Land-use change can influence parasite transmission by reshaping ecological interactions among parasites, vectors, and hosts. In particular, deforestation and agricultural expansion modify habitat structure and resource availability, potentially altering the prevalence and distribution of vector-borne diseases. Fieldwork was conducted on São Tomé Island (Gulf of Guinea, Central Africa) across a land-use gradient from the core of an oil palm plantation to adjacent native forest. Culicoides biting midges and birds were sampled across four habitat types (village, oil palm plantation, at the border between the plantation and the forest, and forested areas) using Centers for Disease Control (CDC) traps and mist nets, respectively. DNA extracted from Culicoides and bird blood was used to screen for Plasmodium, Haemoproteus, and Leucocytozoon using nested polymerase chain reaction (PCR). Blood-fed Culicoides collected in the traps were analyzed by PCR to identify the host species. Linear models were used to assess differences in vector diversity, abundance, host-feeding preferences, and haemosporidian prevalence among habitats. Culicoides species richness did not differ significantly between habitats, but species abundances did vary. Overall abundance was lower in the oil palm plantation than in border and forest areas. Mammophilic Culicoides were more abundant in the village, whereas ornithophilic species were predominated in the forest. We screened 432 bird blood samples and 452 parous Culicoides for haemosporidian infections. Haemosporidian parasites were most frequently detected in Culicoides pools from the border area. Among birds, Plasmodium prevalence was significantly higher in the oil palm plantation than in border and forest habitats, while Leucocytozoon infections were completely absent in plantation birds. Anthropogenic habitat disturbance modifies vector communities and host–parasite associations, influencing the transmission dynamics of Haemoproteus parasites. These findings highlight the ecological consequences of agricultural expansion and the importance of preserving natural habitats to mitigate disease emergence under land-use change scenarios.

The risk of viral transmissions from domestic/wild animals to humans is a major public health concern. Humans can also transmit viruses back to domestic and wild animals, acting as a reservoir for virus maintenance and a source of epidemic diseases re-emergence. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing COVID-19, likely originated from wildlife and has been evidenced to transmit from humans to captive, domestic and wild animals. White-tailed deer (Odocoileus virginianus) show high SARS-CoV-2 prevalence following human contamination, suggesting they could act as an emerging virus reservoir. We completed recent research on European cervid species by investigating whether SARS-CoV-2 had emerged in longitudinally monitored European roe deer (Capreolus capreolus) populations in direct contact with humans in France. We performed indirect tests (serological enzyme-linked immunosorbent assays and seroneutralization) on sera collected before and after the virus emergence in humans, and direct reverse transcriptase polymerase chain reaction tests on nasal swabs collected in 2022. We also investigated the virus exposure and prevalence in three other cervid species. Enzyme-linked immunosorbent assay tests were positive for 2.20% of sera, pre- and post-pandemic, but seroneutralization and polymerase chain reaction tests were negative. Although one population showed increased seroprevalence post-2020, results suggest that SARS-CoV-2 has not emerged in those populations and that enzyme-linked immunosorbent assay cross-reaction with one or several unidentified circulating coronaviruses is possible.

Despite advances in understanding infectious diseases, the persistence and re-emergence of wildlife pathogens continue to raise public and veterinary health concerns. This study investigates the relationship between biodiversity and rodent-borne diseases in Europe, focusing on habitat alterations and their impact on rodent diversity. We present host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals-wildlife interactions are likely to occur. From 2020 to 2022, 3766 specimens comprising 15 different small mammal species were analyzed. Samples were screened for bacteria via 16S rRNA sequencing or PCR, and for viral antibodies using immunofluorescent assays. Pathogens from several genera, including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira, Orthohantavirus, and Orthopoxvirus, were detected at non-negligible prevalence in 11 host species. Host community composition differed between habitats, with more urban adapters in parks than in forests. Pathogen richness increased with an increase in host species diversity, supporting the "host-diversity begets parasite-diversity" hypothesis, though not with anthropization. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community driven by human impact. Host species and intrinsic factors were dominant explanatory variables for Mycoplasma species and Sarcocystidae, while extrinsic environmental and climatic factors influenced variations in several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus served as important connector hosts in urban spaces and temperate forests, respectively. These results improve our understanding of the complex local host-pathogen system, aiding future management decisions and supporting the public health sector.

The risk of viral transmissions from domestic and wild animals to humans is of high concern for human health. Humans can also transmit viral infections back to domestic and wild animals, which can then act as reservoir for the maintenance of viruses, with the risk of epidemic diseases re-emergence. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), causing the COVID-19, likely originated from wildlife and has already been evidenced to be transmitted from humans to captive, domestic and wild animals. In particular, white-tailed deer ( Odocoileus virginianus ) show high-prevalence of SARS-CoV-2 following human contamination, and recent data suggest that white-tailed deer could act as an emerging virus reservoir. Here, we investigated whether SARS-CoV-2 could also have emerged in several longitudinally-monitored populations of European roe deer ( Capreolus capreolus ) in direct contact with humans in France. We performed indirect tests (serological ELISAs and seroneutralization) on serum collected pre- and post-emergence of the virus in human populations. We also performed direct tests (nasal swabs followed by RT-PCR) to detect the presence of SARS-CoV-2 RNA in those populations in 2022. We also investigated the exposure and prevalence of the virus in three other cervid species in France. ELISA tests were positive for 2.20 % of the sera tested, both pre- and post-emergence of the virus, but all positive samples were negative with seroneutralization. Direct PCR testing showed no positive results in 2022. Thus, although seroprevalence increased after the COVID-19 emergence (2022) in one out of three roe deer population, our results suggest that SARS-CoV-2 has not emerged in those populations, and that ELISA cross-reaction with another circulating virus, possibly an unidentified bovine coronavirus, is possible. ### Competing Interest Statement The authors have declared no competing interest.

Recent zoonotic disease emergences emphasize the importance of studying wildlife parasite communities. As wild hosts frequently harbour diverse parasite species, understanding the drivers of multiple infection patterns in free-ranging hosts is critical for elucidating the ecological and epidemiological dynamics of parasite communities. In this study, we analysed co-infection patterns in European roe deer (Capreolus capreolus) inhabiting a fragmented rural landscape in southwestern France. Using data from 130 samples of GPS-tracked deer, we examined the influence of proximity to livestock, host activity levels, age, sex and between-parasite interactions on the presence of 11 parasitic taxa. Hierarchical modelling of species communities (HMSC) revealed that proximity to livestock significantly increased the likelihood of infection with orofecally transmitted parasites (Toxoplasma gondii, gastrointestinal parasites). Sex and age were other key predictors, with males and juveniles exhibiting a higher frequency of parasite presence, likely influenced by hormonal and immune system differences. Activity levels showed distinct age-related effects, with higher activity levels being positively associated with increased parasite prevalence in yearlings, but not in adults. In contrast, parasite association patterns within individual hosts were weak, suggesting minimal interactions between parasite species. Our findings highlight the interplay between exposure and susceptibility in shaping co-infection patterns and underscore the value of hierarchical modelling approaches in multi-parasite systems.

IntroductionInter- and transdisciplinary research (ITDR) is increasingly promoted to address “wicked problems”, particularly in health sectors adopting approaches like Ecohealth. Our Ecohealth-inspired project on rodent-borne diseases, initiated just before the COVID-19 pandemic, provided an opportunity to evaluate ITDR implementation.MethodsWe employed a recently developed semi-quantitative evaluation method to measure our project’s success in achieving ITDR and analyzed factors influencing this achievement.ResultsThe project showed strengths in system description, team task allocation, and data sharing, but had lower scores in engaging societal actors throughout the project cycle.DiscussionWe identified the underexplored influence of problem wickedness as a critical determinant of ITDR success. Addressing rodent-borne diseases, a less wicked problem, limited engagement potential but enabled constructive dialog with local actors. These insights are vital for addressing variably wicked problems in a polycrisis era. We propose recommendations to strengthen researchers’ capacities, particularly in Ecohealth.

The recent emergence of chronic wasting disease (CWD) in Europe has become a new public health risk for monitoring of wild and farmed cervids. This disease, due to prions, has proliferated in North America in a contagious manner. In several mammalian species, polymorphisms in the prion protein gene (PRNP) play a crucial role in the susceptibility to prions and their spread. To obtain a reliable picture of the distribution of PRNP polymorphisms in the two most common cervid species in France, we sequenced the open reading frame (ORF) of this gene in 2114 animals, 1116 roe deer (Capreolus capreolus) and 998 red deer (Cervus elaphus). Selection criteria such as historical origin, spatial distribution and sex ratio have been integrated to establish this sample collection. Except for one heterozygous animal with a non-synonymous mutation at codon 37 (G37A), all the 1116 French roe deer were monomorphic. Red deer showed greater variation with two non-synonymous substitutions (T98A; Q226E), three synonymous substitutions (codons 21, 78 and 136) and a new 24pb deletion (Δ69-77). We found significant regional variations between French regions in the frequency of the identified substitutions. After cloning of the PRNP ORF from animals presenting multiple non-synonymous polymorphisms, we identified six haplotypes and obtained a total of twelve genotypes. As in other European countries, we highlighted the apparent homogeneity of PRNP in the French roe deer and the existence of a greater diversity in the red deer. These results were in line with European phylogeographic studies on these two species.

Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.

(1) Background: Bats are reservoirs and vectors of significant zoonotic diseases. Our study focuses on understanding the role of bats as reservoirs and carriers of coronaviruses, given their epidemiological significance and the recent global health crises stemming from coronavirus outbreaks. (2) Methods: We conducted virological screening of bats hibernating in military bunkers at the Natura 2000 site "Nietoperek" in Western Poland. This involved collecting and analyzing oral and anal swab samples from 138 bats across six species, using a combination of pan-coronavirus and SARS-CoV-2 specific PCR assays. (3) Results: Out of 138 bats, only one anal swab tested positive for coronavirus. However, we were not able to obtain genomic sequence from the sample. No SARS-CoV-2 was detected in any of the samples. The low prevalence of coronavirus in the studied colony contrasts with higher rates found in other regions and may be influenced by the physiological and behavioral conditions of bats during hibernation. (4) Conclusions: Hibernating bats may show a low prevalence of coronavirus, potentially due to the hibernation process itself. This finding indicates that hibernating bats may not be the most optimal subjects for screening zoonotic pathogens. However, continuous monitoring of bat populations for emerging and reemerging diseases is recommended for a comprehensive epidemiological understanding.

Large-scale genotyping platforms are currently being developed for several wild species. By querying thousands of polymorphic loci, genomics can be a useful ecological tool for describing and monitoring populations. Genomics is becoming increasingly useful as a forensic tool because of its ability to identify population of origin for purposes of enforcing anti-poaching laws. Our aim was to test the new SNP chip for caribou/reindeer (Rangifer tarandus) (Illumina iSelect caribou 60 K) under recommended and non-optimal sample conditions. Impact on signal detection (call rate) and error rate were assessed using reference samples. The SNP chip was shown to be robust, highly sensitive, reliable, and accurate at more than 10-fold below the recommended DNA input. Biological source of DNA had minor impact, even with fecal pellets given sufficient amount of host DNA. Hybridization of non-Rangifer samples as well as samples bearing DNA from two Rangifer samples both showed a drop in call rate and shifted levels of heterozygosity. Based on a population-targeted subset of SNPs included in the chip design, reassignment of 981 samples to a functional group (here to a caribou ecotype) was highly accurate (99.59 %) and the relative probability of reassignment error was estimated using the logarithm of odds score. Overall, the SNP chip is suitable for analysis of caribou/reindeer genomes even with suboptimal sampling and hence useful for population management and forensics.

Major advances in the understanding of infectious diseases have been achieved in the last decades. However, the persistence and re-emergence of pathogens continue to raise public and veterinary health concerns, of which the recent COVID-19 pandemic may be one of the most dramatic examples. Understanding the impact of habitat alterations and concomitant biodiversity loss on pathogen transmission and emergence from wildlife remains challenging. Here, we aim to elucidate the interlinkages between biodiversity and rodent-borne diseases at local and European scales. We present recently collected host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals – wildlife interactions are likely to occur. 3766 specimens were analyzed during the period from 2020 to 2022 comprising 15 different small mammal species. Different organ tissues of each specimen were screened for bacteria by either 16S rRNA amplicon sequencing or specific PCR. The presence of antibodies to different families of viruses was screened using immunofluorescent assays. A multitude of pathogens of zoonotic potential from several genera including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira , Orthohantavirus and Orthopoxvirus were detected at non-negligible prevalence in 11 different terrestrial mammal species. A shift in host community composition was observed along the anthropization gradient with more urban adapters in more anthropized sites. Pathogen richness increased with an increase in host species diversity, following the “host-diversity begets parasite-diversity” hypothesis. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community along the anthropization gradient. Host species and host intrinsic factors were dominant explanatory variables for endoparasitic Mycoplasma species and Sarcocystidae , while extrinsic environmental and climatic factors where influential in explaining variations in occurrences of several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus were important connector host species in respectively urban green spaces and temperate forests. Increased host diversity, but not anthropization, correlated with a richer pathogen community. These results ultimately lead to an increased understanding of the complex host-pathogen system at the local landscape that can aid future management decisions and support the public health sector. ### Competing Interest Statement The authors have declared no competing interest.

BackgroundOur study explores the role of bats as reservoirs of coronaviruses.MethodsWe conducted virological screening of bats hibernating in military bunkers at the Natura 2000 site “Nietoperek” in Western Poland collecting oral and anal swab samples from 138 bats across six species to apply a combination of pan-coronavirus and SARS-CoV-2 specific PCR assays.ResultsOnly one anal swab tested positive for coronavirus. No SARS-CoV-2 was detected in any of the samples. The low prevalence of coronavirus in the studied colony contrasts with higher rates found in other regions and may be influenced by hibernation.ConclusionsHibernating bats may show a low prevalence of coronavirus, potentially due to the hibernation process itself. This finding indicates that hibernating bats may not be the most optimal subjects for screening zoonotic pathogens. However, biomonitoring of bats for emerging and reemerging diseases is recommended for comprehensive epidemiological insights.

Mosquito surveillance programmes are essential to assess the risks of local vector-borne disease outbreaks as well as for early detection of mosquito invasion events. Surveys are usually performed with traditional sampling tools (i.e., ovitraps and dipping method for immature stages or light or decoy traps for adults). Over the past decade, numerous studies have highlighted that environmental DNA (eDNA) sampling can enhance invertebrate species detection and provide community composition metrics. However, the usefulness of eDNA for detection of mosquito species has, to date, been largely neglected. Here, we sampled water from potential larval breeding sites along a gradient of anthropogenic perturbations, from the core of an oil palm plantation to the rainforest on São Tomé Island (Gulf of Guinea, Africa). We showed that (i) species of mosquitoes could be detected via metabarcoding mostly when larvae were visible, (ii) larvae species richness was greater using eDNA than visual identification and (iii) new mosquito species were also detected by the eDNA approach. We provide a critical discussion of the pros and cons of eDNA metabarcoding for monitoring mosquito species diversity and recommendations for future research directions that could facilitate the adoption of eDNA as a tool for assessing insect vector communities.

Background: Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining. Results: We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids. Conclusions: Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus .

Background Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. Results From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. Conclusion This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus . This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.

We report serological surveillance for exposure to SARS-CoV-2 in 1,237 wild rodents and other small mammals across Europe. All samples were negative with the possible exception of one. Given the ongoing circulation of this virus in humans and potential host jumps, we suggest such surveillance be continued.

Additional file 1: Details for each step of the stacks workflow

We report results from serologic surveillance for exposure to SARS-CoV-2 among 1,237 wild rodents and small mammals across Europe. All samples were negative, with the possible exception of 1. Despite suspected potential for human-to-rodent spillover, no evidence of widespread SARS-CoV-2 circulation in rodent populations has been reported to date.Esitämme tulokset serologisesta tutkimuksesta, jossa seulottiin SARS-CoV-2 tartuntojen varalta 1,237 luonnonvaraista jyrsijää ja piennisäkästä eri puolilta Eurooppaa. Kaikki näytteet olivat negatiivisia, yhtä näytettä lukuun ottamatta. SARS-CoV-2:n läikkymisen ihmisistä jyrsijöihin on arveltu olevan mahdollista, mutta todisteet viruksen laajamittaisesta leviämisestä jyrsijäpopulaatioissa puuttuvat.