Towards a resource-based habitat approach for spatial modelling of vector-borne disease risks

Given the veterinary and public health impact of vector-borne diseases, there is a clear need to assess the suitability of landscapes for the emergence and spread of these diseases. Current approaches for predicting disease risks neglect key features of the landscape as components of the functional habitat of vectors or hosts, and hence of the pathogen. Empirical–statistical methods do not explicitly incorporate biological mechanisms, whereas current mechanistic models are rarely spatially explicit; both methods ignore the way animals use the landscape (i.e. movement ecology). We argue that applying a functional concept for habitat, i.e. the resource-based habitat concept (RBHC), can solve these issues. The RBHC offers a framework to identify systematically the different ecological resources that are necessary for the completion of the transmission cycle and to relate these resources to (combinations of) landscape features and other environmental factors. The potential of the RBHC as a framework for identifying suitable habitats for vector-borne pathogens is explored and illustrated with the case of bluetongue virus, a midge-transmitted virus affecting ruminants. The concept facilitates the study of functional habitats of the interacting species (vectors as well as hosts) and provides new insight into spatial and temporal variation in transmission opportunities and exposure that ultimately determine disease risks. It may help to identify knowledge gaps and control options arising from changes in the spatial configuration of key resources across the landscape. The RBHC framework may act as a bridge between existing mechanistic and statistical modelling approaches

Modelling the monthly abundance of Culicoides biting midges in nine European countries using Random Forests machine learning

Background: Culicoides biting midges transmit viruses resulting in disease in ruminants and equids such as bluetongue, Schmallenberg disease and African horse sickness. In the past decades, these diseases have led to important economic losses for farmers in Europe. Vector abundance is a key factor in determining the risk of vector-borne disease spread and it is, therefore, important to predict the abundance of Culicoides species involved in the transmission of these pathogens. The objectives of this study were to model and map the monthly abundances of Culicoides in Europe. Methods: We obtained entomological data from 904 farms in nine European countries (Spain, France, Germany, Switzerland, Austria, Poland, Denmark, Sweden and Norway) from 2007 to 2013. Using environmental and climatic predictors from satellite imagery and the machine learning technique Random Forests, we predicted the monthly average abundance at a 1 km2 resolution. We used independent test sets for validation and to assess model performance. Results: The predictive power of the resulting models varied according to month and the Culicoides species/ensembles predicted. Model performance was lower for winter months. Performance was higher for the Obsoletus ensemble, followed by the Pulicaris ensemble, while the model for Culicoides imicola showed a poor performance. Distribution and abundance patterns corresponded well with the known distributions in Europe. The Random Forests model approach was able to distinguish differences in abundance between countries but was not able to predict vector abundance at individual farm level. Conclusions: The models and maps presented here represent an initial attempt to capture large scale geographical and temporal variations in Culicoides abundance. The models are a first step towards producing abundance inputs for R0 modelling of Culicoides-borne infections at a continental scale

Combining dispersion modelling with synoptic patterns to understand the wind-borne transport into the UK of the bluetongue disease vector

Bluetongue, an economically important animal disease, can be spread over long distances by carriage of insect vectors (Culicoides biting midges) on the wind. The weather conditions which influence the midge’s flight are controlled by synoptic scale atmospheric circulations. A method is proposed that links wind-borne dispersion of the insects to synoptic circulation through the use of a dispersion model in combination with principal component analysis (PCA) and cluster analysis. We illustrate how to identify the main synoptic situations present during times of midge incursions into the UK from the European continent. A PCA was conducted on high-pass-filtered mean sea-level pressure data for a domain centred over north-west Europe from 2005 to 2007. A clustering algorithm applied to the PCA scores indicated the data should be divided into five classes for which averages were calculated, providing a classification of the main synoptic types present. Midge incursion events were found to mainly occur in two synoptic categories; 64.8% were associated with a pattern displaying a pressure gradient over the North Atlantic leading to moderate south-westerly flow over the UK and 17.9% of the events occurred when high pressure dominated the region leading to south-easterly or easterly winds. The winds indicated by the pressure maps generally compared well against observations from a surface station and analysis charts. This technique could be used to assess frequency and timings of incursions of virus into new areas on seasonal and decadal timescales, currently not possible with other dispersion or biological modelling methods

Identifying spanish areas at more risk of monthly BTV transmission with a basic reproduction number approach

Bluetongue virus (BTV) causes a disease that is endemic in Spain and its two major biological vector species, C. imicola and the Obsoletus complex species, differ greatly in their ecology and distribution. Understanding the seasonality of BTV transmission in risk areas is key to improving surveillance and control programs, as well as to better understand the pathogen transmission networks between wildlife and livestock. Here, monthly risk transmission maps were generated using risk categories based on well-known BTV R0 equations and predicted abundances of the two most relevant vectors in Spain. Previously, Culicoides spp. predicted abundances in mainland Spain and the Balearic Islands were obtained using remote sensing data and random forest machine learning algorithm. Risk transmission maps were externally assessed with the estimated date of infection of BTV-1 and BTV-4 historical outbreaks. Our results highlight the differences in risk transmission during April-October, June-August being the period with higher R0 values. Likewise, a natural barrier has been identified between northern and central-southern areas at risk that may hamper BTV spread between them. Our results can be relevant to implement risk-based interventions for the prevention, control and surveillance of BTV and other diseases shared between livestock and wildlife host populations

Quantifying the potential for bluetongue virus transmission in Danish cattle farms

We used a mechanistic transmission model to estimate the number of infectious bites (IBs) generated per bluetongue virus (BTV) infected host (cattle) using estimated hourly microclimatic temperatures at 22,004 Danish cattle farms for the period 2000–2016, and Culicoides midge abundance based on 1,453 light-trap collections during 2007–2016. We used a range of published estimates of the duration of the hosts’ infectious period and equations for the relationship between temperature and four key transmission parameters: extrinsic incubation period, daily vector survival rate, daily vector biting rate and host-to-vector transmission rate resulting in 147,456 combinations of daily IBs. More than 82% combinations of the parameter values predicted > 1 IBs per host. The mean IBs (10–90th percentiles) for BTV per infectious host were 59 (0–73) during the transmission period. We estimated a maximum of 14,954 IBs per infectious host at some farms, while a best-case scenario suggested transmission was never possible at some farms. The use of different equations for the vector survival rate and host-to-vector transmission rates resulted in large uncertainty in the predictions. If BTV is introduced in Denmark, local transmission is very likely to occur. Vectors infected as late as mid-September (early autumn) can successfully transmit BTV to a new host until mid-November (late autumn)

Determining and modelling the Bluetongue vector landscape

Bluetongue (BT) is a seasonal vector-borne, viral, disease that causes significant economic and welfare problems in ruminants. It is transmitted by species of Culicoides midges (Diptera: Ceratopogonidae), and as such, the distribution of the disease is restricted to regions where the vectors are present. Once restricted to tropical and subtropical regions of the world, serotypes of BT have been causing outbreaks in southern Europe, following its introduction in 1998, and in 2006, BT serotype-8 emerged in northern Europe, causing devastating economic, welfare and production consequences. The northwards expansion of BT has been attributed to a shift in the geographic limit of the Culicoides imicola Meigen vector, and the involvement of the newly implicated Palaearctic vectors, the Obsoletus and Pulicaris Groups. Little is known about the ecological characteristics of the newly implicated vectors, or indeed those believed to be non-vectors, including their distribution and abundance, making disease risk assessment and management difficult. Within this thesis, a series of field experiments were initiated on a group of farms to gain insight into the distribution and abundance of Culicoides species. The results highlighted that a very high level of variation is seen when trapping Culicoides at the local-scale, yet it is possible to build a strong model explaining this variation using a mixture of host and environmental variables, with satellite-derived ecological correlates. This high level of variation in midge catches present between farms undermines attempts to record their nationwide distribution in larger scale models. The results uniquely model Obsoletus Group abundance, and highlight a difference in host involvement between vector and non-vector models. Further field studies which showed a lack of significant variation both between years and at the within-farm level highlight the robustness of this model in predicting the distribution of the BT vectors species, such that it could prove useful for exploring targeted surveillance and control methods. Culicoides distributions do not remain static, therefore an understanding of their flight behaviour is critical to determining the distance over which an insect may transmit a disease agent and the size of the area over which control should be applied. Laboratory studies were undertaken to validate the use of commercial fluorescent dusts as a quick and effective method of marking Culicoides for both field and laboratory studies, and a ‘self-marking’ technique was conceived. Dispersal studies, using the dusts, determined the distances that Obsoletus Group females and males, as well as C. pulicaris females, are able to disperse over a set period of time. This knowledge of flight speed and distance is of utmost value as a critical component in the modelling of BT disease and other Culicoides-borne diseases. The Obsoletus Group contains four members (C. obsoletus, C. scoticus, C. chiopterus and C. dewulfi¬) which are difficult to differentiate down a microscope. Using morphometric analyses, female C. obsoletus and C. scoticus individuals could be separated under a stereomicroscope based on abdominal measurements. Studies such as those contained in this thesis, therefore, are of utmost value in providing information on critical components in the modelling of BT disease and other Culicoides-borne diseases

Spatio-temporal modelling of bluetongue virus distribution in Northern Australia based on remotely sensed bioclimatic variables

The presence of Bluetongue virus (BTV) in Northern Australia poses an ongoing threat for animal health and although clinical disease has not been detected in livestock, it limits export of livestock from the infected areas. BTV presence is governed by variable environmental conditions, which influence vector and host habitats. The National Arbovirus Monitoring Program (NAMP) was established to determine the extent of virus activity and control the risk of infection spread. Groups of young cattle, previously unexposed to infection, are regularly tested to detect evidence of transmission. This approach is labour and cost intensive and difficult to operate in the remote areas of Northern Australia. The resulting data are therefore characterised by spatial and temporal gaps. The aim of this research is to assess the use of remotely sensed environmental and climatic data as a means of predicting the distribution of BTV seroprevalence throughout Northern Australia to complement conventional surveillance.Environmental factors relating to the viruses’ host and vector habitats and the transmission cycle of BTV have been identified based on the extensive review of virus ecology. Different data sources have been assessed to provide sufficient spatial and temporal coverage for the definition of spatio-temporal environmental variables that can be used to explain and predict the distribution of BTV. Following this assessment, satellite data products from the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Tropical Rainfall Measuring Mission (TRMM) were acquired for the Pilbara in Western Australia, and the Northern Territory. These were reprojected and processed into spatio-temporal variables for the period between the years 2000 and 2009. Due to uncertainty in the precision of the geographic location and timing of animals tested for seropositivity, summary statistics of bioclimatic variables were generated at the station (i.e. property) level for each year. Different combinations of these variables, including vegetation greenness and phenology, land surface temperature and precipitation were screened for correlation with BTV presence using a Generalised Additive Model approach. A final model was developed to predict the presence or absence of BTV seropositivity on the basis of statistical significance of the remotely sensed predictor variables, and informed by knowledge of virus ecological principles.The model, based on the maximum seasonal Normalised Difference Vegetation Index (NDVI), and mean and maximum land surface temperature variables provided excellent discriminatory ability and the basis for the generation of prediction maps of BTV seropositivity for the first eight years. Besides internal assessment, the model’s predictive capabilities were validated using monitoring data from the season 2008/09.It has been demonstrated that the predictions are useful in complementing complement NAMP surveillance by identifying areas at higher risk for seropositivity in cattle, which aids planning of livestock movement and further monitoring activities. Uncertainty in the model was attributed to the spatio-temporal inconsistency in the precision of the available serosurveillance data. The discriminatory ability of models of this type could be further improved by ensuring that exact location details and date of NAMP BTV test events are consistently recorded

Phenotypic and genetic characterization of Culicoides (DIPTERA: CERATOPOGONIDAE) in Portugal and comparison of the effect of pyrethroid insecticides in their control

Tese de Doutoramento em Ciências Veterinárias, especialidade de Sanidade AnimalCulicoides genus is of major importance in animal and human health since hematophagous females are vectors of several pathogens, like viruses (Bluetongue, African Horse Sickness and Schmallenberg) and filarial nematodes, among others. As a consequence, female biting midges are responsible for huge economical losses worldwide. A deeper knowledge of Culicoides fauna present in each country and their ecological preferences is required, so different control strategies can be applied efficiently. The present work was based on Culicoides species captures during the National Entomologic Surveillance Program for Bluetongue disease in mainland Portugal and Azores and Madeira archipelagos (2005-2013), using miniature CDC light traps, and in 2015, with OVI traps, in the framework of VectorNet European network. Biting midges were evaluated phenotypically and genetically, showing the variation of Culicoides species in Portuguese territory. Twenty-two Culicoides species were mentioned for the first time in Portugal, including C. dewulfi and C. montanus in mainland Portugal and species of Obsoletus group in the islands of Azores archipelago where they were never reported, as well as a description of Culicoides paradoxalis, a new species for science. Moreover, a detailed study focused the morphology, genetics and ecology of Obsoletus group, showing that the distribution of those species was unequal in mainland Portugal. Plus, a redefinition of the 3rd palpus segment length/width ratio and spermathecae size intervals, aiming Obsoletus group species identification, together with the reference of anatomical aberrations in these species, was performed, allowing the reduction of errors during midges studies. An identification key for all known Portuguese midges was also created. In this thesis, elaboration of risk assessment maps based on the association of some abiotic variables with the occurrence of C. imicola, C. pulicaris, C. punctatus, C. newsteadi and species from Obsoletus group in mainland Portugal were also performed. Finally, evaluation of C. imicola morphological modifications in sensorial organs localized in the 3rd palpus segment, used for host detection, was performed after an assay with pyrethroid insecticides (permethrin and deltamethrin) at different concentrations, showing complete destruction of sensorial organs with probable feeding implications. The results presented in this scientific work contributed to a better knowledge of Culicoides genus in Portugal, being some of them of worldwide relevance.RESUMO - Caracterização fenotípica e genética de Culicoides (DIPTERA: CERATOPOGONIDAE) em Portugal e comparação do efeito de inseticidas piretróides no seu controlo - Os insetos do género Culicoides (Diptera: Ceratopogonidae) possuem uma grande importância em Saúde Animal e Humana, uma vez que as fêmeas hematófagas são vetores de vários agentes patogénicos, como vírus (da Língua Azul, da Peste Equina Africana, da Doença Hemorrágica Epizoótica e de Schmallenberg), filarídeos, entre outros. Consequentemente, as fêmeas do género Culicoides são responsáveis por elevadas perdas económicas a nível mundial. Um conhecimento profundo da fauna de Culicoides presente em cada país é necessário, assim como as suas preferências ecológicas, de modo a que possam ser aplicadas de modo mais eficaz diferentes estratégias de controlo. Uma das doenças que nos últimos anos afetou gravemente os ovinos em Portugal foi a Doença da Língua Azul. O primeiro foco desta doença em Portugal foi reportado em julho de 1956, afetando os animais da região sul do território abaixo do rio Tejo, excluindo a região algarvia, tendo sido causado pelo serótipo 10 (BTV-10). O país foi considerado livre da doença em 1960 depois da aplicação de uma vacina em ovinos. Nesse período de 4 anos, a doença matou mais de 179 mil ovinos. A Peste Equina Africana foi detetada em Portugal em Agosto de 1989 em Castro Marim, tendo-se alastrado pelo Alentejo, ao longo da zona fronteiriça. As medidas de controlo incluiram o estudo entomológico de insetos do género Culicoides, vacinação massiva dos cavalos, burros e mulas, aspersão de inseticidas nas cavalariças e estábulos e divulgação de informação aos proprietários dos animais sobre prevenção. Até ao final de 1989 a doença vitimou 202 cavalos na zona do rio Guadiana, tendo sido Portugal considerado livre da doença em 1992. Após um silêncio epizoótico de 44 anos, a doença da Língua Azul voltou a surgir em território nacional, nas regiões centro-oeste e sul, em novembro de 2004, sendo desta vez causada pelo serótipo BTV-4. EM 2005, foi criado o Programa Entomológico de Vigilância Nacional para a doença da Língua Azul em Portugal Continental e nos arquipélagos dos Açores e da Madeira (DGV/FMV, 2005-2013) com o objetivo de conhecer a distribuição de Culicoides em território português, reportando às autoridades competentes a presença de espécies com capacidade vetorial, por forma a que se pudesse atuar em tempo real e prevenir a dispersão da Língua Azul em caso de um surto da mesma. Em setembro de 2007, o serótipo BTV-1 foi detetado num concelho do Alentejo perto da fronteira com Espanha. Entre setembro e dezembro de 2007, o serótipo 1 (BTV-1) foi assinalado nas regiões do centro e sul de Portugal continental, tendo-se expandido para o norte do território desde 2008 e mostrando uma diferente distribuição quando comparada com a dos serótipos BTV-4 e BTV-10. As campanhas de vacinação contra os serótipos 4 (2005-2008) e 1 (2007-2010) do vírus da doença da Língua Azul, em ovinos e bovinos, contribuíram para o controlo da emergência e dispersão da doença. Em 2013, o serótipo BTV-4 reemergiu no nosso país, tendo sido adotadas medidas de controlo da doença, que passaram pela vacinação obrigatória dos ovinos e facultativa dos bovinos na região do Algarve contra o referido serótipo. A vacinação contra o mesmo serótipo foi permitida na região do Alentejo como medida profilática. Finalmente, em setembro de 2015, e após um silêncio epizoótico de 3 anos, o serótipo 1 foi novamente detetado na região do Alentejo, nos concelhos de Serpa, Moura e Barrancos. Presentemente, o serótipo 1 encontra-se presente em todo o território português enquanto que o BTV-4 encontra-se em circulação apenas na região do Algarve. Durante o Programa Entomológico de Vigilância Nacional para a doença da Língua Azul em Portugal Continental e nos arquipélagos dos Açores e da Madeira (2005-2013), com recurso a armadilhas do tipo CDC, e em 2015 com armadilhas OVI, no âmbito do grupo de trabalho europeu VectorNet, foram realizadas capturas de insetos do género Culicoides que permitiram a realização do presente trabalho. Os insetos capturados foram analisados fenotípica e geneticamente, mostrando a variação das espécies de Culicoides em território português. C. imicola foi a espécie mais capturada, representando 70,92% do total estimado de insetos capturados. Seguidamente, surgiu C. achrayi (10,34%), C. punctatus (9,34%), espécies do grupo Obsoletus (4,93%) e C. newsteadi (1,93%) como as espécies mais capturadas. C. pulicaris, espécie vetor do vírus da Língua Azul, perfez 0,08% do total estimado de insetos capturados (N=4.384.502). A distribuição espacial das espécies de Culicoides em Portugal Continental apresentou padrões diferentes. Assim, enquanto que algumas espécies deste género estavam dispersas por todo o território (e.g., C. achrayi, C. punctatus), outras localizaram-se preferencialmente nas regiões norte e centro (e.g., C. deltus, C. heliophilus), diversas nas regiões centro e sul (e.g., C. nubeculosus, C. sahariensis) e algumas foram capturadas consistentemente em regiões específicas (e.g., C. impunctatus e C. lupicaris). Vinte e duas espécies de Culicoides foram mencionadas pela primeira vez em Portugal: C. alazanicus, C. deltus, C. dewulfi, C. heliophilus, C. jumineri near C. bahrainensis, C. jurensis, C. kingi, C. lupicaris, C. malevillei, C. montanus, C. paolae, C. picturatus, C. remmi, C. riebi, C. santonicus, C. semimaculatus, C. simulator e C. subfagineus em Portugal continental, C. obsoletus, C. scoticus nas ilhas do arquipélago dos Açores onde ainda não tinham sido referidas e C. circumscriptus e C. newsteadi em todas as ilhas do mesmo arquipélago, com exceção das Flores e do Corvo. Para além destas, foi realizada a descrição de uma nova espécie para a ciência, Culicoides paradoxalis. Outro objetivo deste trabalho focou a morfologia, a genética e a ecologia do grupo Obsoletus, mostrando que a distribuição destas espécies é diferente em Portugal continental. Entre as quatro espécies presentes, C. dewulfi foi apenas identificada em três explorações no Norte do território português. As restantes três espécies do grupo Obsoletus encontravam-se presentes em todo o país, sendo C. obsoletus a espécie mais prevalente no Norte, Centro Sul e Sul de Portugal continental, enquanto que C. scoticus foi a espécie mais prevalente na região Centro Norte. Esta espécie foi menos comum que C. obsoletus e C. montanus nas regiões Centro Sul e Sul. Estas três espécies estão bem adaptadas ao território de Portugal Continental, com a exceção da região Centro Sul. A correta identificação de espécies do complexo Obsoletus nem sempre é possível devido às suas elevadas semelhanças morfológicas. Nesse sentido, foi realizado um estudo com base em várias estruturas anatómicas destes insetos, que levaram à redefinição dos intervalos relativos ao rácio comprimento/largura do 3.º segmento do palpo e ao comprimento das espermatecas. Para além disso, a menção de várias aberrações anatómicas nestas espécies (fossetas sensoriais aberrantes, fossetas sensoriais duplas, segmentos do palpo fundidos, segmentos do palpo com alterações morfológicas, número irregular de espermatecas, espécimens com genitália masculina e simultaneamente com espermatecas, comprimento do 3.º artículo do palpo desigual dentro do mesmo exemplar, flagelómeros antenares fundidos e aberrantes) permitirá uma redução nos erros associados ao estudo destes insetos. Uma chave de identificação para todas as espécies de Culicoides presentes em Portugal foi também elaborada durante este estudo que incidiu sobre cerca de 93.100 exemplares deste género. Nesta tese, a produção de mapas de análise de risco baseados na associação de algumas variáveis abióticas climáticas (temperatura média no período mais seco e no período mais húmido) e edáficas (territórios artificializados, áreas agrícolas e agroflorestais, florestas e meios naturais e seminaturais, zonas húmidas e corpos de água) com a ocorrência de C. imicola, C. pulicaris, C. newsteadi, C. punctatus e espécies do grupo Obsoletus em Portugal Continental foi também efetuada. A partir destes mapas observou-se que a probabilidade de capturar C. imicola é maior nas regiões a sul do rio Tejo e na Beira Baixa, enquanto que C. pulicaris ocorre com maior frequência nas regiões do norte de Portugal continental, na linha costeira e em zonas com elevada altitude. A probabilidade de ocorrência de C. newsteadi é semelhante à de C. imicola, embora aquela espécie possa ser capturada em regiões ligeiramente mais a norte que esta última. C. punctatus pode ocorrer com uma probabilidade maior que 50% em qualquer parte de Portugal Continental e em quase todas as estações do ano. As espécies do grupo Obsoletus surgem nas regiões do norte de Portugal continental, estando estas espécies praticamente ausentes na região Centro Sul durante o outono e inverno. A distribuição do grupo Obsoletus é aproximadamente a oposta de C. imicola. Finalmente, a avaliação de modificações morfológicas dos órgãos sensoriais localizados no 3.º segmento do palpo de C. imicola, usados na deteção do hospedeiro, foi realizada através de microscopia eletrónica de varrimento após um ensaio com inseticidas piretróides (permetrina e deltametrina) em diferentes concentrações. Este estudo revelou a completa destruição dos órgãos sensoriais, com uma provável influência na alimentação destes insetos. Tendo em conta o impacto económico associado aos agentes patogénicos que transmitem, aliado à descoberta recente de novos serótipos do vírus da Língua Azul na Europa (BTV-25 e BTV-27), os resultados apresentados neste trabalho científico evidenciam e sustentam a importância do estudo entomológico dos insetos do género Culicoides.This work was partially funded by the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Ministère en charge de l’Agriculture (France) and by the convention Cherchuer d’Avenir 2011 from Languedoc-Roussillon region (France)