risk map suggests that the majority of AI incursion risk is highly clustered within certain areas of Britain, including in the east, the south west and the coastal north-west of England. The clustering of high risk areas concentrates total risk in a relatively small land area; the top 33% of cells contribute over 80% of total incursion risk. This suggests that targeted risk-based sampling in a relatively small geographical area could be a much more effective and cost-efficient approach than representative sampling. The generic nature of the risk map method, allows rapid updating and application to other diseases transmissible between wild birds and poultry.

Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.Author SummaryA result of the ever-growing poultry industry is a dramatic global increase in the incidence of high pathogenicity avian influenza virus outbreaks. In contrast, wild birds are believed to be the main reservoir for low pathogenic avian influenza A virus. Due to intensive research and surveillance of AIV in waterfowl in the Northern Hemisphere, we have a better understanding of AIV ecology and evolution in that region compared to the Southern Hemisphere, which are characterised by different patterns of avian migration and ecological conditions. We analysed 333 unique AIV genomes collected from wild birds in Australia to understand how Australia fits into global AIV dynamics and how viruses are maintained and dispersed within the continent of Australia. We show that the Southern Hemisphere experiences differing evolutionary dynamics to those seen in Northern Hemisphere with Australia representing a global sink for AIV.

Recent developments in control of highly infectious diseases attempt to improve emergency response efforts by more clearly focusing or targeting response tools according to risk. For example, advances in surveillance testing and sampling deliver their results by more accurately and precisely targeting the population of interest. In this work, targeted implementation of trading zones and vaccination were examined for simulated outbreaks of foot-and-mouth disease (FMD) in Australia. Trading zones allowing unaffected Australian states to resume exports following an outbreak of FMD were assessed using multiple tools. A Victorian incursion scenario with traditional stamping out and vaccination as control options, was simulated using the AADIS model Version 2.47, to characterise the geographic extent of potential outbreaks, the number of animals infected, and the date of last cull indicating duration of the outbreak. Information on disease spread from the AADIS simulations was then used to identify the boundaries of trading zones for the incursion scenario, in which vaccination with trading zones was found to further reduce disease impacts relative to stamping out alone with trading zones. The number of animals culled due to disease provided supply shocks for stamping out alone and vaccinate-to-retain, while the number of vaccinated animals was added to the number of animals culled due to disease for the supply shock of vaccinate-to-remove. The day of last cull was combined with historical FMD trade recovery and Australian export data to estimate the share of Australian exports that would be embargoed under trading zones. The market impacts - changes in equilibrium quantities and prices - of the supply shock, trading zones, and consumer reactions - were simulated within ABARES' AgEmissions partial equilibrium model of Australian agriculture. For this simulated large outbreak, where vaccinate-to-remove was utilised along with trading zones, producer losses were reduced by AUD 4 billion in present value terms over 10 years estimated at a 7% discount rate (PV10,7%) compared to an outbreak where stamping out alone is applied with trading zones. Introducing FMD virus risk mitigation measures for wool to further target trading zones reduced the economic impacts by an additional AUD 3.6 billion (PV10,7%). Outbreak response cost savings and additional potential costs under vaccinate-to-retain with trading zones were also compared to the vaccinate-to-remove control with trading zones. Results emphasised the importance of outbreak characteristics in determining trading zones and targeting of vaccination. Economic analyses identified how additional investments in targeting outbreak response is of value to producers.

A novel Hendra virus (HeV) variant was identified from a horse that suffered acute fatal disease consistent with HeV infection through multidisciplinary and interagency syndromic sentinel surveillance research. Novel molecular assays for HeV detection are described in the light of routine testing failure. In silico analysis of the variant receptor-binding protein in comparison with prototypic HeV supported that the monoclonal antibody m102.4 used for post-exposure prophylaxis, as well as the equine vaccine, should be effective also against this novel variant. Similarity of this virus (99%) to a partial sequence detected from a South Australian grey-headed flying fox, along with case exposure to this species in Queensland, suggests the variant circulates at least across the range of this flying fox species. Investigation into HeV diversity, comparative kinetics and pathogenicity, reservoir-species associations, viral–host co-evolution and spillover dynamics should be prioritized. Biosecurity practices should be updated to appreciate HeV spillover risk across all regions frequented by flying foxes regardless of species. Article Summary Line A novel variant of Hendra virus was discovered and isolated from an Australian horse with fatal disease.

We analyzed the highly pathogenic avian influenza (HPAI) H5 epizootic of 2016-17 in Europe by epidemiologic and genetic characteristics and compared it with 2 previous epizootics caused by the same H5 Guangdong lineage. The 2016-17 epizootic was the largest in Europe by number of countries and farms affected and greatest diversity of wild birds infected. We observed significant differences among the 3 epizootics regarding region affected, epidemic curve, seasonality, and outbreak duration, making it difficult to predict future HPAI epizootics. However, we know that in 2005-06 and 2016-17 the initial peak of wild bird detections preceded the peak of poultry outbreaks within Europe. Phylogenetic analysis of 2016-17 viruses indicates 2 main pathways into Europe. Our findings highlight the need for global surveillance of viral changes to inform disease preparedness, detection, and control.

Versión 2 disponible en: http://hdl.handle.net/10261/225811, Versión editorial disponible en: http://hdl.handle.net/10261/238998, The novel coronavirus SARS-CoV-2 likely emerged from a wildlife source with transmission to humans followed by rapid geographic spread throughout the globe and severe impacts on both human health and the global economy. Since the onset of the pandemic, there have been many instances of human-to-animal transmission involving companion, farmed and zoo animals, and limited evidence for spread into free-living wildlife. The establishment of reservoirs of infection in wild animals would create significant challenges to infection control in humans and could pose a threat to the welfare and conservation status of wildlife. We discuss the potential for exposure, onward transmission and persistence of SARS-CoV-2 in an initial selection of wild mammals (bats, canids, felids, mustelids, great apes, rodents and cervids). Dynamic risk assessment and targeted surveillance are important tools for the early detection of infection in wildlife, and here we describe a framework for collating and synthesising emerging information to inform targeted surveillance for SARS-CoV-2 in wildlife. Surveillance efforts should be integrated with information from public and veterinary health initiatives to provide insights into the potential role of wild mammals in the epidemiology of SARS-CoV-2.

This is the ninth epidemiological report for coronavirus disease 2019 (COVID-19), reported in Australia as at 23:59 Australian Eastern Daylight Time [AEDT] 29 March 2020. It includes data on COVID-19 cases diagnosed in Australia, the international situation and a review of current evidence.

This is the eighth epidemiological report for coronavirus disease 2019 (COVID-19), reported in Australia as at 23:59 Australian Eastern Daylight Time [AEDT] 22 March 2020. It includes data on COVID-19 cases diagnosed in Australia, the international situation and a review of current evidence.

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.

Highlights • Risk assessment for entry of zoonotic bat-borne viruses into the European Union. • Comparison of relative risk of incursion of five viruses by four routes. • An Ebola outbreak similar to 2013–2016 posed the highest risk of introduction. • Relative risk to countries varied due to extent of global trade and human travel. • Model provides a horizon scanning tool for use when available data is limited., This paper presents a quantitative assessment model for the risk of entry of zoonotic bat-borne viruses into the European Union (EU). The model considers four routes of introduction: human travel, legal trade of products, live animal imports and illegal import of bushmeat and was applied to five virus outbreak scenarios. Two scenarios were considered for Zaire ebolavirus (wEBOV, cEBOV) and other scenarios for Hendra virus, Marburg virus (MARV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The use of the same framework and generic data sources for all EU Member States (MS) allows for a relative comparison of the probability of virus introduction and of the importance of the routes of introduction among MSs. According to the model wEBOV posed the highest risk of an introduction event within the EU, followed by MARV and MERS-CoV. However, the main route of introduction differed, with wEBOV and MERS-CoV most likely through human travel and MARV through legal trade of foodstuffs. The relative risks to EU MSs as entry points also varied between outbreak scenarios, highlighting the heterogeneity in global trade and travel to the EU MSs. The model has the capability to allow for a continual updating of the risk estimate using new data as, and when, it becomes available. The model provides an horizon scanning tool for use when available data are limited and, therefore, the absolute risk estimates often have high uncertainty. Sensitivity analysis suggested virus prevalence in bats has a large influence on the results; a 90% reduction in prevalence reduced the risk of introduction considerably and resulted in the relative ranking of MARV falling below that for MERS-CoV, due to this parameter disproportionately affecting the risk of introduction from the trade route over human travel.

Following an FMD eradication program, surveillance will be required to demonstrate that the program has been successful. The World Organization for Animal Health (OIE) provides guidelines including waiting periods and appropriate surveillance to support regaining FMD-free status. Serological surveillance is the recommended method for demonstrating freedom but is time consuming and expensive. New technologies such as real-time reverse transcription polymerase chain reaction (RT-qPCR) tests and sampling techniques such as bulk milk testing (BMT) of dairy cattle, oral swabs, and saliva collection with rope tethers in piggeries could enable surveillance to be done more efficiently. Epidemiological modelling was used to simulate FMD outbreaks, with and without emergency vaccination as part of the response, in Australia. Baseline post-outbreak surveillance approaches for unvaccinated and vaccinated animals based on the European FMD directive were compared with alternative approaches in which the sampling regime, sampling approaches and/or the diagnostic tests used were varied. The approaches were compared in terms of the resources required, time taken, cost, and effectiveness i.e., ability of the surveillance regime to correctly identify the infection status of herds. In the non-vaccination scenarios, the alternative approach took less time to complete and cost less, with the greatest benefits seen with larger outbreaks. In vaccinated populations, the alternative surveillance approaches significantly reduced the number of herds sampled, the total number of tests done and costs of the post-outbreak surveillance. There was no reduction in effectiveness using the alternative approaches, with one of the benefits being a reduction in the number of false positive herds. Alternative approaches to FMD surveillance based on non-invasive sampling methods and RT-qPCR tests have the potential to enable post outbreak surveillance substantiating FMD freedom to be done more quickly and less expensively than traditional approaches based on serological surveys.

SUMMARYPassive surveillance for lyssaviruses in UK bats has been ongoing since 1987 and has identified 13 cases of EBLV-2 from a single species;Myotis daubentonii. No other lyssavirus species has been detected. Between 2005 and 2015, 10 656 bats were submitted, representing 18 species, creating a spatially and temporally uneven sample of British bat fauna. Uniquely, three UK cases originate from a roost at Stokesay Castle in Shropshire, England, where daily checks for grounded and dead bats are undertaken and bat carcasses have been submitted for testing since 2007. Twenty per cent of Daubenton's bats submitted from Stokesay Castle since surveillance began, have tested positive for EBLV-2. Phylogenetic analysis reveals geographical clustering of UK viruses. Isolates from Stokesay Castle are more closely related to one another than to viruses from other regions. Daubenton's bats from Stokesay Castle represent a unique opportunity to study a natural population that appears to maintain EBLV-2 infection and may represent endemic infection at this site. Although the risk to public health from EBLV-2 is low, consequences of infection are severe and effective communication on the need for prompt post-exposure prophylaxis for anyone that has been bitten by a bat is essential.

On Friday 26 May 2017, Biosecurity Queensland announced that an unvaccinated horse in the Gold Coast hinterland had been euthanased following a positive detection of Hendra virus.1 This was the first Hendra virus case for the year and serves as a reminder to horse owners, veterinarians and allied workers to protect themselves and their animals. Given similarities between current environmental conditions and those that preceded a surge of spillover events in 2011, it may be worthwhile to be especially vigilant this year.

Highly pathogenic avian influenza (HPAI) H5Nx viruses of the goose/Guangdong/96 lineage continue to cause outbreaks in poultry and wild birds globally. Shorebirds, known reservoirs of avian influenza viruses, migrate from Siberia to Australia along the East-Asian-Australasian Flyway. We examined whether migrating shorebirds spending nonbreeding seasons in Australia were exposed to HPAI H5 viruses. We compared those findings with those for a resident duck species. We screened >1,500 blood samples for nucleoprotein antibodies and tested positive samples for specific antibodies against 7 HPAI H5 virus antigens and 2 low pathogenicity avian influenza H5 virus antigens. We demonstrated the presence of hemagglutinin inhibitory antibodies against HPAI H5 virus clade 2.3.4.4 in the red-necked stint (Calidris ruficolis). We did not find hemagglutinin inhibitory antibodies in resident Pacific black ducks (Anas superciliosa). Our study highlights the potential role of long-distance migratory shorebirds in intercontinental spread of HPAI H5 viruses.

Influenza A viruses of H5 and H7 subtype in poultry can circulate subclinically and subsequently mutate from low to high pathogenicity with potentially devastating economic and welfare consequences. European Union Member States undertake surveillance of commercial and backyard poultry for early detection and control of subclinical H5 and H7 influenza A infection. This surveillance has moved towards a risk-based sampling approach in recent years; however, quantitative measures of relative risk associated with risk factors utilized in this approach are necessary for optimization. This study describes serosurveillance for H5 and H7 influenza A in domestic and commercial poultry undertaken in the European Union from 2004 to 2010, where a random sampling and thus representative approach to serosurveillance was undertaken. Using these representative data, this study measured relative risk of seropositivity across poultry categories and spatially across the EU. Data were analysed using multivariable logistic regression. Domestic waterfowl, game birds, fattening turkeys, ratites, backyard poultry and the 'other' poultry category holdings had relatively increased probability of H5 and/or H7 influenza A seropositivity, compared to laying-hen holdings. Amongst laying-hen holdings, free-range rearing was associated with increased probability of H7 seropositivity. Spatial analyses detected 'hotspots' for H5 influenza A seropositivity in western France and England, and H7 influenza A seropositivity in Italy and Belgium, which may be explained by the demographics and distribution of poultry categories. Findings suggest certain poultry category holdings are at increased risk of subclinical H5 and/or H7 influenza A circulation, and free-range rearing increases the likelihood of exposure to H7 influenza A. These findings may be used in further refining risk-based surveillance strategies and prioritizing management strategies in influenza A outbreaks.

A novel lyssavirus was isolated from brains of Indian flying foxes (Pteropus medius) in Sri Lanka. Phylogenetic analysis of complete virus genome sequences, and geographic location and host species, provides strong evidence that this virus is a putative new lyssavirus species, designated as Gannoruwa bat lyssavirus.

Rabies is a fatal neurologic disease caused by lyssavirus infection. People are infected through contact with infected animals. The relative increase of human rabies acquired from bats calls for a better understanding of lyssavirus infections in their natural hosts. So far, there is no experimental model that mimics natural lyssavirus infection in the reservoir bat species. Lagos bat virus is a lyssavirus that is endemic in straw-colored fruit bats (Eidolon helvum) in Africa. Here we compared the susceptibility of these bats to three strains of Lagos bat virus (from Senegal, Nigeria, and Ghana) by intracranial inoculation. To allow comparison between strains, we ensured the same titer of virus was inoculated in the same location of the brain of each bat. All bats (n = 3 per strain) were infected, and developed neurological signs, and fatal meningoencephalitis with lyssavirus antigen expression in neurons. There were three main differences among the groups. First, time to death was substantially shorter in the Senegal and Ghana groups (4 to 6 days) than in the Nigeria group (8 days). Second, each virus strain produced a distinct clinical syndrome. Third, the spread of virus to peripheral tissues, tested by hemi-nested reverse transcriptase PCR, was frequent (3 of 3 bats) and widespread (8 to 10 tissues positive of 11 tissues examined) in the Ghana group, was frequent and less widespread in the Senegal group (3/3 bats, 3 to 6 tissues positive), and was rare and restricted in the Nigeria group (1/3 bats, 2 tissues positive). Centrifugal spread of virus from brain to tissue of excretion in the oral cavity is required to enable lyssavirus transmission. Therefore, the Senegal and Ghana strains seem most suitable for further pathogenesis, and for transmission, studies in the straw-colored fruit bat., Author summary Rabies is a neurologic disease that causes severe suffering and is almost always fatal. The disease is caused by infection with a virus of the genus Lyssavirus, of which 16 species are known. These viruses replicate in neurons, are excreted in the mouth, and are transmitted by bites. Dogs are the most important source of rabies for humans, but recently there is a relative increase in people contracting the disease from bats. To better understand the development of human rabies caused by these bat-acquired viruses, we need to study this disease in its bat host under controlled circumstances. To do so, we chose a naturally occurring lyssavirus–host combination: Lagos bat virus in straw-colored fruit bats. We compared three available strains of Lagos bat virus (all isolated from brains of this bat species) for their ability to mimic a natural infection. We used intracranial inoculation to ensure infection of the brain. All three strains infected brain neurons, resulting in fatal neurologic disease, however only two of the strains showed the ability to reach the site of excretion—the mouth—and were considered a suitable virus to use for further studies of this disease in bats.

Avian influenza virus (AIV) subtypes H5 and H7 can infect poultry causing low pathogenicity (LP) AI, but these LPAIVs may mutate to highly pathogenic AIV in chickens or turkeys causing high mortality, hence H5/H7 subtypes demand statutory intervention. Serological surveillance in the European Union provides evidence of H5/H7 AIV exposure in apparently healthy poultry. To identify the most sensitive screening method as the first step in an algorithm to provide evidence of H5/H7 AIV infection, the standard approach of H5/H7 antibody testing by haemagglutination inhibition (HI) was compared with an ELISA, which detects antibodies to all subtypes. Sera (n = 1055) from 74 commercial chicken flocks were tested by both methods. A Bayesian approach served to estimate diagnostic test sensitivities and specificities, without assuming any ‘gold standard’. Sensitivity and specificity of the ELISA was 97% and 99.8%, and for H5/H7 HI 43% and 99.8%, respectively, although H5/H7 HI sensitivity varied considerably between infected flocks. ELISA therefore provides superior sensitivity for the screening of chicken flocks as part of an algorithm, which subsequently utilises H5/H7 HI to identify infection by these two subtypes. With the calculated sensitivity and specificity, testing nine sera per flock is sufficient to detect a flock seroprevalence of 30% with 95% probability.

SUMMARYAs part of further investigations into three linked haemorrhagic fever with renal syndrome (HFRS) cases in Wales and England, 21 rats from a breeding colony in Cherwell, and three rats from a household in Cheltenham were screened for hantavirus. Hantavirus RNA was detected in either the lungs and/or kidney of 17/21 (81%) of the Cherwell rats tested, higher than previously detected by blood testing alone (7/21, 33%), and in the kidneys of all three Cheltenham rats. The partial L gene sequences obtained from 10 of the Cherwell rats and the three Cheltenham rats were identical to each other and the previously reported UK Cherwell strain. Seoul hantavirus (SEOV) RNA was detected in the heart, kidney, lung, salivary gland and spleen (but not in the liver) of an individual rat from the Cherwell colony suspected of being the source of SEOV. Serum from 20/20 of the Cherwell rats and two associated HFRS cases had high levels of SEOV-specific antibodies (by virus neutralisation). The high prevalence of SEOV in both sites and the moderately severe disease in the pet rat owners suggest that SEOV in pet rats poses a greater public health risk than previously considered.

To investigate the risks to Australia of emergent henipaviruses, studies were conducted with the aim of: (1) determining the occurrence of henipaviruses in targeted fruit bat populations in northern Australia, Papua New Guinea, East Timor and Indonesia; (2) investigating the extent and nature of contact between fruit bat populations in Australia with populations in Papua New Guinea, East Timor and Indonesia using satellite telemetry; and (3) investigating the dynamics of henipavirus infection in a fruit bat population. The risk of Nipah virus (NiV) becoming established in Australian fruit bat populations was assessed utilising data generated during this project, together with available literature and expert opinion. Targeted sampling of fruit bat populations found strong evidence for the presence of NiV in Pteropus vampyrus and Rousettus amplexicaudatus in East Timor. Evidence was also found for the presence of henipaviruses that were not Hendra virus (HeV) nor NiV in Pteropus alecto and Acerodon celebensis on Sulawesi and P. alecto on Sumba. The closest to Australia that NiV had previously been detected is Singapore although serological evidence of a henipavirus more closely related to NiV than Hendra virus (HeV) has also been reported from Sumatra and Java. Studies using satellite telemetry showed P. alecto to be capable of crossing Torres Strait (between Papua New Guinea and Australia) thus indicating potential close contact among the populations of this species in northern Queensland, south-western Papua New Guinea and south-eastern Papua, Indonesia. In contrast, an individual P. alecto tracked on Sumba, Indonesia, did not leave this island and two P. vampyrus tracked on Timor remained on that Island although one of these bats moved to Indonesian West Timor. The infection dynamics of HeV in a Pteropus conspicillatus population in northern Queensland was investigated using a serial cross-sectional study over a 25 month period. The results suggested that infection was endemic in the population over the study period and indicated that age, pregnancy and lactation were significant risk factors for a detectable neutralising antibody response. An endemic infection pattern for HeV in this bat population is contrary to a previously proposed episodic infection pattern, but is consistent with recent studies on henipavirus infection in captive bats in Malaysia and free-living bats in Equatorial Guinea. From the current targeted sampling of fruit bat populations and satellite telemetry studies, it appears that an incursion into Australia of a fruit bat infected with NiV is a plausible event, although the probability and consequences of this occurring are not clear. The infection dynamics study has implications for understanding the process of spillover of infection of HeV from bats to horses in Australia, as well as for the consequence of the incursion of a NiV infected bat (or bats) to Australia. Taking the above information into account, a qualitative risk assessment was undertaken to assess the risk of NiV becoming established in Australian fruit bats as a result of movements from nearby regions. Where data gaps were identified, expert opinion was used in this assessment via an Expert Opinion Workshop. The risk was estimated to be very low but was associated with a high level of uncertainty. Different methods for combining expert opinion were also used in the risk assessment model to determine their influence on risk outcome. In addition to estimating the risk of NiV establishing in Australian fruit bats, this study provides a framework for periodically reassessing the risk as further information becomes available. It also identified key areas of data sparsity where future research could be directed.

The straw-coloured fruit bat, Eidolon helvum, is a common and conspicuous migratory species, with an extensive distribution across sub-Saharan Africa, yet hunting and habitat loss are thought to be resulting in decline in some areas. Eidolon helvum is also a known reservoir for potentially zoonotic viruses. Despite E. helvum's importance, ecological and behavioural traits are poorly described for this species. Here we present extensive data on the distribution, migration patterns, roost size, age and sex composition of 29 E. helvum roosts from nine countries across tropical Africa, including roosts not previously described in the literature. Roost age and sex composition were dependent on timing of sampling relative to the annual birth pulse. Rather than a single 'breeding season' as is frequently reported for this species, regional asynchrony of reproductive timing was observed across study sites (with birth pulses variably starting in March, April, September, November or December). Considered together with its genetic panmixia, we conclude that the species has a fluid, fission-fusion social structure, resulting in different roost 'types' at different times of the year relative to seasonal reproduction. Bat-human interactions also varied across the species' geographical range. In the absence of significant hunting, large urban colonies were generally tolerated, yet in regions with high hunting pressure, bats tended to roost in remote or protected sites. The extensive quantitative and qualitative data presented in this manuscript are also valuable for a wide range of studies and provide an historical snapshot as its populations become increasingly threatened., Funding for this study was provided by the Cambridge Infectious Diseases Consortium (grant VT0105 — AJP, DTSH, KSB), The Charles Slater Trust (AJP), Zebra Foundation for Veterinary Zoological Education (AJP), Isaac Newton Trust (AJP), the Wellcome Trust (DTSH, KSB), a David H. Smith postdoctoral fellowship (DTSH), the RAPIDD program of the Science and Technology Directorate, Department of Home - land Security, Fogarty International Center, National Institutes of Health (DTSH, JLNW), The Albo rada Trust (JLNW), a European Union FP7 project ANTIGONE (Antici pat ing Glob - al Onset of Novel Epidemics 278976) (ACB, JLNW, AAC) and a Royal Society Wolfson Research Merit Award (AAC).

SUMMARYA survey of national animal influenza surveillance programmes was conducted to assess the current capacity to detect influenza viruses with zoonotic potential in animals (i.e. those influenza viruses that can be naturally transmitted between animals and humans) at regional and global levels. Information on 587 animal influenza surveillance system components was collected for 99 countries from Chief Veterinary Officers (CVOs) (n = 94) and published literature. Less than 1% (n = 4) of these components were specifically aimed at detecting influenza viruses with pandemic potential in animals (i.e. those influenza viruses that are capable of causing epidemic spread in human populations over large geographical regions or worldwide), which would have zoonotic potential as a prerequisite. Those countries that sought to detect influenza viruses with pandemic potential searched for such viruses exclusively in domestic pigs. This work shows the global need for increasing surveillance that targets potentially zoonotic influenza viruses in relevant animal species.

In Europe and Asia, Ixodid ticks transmit tick-borne encephalitis virus (TBEV), a flavivirus that causes severe encephalitis in humans but appears to show no virulence for livestock and wildlife. In the British Isles, where TBEV is absent, a closely related tick-borne flavivirus, named louping ill virus (LIV), is present. However, unlike TBEV, LIV causes a febrile illness in sheep, cattle, grouse and some other species, that can progress to fatal encephalitis. The disease is detected predominantly in animals from upland areas of the UK and Ireland. This distribution is closely associated with the presence of its arthropod vector, the hard tick Ixodes ricinus. The virus is a positive-strand RNA virus belonging to the genus Flavivirus, exhibiting a high degree of genetic homology to TBEV and other mammalian tick-borne viruses. In addition to causing acute encephalomyelitis in sheep, other mammals and some avian species, the virus is recognized as a zoonotic agent with occasional reports of seropositive individuals, particularly those whose occupation involves contact with sheep. Preventative vaccination in sheep is effective although there is no treatment for disease. Surveillance for LIV in Great Britain is limited despite an increased awareness of emerging arthropod-borne diseases and potential changes in distribution and epidemiology. This review provides an overview of LIV and highlights areas where further effort is needed to control this disease.

To estimate qualitatively the probabilities of release (or entry) of Eurasian lineage H5N1 highly pathogenic avian influenza (HPAI) virus into Great Britain (GB), the Netherlands and Italy through selected higher risk species of migratory water bird.The probabilities of one or more release events of H5N1 HPAI per year (Pre(lease)) were estimated qualitatively for 15 avian species, including swans, geese, ducks and gulls, by assessing the prevalence of H5N1 HPAI in different regions of the world (weighted to 2009) and estimates of the total numbers of birds migrating from each of those regions. The release assessment accommodated the migration times for each species in relation to the probabilities of their surviving infection and shedding virus on arrival. Although the predicted probabilities of release of H5N1 per individual bird per year were low, very low or negligible, Pre(lease) was high for a few species reflecting the high numbers of birds migrating from some regions. Values of Pre(lease) were generally higher for the Netherlands than for GB, while ducks and gulls from Africa presented higher probabilities to Italy compared to the Netherlands and GB.Bird species with high values of Pre(lease) in GB, the Netherlands and Italy generally originate from within Europe based on data for global prevalence of H5N1 between 2003 and 2009 weighted to 2009. Potential long-distance transfer of H5N1 HPAI from North Asia and Eurasia to GB, the Netherlands and Italy is limited to a few species and does not occur from South-East Asia, an area where H5N1 is endemic.The approach accommodates biogeographical conditions and variability in the estimated worldwide prevalence of the virus. The outputs of this release assessment can be used to inform surveillance activities through focusing on certain species and migratory pathways.

SUMMARYNipah virus (NiV) is a recently emerged zoonotic virus that causes severe disease in humans. The reservoir hosts for NiV, bats of the genusPteropus(known as flying-foxes) are found across the Asia-Pacific including Australia. While NiV has not been detected in Australia, evidence for NiV infection has been found in flying-foxes in some of Australia's closest neighbours. A qualitative risk assessment was undertaken to assess the risk of NiV establishing in Australian flying-foxes through flying-fox movements from nearby regions. Events surrounding the emergence of new diseases are typically uncertain and in this study an expert opinion workshop was used to address gaps in knowledge. Given the difficulties in combining expert opinion, five different combination methods were analysed to assess their influence on the risk outcome. Under the baseline scenario where the median was used to combine opinions, the risk was estimated to be very low. However, this risk increased when the mean and linear opinion pooling combination methods were used. This assessment highlights the effects that different methods for combining expert opinion have on final risk estimates and the caution needed when interpreting these outcomes given the high degree of uncertainty in expert opinion. This work has provided a flexible model framework for assessing the risk of NiV establishment in Australian flying-foxes through bat movements which can be updated when new data become available.

This study presents a method for evaluation of surveillance for avian influenza (AI) in wild birds and compares surveillance activities before and after changes in surveillance strategy in Great Britain (GB). In October 2008 the AI Wild Bird Surveillance (AIWBS) system in GB was modified to focus on passive surveillance (birds found dead), including those found during warden patrols of wetlands and wildlife reserves, with less emphasis on public reporting of birds found dead. The number of birds sampled by active surveillance (birds live-trapped or shot) was also reduced. In the present study the impact of these changes was investigated by comparing the 12 mo prior to October 2008 with the subsequent 12 mo. Four factors were considered for each surveillance system component: 1) the number of wild birds tested; 2) whether the tested wild birds were considered "higher risk species" (HRS) for being infected with AI; 3) the location of the birds tested with respect to counties designated as a priority for surveillance; and 4) the probability that the birds tested might yield a positive AI virus result based on surveillance results in wild birds across Europe. The number of birds tested by both surveillance types was greatly reduced after the strategy change. The proportion of birds sampled in priority counties also significantly decreased in the second year for both active and passive surveillance. However, the proportion of HRS sampled by active surveillance significantly increased, while a significant decrease in these species was seen for passive surveillance in the second year. The derived probability scores for detecting AI based on European surveillance results indicated a reduction in sensitivity for H5N1 highly pathogenic AI detection by passive surveillance. The methods developed to evaluate AIWBS in GB may be applicable to other European Union countries. The results also reflect the complex issues associated with evaluation of disease surveillance in wildlife populations in which the disease ecology is only partially understood.

(Published: 4 May 2016) Citation: Infection Ecology and Epidemiology 2016, 6: 31658 - http://dx.doi.org/10.3402/iee.v6.31658

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.

SUMMARYThe aim of this study was to evaluate potential sampling strategies for detection of infected flocks that could be applied during an outbreak of low pathogenicity notifiable avian influenza (LPNAI) initiated in duck holdings, following initial detection. A simulation model of avian influenza virus transmission and spread within and between holdings, respectively, was used to predict the impact on the size and duration of an outbreak of (i) changing the tracing window within which premises that might be the source of infection or that may have been infected by the index premises were sampled and (ii) changing the number of birds sampled in the flock being tested. It has shown that there is potential benefit in increasing the tracing window in terms of reducing the likelihood of a large outbreak. It has also shown that there is comparatively little benefit from increasing the number of birds sampled per flock.

In 2004, the European Union (EU) implemented a pet movement policy (referred to here as the EUPMP) under EU regulation 998/2003. The United Kingdom (UK) was granted a temporary derogation from the policy until December 2011 and instead has in place its own Pet Movement Policy (Pet Travel Scheme (PETS)). A quantitative risk assessment (QRA) was developed to estimate the risk of rabies introduction to the UK under both schemes to quantify any change in the risk of rabies introduction should the UK harmonize with the EU policy. Assuming 100 % compliance with the regulations, moving to the EUPMP was predicted to increase the annual risk of rabies introduction to the UK by approximately 60-fold, from 7.79 × 10(-5) (5.90 × 10(-5), 1.06 × 10(-4)) under the current scheme to 4.79 × 10(-3) (4.05 × 10(-3), 5.65 × 10(-3)) under the EUPMP. This corresponds to a decrease from 13,272 (9,408, 16,940) to 211 (177, 247) years between rabies introductions. The risks associated with both the schemes were predicted to increase when less than 100 % compliance was assumed, with the current scheme of PETS and quarantine being shown to be particularly sensitive to noncompliance. The results of this risk assessment, along with other evidence, formed a scientific evidence base to inform policy decision with respect to companion animal movement.

Fruit bats of the genus Pteropus (commonly known as flying-foxes) are the natural hosts of several recently emerged zoonotic viruses of animal and human health significance in Australia and Asia, including Hendra and Nipah viruses. Satellite telemetry was used on nine flying-foxes of three species (Pteropus alecto n = 5, P. vampyrus n = 2, and P. neohibernicus n = 2) to determine the scale and pattern of their long-distance movements and their potential to transfer these viruses between countries in the region. The animals were captured and released from six different locations in Australia, Papua New Guinea, Indonesia, and Timor-Leste. Their movements were recorded for a median of 120 (range, 47–342) days with a median total distance travelled of 393 (range, 76–3011) km per individual. Pteropus alecto individuals were observed to move between Australia and Papua New Guinea (Western Province) on four occasions, between Papua New Guinea (Western Province) and Indonesia (Papua) on ten occasions, and to traverse Torres Strait on two occasions. Pteropus vampyrus was observed to move between Timor-Leste and Indonesia (West Timor) on one occasion. These findings expand upon the current literature on the potential for transfer of zoonotic viruses by flying-foxes between countries and have implications for disease risk management and for the conservation management of flying-fox populations in Australia, New Guinea, and the Lesser Sunda Islands.

Compared to other viruses, research on Nipah virus has been limited in Indonesia because attributable disease outbreaks have not been reported. However, Nipah virus is a zoonotic Biosafety Level 4 (BSL4) agent, so strategic monitoring is prudent. Farmer interviews and a serologic survey of 610 pig sera and 99 bat sera from West Kalimantan province were conducted. Farmers reported no recent or historic encephalitic or respiratory disease in themselves, their families, workers or pigs. The survey found no evidence of exposure to Nipah virus in pigs. In contrast, 19% of the 84 Pteropus vampyrus bat sera reacted in the ELISA, but none of 15 Cynopterus brachyotis bats reacted.

Primary brain tumours were identified in two Bactrian camels (Camelus bactrianus) living at the Zoological Society of London's two zoos. Histology and immunohistochemistry were used to diagnose a histiocytic sarcoma in a 16-year-old female and a fibroblastic meningioma in a 13-year-old male. Before one died and the other was euthanased both camels had shown progressive neurological signs, including circling and ataxia.

The Middle East is a culturally and politically diverse region at the gateway between Europe, Africa and Asia. Spatial dynamics of the fatal zoonotic disease rabies among countries of the Middle East and surrounding regions is poorly understood. An improved understanding of virus distribution is necessary to direct control methods. Previous studies have suggested regular trans-boundary movement, but have been unable to infer direction. Here we address these issues, by investigating the evolution of 183 rabies virus isolates collected from over 20 countries between 1972 and 2014. We have undertaken a discrete phylogeographic analysis on a subset of 139 samples to infer where and when movements of rabies have occurred. We provide evidence for four genetically distinct clades with separate origins currently circulating in the Middle East and surrounding countries. Introductions of these viruses have been followed by regular and multidirectional trans-boundary movements in some parts of the region, but relative isolation in others. There is evidence for minimal regular incursion of rabies from Central and Eastern Asia. These data support current initiatives for regional collaboration that are essential for rabies elimination., Author Summary Despite being one of the oldest recognised infectious diseases, rabies continues to cause thousands of preventable human deaths per year. As a zoonotic disease, control of infection in the reservoir has been proven the most efficient route to reduction of human cases. In some regions, the epidemiology is well understood, with either dogs or wildlife known to be the primary reservoir and with little or no movement from, or into other regions. This is not the case in the Middle East, where rabies is underreported in animals and humans, there is little laboratory confirmation of infection, and the extent of rabies spread from country to country is not known. Previous studies have demonstrated trans-boundary movement of rabies but have been limited by a low number of available samples from some countries, and the direction of spread has been difficult to estimate. Here we use rabies virus partial genome sequences of 183 viruses from over 20 countries, combined with geographical and temporal information, to reconstruct the evolution of rabies viruses circulating in the Middle East. The results reveal an apparent barrier to spread between some regions but regular movement between others. These analyses will support policy on rabies control by indicating the relative importance of local control and animal movement restrictions when allocating resources.

Wildlife populations are affected by a series of emerging diseases, some of which pose a significant threat to their conservation. They can also be reservoirs of pathogens that threaten domestic animal and human health. In this paper, we review the ecology of two viruses that have caused significant disease in domestic animals and humans and are carried by wild fruit bats in Asia and Australia. The first, Hendra virus, has caused disease in horses and/or humans in Australia every five years since it first emerged in 1994. Nipah virus has caused a major outbreak of disease in pigs and humans in Malaysia in the late 1990s and has also caused human mortalities in Bangladesh annually since 2001. Increased knowledge of fruit bat population dynamics and disease ecology will help improve our understanding of processes driving the emergence of diseases from bats. For this, a transdisciplinary approach is required to develop appropriate host management strategies that both maximise the conservation of bat populations as well as minimise the risk of disease outbreaks in domestic animals and humans.

Summary Horizon scanning techniques can be developed to identify novel routes and sources for the emergence of viruses in the medium to long term. Central to horizon scanning is prediction of the complex scenarios through which viruses could emerge before they occur. One approach involves ‘spidergrams’ in which complex scenarios are generated by combining factors randomly selected from different categories of events. Spidergrams provide a framework for how different factors could interact, irrespective of the virus, and also enable testing of combinations not previously considered but which would be ‘tested’ in nature by a virus. The emergence of viruses through new routes is often related to changes, for example, in environmental and social factors, and the Internet will undoubtedly be used to identify long-term trends for consideration. In addition, online games may provide horizon scanners with suggestions for new routes and strategies that could be used by emerging viruses.

Factors that trigger human infection with animal influenza virus progressing into a pandemic are poorly understood. Within a project developing an evidence-based risk assessment framework for influenza viruses in animals, we conducted a review of the literature for evidence of human infection with animal influenza viruses by diagnostic methods used. The review covering Medline, Embase, SciSearch and CabAbstracts yielded 6,955 articles, of which we retained 89; for influenza A(H5N1) and A(H7N9), the official case counts of the World Health Organization were used. An additional 30 studies were included by scanning the reference lists. Here, we present the findings for confirmed infections with virological evidence. We found reports of 1,419 naturally infected human cases, of which 648 were associated with avian influenza virus (AIV) A(H5N1), 375 with other AIV subtypes, and 396 with swine influenza virus (SIV). Human cases naturally infected with AIV spanned haemagglutinin subtypes H5, H6, H7, H9 and H10. SIV cases were associated with endemic SIV of H1 and H3 subtype descending from North American and Eurasian SIV lineages and various reassortants thereof. Direct exposure to birds or swine was the most likely source of infection for the cases with available information on exposure.