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Human activities have affected the surrounding natural ecosystems, including belowground microorganisms, for millennia. Their short- and medium-term effects on the diversity and the composition of soil microbial communities are well-documented, but their lasting effects remain unknown. When unoccupied for centuries, archaeological sites are appropriate for studying the long-term effects of past human occupancy on natural ecosystems, including the soil compartment. In this work, the soil chemical and bacterial compositions were compared between the Roman fort of Hegra (Saudi Arabia) abandoned for 1500 years, and a preserved area located at 120 m of the southern wall of the Roman fort where no human occupancy was detected. We show that the four centuries of human occupancy have deeply and lastingly modified both the soil chemical and bacterial compositions inside the Roman fort. We also highlight different bacterial putative functions between the two areas, notably associated with human occupancy. Finally, this work shows that the use of soils from archaeological sites causes little disruption and can bring relevant information, at a large scale, during the initial surveys of archaeological sites.

Background: ESBL-producing Escherichia coli (ESBL-Ec) is considered a key indicator for antimicrobial resistance (AMR) epidemiological surveillance in animal, human and environment compartments. There is likelihood of ESBL-Ec animal–human transmission but proof of cross-compartment transmission is still unclear. Objectives: To characterize ESBL-Ec genetic similarity in various compartments (humans, animals and environment) from a rural area of Madagascar. Methods: We collected ESBL-Ec isolates prospectively from humans, animals and the environment (water) between April and October 2018. These isolates were subject to WGS and analysed with cutting-edge phylogenomic methods to characterize population genetic structure and infer putative transmission events among compartments. Results: Of the 1454 samples collected, 512 tested positive for ESBL-Ec. We successfully sequenced 510 samples, and a phylogenomic tree based on 179 365 SNPs was produced. Phylogenetic distances between and amongst compartments were indistinguishable, and 104 clusters of recent transmission events between compartments were highlighted. Amongst a large diversity of ESBL-Ec genotypes, no lineage host specificity was observed, indicating the regular occurrence of ESBL-Ec transfer among compartments in rural Madagascar. Conclusions: Our findings stress the importance of using a phylogenomic approach on ESBL-Ec samples in various putative compartments to obtain a clear baseline of AMR transmissions in rural settings, where one wants to identify risk factors associated with transmission or to measure the effect of 'One Health' interventions in low- and middle-income countries.

In Madagascar, rabies is a significant public health challenge. However, due to the underreporting of many cases and a lack of awareness about post-exposure prophylaxis, the number of rabies cases is likely underestimated. To address this issue, focus groups were conducted following successive awareness- raising sessions about rabies. The main aim of this study was to gain insight into how communities perceive the global goal of eliminating rabies-related human fatalities by 2030. This understanding would help identify effective strategies for addressing the problem. As part of these focus groups, a video in the local language (Malagasy) was presented to all participants, explaining key information about rabies, including its symptoms and what to do in case of animal bites. This video allowed participants to share their own experiences, express their perspectives on rabies surveillance, and suggest practical actions to achieve zero human deaths from rabies by 2030, within their communities. The suggested actions can be summarized into themes (topics), which include improving access to medical care, educating relevant stakeholders, managing the local dog population, fostering collaboration among different stakeholders, reducing the number of stray dogs, implementing vaccination programs, enacting and enforcing relevant laws and regulations, managing dog bites and rabies cases, allocating and utilizing financial resources effectively, and examining local customs. The discussions typically framed these themes in terms of existing deficiencies or inadequacies. According to the insights gathered from these community-driven discussions, activities such as stakeholder education, awareness campaigns, and training should start promptly and continue over a long-term period. In this perspective on tackle rabies, issues related to financial resources were viewed as having a cross-cutting nature, offering potential solutions for short, medium, and long-term challenges. This stud

La maladie du sommeil, ou trypanosomiase humaine africaine (THA), est due à Trypanosoma brucei transmis par la glossine ou mouche tsé-tsé. Après avoir ravagé l'Afrique subsaharienne dans la première moitié du XXe siècle, comme en témoigne l'extraordinaire ouvrage d'Alphonse Laveran et Félix Mesnil en 1912 (Trypanosomes et trypanosomiases), la THA, maladie tropicale négligée mortelle, dite " du bout de la piste " et pour laquelle il n'existe pas de vaccin, semble aujourd'hui à portée de main de l'élimination. Nous passons en revue les stratégies, activités et outils qui ont permis cette forte réduction du fardeau sanitaire pour les populations d'Afrique subsaharienne : environ 300 000 cas estimés dans les années 1990 contre moins de 1000 cas rapportés annuellement depuis 2018. La lutte contre la maladie du sommeil consiste principalement à dépister et traiter les cas ainsi qu'à lutter contre la glossine vectrice pour casser le cycle de transmission. En passant en 30 ans d'un contexte épidémique à un contexte d'élimination, la maladie du sommeil a subi une transition épidémiologique sans précédent à laquelle les stratégies et les outils de lutte ont dû s'adapter. Nous montrons comment la recherche a soutenu ces efforts et examinons certains des défis restants pour rendre effective et durable son élimination.

Rift Valley fever (RVF) is an arboviral disease of zoonotic origin that causes recurrent epidemics in Africa, the Arabic Peninsula, and islands of the South West of the Indian Ocean. RVF occurs mainly in livestock but also affects humans with severe clinical manifestations, including neurological disorders. However, human neuropathogenesis of Rift Valley fever virus (RVFV) is still poorly characterized. To study the interactions between RVFV and the central nervous system (CNS), we focused on RVFV infection of astrocytes, the major glial cells of the CNS that have several supporting roles including immune response regulation. We confirmed the permissiveness of astrocytes to RVFV infection and highlighted a strain-dependent infectivity. We showed that RVFV infection of astrocytes induced cell apoptosis and observed that the RVFV Non-Structural protein NSs, a known virulence factor, potentially delayed apoptosis by sequestrating activated-caspase 3 in the nucleus. Our study also showed that RVFV-infected astrocytes upregulated expression of genes associated with inflammatory and type I interferon responses at the mRNA level, but not at the protein level. This inhibition of immune response is potentially due to a NSs-dependent mechanism of mRNA nuclear export inhibition. Together, these results highlighted the direct impact of RVFV infection on the human CNS through the induction of apoptosis and a possible inhibition of early-onset immune responses that are crucial for the host survival.

Current and likely future changes in the geographic distribution of ticks belonging to the genus Hyalomma are of concern, as these ticks are believed to be vectors of many pathogens responsible for human and animal diseases. However, we have observed that for many pathogens there are no vector competence experiments, and that the level of evidence provided by the scientific literature is often not sufficient to validate the transmission of a specific pathogen by a specific Hyalomma species. We therefore carried out a bibliographical study to collate the validation evidence for the transmission of parasitic, viral, or bacterial pathogens by Hyalomma spp. ticks. Our results show that there are very few validated cases of pathogen transmission by Hyalomma tick species.

Rift Valley fever virus (RVFV) is an arbovirus that causes Rift Valley fever (RVF), a zoonotic disease that mainly affects domestic and wildlife ruminants and humans. The first epidemic in North-Western and West Africa occurred in Senegal and Mauritania in 1987, two countries where RVF is now endemic. Slaughterhouse workers, farmers, herders and veterinarians are at high risk of exposure to RVF. Beyond the health threat, RVF is considered to cause major socio-economic problems, specifically in developing countries where livestock farming and trade are important economic activities. Indeed, the mortality rate linked to RVF infection can reach 95–100% in newborns and young animals. In West Africa, livestock production is a key factor for food production and for national economics. Epizootics caused by RVF can therefore have serious socio-economic consequences by impacting multisectoral economics, the psycho-social health of pastoral communities, and food security. Improving prevention strategies against RVF, including vaccination, enhancing knowledge of RVF and correcting any inappropriate behaviors by populations of endemics areas, as well as better monitoring of RVF ecological factors are effective ways to better foresee and control outbreaks of RVF and its socio-economical side-effects in countries at high risk of occurrence of the disease.

Crimean-Congo haemorrhagic fever virus (CCHF) is an understudied emerging pathogen and the cause of increasingly frequent outbreaks of haemorrhagic fever in humans in sev- eral parts of the world. Here we bring together an important body of work in different aspects of the ecology and epidemiology of CCHF to shed light on its transmission dynamics into humans and the role of environmental drivers. These results show that over the years an endemic pattern of CCHFV transmission has been established within livestock, and the frequency of human cases mirrors the seasonal pattern of livestock transmission. Our analysis further suggests that an important fraction of cases in humans might be subclinical, and the volume of transmission into humans might be much larger than previously thought. We examine the potential impact of vaccination, which suggest that not only human vaccination could be more impactful than animal vaccination, but also that targeted strategies in human high risk groups could be very effective. Our results raise important insights for future vaccine development and important questions on the optimal conditions for conducting Phase III vaccine trials in humans.

Background: Crimean-Congo haemorrhagic fever (CCHF) is a priority emerging pathogen for which a licensed vaccine is not yet available. We aim to assess the feasibility of conducting phase III vaccine efficacy trials and the role of varying transmission dynamics. Methods: We calibrate models of CCHF virus (CCHFV) transmission among livestock and spillover to humans in endemic areas in Afghanistan, Turkey and South Africa. We propose an individual randomised controlled trial targeted to high-risk population, and use the calibrated models to simulate trial cohorts to estimate the minimum necessary number of cases (trial endpoints) to analyse a vaccine with a minimum efficacy of 60%, under different conditions of sample size and follow-up time in the three selected settings. Results: A mean follow-up of 160,000 person-month (75,000–550,000) would be necessary to accrue the required 150 trial endpoints for a target vaccine efficacy of 60 % and clinically defined endpoint, in a setting like Herat, Afghanistan. For Turkey, the same would be achieved with a mean follow-up of 175,000 person-month (50,000–350,000). The results suggest that for South Africa the low endemic transmission levels will not permit achieving the necessary conditions for conducting this trial within a realistic follow-up time. In the scenario of CCHFV vaccine trial designed to capture infection as opposed to clinical case as a trial endpoint, the required person-months is reduced by 70 % to 80 % in Afghanistan and Turkey, and in South Africa, a trial becomes feasible for a large number of person-months of follow-up (>600,000). Increased expected vaccine efficacy > 60 % will reduce the required number of trial endpoints and thus the sample size and follow-time in phase III trials. Conclusions: Underlying endemic transmission levels will play a central role in defining the feasibility of phase III vaccine efficacy trials. Endemic settings in Afghanistan and Turkey offer conditions under which such studi

SARS-CoV-2, the virus responsible for COVID-19 in humans, can efficiently infect a large number of animal species. Like any virus, and particularly RNA viruses, SARS-CoV-2 undergoes mutations during its life cycle some of which bring a selective advantage, leading to the selection of a given lineage. Minks are very susceptible to SARS-CoV-2 and owing to their presence in mass rearing, they make a good model for studying the relative importance of mutations in viral adaptation to host species. Variants, such as the mink-selected SARS-CoV-2 Y453F and D614G or H69del/V70del, Y453F, I692V and M1229I were identified in humans after spreading through densely caged minks. However, not all mink-specific mutations are conserved when the virus infects human populations back. Many questions remain regarding the interspecies evolution of SARS-CoV-2 and the dynamics of transmission leading to the emergence of new variant strains. We compared the human and mink ACE2 receptor structures and their interactions with SARS-CVoV-2 variants. In minks, ACE2 presents a Y34 amino acid instead of the H34 amino acid found in the human ACE2. H34 is essential for the interaction with the Y453 residue of the SARS-CoV-2 Spike protein. The Y453F mink mutation abolishes this conflict. A series of 18 mutations not involved in the direct ACE2 interaction was observed in addition to the Y453F and D614G in 16 different SARS-CoV-2 strains following bidirectional infections between humans and minks. These mutations were not random and were distributed into five different functional groups having an effect on the kinetics of ACE2-RD interaction. The interspecies transmission of SARS-CoV-2 from humans to minks and back to humans, generated specific mutations in each species which improved the affinity for the ACE2 receptor either by direct mutation of the core 453 residue or by associated compensatory mutations.

The acquisition of new hosts is a fundamental mechanism by which parasitic organisms expand their host range and perpetuate themselves on an evolutionary scale. Among pathogens, viruses, due to their speed of evolution, are particularly efficient in producing new emergence events. However, even though these phenomena are particularly important to the human species and therefore specifically studied, the processes of virus emergence in a new host species are very complex and difficult to comprehend in their entirety. In order to provide a structured framework for understanding emergence in a species (including humans), a comprehensive qualitative model is an indispensable cornerstone. This model explicitly describes all the stages necessary for a virus circulating in the wild to come to the crossing of the epidemic threshold. We have therefore developed a complete descriptive model explaining all the steps necessary for a virus circulating in host populations to emerge in a new species. This description of the parameters presiding over the emergence of a new virus allows us to understand their nature and importance in the emergence process.

The rapid intensification of the livestock sector in Southeast Asia has been found to be associated with an expanding use of antibiotics (ABU) and the rise of antimicrobial resistance (AMR) in both humans and livestock. This study aimed to explore the views and practices of commercial pig, poultry and fish farmers regarding antibiotics in Lao People's Democratic Republic, where data on antibiotic use and AMR remain scarce. A multistage cluster sampling method, based on the random selection of villages in two provinces of Vientiane, was used. A total of 364 farmers, corresponding to 454 farm units, were surveyed using a questionnaire and farm visits. This study found a widespread use of antibiotics (261 out of the 454 farm units used antibiotics). The predominance of antibiotics considered critically important antibiotics for human medicine was of great concern. Results from a logistic regression model showed that antibiotics were found less frequently in fish farm units compared to pig and poultry farm units, and more frequently in specialized farms than in livestock-fish farms. Multiple factor analysis and hierarchical cluster analysis revealed three profiles of farmers, each with distinct patterns on knowledge, attitudes and practices regarding ABU and AMR. Cluster 1 held a positive attitude regarding preventive measures and information about antibiotics. In cluster 2, there was a view that antibiotics should be used for prophylactic treatment such as disease prevention. Cluster 3 was characterized by farmers with weak knowledge who were unfamiliar with antibiotics and uncertain about details concerning antibiotic use. This cluster was associated with a significantly lower use of antibiotics than the two other clusters in the regression model. The results of this study may help the Laotian government to adapt strategies to control AMR by focusing on the use of critical antibiotics and prophylactic treatments and by tailoring measures to farmers' profiles.

The whole human society was caught unprepared by the emergence of SARS-CoV-2 and the related COVID-19 pandemic. This should have not been. We already had on hand all information to organize properly and prevent this emergence. However, this information was never translated into preparedness because the current system of sanitary crises management is not adapted. We keep implementing a medical, symptomatic, post-emergence approach which cannot stop an emerging pandemic. The only preventive action considered is the screening for viruses in the wild but it is not efficient since pandemic viruses do not exist in the wild, and indeed, have never been found. The emergence of a viral pandemic is the result of a double accident: the in-host evolution of the causative virus and its amplification to the epidemic threshold by societal factors. To be prepared the society should target this societal dimension of emerging diseases and organize accordingly. Unfortunately, the society is not organized that way and is still unprepared and vulnerable.

Background. Echinococcosis is a zoonotic parasitic disease caused by larval stages of cestodes belonging to the genus Echinococcus. The infection affects people's health and safety as well as agropastoral sector. In China, human echinococcosis is a major public health burden, especially in western China. Echinococcosis affects people health as well as agricultural and pastoral economy. Therefore, it is important to understand the prevalence status and spatial distribution of human echinococcosis in order to advance our knowledge of basic information for prevention and control measures reinforcement. Methods. Report data on echinococcosis were collected in 370 counties in China in 2018 and were used to assess prevalence and spatial distribution. SPSS 21.0 was used to obtain the prevalence rate for CE and AE. For statistical analyses and mapping, all data were processed using SPSS 21.0 and ArcGIS 10.4, respectively. Chi-square test and Exact probability method were used to assess spatial autocorrelation and spatial clustering. Results. A total of 47,278 cases of echinococcosis were recorded in 2018 in 370 endemic counties in China. The prevalence rate of human echinococcosis was 10.57 per 10,000. Analysis of the disease prevalence showed obvious spatial positive autocorrelation in globle spatial autocorrelation with two aggregation modes in local spatial autocorrelation, namely high-high and low-high aggregation areas. The high-high gathering areas were mainly concentrated in northern Tibet, western Qinghai, and Ganzi in the Tibetan Autonomous Region and in Sichuan. The low-high clusters were concentrated in Gamba, Kangma and Yadong counties of Tibet. In addition, spatial scanning analysis revealed two spatial clusters. One type of spatial clusters included 71 counties in Tibet Autonomous Region, 22 counties in Qinghai, 11 counties in Sichuan, three counties in Xinjiang Uygur Autonomous Region, two counties in Yunnan, and one county in Gansu. In the second category, s

MacLean and colleagues recently published a very elegant analysis demonstrating that SARS-CoV-2 carries signs of positive selection and that it was already adapted to humans prior to the emergence of COVID-19. Using the Spillover theory as a reference model for zoonotic emergence, they conclude that SARS-CoV-2 must have acquired this human adaptation in bats. We reinterpreted the data from MacLean et al. using a different model of zoonotic emergence as reference, the Circulation model. The use of the Circulation model provides a more parsimonious interpretation showing that this adaptation to humans occurs in the human population after primo infection.

Dans un contexte d'émergence ou de réémergence des maladies à transmission vectorielle, certaines espèces de Culicoides (Diptera : Ceratopogonidae) sont impliquées dans la transmission de certains virus (Reoviridae : Orbivirus) et de nématodes (Onchocercidae : Mansonella) en région Afrotropicale. Cependant, le schéma systématique et taxonomique ainsi que la bio-écologie des espèces d'intérêt vétérinaire restent à explorer. Ce travail de taxonomie intégrative a pour objectifs de réaliser (i) une révision systématique et taxonomique des espèces appartenant à des sous-genres et des groupes d'intérêt à partir de phylogénie moléculaire multi-marqueur et de délimitation d'espèces, et (ii) de développer des outils moléculaires pour l'étude de la bio-écologie des espèces d'intérêt vétérinaire et de la dynamique de leurs populations d'immatures. Nos résultats mettent en évidence (i) la présence de trois clades monophylétiques le groupe d'espèces Imicola, le groupe d'espèces Milnei et le sous-genre Remmia, (ii) une nouvelle espèce pour la science nommée C. sp. #22 et affiliée au sous-genre Avaritia, groupe Imicola, (iii) la présence d'une nouvelle espèce non - décrite nommée C. sp. #54 appartenant au groupe d'espèces Dasyops, sous-genre Avaritia, (iii) d'affilier les groupes d'espèces Similis et Neavei au sous-genre Synhelea et, (iv) de poser l'hypothèse d'une présence d'espèces cryptiques au sein de C. oxystoma (sous-genre Remmia). D'un point de vue bio-écologique, le travail réalisé combinant suivi entomologique et identification moléculaire avec une librairie de séquences barcodes a permis de décrire le comportement trophique de C. imicola , C. kingi et C. oxystoma ainsi que leurs habitats larvaires dans des environnements équins de la zone des Niayes au Sénégal. L'ensemble de ce travail permet de compléter le corpus de connaissances sur le genre Culicoides en région Afrotropicale afin d'améliorer la compréhension de l'épidémiologie des pathogènes transmis et proposer des

During infection, some intracellular pathogenic bacteria use a dedicated multiprotein complex known as the type IV secretion system to deliver type IV effector (T4E) proteins inside the host cell. These T4Es allow the bacteria to evade host defenses and to subvert host cell processes to their own advantage. Ehrlichia chaffeensis is a tick-transmitted obligate intracellular pathogenic bacterium, which causes human monocytic ehrlichiosis. Using comparative whole genome analysis, we identified the relationship between eight available E. chaffeensis genomes isolated from humans and show that these genomes are highly conserved. We identified the candidate core type IV effectome of E. chaffeensis and some conserved intracellular adaptive strategies. We assigned the West Paces strain to genetic group II and predicted the repertoires of T4Es encoded by E. chaffeensis genomes, as well as some putative host cell targets. We demonstrated that predicted T4Es are preferentially distributed in gene sparse regions of the genome. In addition to the identification of the two known type IV effectors of Anaplasmataceae, we identified two novel candidates T4Es, ECHLIB_RS02720 and ECHLIB_RS04640, which are not present in all E. chaffeensis strains and could explain some variations in inter-strain virulence. We also identified another novel candidate T4E, ECHLIB_RS02720, a hypothetical protein exhibiting EPIYA, and NLS domains as well as a classical type IV secretion signal, suggesting an important role inside the host cell. Overall, our results agree with current knowledge of Ehrlichia molecular pathogenesis, and reveal novel candidate T4Es that require experimental validation. This work demonstrates that comparative effectomics enables identification of important host pathways targeted by the bacterial pathogen. Our study, which focuses on the type IV effector repertoires among several strains of E. chaffeensis species, is an original approach and provides rational putative targets for

Le but de cette thèse est de proposer une double lecture du système d'élevage à ciel ouvert de l'Uruguay et en particulier des relations entre les populations humaines, les populations bovines et l'écosystème de prairies naturelles à travers deux principes antagoniques : la réciprocité et l'échange marchand. La distribution de ces deux principes configure un répertoire de pratiques et d'interactions qui façonne le territoire de l'élevage extensif et ses conditions spécifiques de produire de l'humanité. L'hypothèse de recherche soutient que le processus d'intensification récent de l'élevage tend à substituer les pratiques et relations de réciprocité par des relations d'échange mercantile qui augmentent la vulnérabilité du système d'élevage comme des écosystèmes de prairie naturelle. Cette substitution privilégie des critères technologiques distants de l'expérience concrète et du savoir-faire local. La thèse propose une ethnographie des relations humains/bovins/pâturages et de leurs transformations par une approche sensible qui combine la science et l'art. La recherche montre comment les éleveurs, en même temps qu'ils produisent des richesses matérielles par la commercialisation de la viande, se produisent eux-mêmes à travers des relations de réciprocité qui engendrent une affectivité et des valeurs éthiques productrices d'humanité.

Glossina sp. the tsetse fly that transmits trypanosomes causing the Human or the Animal African Trypanosomiasis (HAT or AAT) can harbor symbiotic bacteria that are known to play a crucial role in the fly's vector competence. We hypothesized that other bacteria could be present, and that some of them could also influence the fly's vector competence. In this context the objectives of our work were: (a) to characterize the bacteria that compose the G. palpalis palpalis midgut bacteriome, (b) to evidence possible bacterial community differences between trypanosome-infected and non-infected fly individuals from a given AAT and HAT focus or from different foci using barcoded Illumina sequencing of the hypervariable V3-V4 region of the 16S rRNA gene. Forty G. p. palpalis flies, either infected by Trypanosoma congolense or uninfected were sampled from three trypanosomiasis foci in Cameroon. A total of 143 OTUs were detected in the midgut samples. Most taxa were identified at the genus level, nearly 50% at the species level; they belonged to 83 genera principally within the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Prominent representatives included Wigglesworthia (the fly's obligate symbiont), Serratia, and Enterobacter hormaechei. Wolbachia was identified for the first time in G. p. palpalis. The average number of bacterial species per tsetse sample was not significantly different regarding the fly infection status, and the hierarchical analysis based on the differences in bacterial community structure did not provide a clear clustering between infected and non-infected flies. Finally, the most important result was the evidence of the overall very large diversity of intestinal bacteria which, except for Wigglesworthia, were unevenly distributed over the sampled flies regardless of their geographic origin and their trypanosome infection status.

Background: WHO developed a global strategy to eliminate hepatitis B by 2030 and set target to treat 80% of people with chronic hepatitis B virus (HBV) infection eligible for antiviral treatment. As a first step to achieve this goal, it is essential to conduct a situation analysis that is fundamental to designing national hepatitis plans. We therefore estimated the prevalence of chronic HBV infection, and described the existing infrastructure for HBV diagnosis in Madagascar. Methods: We conducted a stratified multi-stage serosurvey of hepatitis B surface antigen (HBsAg) in adults aged ≥18 years using 28 sentinel surveillance sites located throughout the country. We obtained the list of facilities performing HBV testing from the Ministry of Health, and contacted the person responsible at each facility. Results A total of 1778 adults were recruited from the 28 study areas. The overall weighted seroprevalence of HBsAg was 6.9% (95% CI: 5.6–8.6). Populations with a low socio-economic status and those living in rural areas had a significantly higher seroprevalence of HBsAg. The ratio of facilities equipped to perform HBsAg tests per 100,000 inhabitants was 1.02 in the capital city of Antananarivo and 0.21 outside the capital. There were no facilities with the capacity to perform HBV DNA testing or transient elastography to measure liver fibrosis. There are only five hepatologists in Madagascar. Conclusion: Madagascar has a high-intermediate level of endemicity for HBV infection with a severely limited capacity for its diagnosis and treatment. Higher HBsAg prevalence in rural or underprivileged populations underlines the importance of a public health approach to decentralize the management of chronic HBV carriers in Madagascar by using simple and low-cost diagnostic tools.

Climate change is expected to threaten human health and well-being via its effects on climate-sensitive infectious diseases, potentially changing their spatial distributions, affecting annual/seasonal cycles, or altering disease incidence and severity. Climate sensitivity of pathogens is a key indicator that diseases might respond to climate change, but the proportion of pathogens that is climate-sensitive, and their characteristics, are not known. The climate sensitivity of European human and domestic animal infectious pathogens, and the characteristics associated with sensitivity, were assessed systematically in terms of selection of pathogens and choice of literature reviewed. Sixty-three percent (N = 157) of pathogens were climate sensitive; 82% to primary drivers such as rainfall and temperature. Protozoa and helminths, vector-borne, foodborne, soilborne and waterborne transmission routes were associated with larger numbers of climate drivers. Zoonotic pathogens were more climate sensitive than human- or animal-only pathogens. Thirty-seven percent of disability-adjusted-life-years arise from human infectious diseases that are sensitive to primary climate drivers. These results help prioritize surveillance for pathogens that may respond to climate change. Although this study identifies a high degree of climate sensitivity among important pathogens, their response to climate change will be dependent on the nature of their association with climate drivers and impacts of other drivers.

Rift Valley fever (RVF) is a major zoonotic and arboviral hemorrhagic fever. The conditions leading to RVF epidemics are still unclear, and the relative role of climatic and anthropogenic factors may vary between ecosystems. Here, we estimate the most likely scenario that led to RVF emergence on the island of Mayotte, following the 2006–2007 African epidemic. We developed the first mathematical model for RVF that accounts for climate, animal imports and livestock susceptibility, which is fitted to a 12-years dataset. RVF emergence was found to be triggered by the import of infectious animals, whilst transmissibility was approximated as a linear or exponential function of vegetation density. Model forecasts indicated a very low probability of virus endemicity in 2017, and therefore of re-emergence in a closed system (i.e. without import of infected animals). However, the very high proportion of naive animals reached in 2016 implies that the island remains vulnerable to the import of infectious animals. We recommend reinforcing surveillance in livestock, should RVF be reported is neighbouring territories. Our model should be tested elsewhere, with ecosystem-specific data.

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causing infections in humans is genetically indistinguishable from the virus found in Arabian camels (dromedaries) in the Middle East. Although no primary human case of MERS was reported outside the Arabian Peninsula, camel populations in Africa are known to have high prevalence of antibodies against MERS-CoV. We carried out surveillance for MERS-CoV in dromedaries in Africa and Central Asia. By MERS-CoV spike pseudoparticle neutralization assay we confirmed that camel serum samples from African countries have high prevalence of MERS-CoV antibodies. Using RT-qPCR we detected MERS-CoV positives in camel nasal swabs from all different African countries from which samples were collected. However, dromedary serum and swab samples from Kazakhstan in Central Asia were negative for MERS-CoV by these assays. Phylogenetic analysis of the spike gene revealed that MERS-CoVs from Africa formed a cluster closely related to but distinct from the viruses from the Arabian Peninsula. Results from this study suggest that MERS-CoV is actively circulating in dromedary populations in Africa and the virus in Africa is phylogenetically distinct from that in the Middle East.

Rift Valley fever (RVF) is a vector-borne viral disease widespread in Africa. The primary cycle involves mosquitoes and wild and domestic ruminant hosts. Humans are usually contaminated after contact with infected ruminants. As many environmental, agricultural, epidemiological, and anthropogenic factors are implicated in RVF spread, the multidisciplinary One Health approach was needed to identify the drivers of RVF epidemics in Madagascar. We examined the environmental patterns associated with these epidemics, comparing human and ruminant serological data with environmental and cattle-trade data. In contrast to East Africa, environmental drivers did not trigger the epidemics: They only modulated local Rift Valley fever virus (RVFV) transmission in ruminants. Instead, RVFV was introduced through ruminant trade and subsequent movement of cattle between trade hubs caused its long-distance spread within the country. Contact with cattle brought in from infected districts was associated with higher infection risk in slaughterhouse workers. The finding that anthropogenic rather than environmental factors are the main drivers of RVF infection in humans can be used to design better prevention and early detection in the case of RVF resurgence in the region.

Bacteria of the species Treponema pallidum are causative agents of venereal syphilis (Treponema pallidum pallidum), Bejel (T. p. endemicum), and yaws (T. p. pertenue) in humans. We documented Treponema pallidum infections associated with disease in wild sooty mangabeys (Cercocebus atys) in Taï National Park, Côte d'Ivoire, and green monkeys (Chlorocebus sabaeus) from Bijilo Forest Park, Gambia and Niokolo-Koba National Park, Senegal. To examine the evolutionary relatedness of these treponemes to those responsible for diseases in humans and for previously documented infections in baboons (Papio papio), we conducted a hybridization capture experiment to enrich Treponema pallidum DNA from samples collected from symptomatic individuals. This approach allowed us to sequence the full genomes of Treponema pallidum strains infecting sooty mangabeys (n = 2) and green monkeys (n = 4). Phylogenomic analyses revealed that all Treponema pallidum strains infecting non-human primates are most closely related to the sub-species T. p. pertenue. Strains infecting humans and non-human primates do not appear to be reciprocally monophyletic. The star-like phylogenetic branching pattern of the T. p. pertenue clade, with short basal branches receiving low statistical support, suggests a rapid initial radiation across humans and non-human primates. These results greatly broaden the known host range of T.p. pertenue and suggest the existence of a vast zoonotic reservoir that could possibly contribute to the failure of global eradication efforts.

Humans and African great apes (AGAs) are naturally infected with several species of closely related malaria parasites. The need to understand the origins of human malaria as well as the risk of zoonotic transmissions and emergence of new malaria strains in human populations has markedly encouraged research on great ape Plasmodium parasites. Progress in the use of non-invasive methods has rendered investigations into wild ape populations possible. Present knowledge is mainly focused on parasite diversity and phylogeny, with still large gaps to fill on malaria parasite ecology. Understanding what malaria infection means in terms of great ape health is also an important, but challenging avenue of research and has been subject to relatively few research efforts so far. This paper reviews current knowledge on African great ape malaria and identifies gaps and future research perspectives.