Virome analysis of Eurasian red squirrels (Sciurus vulgaris)
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PROVIDER: PRJEB48612 | ENA |
REPOSITORIES: ENA
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Project description:Cryptosporidium spp. are common protozoan pathogens in mammals. The diversity and biology of Cryptosporidium in tree squirrels are not well studied. A total of 258 Eurasian red squirrels (Sciurus vulgaris) from 25 and 15 locations in the Czech Republic and Slovakia, respectively, were examined for Cryptosporidium spp. oocysts and specific DNA at the SSU, actin, HSP70, TRAP-C1, COWP, and gp60 loci. Out of 26 positive animals, only juveniles (9/12) were microscopically positive (18,000 to 72,000 OPG), and molecular analyses revealed the presence of Cryptosporidium sp. ferret genotype in all specimens. Oocysts obtained from naturally-infected squirrels measured 5.54-5.22 μm and were not infectious for laboratory mice (BALB/c and SCID), Mongolian gerbils, Guinea pigs, Southern multimammate mice, chickens, or budgerigars. None of naturally infected squirrels showed clinical signs of disease. The frequency of occurrence of the ferret genotype in squirrels did not vary statistically based on host age, gender or country of capture. Phylogenetic analysis of sequences from six loci revealed that Cryptosporidium sp. ferret genotype is genetically distinct from the currently accepted Cryptosporidium species. Morphological and biological data from this and previous studies support the establishment of Cryptosporidium sp. ferret genotype as a new species, Cryptosporidium sciurinum n. sp.
| S-EPMC8537388 | biostudies-literature
Project description:BackgroundSquirrel poxvirus (SQPV) is highly pathogenic to red squirrels (Sciurus vulgaris), and is a significant contributing factor to the local extinction of the species in most parts of England and Wales, where infection is endemic in Eastern grey squirrel (Sciurus carolinensis) populations. Although a nested PCR assay has been used successfully to study the epidemiology of SQPV, samples have a long processing time and the assay is not quantifiable.ResultsThis project describes the design and optimization of a real-time PCR for SQPV. Comparison with the nested PCR showed the real-time assay to be more sensitive by one log and able to detect approximately 144 genome copies per mg of tissue.ConclusionsThe real-time PCR has been used to quantify viral genome load in tissues from diseased and apparently healthy red and grey squirrels, and suggests that the titre of virus in tissues from diseased red squirrels is considerably higher than that found even in a grey squirrel with cutaneous lesions.
| S-EPMC2887832 | biostudies-literature
Project description:We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
| S-EPMC7309416 | biostudies-literature
Project description:TLR1 variation linked with leprosy in Sciurus vulgaris from the British Isles
| PRJNA325827 | ENA
Project description:Conservation translocations, including reintroductions, are practices that are vital to restoring biodiversity and ecosystem function within conservation schemes globally. Sadly, population translocations have had a poor success rate historically. At a time where biodiversity is constantly decreasing, improving translocation success is vital for future conservation schemes. Often, to improve success, the selection of individuals is based on genetic characteristics and behaviours linked directly to survival. Further development to improve selection is proposed within this paper using animal personality. The study took place opportunistically to test how personality, in particular an animal's boldness/timidness, may influence a population restoration of red squirrels into the Ogwen Valley, North Wales. Despite frequent translocations, data on how boldness and timidness may affect the establishment of this species are low. Testing was performed on key survival behaviours and boldness/timidness pre-release. This was performed via video data collection and identification of key behaviours that could be used to identify boldness or behaviours that could be linked to reduced fitness once released. Encounters at different distance intervals were monitored post-release via camera trapping to identify if boldness/timidness may change the furthest encounter distance of focal animals away from their release site. Relationships between the period for an individual to reappear post-threat was significantly linked to boldness, with other behavioural results and the encounter distance also showing trends of a potential relationship. Our results indicate that bolder individuals have a higher chance of expressing behavioural traits that will increase exposure to risks and, therefore, reduce the likelihood of successfully establishing populations. However, the small sample size of this study means that further research is needed. We suggest that during early stages of conservation translocation programmes, personality testing for boldness should become common practice, and we recommend selecting timid individuals for an initial release to improve population establishment, with bolder individuals utilised later to expand population distribution.
| S-EPMC7599904 | biostudies-literature
Project description:Cryptosporidium spp. and Enterocytozoon bieneusi are two well-known protist pathogens which can result in diarrhea in humans and animals. To examine the occurrence and genetic characteristics of Cryptosporidium spp. and E. bieneusi in pet red squirrels (Sciurus vulgaris), 314 fecal specimens were collected from red squirrels from four pet shops and owners in Sichuan province, China. Cryptosporidium spp. and E. bieneusi were examined by nested PCR targeting the partial small subunit rRNA (SSU rRNA) gene and the ribosomal internal transcribed spacer (ITS) gene respectively. The infection rates were 8.6% (27/314) for Cryptosporidium spp. and 19.4% (61/314) for E. bieneusi. Five Cryptosporidium species/genotypes were identified by DNA sequence analysis: Cryptosporidium rat genotype II (n = 8), Cryptosporidium ferret genotype (n = 8), Cryptosporidium chipmunk genotype III (n = 5), Cryptosporidium rat genotype I (n = 4), and Cryptosporidium parvum (n = 2). Additionally, a total of five E. bieneusi genotypes were revealed, including three known genotypes (D, SCC-2, and SCC-3) and two novel genotypes (RS01 and RS02). Phylogenetic analysis revealed that genotype D fell into group 1, whereas the remaining genotypes clustered into group 10. To our knowledge, this is the first study to report Cryptosporidium spp. and E. bieneusi in pet red squirrels in China. Moreover, C. parvum and genotype D of E. bieneusi, previously identified in humans, were also found in red squirrels, suggesting that red squirrels may give rise to cryptosporidiosis and microsporidiosis in humans through zoonotic transmissions. These results provide preliminary reference data for monitoring Cryptosporidium spp. and E. bieneusi infections in pet red squirrels and humans.
| S-EPMC6978461 | biostudies-literature
Project description:Members of the genus Bartonella are fastidious Gram-negative facultative intracellular bacteria that are typically transmitted by arthropod vectors. Several Bartonella spp. have been found to cause culture-negative endocarditis in humans. Here, we report the case of a 75-year-old German woman with prosthetic valve endocarditis due to Bartonella washoensis The infecting agent was characterized by sequencing of six housekeeping genes (16S rRNA, ftsZ, gltA, groEL, ribC, and rpoB), applying a multilocus sequence typing (MLST) approach. The 5,097 bp of the concatenated housekeeping gene sequence from the patient were 99.0% identical to a sequence from a B. washoensis strain isolated from a red squirrel (Sciurus vulgarisorientis) from China. A total of 39% (24/62) of red squirrel (S. vulgaris) samples from the Netherlands were positive for the B. washoensisgltA gene variant detected in the patient. This suggests that the red squirrel is the reservoir host for human infection in Europe.
| S-EPMC6935924 | biostudies-literature
Project description:The Eurasian red squirrel (Sciurus vulgaris) is an emblematic species for conservation, and its decline in the British Isles exemplifies the impact that alien introductions can have on native ecosystems. Indeed, red squirrels in this region have declined dramatically over the last 60 years due to the spread of squirrelpox virus following the introduction of the gray squirrel (Sciurus carolinensis). Currently, red squirrel populations in Britain are fragmented and need to be closely monitored in order to assess their viability and the effectiveness of conservation efforts. The situation is even more dramatic in the South of England, where S. vulgaris survives only on islands (Brownsea Island, Furzey Island, and the Isle of Wight). Using the D-loop, we investigated the genetic diversity and putative ancestry of the squirrels from Southern England and compared them to a European dataset composed of 1,016 samples from 54 populations. We found that our three populations were more closely related to other squirrels from the British Isles than squirrels from Europe, showed low genetic diversity, and also harbored several private haplotypes. Our study demonstrates how genetically unique the Southern English populations are in comparison with squirrels from the continental European range. We report the presence of four private haplotypes, suggesting that these populations may potentially harbor distinct genetic lineages. Our results emphasize the importance of preserving these isolated red squirrel populations for the conservation of the species.
| S-EPMC6580283 | biostudies-literature
Project description:Effective methods for monitoring animal populations are crucial for species conservation and habitat management. Motion-activated cameras provide an affordable method for passively surveying animal presence across the landscape but have mainly been used for studying large-bodied mammals. This paper explores the relative abundance and habitat preferences of red squirrels (Sciurus vulgaris) in coniferous forests using cameras and live trapping. The study was conducted in two forests (Newborough and Pentraeth) on Anglesey, North Wales, with a total of 50 sampling locations across four habitat categories. Detailed woodland structure and composition data were gathered around each sampling location. We found a strong positive correlation between the number of individual red squirrels live trapped over 10 days with the number of camera images of squirrels recorded during a previous 5-day period. The time interval between camera deployment and the first recorded image of a red squirrel showed a significant negative correlation with the number of individuals live trapped. Red squirrel relative abundance was negatively related to forest canopy openness, while the presence of Scots pine and increased tree species diversity were positively associated with the relative abundance of squirrels. There was also a strong site difference with lower relative abundance at Newborough compared with Pentraeth, which likely reflects the heavy thinning of mature forest at Newborough reducing tree crown connectivity. The results show that remotely activated cameras are an effective method for monitoring red squirrel populations across varying animal densities. The cameras also provided crucial information on red squirrel habitat preferences that can aid in woodland management and conservation efforts. Cameras have great potential to collect data on the population status of other small mammals, but it is essential that these methods are validated on a species-by-species basis.
| S-EPMC10546084 | biostudies-literature