Animal, Santé, Territoires, Risques et Ecosystèmes

Over the past decade, a significant increase in the circulation of infectious agents was observed. With the spread and emergence of epizootics, zoonoses and epidemics, the risks of pandemics became more and more critical. Human and animal health has also been threatened by antimicrobial resistance, environmental pollution and the development of multifactorial and chronic diseases. This highlighted the increasing globalization of health risks and the importance of the human-animal-ecosystem interface in the evolution and emergence of pathogens. A better knowledge of causes and consequences of certain human activities, lifestyles and behaviors in ecosystems is crucial for a rigorous interpretation of disease dynamics and to drive public policies. As a global good, health security must be understood on a global scale and from a global and cross-cutting perspective, integrating human health, animal health, plant health, ecosystems health and biodiversity. In this paper, we discuss how crucial it is to consider ecological, evolutionary and environmental sciences in understanding the emergence and re-emergence of infectious diseases and in facing the challenges of antimicrobial resistance. We also discuss the application of the “One Health” concept to non-communicable chronic diseases linked to exposure to multiple stresses, including toxic stress, and new lifestyles. Finally, we draw up a list of barriers that need removing and the ambitions that we must nurture for the effective application of the “One Health” concept. We conclude that the success of this One Health concept now requires breaking down the interdisciplinary barriers that still separate human and veterinary medicine from ecological, evolutionary and environmental sciences. The development of integrative approaches should be promoted by linking the study of factors underlying stress responses to their consequences on ecosystem functioning and evolution. This knowledge is required for the development of novel control strategies inspired by environmental mechanisms leading to desired equilibrium and dynamics in healthy ecosystems and must provide in the near future a framework for more integrated operational initiatives.

Although copper (Cu) is recognized as an essential trace element, uncertainties remain regarding Cu reference values for humans, as illustrated by discrepancies between recommendations issued by different national authorities. This review examines human studies published since 1990 on relationships between Cu intake, Cu balance, biomarkers of Cu status, and health. It points out several gaps and unresolved issues which make it difficult to assess Cu requirements. Results from balance studies suggest that daily intakes below 0.8 mg/day lead to net Cu losses, while net gains are consistently observed above 2.4 mg/day. However, because of an incomplete collection of losses in all studies, a precise estimation of Cu requirements cannot be derived from available data. Data regarding the relationship between Cu intake and potential biomarkers are either too preliminary or inconclusive because of low specificity or low sensitivity to change in dietary Cu over a wide range of intakes. Results from observation and intervention studies do not support a link between Cu and a risk of cardiovascular disease, cognitive decline, arthritis or cancer for intakes ranging from 0.6 to 3mg/day, and limited evidence exists for impaired immune function in healthy subjects with a very low (0.38 mg/day) Cu intake. However, data from observation studies should be regarded with caution because of uncertainties regarding Cu concentration in various foods and water. Further studies that accurately evaluate Cu exposure based on reliable biomarkers of Cu status are needed.

Panzootic chytrid fungus out of Asia Species in the fungal genus Batrachochytrium are responsible for severe declines in the populations of amphibians globally. The sources of these pathogens have been uncertain. O'Hanlon et al. used genomics on a panel of more than 200 isolates to trace the source of the frog pathogen B. dendrobatidis to a hyperdiverse hotspot in the Korean peninsula (see the Perspective by Lips). Over the past century, the trade in amphibian species has accelerated, and now all lineages of B. dendrobatidis occur in traded amphibians; the fungus has become ubiquitous and is diversifying rapidly. Science , this issue p. 621 ; see also p. 604

Abstract During the last decades, climate and land use changes led to an increased prevalence of megafires in Mediterranean-type climate regions (MCRs). Here, we argue that current wildfire management policies in MCRs are destined to fail. Focused on fire suppression, these policies largely ignore ongoing climate warming and landscape-scale buildup of fuels. The result is a ‘firefighting trap’ that contributes to ongoing fuel accumulation precluding suppression under extreme fire weather, and resulting in more severe and larger fires. We believe that a ‘business as usual’ approach to wildfire in MCRs will not solve the fire problem, and recommend that policy and expenditures be rebalanced between suppression and mitigation of the negative impacts of fire. This requires a paradigm shift: policy effectiveness should not be primarily measured as a function of area burned (as it usually is), but rather as a function of avoided socio-ecological damage and loss.

African swine fever is a devastating disease that can result in death in almost all infected pigs. The continuing spread of African swine fever from Africa to Europe and recently to the high-pig production countries of China and others in Southeast Asia threatens global pork production and food security. The African swine fever virus is an unusual complex DNA virus and is not related to other viruses. This has presented challenges for vaccine development, and currently none is available. The virus is extremely well adapted to replicate in its hosts in the sylvatic cycle in East and South Africa. Its spread to other regions, with different wildlife hosts, climatic conditions, and pig production systems, has revealed unexpected epidemiological scenarios and different challenges for control. Here we review the epidemiology of African swine fever in these different scenarios and methods used for control. We also discuss progress toward vaccine development and research priorities to better understand this complex disease and improve control.

Very large fires (VLFs) have important implications for communities, ecosystems, air quality and fire suppression expenditures. VLFs over the contiguous US have been strongly linked with meteorological and climatological variability. Building on prior modelling of VLFs (>5000 ha), an ensemble of 17 global climate models were statistically downscaled over the US for climate experiments covering the historic and mid-21st-century periods to estimate potential changes in VLF occurrence arising from anthropogenic climate change. Increased VLF potential was projected across most historically fire-prone regions, with the largest absolute increase in the intermountain West and Northern California. Complementary to modelled increases in VLF potential were changes in the seasonality of atmospheric conditions conducive to VLFs, including an earlier onset across the southern US and more symmetric seasonal extension in the northern regions. These projections provide insights into regional and seasonal distribution of VLF potential under a changing climate, and serve as a basis for future strategic and tactical fire management options.

BACKGROUND: Landscape attributes influence spatial variations in disease risk or incidence. We present a review of the key findings from eight case studies that we conducted in Europe and West Africa on the impact of land changes on emerging or re-emerging vector-borne diseases and/or zoonoses. The case studies concern West Nile virus transmission in Senegal, tick-borne encephalitis incidence in Latvia, sandfly abundance in the French Pyrenees, Rift Valley Fever in the Ferlo (Senegal), West Nile Fever and the risk of malaria re-emergence in the Camargue, and rodent-borne Puumala hantavirus and Lyme borreliosis in Belgium. RESULTS: We identified general principles governing landscape epidemiology in these diverse disease systems and geographic regions. We formulated ten propositions that are related to landscape attributes, spatial patterns and habitat connectivity, pathways of pathogen transmission between vectors and hosts, scale issues, land use and ownership, and human behaviour associated with transmission cycles. CONCLUSIONS: A static view of the "pathogenecity" of landscapes overlays maps of the spatial distribution of vectors and their habitats, animal hosts carrying specific pathogens and their habitat, and susceptible human hosts and their land use. A more dynamic view emphasizing the spatial and temporal interactions between these agents at multiple scales is more appropriate. We also highlight the complementarity of the modelling approaches used in our case studies. Integrated analyses at the landscape scale allows a better understanding of interactions between changes in ecosystems and climate, land use and human behaviour, and the ecology of vectors and animal hosts of infectious agents.

Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.

Area-wide integrated pest management is designed for specific purposes, and an economic evaluation should determine its performance against those purposes. The sterile insect technique is used for eradication, suppression, containment and prevention, each of which has different performance measures. Eradication or suppression of insect pest populations using the sterile insect technique (SIT), together with other area-wide control measures, may require significant initial capital investments to achieve long-term returns in subsequent periods. It may also raise questions about the distribution of benefits or the justification of public or private pest control efforts, given long-term uncertainties about the pest challenge and the potential of new control options. A consistent and transparent evaluation is needed to analyse the benefits and costs of such projects and to demonstrate their value, or in some cases to assess appropriate contributions to the costs by the various stakeholders who gain the benefits. Suppression must be compared with expected losses and costs in alternative conditions without SIT application, either from recent experience prior to implementation of the SIT or with similar areas without SIT treatment. Preventive SIT should reduce the frequency of outbreaks compared with experience prior to the application of the SIT or in similar areas elsewhere without SIT use. This chapter outlines the process of benefit/cost analysis, in which itemized future costs and benefits are compared in terms of present values. It also provides a review and examples of the application of benefit/cost analysis to the SIT. A checklist of benefit/cost analysis inputs and some example benefit/cost outputs are also presented.

Wildfire activity is expected to increase across the Mediterranean Basin because of climate change. However, the effects of future climate change on the combinations of atmospheric conditions that promote wildfire activity remain largely unknown. Using a fire-weather based classification of wildfires, we show that future climate scenarios point to an increase in the frequency of two heat-induced fire-weather types that have been related to the largest wildfires in recent years. Heat-induced fire-weather types are characterized by compound dry and warm conditions occurring during summer heatwaves, either under moderate (heatwave type) or intense (hot drought type) drought. The frequency of heat-induced fire-weather is projected to increase by 14% by the end of the century (2071-2100) under the RCP4.5 scenario, and by 30% under the RCP8.5, suggesting that the frequency and extent of large wildfires will increase throughout the Mediterranean Basin.

Atmospheric correction over inland and coastal waters is one of the major remaining challenges in aquatic remote sensing, often hindering the quantitative retrieval of biogeochemical variables and analysis of their spatial and temporal variability within aquatic environments. The Atmospheric Correction Intercomparison Exercise (ACIX-Aqua), a joint NASA – ESA activity, was initiated to enable a thorough evaluation of eight state-of-the-art atmospheric correction (AC) processors available for Landsat-8 and Sentinel-2 data processing. Over 1000 radiometric matchups from both freshwaters (rivers, lakes, reservoirs) and coastal waters were utilized to examine the quality of derived aquatic reflectances (ρ̂w). This dataset originated from two sources: Data gathered from the international scientific community (henceforth called Community Validation Database, CVD), which captured predominantly inland water observations, and the Ocean Color component of AERONET measurements (AERONET-OC), representing primarily coastal ocean environments. This volume of data permitted the evaluation of the AC processors individually (using all the matchups) and comparatively (across seven different Optical Water Types, OWTs) using common matchups. We found that the performance of the AC processors differed for CVD and AERONET-OC matchups, likely reflecting inherent variability in aquatic and atmospheric properties between the two datasets. For the former, the median errors in ρ̂w560 and ρ̂w664 were found to range from 20 to 30% for best-performing processors. Using the AERONET-OC matchups, our performance assessments showed that median errors within the 15–30% range in these spectral bands may be achieved. The largest uncertainties were associated with the blue bands (25 to 60%) for best-performing processors considering both CVD and AERONET-OC assessments. We further assessed uncertainty propagation to the downstream products such as near-surface concentration of chlorophyll-a (Chla) and Total Suspended Solids (TSS). Using satellite matchups from the CVD along with in situ Chla and TSS, we found that 20–30% uncertainties in ρ̂w490≤λ≤743nm yielded 25–70% uncertainties in derived Chla and TSS products for top-performing AC processors. We summarize our results using performance matrices guiding the satellite user community through the OWT-specific relative performance of AC processors. Our analysis stresses the need for better representation of aerosols, particularly absorbing ones, and improvements in corrections for sky- (or sun-) glint and adjacency effects, in order to achieve higher quality downstream products in freshwater and coastal ecosystems.

African swine fever virus (ASFV) is one of the most threatening infectious diseases of pigs. There are not sufficient data to indicate the importance of the sylvatic cycle in the spread and maintenance of the disease locally and potentially, globally. To assess the capacity to maintain ASF in the environment, we investigated the presence of soft tickreservoirs of ASFV in Gorongosa National Park (GNP) and its surrounding villages. A total of 1,658 soft ticks were recovered from warthog burrows and pig pens at the wildlife/livestock interface of the GNP and viral DNA was confirmed by nested PCR in 19% of Ornithodoros porcinus porcinus and 15% of O. p. domesticus. However, isolation of ASFV was only achieved in approximately 50% of the PCR-positive samples with nineteen haemadsorbing virus isolates recovered. These were genotyped using a combination of partial sequencing of the B646L gene (p72) and analysis of the central variable region (CVR) of the B602L gene. Eleven isolates were classified as belonging to genotype II and homologous to contemporary isolates from southern Africa, the Indian Ocean and eastern Europe. Three isolates grouped within genotype V and were similar to previous isolates from Mozambique and Malawi. The remaining five isolates constituted a new, previously unidentified genotype, designated genotype XXIV. This work confirms for the first time that the virus currently circulating in eastern Europe is likely to have a wildlife origin, and that the large diversity of ASFV maintained in wildlife areas can act as a permanent sources of different strains for the domestic pig value chain in Mozambique and beyond its boundaries. Their genetic similarity to ASFV strains currently spreading across Europe justifies the need to continue studying the sylvatic cycle in this African country and other parts of southern Africa in order to identify potential hot spots of ASF emergence and target surveillance and control efforts.

While the epidemic of SARS-CoV-2 has spread worldwide, there is much concern over the mortality rate that the infection induces. Available data suggest that COVID-19 case fatality rate had varied temporally (as the epidemic has progressed) and spatially (among countries). Here, we attempted to identify key factors possibly explaining the variability in case fatality rate across countries. We used data on the temporal trajectory of case fatality rate provided by the European Center for Disease Prevention and Control, and country-specific data on different metrics describing the incidence of known comorbidity factors associated with an increased risk of COVID-19 mortality at the individual level. We also compiled data on demography, economy and political regimes for each country. We found that temporal trajectories of case fatality rate greatly vary among countries. We found several factors associated with temporal changes in case fatality rate both among variables describing comorbidity risk and demographic, economic and political variables. In particular, countries with the highest values of DALYs lost to cardiovascular, cancer and chronic respiratory diseases had the highest values of COVID-19 CFR. CFR was also positively associated with the death rate due to smoking in people over 70 years. Interestingly, CFR was negatively associated with share of death due to lower respiratory infections. Among the demographic, economic and political variables, CFR was positively associated with share of the population over 70, GDP per capita, and level of democracy, while it was negatively associated with number of hospital beds ×1000. Overall, these results emphasize the role of comorbidity and socio-economic factors as possible drivers of COVID-19 case fatality rate at the population level.

The variation in viral gene frequencies remains a largely unexplored aspect of within-host genetics. This phenomenon is often considered to be specific to multipartite viruses. Multipartite viruses have segmented genomes, but in contrast to segmented viruses, their segments are each encapsidated alone in a virion. A main hypothesis explaining the evolution of multipartism is that, compared to segmented viruses, it facilitates the regulation of segment abundancy, and the genes the segments carry, within a host. These differences in gene frequencies could allow for expression regulation. Here, we show that wild populations of a segmented virus, bluetongue virus (BTV), also present unequal segment frequencies. BTV cycles between ruminants and Culicoides biting midges. As expected from a role in expression regulation, segment frequencies tended to show specific values that differed between ruminants and midges. Our results expand previous knowledge on gene frequency variation and call for studies on its role and conservation beyond multipartite viruses.

River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.

Jellyfish blooms occur in many estuarine and coastal regions and may be increasing in their magnitude and extent worldwide. Voracious jellyfish predation impacts food webs by converting large quantities of carbon (C), fixed by primary producers and consumed by secondary producers, into gelatinous biomass, which restricts C transfer to higher trophic levels because jellyfish are not readily consumed by other predators. In addition, jellyfish release colloidal and dissolved organic matter (jelly-DOM), and could further influence the functioning of coastal systems by altering microbial nutrient and DOM pathways, yet the links between jellyfish and bacterioplankton metabolism and community structure are unknown. Here we report that jellyfish released substantial quantities of extremely labile C-rich DOM, relative to nitrogen (25.6 ± 31.6 C:1N), which was quickly metabolized by bacterioplankton at uptake rates two to six times that of bulk DOM pools. When jelly-DOM was consumed it was shunted toward bacterial respiration rather than production, significantly reducing bacterial growth efficiencies by 10% to 15%. Jelly-DOM also favored the rapid growth and dominance of specific bacterial phylogenetic groups (primarily γ-proteobacteria) that were rare in ambient waters, implying that jelly-DOM was channeled through a small component of the in situ microbial assemblage and thus induced large changes in community composition. Our findings suggest major shifts in microbial structure and function associated with jellyfish blooms, and a large detour of C toward bacterial CO(2) production and away from higher trophic levels. These results further suggest fundamental transformations in the biogeochemical functioning and biological structure of food webs associated with jellyfish blooms.

African swine fever (ASF) is a complex disease of swine, caused by a large DNA virus belonging to the family Asfarviridae. The disease shows variable clinical signs, with high case fatality rates, up to 100%, in the acute forms. ASF is currently present in Africa and Europe where it circulates in different scenarios causing a high socio-economic impact. In most affected regions, control has not been effective in part due to lack of a vaccine. The availability of an effective and safe ASFV vaccines would support and enforce control-eradication strategies. Therefore, work leading to the rational development of protective ASF vaccines is a high priority. Several factors have hindered vaccine development, including the complexity of the ASF virus particle and the large number of proteins encoded by its genome. Many of these virus proteins inhibit the host's immune system thus facilitating virus replication and persistence. We review previous work aimed at understanding ASFV-host interactions, including mechanisms of protective immunity, and approaches for vaccine development. These include live attenuated vaccines, and "subunit" vaccines, based on DNA, proteins, or virus vectors. In the shorter to medium term, live attenuated vaccines are the most promising and best positioned candidates. Gaps and future research directions are evaluated.

Wildlife species as reservoirs of infectious pathogens represent a serious constraint in the implementation of disease management strategies. In the Mediterranean island of Corsica, the dynamics of hepatitis E virus (HEV) and Aujeszky's disease virus (ADV) are suspected to be influenced by interactions between wild and domestic pigs. To improve our understanding of these influences, we first compared the seroprevalences of both viruses in domestic pig populations from different locations with contrasted levels of wild-domestic interactions, ADV vaccination, biosafety, and farm husbandry. Second, we performed an analysis at a more restricted geographical scale, to assess the matching of ADV or HEV prevalence between sympatric wild boar and outdoor pig farms most exposed to interactions with wildlife. Logistic models were adjusted to the observed data. A high seroprevalence of HEV (>80%) and ADV (40%) in pigs, with no significant difference according to the region, confirms that both pathogens are enzootic in Corsica. Vaccination against ADV had a strong protective effect, even when performed voluntarily by farmers. Farm biosafety had an additional effect on pigs' exposure, suggesting that contact between wild boars and pigs were involved in disease transmission. A strong correlation in HEV seroprevalence was observed between pigs and wild boars that were in close contact, and significantly lower seroprevalence was observed in pigs when they had little contact with wild boars due to spatial segregation. These results suggest a regular HEV circulation between sympatric wild boar and domestic pigs. The high HEV seroprevalence observed in domestic pigs (>80%) suggests a spillover of the virus from domestic to wild populations through environmental contamination, but this hypothesis has to be confirmed. Conversely, even though avoiding sows' release on pasture during estrus showed some protecting effect in the free ranging pig farms regarding ADV, ADV seroprevalence was not dependent on the swine populations (wild or domestic) or on the wild-domestic spatial overlap, suggesting two quasi-separate enzootic cycles. This information will prove useful for designing more efficient disease management strategies in Corsica and similar contexts.

Significance Middle East respiratory syndrome (MERS) is a zoonotic disease of global health concern, and dromedary camels are the source of human infection. Although Africa has the largest number of dromedary camels, and MERS-coronavirus (MERS-CoV) is endemic in these camels, locally acquired zoonotic MERS is not reported from Africa. However, little is known of the genetic or phenotypic characterization of MERS-CoV from Africa. In this study we characterize MERS-CoV from Burkina Faso, Nigeria, Morocco, and Ethiopia. We demonstrate viral genetic and phenotypic differences in viruses from West Africa, which may be relevant to differences in zoonotic potential, highlighting the need for studies of MERS-CoV at the animal–human interface.

Source Agritrop Cirad (https://agritrop.cirad.fr/596835/)