Non-invasive genomics of respiratory pathogens infecting wild great apes using hybridisation capture

Human respiratory pathogens have repeatedly caused lethal outbreaks in wild great apes across Africa, leading to population declines. Nonetheless, our knowledge of potential genomic changes associated with pathogen introduction and spread at the human-great ape interface remains sparse. Here, we made use of target enrichment coupled with next generation sequencing to non-invasively investigate five outbreaks of human-introduced respiratory disease in wild chimpanzees living in Taï National Park, Ivory Coast. By retrieving 34 complete viral genomes and three distinct constellations of pneumococcal virulence factors, we provide genomic insights into these spillover events and describe a framework for non-invasive genomic surveillance in wildlife.Peer Reviewe

Assessment of metallic pollution (Hg, Pb, Cd, Cu) of water and sediment in fish ponds located in a lowland in the city of Daloa

The Assessment of the metallic pollution of the water and sediment of four fish ponds located in the town of Daloa has been determined. To do this, water and sediment samples were taken from these ponds for the determination of Hg, Pb, Cd and Cu with the atomic absorption spectrophotometer. The results of the analysis show that the water quality of the various fish ponds is influenced by the variation of the physicochemical parameters and that these waters are vulnerable to organic and inorganic pollution. Moreover, these results also revealed Cu (5.039 mg.L-1) and Hg (5.191 mg.L-1) are the metals most accumulated in the waters of fish ponds, while for sediments we have Cu (708.909 mg.kg-1) and Pb (1.22 mg.kg-1). The order of preferential accumulation of ETM in the water of these ponds is as follows: [Cu]>[Hg]>[Pb]>[Cd]. That of the sediments is [Cu]>[Pb]>[Hg]>[Cd]. This shows that whatever the study matrix, Cu is the most predominant metal. On the other hand, the values of the Geo index did indeed show a high intensity of the pollution of the sediment of fish ponds by Hg and Cu. These two metals would therefore present risks of metallic bioaccumulation of living organisms in this environment due to their presence and their strong accumulatio

Data from: Lassa virus in multimammate rats, Côte d’Ivoire, 2013

Lassa fever is a zoonosis caused by Lassa virus (LASV; family Arenaviridae, genus Lassavirus). The primary reservoir of LASV is the multimammate rat (Mastomys natalensis), which is found throughout sub-Saharan Africa. For a study investigating zoonotic pathogens in rural habitats, we caught small mammals in 3 ecologic zones of Côte d’Ivoire: dry bushland in northern Côte d’Ivoire, around Korhogo; semiarid bushland in central Côte d’Ivoire, around Bouake; and rainforest in southwestern Côte d’Ivoire, near the Taï National Park

Fly iDNA suggests strict reliance of the causative agent of sylvatic anthrax on rainforest ecosystems

Abstract Metabarcoding of invertebrate‐derived DNA (iDNA) is increasingly used to describe vertebrate diversity in terrestrial ecosystems. Fly iDNA has also shown potential as a tool for detecting pathogens. Combining these approaches makes fly iDNA a promising tool for understanding the ecology and distribution of novel pathogens or emerging infectious diseases. Here, we use fly iDNA to explore the geographic distribution of Bacillus cereus biovar anthracis (Bcbva) along a gradient from the forest within Taï National Park, Côte d'Ivoire, out to surrounding villages. We tested fly pools (N = 100 pools of 5 flies) collected in the forest (N = 25 pools), along the forest edge (N = 50 pools), and near surrounding villages (N = 25 pools) for Bcbva. Using the same iDNA, we sought to reconstruct fly and mammal communities with metabarcoding, with the aim of investigating potential links with Bcbva detection. We detected Bcbva in 5/100 fly pools and positivity varied significantly across the habitat types (forest = 4/25, edge = 1/50, village = 0/25). It was possible to culture Bcbva from all positive fly pools, confirming their positivity, while sequencing of their whole genomes revealed a considerable portion of known genomic diversity for this pathogen. iDNA generated data about the mammal and fly communities in these habitats, revealing the highest mammal diversity in the forest and considerable changes in fly community composition along the gradient. Bcbva host range estimates from fly iDNA were largely identical to the results of long‐term carcass monitoring efforts in the region. We show that fly iDNA can generate data on the geographic distribution and host range of a pathogen at kilometer scales, as well as reveal the pathogen's phylogenetic diversity. Our results highlight the power of fly iDNA for mammal biomonitoring and pathogen surveillance

Rodent and eulipotyphlan partial cytochrome b sequences

FASTA file comprising 248 sequences generated during this study

Role of Wildlife in Emergence of Ebola Virus in Kaigbono (Likati), Democratic Republic of the Congo, 2017

International audienceAfter the 2017 Ebola virus (EBOV) outbreak in Likati, a district in northern Democratic Republic of the Congo, we sampled small mammals from the location where the primary case-patient presumably acquired the infection. None tested positive for EBOV RNA or antibodies against EBOV, highlighting the ongoing challenge in detecting animal reservoirs for EBOV