Facing increasing needs to feed human populations requires, more than ever, enhancing quantity, quality, safety and security of agricultural products, and, at the same time, to reduce environmental contamination. Thus, in livestock production, it is required to control blood-feeding flies such as tabanids and stable flies which are responsible of annual losses estimated at 130Kg of milk/cow and 25-60Kg of meat/ox. To the huge blood spoliation (up to 0.5 liter/day) are added: stress, loss of appetite and energy, immunosuppression and mechanical transmission of viruses (equine infectious anemia, ovine catarrhal fever), bacteria (Q fever, anthrax) and parasites (Besnoitia, Trypanosoma), with dramatic medical and economic consequences. Control of hematophagous flies is most often neglected or occasional, since insecticide spraying on walls or animals (spray, pour on) is expensive, of low efficacy and meets increasing chemo-resistance problems. Moreover, residues contamination of animal products and environment is unacceptable, especially for organic farming. Tsetse fly control using insecticide impregnated targets proved to be efficient in Africa, because tsetse flies have low prolificacy and are very sensitive to insecticides. Unfortunately this does not apply to other hematophagous flies such as Tabanids (> 4000 species present in all types of environments and climates), Stomoxys (one species is cosmopolite) and other hematophagous insects such as Haematobia and Musca crassirostris, which are highly prolific, and may develop early chemo-resistance to insecticides. FlyScreen project aims at the development and optimization of efficient, low cost and low or non-polluting methods for the control of hematophagous insects. It will consist in: (i) designing and optimizing specific color baited attractant screens/traps (excluding pollinators); (ii) developing and evaluating in laboratory conditions various toxic systems including: growth hormones or insecticides incorporation into polymers (slow release), single or combined, UV and water-protection and/or special abrasive coating (which advantage is the absence of chemo-resistance) and attractants; (iii) evaluating and validating these screens in semi-liberty and field conditions to measure efficacy and environmental safety; and (iv) promoting low-cost, low-polluting, and possibly insecticide-free control methods. FlyScreen project will be carried out in partnership by UMR17/InterTryp (CIRAD-bios) bringing expertise in biting insects and tropical field spots for evaluation, as well as expertise on mathematical modeling to support impact and cost studies; UMR1225/ IHAP (National Veterinary School of Toulouse ; ENVT), bringing biological material (evaluation on laboratory reared stomoxes) and field spots in France, UMR 5175/CEFE UPVM (University Paul-Valery, Montpellier), bringing expertise in stomoxes and biting insect trapping technologies, Kasetsart University (Bangkok, Thailand) offering facilities for field experimentation in a rich entomofauna area, and “AtoZ” enterprise, specialized in the development, production and commercialization of attractive fabrics and/or mosquito nets, processed under various technologies including biocide incorporation and coating. Additional support from CIRDES and IRD will allow extending the evaluation of toxic fabrics and screens to tsetse flies. Relevant treatment technologies and prototyping will be handled by AtoZ enterprise, while optimization, validation and safety assessment of screens will be handled by public organisms. These low cost targeted and environmentally friendly control tools should be easy to adopt. They will bring a major breakthrough in the control of hematophagous flies, so far neglected due to the low efficacy and high cost of current insecticide spraying systems. Development of insecticide-free attractive lethal screens is the ultimate goal of FlyScreen.

Our capacity to predict areas at risk of emergence of infectious animal diseases (ID) and to minimize pathogen spreading is directly linked to our understanding of population dynamics of pathogens within and outside hosts, including interactions within and between hosts and within a community of hosts. These relationships are complexified by global changes (mobility intensification, land-use, and climate changes), which highly influence contacts among hosts and vectors’ distribution. Therefore, there is a crucial need to produce knowledge regarding population dynamics of pathogens. This relies on three main issues, which are: (i) identify mechanisms and drivers promoting an increase in virulence, transmissibility and host-shift, (ii) well understand the impact of host factors as a key parameter of pathogen evolution and dynamics, in particular those provided by vaccination or pre-existing immunity or by host genetics, and (iii) identify transmission routes, including the role of vectors and of the environment in dissemination and transmission to highlight areas at risk of emergence and spread. Addressing these issues is essential for ID management, in providing stakeholders and policy makers with strategies and methods for surveillance, prevention and control of IDs (breaking the route of transmission, detection, inactivation of pathogens…) within the context of global changes. Within the frame of the Research Innovation Action HORIZON-CL6-2022-FARM2FORK-02-03 call, WiLiMan-ID intends to tackle these issues using IDs that each represent both a threat and a model for studying the ecology of infectious animal diseases, thanks to the diversity of transmission pathways and hosts and putative vectors involved. The communities of hosts considered vary depending on the disease and include humans, domestic animals (poultry, horses and pigs) and wildlife (wild birds, wild boars and cervids). The selected IDs are avian influenza, caused by avian influenza virus; African horse sickness caused by African horse sickness virus, fatal neuronal disease caused by West Nile virus (that will be studied together with the Usutu virus as a co-infecting agent); African swine fever caused by African swine fever virus; and chronic wasting disease caused by an atypical pathogen belonging to the prion-like family. The two main innovative aspects of WiLiMan-ID are (i) the integration of fine-grained features of pathogens and host behaviour with large scale observations across different compartments of the ecosystem to gain an integrated vision of ID (re-)emergence, persistence and spread, and (ii) the study of contrasted patho-ecosystems in order to gain a more complete view of their intertwinement. This will help us gain relevant knowledge and develop methods to anticipate and face future, mostly unknown, infectious health threats with better proficiency. Overall, WiLiMan-ID aims at (i) improving the capacity for risk-based surveillance thanks to a better understanding of sources and pathways of emergence and spread of animal IDs, (ii) enhancing the capacity to prevent and control IDs in animals, and their potential impact in human populations, and (iii) improving our understanding of the impact of climate change on pathogen ecology and animal IDs to predict and possibly anticipate with appropriate countermeasures. To tackle this challenge and reach the expected outcomes of the call, the consortium will bring together a strong group of academic and non-academic (private companies, stakeholders…) partners with the wide range of expertise needed to intregrate the multiple levels of complexity (pathogen, host, communities of hosts, territory) of WiLiMan-ID and to interlink complementary disciplines. WiLiMan-ID will be embeded within Prezode and will thus benefit from the network developed by this initiative.

Chronic Wasting Disease (CWD) is a prion disease that affects wild and farmed cervids. CWD is a highly contagious: over the last 15 years the disease has spread across the whole United States of America and Canada. The CWD epidemics reached a stage where it now threatens the long term survival of cervid populations. Beside the ecological disaster it represents, major concerns exist with regard to the risk that CWD prions might represent for human (zoonosis) and other animal species (propagation in farmed ruminants) During three decades Europe was considered to be free of CWD. However, CWD cases have now been identified in three European countries. The goals of this project are: • to provide the necessary elements for an in depth assessment of the public health risks that are associated with the emergence of CWD prions in Europe. • to identify allele that would be associated with genetic resistance/ susceptibility to the disease in the cervid populations.

The aim of the Path2Bos project is to reconstruct the evolutionary path of cattle from its domestication starting about 10,000 years ago in Anatolia, during its later spread into Europe and Africa and up to now, through a paleogenomic analysis of fossils, the direct witnesses of evolution. The goal is to identify genomic regions that were selected at the early stages of domestication, corresponding to basic phenotypes that should be preserved in ongoing genetic selection schemes. The project is based on a previous paleogenetic characterization of a large number (~ 700) of 9,000- to 1,000-year-old archaeological bones of ancient domesticated cattle and their wild ancestors, the aurochs. We have genotyped the mitochondrial genomes and sequenced the hypervariable regions of almost 200 of these ancient bones, allowing us to assign reliably their mitochondrial haplogroups and to follow the evolution of populations from their initial domestication in Anatolia during the Neolithic as well as their spread and evolution in Europe and North Africa until the Middle Ages. Using sequence capture, we obtained complete mitogenomes from 40 of these samples representing the various clades, reconstructed the evolution and timing of radiation of aurochs’ populations, and untangled the impacts on population diversity of both climate changes during the Pleistocene-Holocene transition and initial domestication. We have sequenced the genome of a 9,000-year-old aurochs from the domestication centre in Anatolia that will serve as a reference genome to follow the genomic changes and selective sweeps during the domestication process. We propose to sequence about 30 of these ancient genomes and to compare them with genomes and phenotypic records from modern domestic animals to reconstruct many aspects of the selection pressure exerted during different prehistoric and historic periods. We will also sequence several individuals from modern hardy breeds to generate reference genetic data from breeds that have escaped recent selection schemes or that were selected for alternative phenotypes. Our data will be used in combination with modern genomic data from the 1,000 Bull Genomes consortium in various complementary ways to identify and to date signatures of selection during the cattle domestication process. We will screen for selection events that are either recent or old, complete or ongoing, acting on new variants or on standing variation. Using powerful tools to detect selective sweeps in genomes, ancient genomic data will provide the ability to date the various selection events, to identify the population(s) of origins onto which selection was exerted and to explore the validity of the various demographic models used to detect selective sweeps from modern genomic data. We will also use extensive GWAS data, produced by one of us using modern cattle, to reconstruct the past evolution of complex multigenic traits. Path2Bos will (1) improve the power and accuracy of the identification of genomic regions under selection, (2) estimate the strength of selection and date the origin of the corresponding selective events, (3) identify variants that were selected in the past and that have been lost in modern selection schemes, thereby pinpointing the genetic bases of phenotypic traits that might be useful to preserve for the long-term sustainability of cattle husbandry. Thus, it will provide an original and very useful cattle genome annotation data source to complement the genomic characterization efforts of modern cattle breeds and enrich the current selection strategies. A strong point of Path2Bos is the complementarity of the expertise and resources, including preliminary data, of the consortium partners, in particular paleogenomics and a large collection of characterized archeological samples, involvement in the 1000 Bull Genomes consortium and GWAS, selective sweep method developments and analyses of genomes and a high-throughput sequencing facility.