Erik Verheyen

Because of their arboreal lifestyle, the diversity and life history of squirrels in low-altitude Afrotropical forests are currently under-researched. Following a 72-day inventory using traditional ...

The taxonomy, distribution, and ecology of sub-Saharan squirrels are poorly documented. This study focuses on the diversity and distribution of rope squirrels (Funisciurus Trouessart, 1880) in the Congo Basin. We compiled the most comprehensive genetic (n = 397 sequences) and morphometric (n = 219 measured skulls) dataset to date, covering much of their geographical and taxonomic range. Analysis of mitochondrial markers recovered 10 MOTUs (Molecular Operational Taxonomic Unit), nuclear markers 2 MOTUs, and morphometrics 5 Operational Taxonomic Units. Integrating this evidence suggests at least six species-level lineages in our dataset: four allopatric taxa related to F. anerythrus; four genetically different taxa (of which two are sympatric species) that resemble F. cf. bayonii; one taxon corresponding to F. pyrropus akka de Winton, 1895; one morphologically distinct taxon that resembles F. cf. congicus; and one unidentified taxon. Their distributional ranges reveal that the Congo and Kasaï Rivers act as major biogeographical barriers, suggesting that they originated by allopatric speciation. Our findings provide a baseline for studying the effects of habitat loss on rope squirrel populations in the Congo Basin and inform research into their role as reservoirs of zoonotic pathogens, including mpox virus.

The full text of this preprint has been withdrawn by the authors since they no longer stand by the findings/conclusions of this work. Therefore, the authors do not wish this work to be cited as a reference. Questions should be directed to the corresponding author.

The diversity, taxonomy, distribution and ecology of sub-Saharan tree squirrels remain under-researched. This study aims to elucidate the diversity and distribution of rope squirrels, genus Funisciurus Trouessart 1880, in the Congo Basin. We assembled the most comprehensive genetic and morphometric data set to date, on a significant portion of the geographical and taxonomic range of these squirrels (470 specimens from seven provinces of the Democratic Republic of Congo). We identified six main taxa: a previously undescribed Funisciurus species (here, Fx), three allopatric taxa of Funisciurus anerythrus (Fc, FaRB and FaLB), and two sympatric genetically distinct taxa (FbLB1, FbLB2), potentially belonging to a Funisciurus bayonii species complex. We then mapped their distribution, showing that the Congo and Kasaï Rivers represent significant biogeographical barriers limiting the distribution of Funisciurus species. In addition to providing a baseline for research on the impact of climate change and habitat degradation on the abundance and distribution of rope squirrels, our findings support research on the role of rope squirrel species in the transmission of pathogens of public health importance. Teaser text: We studied the diversity and distribution of rope squirrels, genus Funisciurus Trouessart 1880, in the Congo Basin. By gathering the most comprehensive genetic and morphometric data to date on a significant part of the geographical and taxonomic range of these squirrels (specimens from seven provinces of the Democratic Republic of Congo), we identified six main taxa: one previously undescribed species, three allopatric taxa, and two genetically distinct sympatric taxa. We then mapped their distribution, showing that the Congo and Kasai rivers represent significant biogeographical barriers limiting the distribution of Funisciurus species. These results support research into the role of rope squirrel species in the transmission of pathogens of public health importance. Image for the online table of contents: African rope squirrel Photo credit: Bushnell photo trap set by Pascal Baelo

Altough zoonotic spillover events continue to drive human mpox outbreaks in the Democratic Republic of the Congo (DRC), the wildlife reservoir of mpox virus (MPXV) remains unkown. To address this gap, we screened samples from 2,701 wild mammals, mainly rodents (59.7%), bats (26.4%) and shrews (12.1%). Only six (0.2%) animals were Orthopoxvirus (OPV) PCR positive. Near full-length MPXV sequences were obtained from two squirrels ( Funisciurus anerythrus and Paraxerus sp.) and one soft furred mouse ( Praomys jacksoni ). A novel Taterapox virus was identified in a shrew ( Crocidura cf. denti ). All newly identified MPXV strains belong to clade Ia, but they cluster into different groups or subgroups, despite being collected from geographically close locations, and all are closely related to human MPXV strains from the same regions. Our study provides for the first time clear evidence that MPXV diversity is not restricted to a single rodent host species nor confined to a geographic area. Importantly, MPXV positive Paraxerus and Praomys specimens were sampled close to Kisangani, a city with more than one million habitants, highlighting that spillover events can also occur in or near major cities, with more favorable conditions for interhuman transmissions and potential emergence of new lineages.

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 in many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens. This report presents the findings of a metagenomic viral screening of 99 specimens belonging to 27 wild African mammal species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected from various regions in the Democratic Republic of the Congo and in Brussels, Belgium. A total of fifteen 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 the close interactions with wildlife in the wild meat supply chain.

The wildlife reservoir and spillover mechanisms of the 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. In 2021, we collected 1015 samples from 888 animals, predominantly small mammals, and 380 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 one orthoebolavirus antigen, with 12 showing seropositivity for two antigens of the same orthoebolavirus, despite not having a prior Ebola disease diagnosis. Furthermore, over 50% 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, like those observed in bats. Similarly, seasonal human activities, like 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.

Background: Over five billion people globally rely on a plant- and animal-based pharmacopoeia for their healthcare needs. The inhalation, topical application, subcutaneous injection, or ingestion of animal products – such as faeces, fur, milk, blood, brain tissue, or meat – likely facilitates the spill over of zoonotic pathogens. Certain practices use species known to be involved in the transmission of pathogens of public health relevance, such as reservoir species for filoviruses, poxviruses, and coronaviruses. These practices and the public health risk they entail have not been previously reviewed and analysed for the African continent. Methods: We first conducted a systematic review of literature using web-scraping algorithms targeted at peer-reviewed (PubMed) and peer-reviewed or grey literature (Google Scholar) databases, followed by manual search of reference lists published before July 30th, 2023. We used terms encompassing zoo*, animal*, health*, practice*, tradition* followed by a list of all 54 African countries in combination with Boolean operators. We then created a categorical score reflecting the risk of zoonotic pathogen spill over for each recorded zootherapeutic practice, and compared this risk between geographic regions and between demographic groups. Findings: A total of 53 studies were included, reporting the use of over 2,000 zootherapeutic practices. Half of the included studies were published after 2020. Nigerian, Ethiopian, Tanzanian and South African practices were comparatively well documented. The mean total risk score was significantly lower in western (13.27 ± 0.13, p < 0.0001), central (14.80 ± 0.27, p < 0.003), and southern (13.48 ± 0.23, p < 0.0001) Africa, compared to eastern Africa, while there was no significant difference between eastern and northern Africa (15.25 ± 0.26, p = 0.16). Further, we found that physically sick children are overall at increased risk for pathogen spill over (13.20 ± 0.36 out of a possible sub-score of 20, p = 0.001 < 0.05) compared to physically sick adults, and that pregnant or lactating women are exposed to animal tissues of significantly greater infectious potential (4.01 ± 0.15, p = 0.032 <0.05). Interpretation: The WHO recently hosted its first global summit on Traditional, Complementary and Integrative Medicine (TCIM), highlighting its importance to fulfil SDG 3: Good Health and Wellbeing. Where other forms of healthcare are unavailable or inefficient, zootherapeutic practices can provide valuable solutions to acute, chronic, physical, and psychological issues. However, significant risks of zoonotic disease transmission exist. This article aims to guide research on sustainable alternatives to mainstream medical treatments that balance cultural significance and public health.

Previous literature suggests that Indigenous cultural practices, specifically traditional medicine, are commonplace among urban communities contrary to the general conception that such practices are restricted to rural societies. We reviewed previous literature for records of herptiles (frog and reptile species) sold by traditional health practitioners in urban South Africa, then used visual confirmation surveys, DNA barcoding and folk taxonomy to identify the herptile species that were on sale. Additionally, we interviewed 11 IsiZulu and SePedi speaking traditional health practitioners to document details of the collection and pricing of herptile specimens along with the practitioners' views of current conservation measures for traditional medicine markets. The 34 herptile species recorded in previous literature on traditional medicine markets included endangered and non‐native species. Spectrophotometry measurements of the DNA we extracted from the tissue of herptiles used in traditional medicine were an unreliable predictor of whether those extractions would be suitable for further experimental work. From our initial set of 111 tissue samples, 81 sequencing reactions were successful and 55 of those sequences had species‐level matches to COI reference sequences on the NCBI GenBank and/or BOLD databases. Molecular identification revealed that traditional health practitioners correctly labelled 77% of the samples that we successfully identified with DNA barcoding in this study. Our mixed methodology approach is useful for conservation planning as it updates knowledge of animal use in Indigenous remedies and can accurately identify species of high conservation priority. Furthermore, this study highlights the possibility of collaborative conservation planning with traditional health practitioners.

The wild meat trade poses a significant threat to public health as it facilitates the spillover of zoonotic pathogens through high-risk activities such as the hunting, butchering, trade, and consumption of wild animals. Despite the health risks and association with marking epidemics including SARS, Ebola, and COVID-19, the global wild meat trade continues to thrive. To summarize the evidence available, primary literature published between 2000 and 2022 was systematically and critically assessed for evidence of zoonotic pathogens or other infectious organisms detected in samples directly from wild meat, from animals hunted for wild meat, or from humans exposed through high-risk activities. Within the 97 articles analyzed, a total of 114 pathogen genera (15 viruses, 40 bacteria, 54 parasites, and 5 fungi) were detected in wild meat animals belonging to 168 vertebrate species including mammals, reptiles and birds sampled in 32 countries. In the context of wild meat specifically, infectious organisms were differentiated between those with zoonotic potential (32 of reported genera), ectoparasitic vectors (1), and possible opportunistic or environmental contaminants. Thirteen viral, four bacterial, and one parasitic genera were also documented in humans participating in wild meat trade activities, supporting pathogen spillover potential. Most studies employed a targeted approach to evaluate the presence of (i.e., polymerase chain reaction (PCR); n65) or exposure to (i.e., ELISA; n19) a specific pathogen, while only one study employed broad-spectrum metabarcoding techniques. The diversity of infectious organisms associated with wild meat are highlighted through this review and could be used to guide policy development. However, the common use of a selected set of targeted detection assays likely biases the exploration of pathogen diversity, therefore potentially preventing the discovery of disease x. The global health risk demonstrated should make the illegal wild meat trade a priority for law-enforcement agencies and future research.