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Additional file1: Table S1. Variables and values considered for the environmental analysis. Table S2. Values of the categorical variables for each trap. Table S3. Host choices of blood-fed mosquitoes captured in Chester Zoo, 2017. Table S4. Host choices of blood-fed mosquitoes captured in Chester Zoo, 2018. Table S5. Host choices of blood-fed mosquitoes captured in Chester Zoo, 2019. Table S6. Host choices of blood-fed mosquitoes captured in Flamingo Land, 2017. Table S7. Values of the generalised linear models for the significant variables in relation to the capture of blood-fed mosquitoes. Figure S1. Host patterns of blood-fed mosquitoes. Birds in shades of blue, non-human mammals in shades of red. Zoo vertebrates are indicated with an asterisk.

Novel pathogenic coronaviruses – such as SARS-CoV and probably SARS-CoV-2 – arise by homologous recombination between co-infecting viruses in a single cell. Identifying possible sources of novel coronaviruses therefore requires identifying hosts of multiple coronaviruses; however, most coronavirus-host interactions remain unknown. Here, by deploying a meta-ensemble of similarity learners from three complementary perspectives (viral, mammalian and network), we predict which mammals are hosts of multiple coronaviruses. We predict that there are 11.5-fold more coronavirus-host associations, over 30-fold more potential SARS-CoV-2 recombination hosts, and over 40-fold more host species with four or more different subgenera of coronaviruses than have been observed to date at >0.5 mean probability cut-off (2.4-, 4.25- and 9-fold, respectively, at >0.9821). Our results demonstrate the large underappreciation of the potential scale of novel coronavirus generation in wild and domesticated animals. We identify high-risk species for coronavirus surveillance., Homologous recombination between co-infecting coronaviruses can produce novel pathogens. Here, Wardeh et al. develop a machine learning approach to predict associations between mammals and multiple coronaviruses and hence estimate the potential for generation of novel coronaviruses by recombination.

Additional file 2: Text S1. Derivation of ‘estimated relative quantity’ of RNA from Cq values.

Supplementary notes 1 - 5.

Table S1. Regression coefficients for the final negative binomial GLMs for subgenus Avaritia female Culicoides collected on two breeds of sheep. Table S2. Regression coefficients for the final negative binomial GLMs for C. scoticus females collected on two breeds of sheep. Table S3. Regression coefficients for the final negative binomial GLMs for C. dewulfi females collected on two breeds of sheep. Table S4. Regression coefficients for the final negative binomial GLMs for C. chiopterus females collected on two breeds of sheep. Table S5. Regression coefficients for the final negative binomial GLMs for collections of C. obsoletus females collected on sheared and unsheared sheep. Table S6. Differences in collections between sheared and unsheared sheep and UV suction-light trap controls for C. obsoletus for total females (a), unpigmented females (b), pigmented females (c) and blood-fed females (d). Table S7. Regression coefficients for the final negative binomial GLMs for collections of C. scoticus females from sheared and unsheared sheep. Table S8. Differences in collections between sheared and unsheared sheep and UV light-suction trap controls for C. scoticus females (a), unpigmented females (b) and pigmented females (c). Table S9. Regression coefficients for the final negative binomial GLMs for collections of C. dewulfi females from sheared and unsheared sheep. Table S10. Differences in catch collections between sheared and unsheared sheep and UV light-suction trap controls for C. dewulfi females (a), unpigmented females (b) and pigmented females (c). Table S11. Regression coefficients for the final negative binomial GLMs for collections of C. chiopterus females on sheared and unsheared sheep. (DOCX 37 kb)

The liver fluke Fasciola hepatica is a trematode parasite with a worldwide distribution and is the cause of important production losses in the dairy industry. The aim of this observational study was to assess the prevalence of exposure to F. hepatica in a group of high yielding dairy herds, to determine the risk factors and investigate their associations with production and fertility parameters. Bulk milk tank samples from 606 herds that supply a single retailer with liquid milk were tested with an antibody ELISA for F. hepatica. Multivariable linear regression was used to investigate the effect of farm management and environmental risk factors on F. hepatica exposure. Higher rainfall, grazing boggy pasture, presence of beef cattle on farm, access to a stream or pond and smaller herd size were associated with an increased risk of exposure. Univariable regression was used to look for associations between fluke exposure and production-related variables including milk yield, composition, somatic cell count and calving index. Although causation cannot be assumed, a significant (p

Increased globalisation and climate change have led to concern about the increasing risk of arthropod-borne virus (arbovirus) outbreaks globally. An outbreak of equine arboviral disease in northern Europe could impact significantly on equine welfare, and result in economic losses. Early identification of arboviral disease by horse owners may help limit disease spread. In order to determine what horse owners understand about arboviral diseases of horses and their vectors, the authors undertook an open, cross-sectional online survey of UK horse owners. The questionnaire was distributed using social media and a press release and was active between May and July 2016. There were 466 respondents, of whom 327 completed the survey in full. High proportions of respondents correctly identified photographic images of biting midges (71.2 per cent) and mosquitoes (65.4 per cent), yet few were aware that they transmit equine infectious diseases (31.4 per cent and 35.9 per cent, respectively). Of the total number of respondents, only 7.4 per cent and 16.2 per cent correctly named a disease transmitted by biting midges and mosquitoes, respectively. Only 13.1 per cent and 12.5 per cent of participants identified specific clinical signs of African horse sickness (AHS) and West Nile virus (WNV), respectively. This study demonstrates that in the event of heightened disease risk educational campaigns directed towards horse owners need to be implemented, focussing on disease awareness, clinical signs and effective disease prevention strategies.

Open peer review. (PDF 357Â kb)

The emergence of Japanese encephalitis virus (JEV) in the Himalayan highlands is of significant veterinary and public health concern and may be related to climate warming and anthropogenic landscape change, or simply improved surveillance. To investigate this phenomenon, a One Health approach focusing on the phylogeography of JEV, the distribution and abundance of the mosquito vectors, and seroprevalence in humans and animal reservoirs would be useful to understand the epidemiology of Japanese encephalitis in highland areas.

Avian malaria is one of the most serious diseases in penguins under human care and could become a severe threat to the conservation of vulnerable wild populations. It is caused by the Haemosporidia parasites of the genus Plasmodium and needs a mosquito vector for its transmission. We captured mosquitoes during two years in Chester Zoo (Cheshire) and one year in Flamingo Land (Yorkshire); both zoos house Humboldt penguins (Spheniscus humboldti). The mosquito temporal and spatial abundance across the seasons and sites were analysed. It was found that Culex pipiens, the principal avian malaria vector in Europe, was the most abundant species. There was a peak in the mosquito abundance during the summer as expected, but it was at different months between sites and years. The abundance of mosquitoes also varied among sampling areas; one area in Chester Zoo captured a greater proportion of mosquitoes than the others in both years, and in Flamingo Land, we also found an area with consistent high catches. Blood-fed mosquitoes were captured and analysed to identify the host on which they had fed. Different proportions of blood-fed mosquitoes were captured by areas and months; more were collected during the summer and in certain areas that not in all cases were related to a high abundance of un-fed mosquitoes. Most of these mosquitoes were Culex pipiens and Culiseta annulata; it was confirmed that the first one prefers to feed on birds and the second one on non-human mammals. However, many Culex pipiens fed on humans, which alert us about the possible nuisance for visitors and the potential transmission risk of zoonotic diseases. A partially identified Culicinae mosquito, likely to be Culex pipiens, and an Anopheles maculipennis s. l. fed on penguins; so, they could be involved in avian malaria transmission. It was found that mosquitoes travel variable distance after feeding and therefore, the control measures against mosquitoes should cover more than the areas of immediate concern. The environmental variables were analysed to understand the drivers of the diverse mosquito captures. The temperature was the most important variable related to mosquito abundance, and the dense vegetation, proximity to mosquito oviposition sites and closeness to animal exhibits were also significant. Therefore, the temperature could guide actions for mosquito control and avian malaria prevention and avoiding those surrounding features near the penguin exhibits could prevent high densities of mosquitoes. Many aspects of avian malaria epidemiology are uncertain so, through an online survey, the knowledge of the staff in zoos and wildlife parks about the disease was gathered. It was found that avian malaria had affected penguins in more than half of the answering institutions, involving mainly Humboldt and African penguins (Spheniscus demersus) with high lethality rates; therefore, efforts on preventive actions are encouraged. Avian malaria parasites were found in Culex pipiens mosquitoes and their saliva, wild birds and penguins, suggesting that the transmission process happens locally. Mosquito populations are dynamic, and the biosurveillance of their populations is needed to better understand their role as disease vectors and to implement effective control measures at the right time, assisting in this way the prevention of avian malaria in captive penguins.

Culicoides biting midges (Diptera: Ceratopogonidae), are the vectors of several viruses affecting livestock including bluetongue and Schmallenberg viruses. There are no effective control methods of the vectors, and disease control therefore relies on vaccines which, given the rapid emergence/spread of the viruses, are often not available. Thus, there is increasing interest in the heritable bacteria (endosymbionts) of invertebrates as they present novel targets for control initiatives. For example, the endosymbiont Wolbachia is capable of inducing a “virus blocking” phenotype in mosquito hosts. Previous studies on biting midges, have revealed infections with the endosymbiotic bacteria, Wolbachia and Cardinium. However, other common symbionts, such as Rickettsia, are underexplored. I first clarify which Culicoides vector species are appropriate for further study of Cardinium-midge interactions. Reinvestigation of a previous UK screening study indicates spurious identification of Cardinium infection in the vector species C. pulicaris, as a result of inappropriate methodology and interpretation. In addition, this chapter establishes associations between mitochondrial haplotypes (mitotypes), used as a phylogeographic marker, and Cardinium infection in the globally important vector C. imicola. The concordance of mitotypes and Cardinium infection in populations of C. imicola from different geographic regions suggests a potential confounding of future biodiversity studies which fail to consider the presence of Cardinium. I then describe the results of a targeted screening of Culicoides populations for Rickettsia symbionts. Through conventional PCR, I demonstrated that Rickettsia represent a widespread but previously overlooked association, reaching high frequencies in midge populations and present in over a third of the species tested. Sequence typing clusters the Rickettsia within the Limoniae group of the genus, a group known to infect several aquatic and haematophagous taxa. Considering the presence of Rickettsia in several vector species, this result highlights the need to establish the impact of this newly-found association on vector competence. Leading from this, I describe the tropism of a Rickettsia endosymbiont present in the Scottish Highland midge, Culicoides impunctatus. Fluorescence in-situ hybridisation (FISH) and transmission electron microscopy (TEM) analysis indicated the presence of Rickettsia bacteria in ovarian tissue and the ovarian suspensory ligament suggesting a novel germline targeting strategy. In addition, Rickettsia presence in the fat body of larvae indicates potential host fitness effects to be investigated in the future. In the final study, I investigate inadvertent amplification of Rickettsia DNA through the common taxonomic identification technique of DNA barcoding. Through collaboration with the Barcoding of Life Data System (BOLD) curators, I undertook a systematic survey to determine the scale of this phenomenon, as well as investigate its potential to unveil new Rickettsia-infected host species. My results determine that unintended Rickettsia amplification is common and should be considered when designing future barcoding studies. In addition, a new wealth of host information was uncovered which can inform future directions of investigation pertaining to Rickettsia.

This thesis considers the uncertainty in forecasts of climate-driven disease risk, focusing on seasonal and decadal timescales. An analysis of the skill of decadal climate predictions is carried out, looking at the first multi-model decadal hindcast set produced as part of the ENSEMBLES project. Some skill in the prediction of global average temperature trends over the forthcoming decade is shown, with no skill evident for precipitation. Focusing on smaller areas shows limited skill in predicting temperature trends and no skill for precipitation trends, suggesting that decadal climate models cannot currently make useful predictions of disease risk. Seasonal climate forecasting skill is then considered. Seasonal hindcasts produced by two research projects, DEMETER and ENSEMBLES, are compared with the most recent version of the European Centre for Medium-Range Weather Forecast’s seasonal forecast model, System 4. The models are validated over Africa and the Indian subcontinent, and it is shown that in general System 4 forecasts are an improvement over the DEMETER and ENSEMBLES multimodel ensembles, particularly for West Africa. A more in depth study of System 4 is subsequently carried out, comparing the variation in skill between forecast start dates. Forecast value is demonstrated at multiple lead times, with most skill found for West African regions and Botswana and limited skill for India; indicating when and where forecasts can potentially be issued to users. Forecasting malaria is then studied by using Liverpool Malaria Model (LMM) driven by System 4. Skill is demonstrated over Botswana, particularly for forecasts issued in November, validating against laboratory confirmed cases of malaria. This is an improvement on previous work where the LMM was driven with the DEMETER seasonal hindcasts. Where malaria data is not available, System 4-driven LMM hindcasts are compared to LMM driven by ERA-Interim in a tier-2 validation context. Skill is demonstrated at the epidemic fringe of the Sahel and in north west Malawi, whilst the Gulf of Guinea shows no skill. This is consistent with previous work suggesting the LMM performs better in epidemic than in endemic regions. A method for interpreting hindcast validation results as uncertainty quantification is then presented. Finally, the uncertainty in the relationship between seasonal average climate and malaria risk is analysed, using the LMM driven by the 20th century reanalysis dataset. The relationship parameters describing seasonal average climate and malaria risk is explored and impact surfaces are created, relating seasonal average temperature and precipitation to average seasonal malaria incidence. The robustness of these impact surfaces is investigated by comparing the surfaces associated with different LMM survival schemes. A method of combining impact surfaces based on tercile categories is described and implemented and it is demonstrated how the resulting graphic could be integrated with a seasonal ensemble forecast system. Such a tool is potentially useful for decision-makers, allowing an intuitive visual communication of the quantified uncertainty in predicting climate-driven disease risk at seasonal timescales.

Background Plague, a zoonosis caused by Yersinia pestis, is found in Asia and the Americas, but predominantly in Africa, with the island of Madagascar reporting almost one third of human cases worldwide. Plague's occurrence is affected by local climate factors which in turn are influenced by large-scale climate phenomena such as the El Niño Southern Oscillation (ENSO). The effects of ENSO on regional climate are often enhanced or reduced by a second large-scale climate phenomenon, the Indian Ocean Dipole (IOD). It is known that ENSO and the IOD interact as drivers of disease. Yet the impacts of these phenomena in driving plague dynamics via their effect on regional climate, and specifically contributing to the foci of transmission on Madagascar, are unknown. Here we present the first analysis of the effects of ENSO and IOD on plague in Madagascar. Methodology/principal findings We use a forty-eight year monthly time-series of reported human plague cases from 1960 to 2008. Using wavelet analysis, we show that over the last fifty years there have been complex non-stationary associations between ENSO/IOD and the dynamics of plague in Madagascar. We demonstrate that ENSO and IOD influence temperature in Madagascar and that temperature and plague cycles are associated. The effects on plague appear to be mediated more by temperature, but precipitation also undoubtedly influences plague in Madagascar. Our results confirm a relationship between plague anomalies and an increase in the intensity of ENSO events and precipitation. Conclusions/significance This work widens the understanding of how climate factors acting over different temporal scales can combine to drive local disease dynamics. Given the association of increasing ENSO strength and plague anomalies in Madagascar it may in future be possible to forecast plague outbreaks in Madagascar. The study gives insight into the complex and changing relationship between climate factors and plague in Madagascar., Author Summary Plague is a vector-borne bacterial infection with rodents and their fleas as its principal hosts. Transmission to humans occurs via the bite of an infected flea. In the highlands of Madagascar, plague is endemic and more than one hundred human cases are reported every year. Global climate is known to affect many infectious diseases and has been shown to affect plague incidence in other areas of the world. The ENSO and the IOD are global climate drivers affecting rainfall and temperature in Madagascar. Our study investigates the effect of global climate drivers on human plague incidence on the island. We found a link between ENSO, IOD, temperature and precipitation and plague incidence throughout the 48-year time-series although it was not constant over time. The correlation between ENSO and plague turned from weakly positive to strongly negative and then to positive, and the association with the IOD became stronger with time. We demonstrate that during periods of high ENSO intensity, plague incidence is likely to increase via ENSO's impact on temperature and precipitation. This shows that climate indices can be a tool to help predict human plague incidence.

BACKGROUND: Prions are known to cause transmissible spongiform encephalopathies (TSE) after accumulation in the central nervous system. There is increasing evidence that prions are also present in body fluids and that prion infection by blood transmission is possible. The low concentration of the proteinaceous agent in body fluids and its long incubation time complicate epidemiologic analysis and estimation of spreading and thus the risk of human infection. This situation is particularly unsatisfactory for food and pharmaceutical industries, given the lack of sensitive tools for monitoring the infectious agent. METHODOLOGY/PRINCIPAL FINDINGS: We have developed an adsorption matrix, Alicon PrioTrap, which binds with high affinity and specificity to prion proteins. Thus we were able to identify prion protein (PrP(C))--the precursor of prions (PrP(Sc))--in milk from humans, cows, sheep, and goats. The absolute amount of PrP(C) differs between the species (from microg/l range in sheep to ng/l range in human milk). PrP(C) is also found in homogenised and pasteurised off-the-shelf milk, and even ultrahigh temperature treatment only partially diminishes endogenous PrP(C) concentration. CONCLUSIONS/SIGNIFICANCE: In view of a recent study showing evidence of prion replication occurring in the mammary gland of scrapie infected sheep suffering from mastitis, the appearance of PrP(C) in milk implies the possibility that milk of TSE-infected animals serves as source for PrP(Sc).