Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020

Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.

Characterising the relationship between suitable habitat and gene flow for Myotis bechsteinii and Eptesicus serotinus in Britain

Context Habitat suitability models (HSM) have been used to understand the impacts of landscape-scale habitat connectivity and gene flow mostly by assuming a regular decrease in the cost of movement as habitat improves. Yet, habitat selection and gene flow are governed by different behavioural processes which may limit the reliability of this approach as individuals are likely to disperse through unsuitable habitat for breeding. Objectives The aim of this study was to identify the optimal relationship between gene flow and HSMs for two bat species (Myotis bechsteinii and Eptesicus serotinus) in Britain by testing a range of nonlinear negative exponential functions for the transformation of HSMs into resistance surfaces. Methods We modelled habitat suitability using a hierarchical, multi-level approach that integrates models across three nested levels. Then, we measured the relationship between published genetics data of both species and six negative exponential transformations of the predicted outputs. Results The two most extreme transformations provided the best fit to genetic data for both M. bechsteinii (c = 32; R2 = 0.87) and E. serotinus (c = 16; R2 = 0.42). The negative linear transformations had the poorest fit. Conclusions These results suggest that bats are able to disperse through areas of poor habitat for breeding, but will avoid the most unsuitable areas. We recommend comparing multiple transformations of HSMs at different resolutions to gain a more accurate representation of gene flow across heterogeneous landscapes and to inform cost-effective, targeted management.

Retrospective Enhanced Bat Lyssavirus Surveillance in Germany between 2018–2020

Lyssaviruses are the causative agents for rabies, a zoonotic and fatal disease. Bats are the ancestral reservoir host for lyssaviruses, and at least three different lyssaviruses have been found in bats from Germany. Across Europe, novel lyssaviruses were identified in bats recently and occasional spillover infections in other mammals and human cases highlight their public health relevance. Here, we report the results from an enhanced passive bat rabies surveillance that encompasses samples without human contact that would not be tested under routine conditions. To this end, 1236 bat brain samples obtained between 2018 and 2020 were screened for lyssaviruses via several RT-qPCR assays. European bat lyssavirus type 1 (EBLV-1) was dominant, with 15 positives exclusively found in serotine bats (Eptesicus serotinus) from northern Germany. Additionally, when an archived set of bat samples that had tested negative for rabies by the FAT were screened in the process of assay validation, four samples tested EBLV-1 positive, including two detected in Pipistrellus pipistrellus. Subsequent phylogenetic analysis of 17 full genomes assigned all except one of these viruses to the A1 cluster of the EBLV-1a sub-lineage. Furthermore, we report here another Bokeloh bat lyssavirus (BBLV) infection in a Natterer’s bat (Myotis nattereri) found in Lower Saxony, the tenth reported case of this novel bat lyssavirus.

Features of the chromosome set of representatives of smoothnosed bats of the North Caucasus

Aim. The aim of this work was to study the chromosome set of some representatives of smooth-nosed bats of the North Caucasus.Material and Methods. Various research methods were used to achieve this goal, including that of dried preparations (the main method for obtaining chromosomal preparations) and that of constructing karyograms.Results. A comparative analysis of the karyological data of 11 species of smooth-nosed bats of the North Caucasus was undertaken and the karyological characteristics of the species accepted in the latest reports on the fauna of Russia and the Caucasus were clarified. The similarity of G -bands in large pairs of meta- and submetacentric chromosomes in Myotis blythi, Myotis mystacinus, Pipistrellus pipistrellus, Pipistrellus kuhli and Vepertilio murinus with bands in small and medium-sized acrocentric chromosomes such as in Eptesicus seotinus may indicate the evolution of the karyotype of the first species by Robertsonian translocation, i.e. compounds of acrocentric chromosomes of Eptesicus serotinus in various combinations. When comparing karyotypes in the family Vespertilionidae, it was found that the karyotype of Eptesicus serotinus is "archaic" (2n=50, NFa=48). With the help of karyological data, the authors composed schemes of phylogenetic relationships of genera in the family Vespertilionidae, which differ to a certain extent from the schemes compiled by taxonomists for representatives of this family.Conclusions. Based on the results obtained, we can conclude that the karyotype of Eptesicus serotinus is the most primitive among the representatives of the order of bats. The primary role in the evolution of this group was played by Robertsonian rearrangements and pericentric inversions (reduction of NFa and 2n from 50 to 38).

Macrospatial structure and biodiversity of bat communities (Chiroptera) of the European fauna in the forest-steppe habitat

Twelve bat species of seven genera of the family Vespertilionidae were studied in conditions of the Central Forest-steppe of Ukraine (Myotis nattereri, M. daubentonii, M. dasycnemе, Barbastella barbastellus, Plecotus auritus, Pl. аustriacus, Pipistrellus pуgmaeus, P. kuhlii, P. nathusii, Nyctalus noctula, N. leisleri, Vespertilio murinus, and Eptesicus serotinus). The data were collected during decade-long surveys (2007–2016) in the Central Forest-Steppe (Cherkasy, Kirovohrad, and Kyiv Oblasts, Ukraine) at 23 localities. The census route included 680 km walked along the surveyed territory. The species composition of different habitats was determined during faunal and indoor surveys, when a certain type of landscape changes to another, and also by comparing the species composition of communities in different types of habitats. For species diversity comparison, five types of habitats were selected: forest (W), towns and villages (A-W), wood lines and fields (F-W), wetland areas (A-W), and fores parks (W-P). The analysis of record localities of bats and the character of their biotopic distribution shows that most species prefer floodplains with trees (wetland areas (A-W) and forest parks (W-P)), where the maximum number of species was noted. Quite high diversity was also noted for settlements (T-W). Based on abundance, a noticeable decrease of the diversity index occurs during the transfer from the area of wetland types to fields and wood lines. Due to the character of differences between groups of local bat species, relative to spatial distribution of species on topical and trophic levels, the performed analyses helped us to outline four groups of species. The first group includes species united by open type habitats (N. noctula and N. leisleri). The second group comprises V. murinus, E. serotinus, P. pуgmaeus, and P. kuhlii, which are very hard to relate to a separate type of locality. The third group includes species that prefer closed habitats: M. nattereri, M. daubentonii, Pl. auritus, P. nathusii, and B. barbastellus. The fourth group comprises M. dasycnemе, a species that is relatively rare in the studied territory and is related to lakes and slow flowing water bodies.

Seroprevalence of Toscana Virus and Sandfly Fever Sicilian Virus in European Bat Colonies Measured Using a Neutralization Test

Toscana phlebovirus (TOSV) and Sicilian phlebovirus (SFSV) are endemic in the Mediterranean area where they are transmitted to humans by infected sandflies. Vertebrates of several species have been postulated to act as reservoirs of these viruses, but convincing evidence is still awaited. Among them, bats have been suggested, however documented evidence is lacking. Here we tested a total of 329 bats belonging to eight species collected from twelve localities in southern Spain for the presence of neutralizing antibodies specific to TOSV and SFSV. Positive sera were detected in Schreiber’s long-fingered bat (Miniopterus schreibersii), mouse-eared Myotis (Myotis myotis), European free-tailed bat (Tadarida teniotis), and common serotine (Eptesicus serotinus) with the latter showing the highest prevalence rates for SFSV (22.6%) and TOSV (10%). There was no difference between females and males. Results suggest that bats are not likely to play a major role in the natural cycle of these two sandfly-borne phleboviruses. However, large breeding colonies of bats can be used as sentinels for surveillance of the presence of such viruses in a given locality. In addition, capture–recapture studies should be initiated in order to understand better the dynamics of TOSV and SFSV in bat populations.

On the bat fauna of the Dnipro-Orilskiy Nature Reserve

Data on visual observations of bats in the territory of the Dnipro-Orilskiy Nature Reserve during 2013–2020 are given. The photos that were taken at the same time are presented. From the existing checklist of bats occurring in the reserve, four species were recorded during the mentioned period: Eptesicus serotinus (2 specimens), Pipistrellus pipistrellus (1 specimen), Nyctalus noctula (about 40 specimens), and Pipistrellus kuhlii (about 30 specimens). The most interesting fact is the finding of Nyctalus noctula in November, which is due to the tendency to expand its wintering range. The occurrence of Pipistrellus kuhlii in natural habitats was also revealed, which is uncommon for this species.

Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity

To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum, Eptesicus serotinus, Myotis blythii, Myotis nattereri and Myotis emarginatus) conducted in Mediterranean and continental Croatia. Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing. The presence of 63 different viral families representing all seven Baltimore groups were confirmed, most commonly insect viruses likely reflecting the diet of insectivorous bats. Virome compositions of our samples were largely impacted by the sample type: invertebrate-infecting viruses were most frequently found in feces, bacterial viruses in guano, whereas vertebrate-infecting viruses were most common in swabs. Most vertebrate-infecting virus sequences were assigned to retroviruses, parvoviruses, iridoviruses, and poxviruses. We further report the complete genome sequence of a novel adeno-associated virus, densovirus and a near complete length genome sequence of a novel iflavirus. Additionally, one of the most interesting findings in this study was the difference in viromes between two contrasting habitats, the continental and Mediterranean Croatia.