Detection of Novel RNA Viruses in wild Noble Crayfish (Astacus astacus): a Virome Analysis in Swiss water bodies.

European native crayfish populations are undergoing a strong decline due to environmental factors and the introduction of highly competitive non-native species. Pathogens are an additional threat to native crayfish. However, aside from the crayfish plague, other infectious diseases are still widely unknown. This study aimed to investigate viruses present in seven populations of wild noble crayfish (Astacus astacus) in Switzerland, through high-throughput sequencing. Sequence analysis revealed the presence of 11 novel RNA viruses (one bunya-like, four hepe-like, two dicistro-like, three picorna-like, and one permutotetra-like) in the samples. The discovery of a novel bunya-like virus in noble crayfish without associated mortality or macroscopical alterations is of particular interest since it is closely related to the bunya-like brown spot virus, a virus described in 2019 from diseased native white-clawed crayfish (Austropotamobius pallipes) during a mass mortality event in France. It seems that these two closely related viruses have very different impacts on their respective hosts, raising the need for further investigations on virulence factors and host susceptibility towards these viruses. This study provides a basis for future investigations, permitting to gradually fill the knowledge gap in crayfish viral diseases

Description of a Sarcoptic Mange Outbreak in Alpine Chamois Using an Enhanced Surveillance Approach

Since 1995, the Alpine chamois (Rupicapra r. rupicapra) population of the Dolomites has been affected by sarcoptic mange with considerable management concerns. In this study, 15 years (2006–2020) of passive surveillance and demographic data were analyzed in order to describe a mange outbreak. Furthermore, an enhanced passive surveillance protocol was implemented in order to evaluate the efficiency of ordinary vs. enhanced surveillance protocol in identifying dead chamois in the field and in reaching a correct diagnosis. Our results confirm the role of mange as a determining factor for chamois mortality, while stressing the importance of a wider view on the factors affecting population dynamics. The enhanced passive surveillance protocol increased the probability of carcass retrieval and identification of the cause of death; however, its adoption may be too costly if applied for long periods on a wide scale. Passive surveillance, in both ordinary and enhanced surveillance protocol, should encompass the use of other strategies in the future to study the eco-epidemiology of the disease in wild Caprinae

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

n the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was en-acted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and as-sess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immi-gration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad- scale geographic origin assignment using nuclear markers to support law enforcement

Sarcoptic mange in Felidae: does Sarcoptes scabiei var. felis exist? A first molecular study.

Domestic and wild felids are considered suitable hosts for the parasitic mite Sarcoptes scabiei, and sarcoptic mange is reported in several felid species in the scientific literature. However, the historic classification of Sarcoptes mites into host-specific varieties does not include S. scabiei var. felis. It is unclear whether sarcoptic mange transmission in felids involves canids, other sympatric species, or exclusively felids. This study aimed to characterize the genetic structure of S. scabiei mites from domestic cats (Felis catus) and Eurasian lynx (Lynx lynx carpathicus), comparing them with Sarcoptes mites from sympatric domestic and wild carnivores. Ten Sarcoptes microsatellite markers were used to genotype 81 mites obtained from skin scrapings of 36 carnivores: 4 domestic cats, one dog (Canis lupus familiaris), 4 Eurasian lynx, 23 red foxes (Vulpes vulpes), and 4 grey wolves (Canis lupus lupus) from either Italy, Switzerland or France. Two genetic clusters of S. scabiei with a geographical distribution pattern were detected: mites from cats originating from Central Italy clustered with those from sympatric wolves. In contrast, all the other mites from Switzerland, France and Northern Italy clustered together. These results strengthen the previously advanced hypothesis that genetic variants of S. scabiei have a predominant geographic-related distribution with cryptic transmission patterns. These patterns may rely on the interactions between different hosts living in the same ecological niche rather than a simple infection among hosts belonging to the same taxon, reinforcing the idea that the S. scabiei historic classification into "var" might have little ongoing relevance

Sarcoptic mange in Felidae: does Sarcoptes scabiei var. felis exist? A first molecular study

Domestic and wild felids are considered suitable hosts for the parasitic mite Sarcoptes scabiei, and sarcoptic mange is reported in several felid species in the scientific literature. However, the historic classification of Sarcoptes mites into host-specific varieties does not include S. scabiei var. felis. It is unclear whether sarcoptic mange transmission in felids involves canids, other sympatric species, or exclusively felids. This study aimed to characterize the genetic structure of S. scabiei mites from domestic cats (Felis catus) and Eurasian lynx (Lynx lynx carpathicus), comparing them with Sarcoptes mites from sympatric domestic and wild carnivores. Ten Sarcoptes microsatellite markers were used to genotype 81 mites obtained from skin scrapings of 36 carnivores: 4 domestic cats, one dog (Canis lupus familiaris), 4 Eurasian lynx, 23 red foxes (Vulpes vulpes), and 4 grey wolves (Canis lupus lupus) from either Italy, Switzerland or France. Two genetic clusters of S. scabiei with a geographical distribution pattern were detected: mites from cats originating from Central Italy clustered with those from sympatric wolves. In contrast, all the other mites from Switzerland, France and Northern Italy clustered together. These results strengthen the previously advanced hypothesis that genetic variants of S. scabiei have a predominant geographic-related distribution with cryptic transmission patterns. These patterns may rely on the interactions between different hosts living in the same ecological niche rather than a simple infection among hosts belonging to the same taxon, reinforcing the idea that the S. scabiei historic classification into “var” might have little ongoing relevance

Potential effect of managing connectivity to contain disease spread among free‐ranging wild boar (Sus scrofa) in disparate landscapes

1. Landscape connectivity is a major factor shaping the spread of pathogens in wildlife populations. By managing connectivity, transmission pathways can be broken and disease spread be contained, particularly in the early phases of an outbreak. Having witnessed recent outbreaks of African Swine Fever in free-ranging wild boar (Sus scrofa) in Belgium, Germany and Italy, offices for disease control are on the alert also in other western European countries. 2. This study investigates the potential effect of managing landscape connectivity to contain disease spread among free-ranging wild boar in disparate landscapes. It involves research into (1) the ease with which wildlife corridors can be blocked for wild boar, (2) the connectivity of wild boar habitat and (3) the impact of landscape fragmentation on connectivity management. This is addressed by carrying out GIS analyses and performing graph operations on the wild boar networks in different biogeographical regions of Switzerland. 3. The results of doing research into the three above-mentioned objects show that, regarding the first, most wildlife corridors are hard to block for wild boar, because their features or location make fencing difficult. Regarding the second, the wild boar habitat is connected. Opening wildlife passages that are currently under construction may allow wild boar to disperse to hitherto uncolonized areas. Regarding the third, all wild boar networks could be partially decomposed by blocking the easy to block corridors and closing the passages. Network decomposition would be easiest to achieve in the region where the built infrastructure is most abundant. All over Switzerland, the potential epidemic size could be reduced by 25% when blocking the minimal set of corridors and passages that cut the networks to non-decomposable components. 4. This study suggests that (a) combining connectivity analysis with fragmentation analysis is key to explaining why a specific measure of disease containment is more effective in one landscape than in the other, (b) complementing the permeability model with a species distribution model is essential to identify connected habitat patches for the species of concern and (c) connectivity metrics should consider also the surface area of occupied habitat patches and relative abundance of the species of concern

Analysis of a European general wildlife health surveillance program: Chances, challenges and recommendations.

In a One Health perspective general wildlife health surveillance (GWHS) gains importance worldwide, as pathogen transmission among wildlife, domestic animals and humans raises health, conservation and economic concerns. However, GWHS programs operate in the face of legal, geographical, financial, or administrative challenges. The present study uses a multi-tiered approach to understand the current characteristics, strengths and gaps of a European GWHS that operates in a fragmented legislative and multi-stakeholder environment. The aim is to support the implementation or improvement of other GWHS systems by managers, surveillance experts, and administrations. To assess the current state of wildlife health investigations and trends within the GWHS, we retrospectively analyzed 20 years of wildlife diagnostic data to explore alterations in annual case numbers, diagnosed diseases, and submitter types, conducted an online survey and phone interviews with official field partners (hunting administrators, game wardens and hunters) to assess their case submission criteria as well as their needs for post-mortem investigations, and performed in-house time estimations of post-mortem investigations to conduct a time-per-task analysis. Firstly, we found that infectious disease dynamics, the level of public awareness for specific diseases, research activities and increasing population sizes of in depth-monitored protected species, together with biogeographical and political boundaries all impacted case numbers and can present unexpected challenges to a GWHS. Secondly, we found that even a seemingly comprehensive GWHS can feature pronounced information gaps, with underrepresentation of common or easily recognizable diseases, blind spots in non-hunted species and only a fraction of discovered carcasses being submitted. Thirdly, we found that substantial amounts of wildlife health data may be available at local hunting administrations or disease specialist centers, but outside the reach of the GWHS and its processes. In conclusion, we recommend that fragmented and federalist GWHS programs like the one addressed require a central, consistent and accessible collection of wildlife health data. Also, considering the growing role of citizen observers in environmental research, we recommend using online reporting systems to harness decentrally available information and fill wildlife health information gaps

First description of peritoneal and pleural metacestodosis caused by Mesocestoides vogae in a European wild cat (Felis silvestris silvestris)

Tapeworms of the genus Mesocestoides (Cestoda: Cyclophyllidea: Mesocestoididae) are still enigmatic to scientists, due to their high morphological variability, low host specificity, and unknown details of their life cycle. They are found worldwide, with carnivorous mammals as the main definitive hosts, and the disease is potentially zoonotic. After ingestion by a definitive host, the tetrathyridium can occasionally migrate through the intestinal wall and reach the peritoneal cavity or abdominal organs causing peritoneal metacestodosis. Here, we report on a case of metacestodosis of a European wild cat (Felis silvestris silvestris) found dead in Croatia. At necropsy, a large number of white, rice-like structures were found free in the abdominal and thoracic cavities, as well as along the serous surfaces and in the lungs. DNA isolated from the nodules was genotyped and based on a 320-base pair long 12S fragment classified as Mesocestoides vogae. Although post-mortem changes were advanced, severe emaciation due to the severe parasitic infection and gastrointestinal bleeding was diagnosed as the likely cause of death. Intestinal cestodosis was previously reported in wild cats, but according to our knowledge, this is the first description of peritoneal and pleural metacestodosis caused by M. vogae tetrathyridia (metacestodes) in any wild carnivore species

The Atacama Cosmology Telescope: DR4 Maps and Cosmological Parameters

International audienceWe present new arcminute-resolution maps of the Cosmic Microwave Background temperature and polarization anisotropy from the Atacama Cosmology Telescope, using data taken from 2013–2016 at 98 and 150 GHz. The maps cover more than 17,000 deg2, the deepest 600 deg2 with noise levels below 10μK-arcmin. We use the power spectrum derived from almost 6,000 deg2 of these maps to constrain cosmology. The ACT data enable a measurement of the angular scale of features in both the divergence-like polarization and the temperature anisotropy, tracing both the velocity and density at last-scattering. From these one can derive the distance to the last-scattering surface and thus infer the local expansion rate, H0. By combining ACT data with large-scale information from WMAP we measure H0=67.6± 1.1 km/s/Mpc, at 68% confidence, in excellent agreement with the independently-measured Planck satellite estimate (from ACT alone we find H0=67.9± 1.5 km/s/Mpc). The ΛCDM model provides a good fit to the ACT data, and we find no evidence for deviations: both the spatial curvature, and the departure from the standard lensing signal in the spectrum, are zero to within 1σ; the number of relativistic species, the primordial Helium fraction, and the running of the spectral index are consistent with ΛCDM predictions to within 1.5–2.2σ. We compare ACT, WMAP, and Planck at the parameter level and find good consistency; we investigate how the constraints on the correlated spectral index and baryon density parameters readjust when adding CMB large-scale information that ACT does not measure. The DR4 products presented here will be publicly released on the NASA Legacy Archive for Microwave Background Data Analysis