Malaria parasite detection increases during pregnancy in wild chimpanzees

Background: The diversity of malaria parasites (Plasmodium sp.) infecting chimpanzees (Pan troglodytes) and their close relatedness with those infecting humans is well documented. However, their biology is still largely unexplored and there is a need for baseline epidemiological data. Here, the effect of pregnancy, a well-known risk factor for malaria in humans, on the susceptibility of female chimpanzees to malaria infection was investigated. Methods: A series of 384 faecal samples collected during 40 pregnancies and 36 post-pregnancies from three habituated groups of wild chimpanzees in the Tai National Park, Cote d'Ivoire, were tested. Samples were tested for malaria parasites by polymerase chain reaction (PCR) and sequencing. Data were analysed using a generalized linear mixed model. Results: Probability of malaria parasite detection significantly increased towards the end of pregnancy and decreased with the age of the mother. Conclusions: This study provides evidence that susceptibility to malaria parasite infection increases during pregnancy, and, as shown before, in younger individuals, which points towards similar dynamics of malaria parasite infection in human and chimpanzee populations and raises questions about the effects of such infections on pregnancy outcome and offspring morbidity/mortality

Assessing the feasibility of fly based surveillance of wildlife infectious diseases

Monitoring wildlife infectious agents requires acquiring samples suitable for analyses, which is often logistically demanding. A possible alternative to invasive or non-invasive sampling of wild-living vertebrates is the use of vertebrate material contained in invertebrates feeding on them, their feces, or their remains. Carrion flies have been shown to contain vertebrate DNA; here we investigate whether they might also be suitable for wildlife pathogen detection. We collected 498 flies in Taï National Park, Côte d’Ivoire, a tropical rainforest and examined them for adenoviruses (family Adenoviridae), whose DNA is frequently shed in feces of local mammals. Adenoviral DNA was detected in 6/142 mammal-positive flies. Phylogenetic analyses revealed that five of these sequences were closely related to sequences obtained from local non-human primates, while the sixth sequence was closely related to a murine adenovirus. Next-generation sequencing-based DNA-profiling of the meals of the respective flies identified putative hosts that were a good fit to those suggested by adenoviral sequence affinities. We conclude that, while characterizing the genetic diversity of wildlife infectious agents through fly-based monitoring may not be cost-efficient, this method could probably be used to detect the genetic material of wildlife infectious agents causing wildlife mass mortality in pristine areas

Detection of Retroviral Super-Infection from Non-Invasive Samples

While much attention has been focused on the molecular epidemiology of retroviruses in wild primate populations, the correlated question of the frequency and nature of super-infection events, i.e., the simultaneous infection of the same individual host with several strains of the same virus, has remained largely neglected. In particular, methods possibly allowing the investigation of super-infection from samples collected non-invasively (such as faeces) have never been properly compared. Here, we fill in this gap by assessing the costs and benefits of end-point dilution PCR (EPD-PCR) and multiple bulk-PCR cloning, as applied to a case study focusing on simian foamy virus super-infection in wild chimpanzees (Pan troglodytes). We show that, although considered to be the gold standard, EPD-PCR can lead to massive consumption of biological material when only low copy numbers of the target are expected. This constitutes a serious drawback in a field in which rarity of biological material is a fundamental constraint. In addition, we demonstrate that EPD-PCR results (single/multiple infection; founder strains) can be well predicted from multiple bulk-PCR clone experiments, by applying simple statistical and network analyses to sequence alignments. We therefore recommend the implementation of the latter method when the focus is put on retroviral super-infection and only low retroviral loads are encountered

Ebola virus disease: an orphan zoonosis ?

The gigantic Ebola virus disease outbreak that recently swept several West African countries has revealed how little we know about this infectious disease. The question of the animal reservoir of this zoonosis remains particularly mysterious. Bats seem to be involved in the ecology of the virus but it remains unclear whether or not they may be at the origin of spill-over events towards humans. Almost 40 years after the discovery of the Ebola virus, this short communication offers a summary of the progresses made and an outlook on upcoming efforts to solve this outstanding question.La terrible épidémie de maladie à virus Ebola qui a balayé l’Afrique de l’Ouest a mis en évidence combien nos connaissances sur cette maladie infectieuse sont limitées. Une question particulièrement mystérieuse reste celle du réservoir animal de cette zoonose. L’implication des chauves-souris dans l’écologie du virus semble probable mais il n’est pas encore établi qu’elles jouent un rôle dans sa transmission à l’homme. Près de 40 ans après la découverte du virus, cette communication se propose de faire le point sur les savoirs accumulés et de dégager des pistes de réflexion utiles

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

Comparison of mosquito and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany

The use of invertebrate‐derived DNA (iDNA) is a promising non‐invasive tool to monitor wildlife. While most studies have been carried out in dense tropical and sub‐tropical forests and have focused on the use of a single category of invertebrates, this study compares the use of flies and mosquitoes‐derived DNA to assess vertebrate diversity in semi‐urban environments. We conducted our sampling in four different forest plots in Berlin, Germany. Pools of flies and non‐bloodfed mosquitoes were metabarcoded using 108‐bp vertebrate‐specific 12 S rRNA (12 S‐V5) and 94‐bp mammal‐specific 16 S rRNA (16Smam) mitochondrial markers, and individual bloodfed mosquitoes were sequenced using the 340‐bp vertebrate‐specific 12 S rRNA fragment (Mam‐12 S‐340). Most sequencing was only successful for mammal species. From the fly pools, we detected 10 mammal species using 16Smam, and six species using 12 S‐V5. From the non‐bloodfed mosquito pools, we only amplified putative contaminant DNA, indicating that mosquito females without visual signs of a blood meal carry no traces of vertebrate DNA. Finally, in the bloodfed mosquitoes, we identified four mammal species. We did not find significant differences in the proportion of mammal species detected regarding the total available number of species between sampling localities. Fly samples were easier to obtain and more abundant over the sampled localities compared to mosquito samples. We conclude that, while there are a few advantages in using mosquito blood meals, the use of flies in the detection of wildlife in a suburban environment is more effective in terms of collection of samples and detection of vertebrates, although this technique is limited to few mammal species in the urban environment

Novel Mycobacterium tuberculosis Complex Isolate from a Wild Chimpanzee

Tuberculosis (TB) is caused by gram-positive bacteria known as the Mycobacterium tuberculosis complex (MTBC). MTBC include several human-associated lineages and several variants adapted to domestic and, more rarely, wild animal species. We report an M. tuberculosis strain isolated from a wild chimpanzee in Côte d’Ivoire that was shown by comparative genomic and phylogenomic analyses to belong to a new lineage of MTBC, closer to the human-associated lineage 6 (also known as M. africanum West Africa 2) than to the other classical animal-associated MTBC strains. These results show that the general view of the genetic diversity of MTBC is limited and support the possibility that other MTBC variants exist, particularly in wild mammals in Africa. Exploring this diversity is crucial to the understanding of the biology and evolutionary history of this widespread infectious disease

The cost of living in larger primate groups includes higher fly densities

Flies are implicated in carrying and mechanically transmitting many primate pathogens. We investigated how fly associations vary across six monkey species (Cercopithecus ascanius, Cercopithecus mitis, Colobus guereza, Lophocebus albigena, Papio anubis, and Piliocolobus tephrosceles) and whether monkey group size impacts fly densities. Fly densities were generally higher inside groups than outside them, and considering data from these primate species together revealed that larger groups harbored more flies. Within species, this pattern was strongest for colobine monkeys, and we speculate this might be due to their smaller home ranges, suggesting that movement patterns may influence fly–primate associations. Fly associations increase with group sizes and may thus represent a cost to sociality