The processes involved in acquiring, trading, preparing, and consuming wild meat pose significant risks for the emergence of zoonotic infectious diseases. Several major viral outbreaks have been directly linked to the wild meat supply chain, yet our knowledge of the virome of many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens. Here, we present the findings of a metagenomic viral screening of 101 mammalian specimens belonging to 28 wild African species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected in various regions in the Democratic Republic of the Congo and in Brussels, Belgium. A total of sixteen virus strains were detected, belonging to the families Arteriviridae, Retroviridae and Sedoreoviridae (primates), Picobirnaviridae (primates and rodents), Picornaviridae (rodents), Hepadnaviridae (hyrax), Orthoherpesviridae (artiodactylid and carnivore) and Spinareoviridae (carnivore). Several strains were detected in mammalian hosts for the first time, expanding their host range and genetic diversity. Of note is the presence of viruses genetically related to recognised zoonotic pathogens, i.e., human picobirnavirus (Orthopicobirnavirus hominis) (primates and rodents), simian foamy viruses (Simiispumavirus) (primates), and rotavirus A (Rotavirus alphagastroenteritidis) (primates). The presence of these viruses in primates is concerning as non-human primates are phylogenetically closely related to humans, which can facilitate interspecies viral transmission. These findings underscore the high diversity of mammalian viruses and the potential risk of human infection through cross-species transmission during close interactions with wildlife in the wild meat supply chain.

The wildlife reservoir and spillover mechanisms of Ebola virus remain elusive despite extensive research efforts in endemic areas. This study employed a One Health approach to examine the virus' circulation in wildlife and the associated human exposure risks in the Tshuapa province of the Democratic Republic of the Congo. We screened 1049 samples from 919 animals, predominantly small mammals, collected in 2021, and 380 samples from inhabitants of Inkanamongo village, the site of an Ebola virus disease outbreak in 2014. These samples were screened for evidence of current (RNA) or past (IgG antibodies) Ebola virus infections. We also conducted interviews with 167 individuals in the surrounding districts to assess their interactions with wildlife. While no Ebola virus RNA was detected in the wildlife samples, anti-orthoebolavirus IgG antibodies were found in 13 bats and 38 rodents. Among the human participants, 120 individuals had IgG antibodies against at least 1 orthoebolavirus antigen, with 12 showing seropositivity for 2 antigens of the same orthoebolavirus, despite not having a prior Ebola disease diagnosis. Furthermore, the majority of respondents reported frequent visits to the forest to hunt a variety of wild animals, particularly ungulates and rodents, which could account for occasional viral spillovers. The absence of active Ebola virus circulation in wildlife may reflect seasonal patterns in reservoir ecology, as those observed in bats. Similarly, seasonal human activities, such as hunting and foraging, may result in periodic exposure risks. These findings highlight the importance of continuous, multidisciplinary surveillance to monitor changes in seasonal spillover risks.

Abstract We determined a near complete and complete monkeypox virus (Mpox) genome in an elephant shrew (Petrodromus tetradactylus), a squirrel (Funisciurus bayonii), and produced shorter sequencesobtained from two rats (Stochomys longicaudatus, Cricetomys sp. 2) originating from the Democratic Republic of the Congo. We also ran a series of molecular clock analyses that all agree on a recent, clearly post Dahomey gap opening diversification of Mpox. This suggests that, besides squirrels, a number of rodents and elephant shrews are involved in Mpox ecology, whose current genomic diversity and distribution was likely shaped in the last 1,000 years.

Abstract Many tropical biosphere reserves face the problem of overexploiting biological resources, which is a major cause of biodiversity loss. We used an integrative approach, combining camera trapping and bat trapping in diverse habitats over multiple surveys in Yangambi Biosphere Reserve, Democratic Republic of the Congo. We investigated whether species-level traits of volant and nonvolant mammals, as well as key features of their habitats, can predict effects on species detectability and occupancy, and thus on community-level species richness. We applied single-season occupancy models using multi-species data for camera trap and bat trap datasets. We found a positive effect of denser woodlands on occupancy estimates over 6480 camera-days. Average adult body weight and whether species were group-living negatively influenced species detection estimates. Species richness and body size assemblages approximated marginal rainforest diversity. This included small-bodied, generally high-hunting-resilient arboreal and terrestrial species. During 324 trap-nights, site location was the main determinant of habitat occupancy at the community level. Occupancy estimates were not, however, directly linked to variables measured in different stands. This may be a consequence of habitat patterns at larger spatial scales, which require additional data to clarify. Species-level characteristics that might influence detection estimates were not, however, included in the parsimonious output of the model used. Our findings indicate specific mechanisms triggering mammalian impoverishment above a critical size that may drive ecological changes. Thanks to certain life-history traits, bats can compensate for some of the lost services previously provided by large mammals, thus contributing to the maintenance of biodiversity dynamics.

In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.

Abstract This paper documents a community of eastern chimpanzees (Pan troglodytes schweinfurthii Giglioli, 1872) inhabiting three relict forest fragments situated on the Lake Albert escarpment, down the Ituri highlands, of eastern Democratic Republic of the Congo (DRC). The area explored had a combined forested surface of ±18.15 km2 in 2017, shrinking by 1.2% per year between 2010 and 2015. Between 2015 and 2017, we found 160 chimpanzee nests along 37.6 km of pilot walks, some up to 2,000 m altitude. Another 123 nests logged along 6.7 km transects led to an estimate of chimpanzee density of 4.62 weaned individuals per square kilometer of forest habitat. Camera‐trap images and direct observations revealed that this community is comprised of a minimum of 42 weaned individuals, which translates into an estimated density of 2.3 chimpanzees per square kilometer. The increasing rate of forest degradation threatens to erode the cultural and genetic diversity of nonhuman primates in eastern DRC; the local people however exhibit willingness to establish a community managed reserve. We hope that this report will lead to the recognition of this site as a Chimpanzee Conservation Unit, facilitating further research in these “Relict Altitude Forests Fragments of the Albert Lake Escarpment” (or RAFALE landscape) and the Ituri highlands where other undocumented chimpanzee communities occur.

We determined near complete and complete monkeypox virus genomes in a shrew ( Crocidura littoralis ), two squirrels ( Funisciurus anerythrus, Funisciurus bayonii ), and produced shorter sequences from two rats ( Stochomys longicaudatus, Cricetomys sp. 2) originating from the Democratic Republic of the Congo. This suggests that a number of rodents besides squirrels (families Muridae and Nesomyidae) and shrews (order Eulipotyphla) are potential monkeypox virus reservoirs.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) has recently emerged as an alternative to morphological and molecular tools to identify tick species. In this study, we set out to evaluate and confirm the ability of MALDI-TOF MS to identify different species of ticks collected in the Democratic Republic of the Congo and preserved in 70% ethanol. A total of 575 ticks, of which 530 were collected from domestic pigs and 45 from wild animals, were subjected to MALDI-TOF MS analysis to evaluate the intraspecies reproducibility and interspecies specificity of MS profiles obtained from the different species. Morphologically, the ticks belonged to seven different species, namely Rhipicephalus complanatus , Rhipicephalus congolensis , Haemaphysalis muhsamae , Ixodes cumulatimpunctatus , Amblyomma exornatum , Amblyomma compressum and an unidentified Rhipicephalus sp. A total of 535/575 (93%) of the spectra obtained were of good enough quality to be used for our analyses. Our home-made MALDI-TOF MS arthropod database was upgraded with spectra obtained from between one and five randomly selected specimens per species. For these reference specimens, molecular identification of the ticks was also made using 16S, 12S rDNA genes and the Cox1 mtDNA gene sequencing. The remaining good quality spectra were then queried against the upgraded MALDI-TOF MS database, showing that 100% were in agreement with the morphological identification, with logarithmic score values (LSVs) between 1.813 and 2.51. The consistency between our morphological, molecular and MALDI-TOF MS identification confirms the capability and precision of MALDI-TOF MS for tick identification.

After 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.

Amongst small mammals, rodents are the largest order in terms of both species and population numbers. They have a high rate of reproduction, are cosmopolitan and have the ability to adapt to a wide variety of habitats. Several studies were carried out on myomorphic rodents in the Kisangani ecoregion, while those on sciuromorphic rodents are very scarce. Therefore, the purpose of this study was to determine the composition of the sciuromorph rodent population in the Kisangani ecoregion. This investigation was conducted in five stations of Kisangani and the sampling was performed between April 2014 and December 2016. The external morphometry method was used for species identification according to Kingdon and Schouteden. Using traditional traps, the trapping was done randomly and 75 specimens of squirrels were captured knowing that 75 traps were installed in each station. In total, the capture success was of 27750 night traps with a weak yield of 0.27%. The findings revealed that the highest rate of species was recorded in the Masako station with a capture success of 1.89% while the lowest in the Mombongo station with a capture success of 0.38%. The 75 specimens of squirrels captured belong to 4 genera and 7 species Masako and Yasikia stations presented a high specific richness (SR = 4) than other stations. Funisciurus anerythrus, Heliosciurus rufobrachium, Paraxerus boehmi are constant (C> 50%) and Funisciurus pyrropus, Protoxerus stangeri, Funisciurus bayonii, Funisciurus congicus are accessory taxa (25%

In this 21 century, the world's attention is focused on the accelerated degradation of the biodiversity. This phenomenon of degradation seems to hasten the process of climate change and habitats that would amplify the lack of biological resources. The main objective of this work was to acquire scientific information on rodents and shrews biodiversity that colonize future TshuapaLomami-Lualaba National Park. The study was conducted in the Congolese Central Cuvette precisely in Obenge village, in this national park the future Tshuapa-Lomami-Lualaba National Park. The trapping was carried out for 5 days, divided as follows: 2 days for traps installed in the secondary forest, 3 days for the traps installed in the village, its surroundings and in the fallow, 5 days for the traps installed in the primary forest. We combined Pitfall, Victor and Sherman traps to form devices to capture Rodents and Shrews. Specific richness, capture effort, trapping success, Shannon-Wiener alpha index and maximum equitability were the ecological indices used. We collected a total of 159 small mammals of which 110 rodents, 43 Soricidae and 6 macroselidae. From this study, CSB brought a new idea regarding the knowledge of rodent as well as shrew biodiversity in Tshuapa-Lomami-Lualaba future National Park and making available data for Natural Resource Managers for a sustainable development. These results show that body biomass of rodents’ ranges between 3 and 31g. The calculated biodiversity indices for different habitats show that rodent communities are less diversified. For the distribution of shrews sampled in different habitats, the most interesting was performed in primary forest at G dewevrei (42 out of 49 specimens where Crocidura sp. is the most captured with 16 out of 49 specimens). The body biomass ranges between 24 and 190g. The calculated indices of biodiversity for different habitats revealed that shrew communities are less diversified.

The study concerns the reproduction and structure of the populations of Sciuridae from the forest reserve of Yoko and has for objectives to identify the dominant species present in this reserve, to determine and to analyze the structure of the populations of squirrels and their reproduction phonology in order to estimate the stability of this group facing the local and global changes. The animals were harvested with the help of traditional traps from May 2014 to April 2015. From the six species captured, Funisciurus anerythrus was the most abundant, followed by the Funisciuruses bayonii, Funisciurus congicus, Paraxerus boehmi, Heliosciurus rufobrachium and Protoxerus stangeri. Their activities seem to achieve themselves in the fallows except the last two species that prefer the primary forest. The reproductive activities increase toward the middle of the rainy season (September-November) with a great proportion of the gravid females from December to February, which accompanies of a massive entry of the young during the active period from June to November. The sex-ratio is in favor of the males but the difference is not significative (p>0.05). The middle range is of two for Funisciurus anerythrus, and one for the other. The adults are abundant; the continuous presence of the young adult and juvenile reveals a continuous reproduction and the stability of the population.

The study is a contribution to the knowledge of Rodents and Shrews diversity in Yasikia forest, located at 31 Km from Kisangani, on the road towards Opala. On transects, Rodents and Shrews were sampled using the protocol with (xPF, ySH). A total of 13 sampling lines were observed during 15 days (from March 26 to 11 April 2015). As results, we collected 74 shrews, belonging to two genera at least 9 species; 68 rodents which represent 9 genera and 12 species. In total, we collected 145 small mammals, with a trapping effort of 6478 trap-nights. The specific biodiversity and trappingsuccess showed that Pitfall traps are the most efficient to capture Shrews. It also catches small Rodents and adult such as N.cf.grata, and other adults' rodents as Praomys genera, but with reduced number. Sherman traps are more effective to catch Rodents. They also catch shrews in reduced number. The trappings were conducted in three habitats. In the primary forest G. dewevrei (EC = 1060 night-traps, 50 specimens, 14 species, and TS = 4.72%), mixed primary forest (EC = 1500 night-traps, 69 specimens, 15 species, and TS = 4.6%) and fallow land (EC = 440 night-traps, 23 specimens, 9 species, and TS = 5.23%). No new species was announced but rather the presence of three endemic species of which two ( C. Goliath and L. huttereri ) are rare.