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Additional file 3: Text S3. Structure of the African animal trypanosomosis database

Additional file 1: Text S1. List of scientific publications that contributed to developing the national atlas of tsetse and African animal trypanosomosis in Burkina Faso.

Vector-borne diseases affecting livestock have serious impacts in Africa. Trypanosomosis is caused by parasites transmitted by tsetse flies and other blood-sucking Diptera. The animal form of the disease is a scourge for African livestock keepers, is already present in Latin America and Asia, and has the potential to spread further. A human form of the disease also exists, known as human African trypanosomosis or sleeping sickness. Controlling and progressively minimizing the burden of animal trypanosomosis (COMBAT) is a four-year research and innovation project funded by the European Commission, whose ultimate goal is to reduce the burden of animal trypanosomosis (AT) in Africa. The project builds on the progressive control pathway (PCP), a risk-based, step-wise approach to disease reduction or elimination. COMBAT will strengthen AT control and prevention by improving basic knowledge of AT, developing innovative control tools, reinforcing surveillance, rationalizing control strategies, building capacity, and raising awareness. Knowledge gaps on disease epidemiology, vector ecology and competence, and biological aspects of trypanotolerant livestock will be addressed. Environmentally friendly vector control technologies and more effective and adapted diagnostic tools will be developed. Surveillance will be enhanced by developing information systems, strengthening reporting, and mapping and modelling disease risk in Africa and beyond. The socio-economic burden of AT will be assessed at a range of geographical scales. Guidelines for the PCP and harmonized national control strategies and roadmaps will be developed. Gender equality and ethics will be pivotal in all project activities. The COMBAT project benefits from the expertise of African and European research institutions, national veterinary authorities, and international organizations. The project consortium comprises 21 participants, including a geographically balanced representation from 13 African countries, and it will engage a larger number of AT-affected countries through regional initiatives.

International audience; 1. Tsetse flies (Diptera: Glossinidae) are K‐strategist species and deposit a single larva at 10‐day intervals in specific sites. As larviposition site selection strongly impacts reproductive success, the selection of larviposition sites is unlikely to be random and will be subject to strong selective processes, probably mediated by specific cues.2. This study was designed to assess the existence of an aggregation effect in the palpalis group and to test its potential chemical nature (contact or volatile compounds). The larviposition site selection of Glossina palpalis gambiensis was studied according to the presence of conspecific and heterospecific larvae (morsitans group) buried in substrates. Three sets of experiments were performed with either individual or grouped gravid females and with or without physical access to the substrate.3. In individual larviposition experiments, females were more likely to select trays with buried larvae than unconditioned sand (63.2% and 36.8%, respectively; P

Tsetse flies (Diptera: Glossinidae) are the cyclical vectors of trypanosomes, the causative agents of African animal trypanosomosis or nagana in animals and human African trypanosomosis or sleeping sickness in humans. Tsetse flies are K-strategist species with the deposition of a single larva at 10 days intervals in specific sites. As larviposition site selection will strongly impact reproductive success, it is obvious that the selection of larviposition sites is not random and is under strong selective processes, probably mediated by specific cues as suggested by the existence of an aggregation factor in the Morsitans and Fusca groups. This study aimed to highlight the existence of an aggregation effect in the Palpalis group and to test for its chemical nature. We studied the larviposition site selection of Glossina palpalis gambiensis according to the presence of conspecific and heterospecific larvae buried in substrates in different settings. Three sets of experiments were performed with either individual or grouped (n = 50) gravid females, and with physical access to substrate or not. In both individual and grouped larviposition experiments, females selected significantly more often trays conditioned by larvae (PGlossina palpalis gambiensis. However, these compounds seem not to be species-specific and therefore offer new avenues for the behavioural manipulation of these vectors and for the development of new vector control tools targeting gravid females.Author summaryLarviposition site selection in tsetse flies is govern by several biotic and abiotic factors that lead to an aggregation effect of larvae. Among those, larvae are suspected to produce chemicals that drive females to breeding site but little information is available. This study aimed to highlight the existence of an aggregation effect of larval origin in the Palpalis group and to test for its chemical nature. Through behavioural larviposition choice experiments, we showed that females of Glossina palpalis gambiensis deposit their larvae significantly more often in trays conditioned either by conspecific or heterospecific larvae, even in the absence of physical contact with the substrate. These results highlight the first evidence for aggregation effect in Glossina palpalis gambiensis mediated by volatile semiochemicals of larval origin. Isolation and identification of these chemicals should offer new avenues for the behavioural manipulation of these vectors and for the development of new vector control tools targeting gravid females.

Our understanding on the structure and role of viral communities in animal hosts has not yet reached the knowledge level attained on the bacteriome. This situation is, among others, probably due to technical constraints in adapting metagenomics, a main tool in bacteriome studies, to the characterisation of viral communities. Technical developments have been achieved for most steps of viral metagenomics. However, there is yet a key step that has received little attention, that of library preparation. This situation is surprising because developments in library preparation have largely facilitated bacteriome studies. Here, we present a library preparation optimized for metagenomics of RNA viruses from animals. The library has been designed to provide advantages found in metabarcoding libraries used in bacteriome studies, while allowing shotgun sequencing as required in viral metagenomics. We have validated a full metagenomics approach incorporating our library preparation and using mock viral communities. We have further tested our approach in two pilot studies with field-caught insects, all vectors of viral diseases. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition in a mosquito species, and thus the existence of deterministic forces shaping its virome. Finally, the sensitivity of our approach was relatively good when compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught vectors. Our approach could facilitate studies on viral communities from animals and the democratisation of metagenomics in virus ecology.

International audience; In many parts of Africa, tsetse eradication is impossible due to political, environmental or economic circumstances. In these situations, African animal trypanosomosis control relies on communities or farmer-based control, implemented at a local scale in accordance to the eco-epidemiological context and the cattle rearing system to be sustainable. Management of the African animal trypanosomosis requires integrated controls strategies that combine the use of more than one locally-based tool and where possible, needs to be assisted by veterinarians and other animal health professionals. Several tsetse control methods based on insecticide treated cattle (i.e. pour-on, manual spraying, community bath) and insecticide treated target (traps and screens impregnated with insecticides) are available and should be complemented with diagnostic tests and medication (active trypanocides with prophylactic and/or therapeutic action). However, their adoption is mainly dependent on the engagement of communities, farmers and herders. Indeed, the adoption of a locally-adapted control strategy will depend on farmers socio-technical networks, the cost-effectiveness of the control activities, as well as the time and cost for implementation. In general, insecticide treated cattle methods are the most suitable and acceptable for farmers, because they protect a private good i.e. cattle, whereas insecticide treated targets are generally considered to provide a public good. Nonetheless, selection of the most appropriate tools requires consideration of local disease epidemiology (including host-parasite coevolution), local environmental and socioeconomic constraints. The active involvement of communities, farmers and herders is essential from the beginning of the conception of innovative control strategies, and the cost of local integrated pest management should be reduced as much as possible, to be adopted as an acceptable and sustainable animal production cost.

Introduction : Les trypanosomoses africaines sont transmises par la mouche tsé-tsé aux humains et au bétail. En Côte d'Ivoire, la Trypanosomiase Humaine Africaine (THA) sévit principalement dans la région de la Marahoué, sous forme de foyers où sévit également la Trypanosomose Animale Africaine (TAA). Cependant, le réservoir animal à T.b.gambiense, qui intervient probablement dans le cycle pathogène de la maladie chez l'homme, n'a jamais été pris en compte dans la lutte contre la THA en Côte d'Ivoire. Matériel et méthodes : Dans le but de mener une lutte durable, des enquêtes géographiques, entomologiques et parasitologiques de bases ont été menées dans le foyer de THA de Sinfra ; et des actions de lutte combinées et intégrées ciblant les humains, les tsé-tsé, le bétail et les porcs domestiques ont été proposées. Résultats : Les plus fortes densités de Glossina palpalis palpalis, ont été trouvées dans et autour des villages où les porcs villageois en divagation sont présents. Ces porcs sont les plus infectés de tous les animaux par des trypanosomes (85,7%) et constituent l'alimentation préférée des tsé-tsé (87%). Conclusion: Les animaux domestiques comme les porcs pourraient jouer un rôle dans l'épidémiologie de la THA. Cela suggère leur prise en compte dans les stratégies de lutte basées sur le concept one health, dans un contexte d'élimination durable.

Contexte Dans les programmes d'éradication des glossines, les mâles stériles sont marqués avec de la poudre fluorescente avant d'être lâchés afin de pouvoir différencier les mâles stériles des sauvages dans les pièges de suivi de l'impact des opérations de lutte. Cependant, il arrive que la couleur disparaisse de la mouche à un moment de leur vie sur le terrain et il devient difficile de différencier les mâles sauvages des stériles à l'aide d'une caméra UV. Dans un contexte d'éradication, comme c'est le cas dans la zone des Niayes au Sénégal, tout doute doit être levé quant à la nature de la mouche qui est capturée sur le terrain (stérile ou sauvage), surtout en phase finale. En effet, les lâchers doivent être poursuivis pendant 6-12 mois après la capture de la dernière mouche sauvage. Méthodologie Nous avons développé une technique moléculaire basée sur la détermination des haplotypes du cytochrome oxydase de G. p. gambiensis pour faire la distinction entre les mâles sauvages et stériles. L'ADN a été isolé à partir de la tête des mouches (sauvages du Sénégal et du Burkina et stériles d'élevage) et une partie de l'extrémité 5' du cytochrome oxydase I du gène mitochondrial a été amplifiée pour finalement être séquencée. Les séquences ont été alignées et comparées en utilisant "Blast" dans GenBank. Résultats Tous les mâles stériles de la colonie du Burkina Faso présentaient le même haplotype et différaient systématiquement des mouches mâles sauvages piégés au Sénégal et au Burkina Faso. Ceci a permis une discrimination à 100% entre les mâles stériles et sauvages de G. p. gambiensis. Conclusions Cet outil pourrait être utile pour d'autres campagnes de lutte contre la tsé-tsé avec une composante SIT dans le cadre de la PATTEC et, plus généralement, pour d'autres programmes de lutte contre d'autres insectes vecteurs.

In order to assess the effect of irradiation on male pupae of Glossina palpalis gambiensis, we assessed quality parameters of the irradiated male pupae, notably the hatching rate of the pupae, the flying ability of emerged tsetse flies and survival rate of young flies in starving condition following an available quality control protocol. The fertility of male flies from irradiated pupae was also assessed through female productivity and the insemination ability of irradiated males. For this purpose 30 virgin females of 3 days old were mated with 10 irradiated males aged 6 days in breeding cages. Productivity (number of pupae) was compared to a control batch. Simultaneously to this test, other cages of 30 virgin females of 3 days old, mated with 10 irradiated males of 6 days old were followed for the insemination capacity of the irradiated males. Dissections were performed to evaluate the filling level of spermatheca of females mated with irradi-ated males and those mated with control males. Irradiation had no effect on pupae hatching (p=0.083). The fly ability rate was significantly greater in the control group than in the treated lot (p

Figure S2. Line plot of the barcode gap for our DNA reference libraries. For each individual in the dataset, the light sky-blue lines represent the maximum intraspecific distance (bottom of line value), and the minimum interspecific distance (top of line value). The red lines show where this relationship is reversed, and the closest non-conspecific is actually closer to the query than its nearest conspecific, i.e. the situation where there is no barcoding gap. (PDF 3 kb)

Generalized linear model (GLM) fixed effect statistical results. (DOC 269 kb)

L'éradication des glossines par la technique de l'insecte stérile, nécessite une production en masse de glossines de bonne qualité biologique. La présente étude a été menée pour évaluer l'impact de la durée de congélation du sang utilisé pour les repas sanguin sur les performances des glossines afin de décider de l'utilisation de ce type de sang en élevage des glossines du Centre International de Recherche-Développement sur l'Elevage en zone Subhumide. Méthodes : Trois lots de glossines ont été alimentés avec 3 groupes de sang congelé de différente durée de conservation : 1 mois (E1), 3 mois (E2) et 5 mois (E3) en comparaison avec un lot témoin alimenté avec du sang frais (C) non congelé. 810 glossines ont été utilisées pour les 3 groupes de sang congelé et 270 glossines pour le sang frais non congelé soit un total de 1080 glossines. Les paramètres biologiques suivis ont été la survie, la productivité, le taux d'éclosion de la descendance et les performances de vol. Résultats : Aucune différence significative n'a été observée entre les différents traitements en ce qui concerne la survie, le taux d'éclosion des pupes et la performance de vol des glossines. Pour ce qui est de la productivité, celle du témoin était significativement supérieure à celle du lot alimenté avec le sang congelé de 5 mois. Conclusion : le sang congelé en provenance de l'abattoir de Bobo-Dioulasso pourrait être conservé jusqu'à 4 mois à – 18°C, sans que cela n'affecte la qualité des mouches.

Introduction En Côte d'Ivoire, la région de Méagui a été mise en valeur tardivement, mais elle affiche des densités de population pouvant atteindre plus de 400 hab/km2. Dans cette région, parallèlement aux fortes densités de population humaine, il a été mis en évidence une disparition des glossines sur de vastes superficies. On suspecte l'impact de l'anthropisation sur la disparition des glossines, et notamment l'utilisation massive de pesticides. Matériels et méthodes Nous avons cherché à déterminer les modalités d'utilisation des pesticides (produits, quantité, fréquence) dans une zone allant de la ville de Méagui jusqu'au parc national de Tai. Pour cela, à l'aide du GPS, nous avons délimité 100 parcelles de cultures (cacao-café, hévéa, riz, maraicher) traitées avec des pesticides. Un questionnaire sur les modalités d'utilisation des pesticides a été soumis aux paysans propriétaires des parcelles délimitées. Résultats Au total, 74 pesticides différents ont été cités par les paysans, parmi lesquels 48 insecticides et 26 herbicides. En moyenne, la fréquence de pulvérisation des parcelles à l'aide de pesticides est estimée à 3 fois dans l'année. L'ensemble des parcelles enquêtées, d'une superficie totale de 335 hectares, reçoit une application annuelle de 1623 litres de pesticides (4,8 l/hectare). L'insecticide le plus utilisé par les paysans est la grosudine dont la substance active contient la bifenthrine appartenant à la famille des pyréthrinoides de synthèse. Conclusion Les modalités d'épandage de pesticides adoptées par les paysans ont probablement des conséquences sur les densités de glossines et donc sur le risque des trypanosomoses.

International audience; Phylogenetic relationships of Culicoides species of the Afrotropical region are problematic as different authors disagree on the placement of species into specific subgenera or groups. In this study we sequenced two mitochondrial (COI and 16S rDNA) and two nuclear (CAD and 28S rDNA) gene fragments to reconstruct phylogenetic relationships within the Avaritia, Remmia and Synhelea subgenera and the Milnei, Neavei and Similis groups of Culicoides using both Bayesian inference and maximum-likelihood approaches. Based on phylogenetic trees, we used the bGMYC (Bayesian General Mixed Yule Coalescent model) and the PTP (Bayesian Poisson Tree Processes) to investigate species boundaries. All species relationships within the studied subgenera and groups were well-supported by using morphological characters and molecular analyses. The subgenus Avaritia includes (i) all of the species of the Imicola group, as well as the putative new species, C.sp. #22, and we confirmed the monophyly of this group; (ii) the Dasyops group includes C.kanagai and C.sp. #54 Meiswinkel (new species), shown to be monophyletic; (iii) the C.sp. #20 belongs to the Orientalis group; (iv) C.grahamii, C.gulbenkiani and C. kibatiensis. Our results also show that subgenus Remmia is monophyletic. Relationships of species of the Milnei group were well-supported and demonstrate the monophyly of this group. Borkent's classification for Similis group is confirmed. In addition, C.neavei and C.ovalis (Neavei group) are placed in the subgenus Synhelea.

The study of viral communities has recently been boosted by the use of the so-called high-throughput sequencing (HTS) technologies. Coupled with random amplification of nucleic acids, HTS allows the identification of viral species present in a given sample without a-priori knowledge on their identity but their resemblance to known viruses. The huge interest of this approach for virus ecology and diagnostics has triggered several technical improvements in most steps required in virus metagenomics, from nucleic-acid extraction to bioinformatics analysis of sequencing results. Surprisingly, there is yet a key step that has received little attention, that of library preparation. Here, we describe a library preparation for exploring viral diversity in a large number of samples with the use of high-throughput sequencing. This method uses custom adaptors that are PCR ligated, allowing low cost, high multiplexing and fully exploitable read lengths. After validation of our method with artificial viral communities, we have tested it with two samples set from wild-caught arthropod vectors showing that our approach allows to identify an arbovirus in highly-degraded samples with a relatively high sensitivity.

En Afrique subsaharienne, la Trypanosomiase Humaine Africaine (THA ou maladie du sommeil) est une maladie parasitaire négligée provoquée par un trypanosome (protozoaire flagellé), transmis à l'homme par la mouche tsé-tsé (Glossina spp.). Cette mouche hématophage est également en grande partie responsable de la transmission de trypanosomes aux animaux, provoquant la Trypanosomose Animale Africaine (TAA ou nagana). Ce complexe de maladies a un impact important sur la santé humaine et animale et sur la productivité en Afrique. L'élevage du bétail dans les zones endémiques est difficile, et entraîne des pertes économiques de plusieurs milliards de dollars par an. La mouche tsé-tsé reste cependant un insecte vulnérable, sensible aux modifications environnementales et aux insecticides. En 2015 en Côte d'Ivoire, il a été mis en évidence une grande zone forestière (200 km2) où les glossines (Glossina palpalis palpalis) ont totalement disparues, en l'absence de lutte anti-vectorielle bien que l'environnement semble rester propice à leur développement. L'hypothèse sous-jacente à la disparition des glossines serait liée aux fortes densités de population humaines et aux pratiques agricoles associées qui se caractérisent par une utilisation importante de de produits phytosanitaires et qui affecteraient la survie des mouches. Après avoir caractérisé les produits les plus utilisés par les agriculteurs, nous les avons testés en bioessays par contact tarsal sur l'espèce Glossina palpalis gambiensis. Cette étude actuellement en cours nous permettra de mettre en évidence l'impact collatéral des traitements phytosanitaires en forêt de Côte d'Ivoire sur les populations de glossines.