Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat

Effective prediction of future viral zoonoses requires an in-depth understanding of the heterologous viral population in key animal species that will likely serve as reservoir hosts or intermediates during the next viral epidemic. The importance of bats as natural hosts for several important viral zoonoses, including Ebola, Marburg, Nipah, Hendra, and rabies viruses and severe acute respiratory syndrome-coronavirus (SARS-CoV), has been established; however, the large viral population diversity (virome) of bats has been partially determined for only a few of the ～1,200 bat species. To assess the virome of North American bats, we collected fecal, oral, urine, and tissue samples from individual bats captured at an abandoned railroad tunnel in Maryland that is cohabitated by 7 to 10 different bat species. Here, we present preliminary characterization of the virome of three common North American bat species, including big brown bats (Eptesicus fuscus), tricolored bats (Perimyotis subflavus), and little brown myotis (Myotis lucifugus). In samples derived from these bats, we identified viral sequences that were similar to at least three novel group 1 CoVs, large numbers of insect and plant virus sequences, and nearly full-length genomic sequences of two novel bacteriophages. These observations suggest that bats encounter and disseminate a large assortment of viruses capable of infecting many different animals, insects, and plants in nature.     

Evidence Supporting a Zoonotic Origin of Human Coronavirus Strain NL63

The relationship between bats and coronaviruses (CoVs) has received considerable attention since the severe acute respiratory syndrome (SARS)-like CoV was identified in the Chinese horseshoe bat (Rhinolophidae) in 2005. Since then, several bats throughout the world have been shown to shed CoV sequences, and presumably CoVs, in the feces; however, no bat CoVs have been isolated from nature. Moreover, there are very few bat cell lines or reagents available for investigating CoV replication in bat cells or for isolating bat CoVs adapted to specific bat species. Here, we show by molecular clock analysis that alphacoronavirus (α-CoV) sequences derived from the North American tricolored bat (Perimyotis subflavus) are predicted to share common ancestry with human CoV (HCoV)-NL63, with the most recent common ancestor between these viruses occurring approximately 563 to 822 years ago. Further, we developed immortalized bat cell lines from the lungs of this bat species to determine if these cells were capable of supporting infection with HCoVs. While SARS-CoV, mouse-adapted SARS-CoV (MA15), and chimeric SARS-CoVs bearing the spike genes of early human strains replicated inefficiently, HCoV-NL63 replicated for multiple passages in the immortalized lung cells from this bat species. These observations support the hypothesis that human CoVs are capable of establishing zoonotic-reverse zoonotic transmission cycles that may allow some CoVs to readily circulate and exchange genetic material between strains found in bats and other mammals, including humans.     

Rabies in insectivorous bats of western Canada, 1979 to 1983

A total of 1,745, 362, and 536 bats collected in Alberta, British Columbia, and Saskatchewan, respectively, was tested for rabies virus between 1979 and 1983. Only one (0.1%) of 769 bats collected at random from buildings was infected with rabies virus in contrast to 95 (5%) of 1,874 symptomatic, rabies-suspect bats submitted for testing. The pattern of infection in the rabies-suspect bats was similar in Alberta and Saskatchewan, but differed in British Columbia. Rabies was diagnosed in four species of bats in each of Alberta and Saskatchewan, but in seven species in British Columbia. Annual prevalence in rabies-suspect bats was similar in colonial species within each province. Rabies was found rarely in suspect little brown bats (Myotis lucifugus) (less than 1%). In suspect big brown bats (Eptesicus fuscus), the prevalence was low in Saskatchewan (3%), moderate in Alberta (10%), and high in British Columbia (25%). Big brown bats accounted for over 55% of the rabid bats detected in each province. Annual prevalence reported in silver-haired bats (Lasionycteris noctivagans) and hoary bats (Lasiurus cinereus) was variable in all three provinces. Rabies is enzootic in northern insectivorous bats.     

Coronavirus and paramyxovirus in bats from Northwest Italy

Background

Bat-borne virus surveillance is necessary for determining inter-species transmission risks and is important due to the wide-range of bat species which may harbour potential pathogens. This study aimed to monitor coronaviruses (CoVs) and paramyxoviruses (PMVs) in bats roosting in northwest Italian regions. Our investigation was focused on CoVs and PMVs due to their proven ability to switch host and their zoonotic potential. Here we provide the phylogenetic characterization of the highly conserved polymerase gene fragments.

Results

Family-wide PCR screenings were used to test 302 bats belonging to 19 different bat species. Thirty-eight animals from 12 locations were confirmed as PCR positive, with an overall detection rate of 12.6% [95% CI: 9.3–16.8]. CoV RNA was found in 36 bats belonging to eight species, while PMV RNA in three Pipistrellus spp. Phylogenetic characterization have been obtained for 15 alpha- CoVs, 5 beta-CoVs and three PMVs; moreover one P. pipistrellus resulted co-infected with both CoV and PMV. A divergent alpha-CoV clade from Myotis nattereri SpA is also described. The compact cluster of beta-CoVs from R. ferrumequinum roosts expands the current viral sequence database, specifically for this species in Europe. To our knowledge this is the first report of CoVs in Plecotus auritus and M. oxygnathus, and of PMVs in P. kuhlii.

Conclusions

This study identified alpha and beta-CoVs in new bat species and in previously unsurveyed Italian regions. To our knowledge this represents the first and unique report of PMVs in Italy. The 23 new bat genetic sequences presented will expand the current molecular bat-borne virus databases. Considering the amount of novel bat-borne PMVs associated with the emergence of zoonotic infections in animals and humans in the last years, the definition of viral diversity within European bat species is needed. Performing surveillance studies within a specific geographic area can provide awareness of viral burden where bats roost in close proximity to spillover hosts, and form the basis for the appropriate control measures against potential threats for public health and optimal management of bats and their habitats.

     

Geographic Variation in Roost-Site Selection of Long-Legged Myotis in the Pacific Northwest

Abstract: Several species of bats in the Pacific Northwest of the United States, including long-legged myotis (Myotis volans), are dependent on snags in coniferous forests during summer for roosting and rearing young. Thus, data on roosting preferences of this species are needed to integrate their habitat requirements into shifting plans for management of forests in this region. Therefore, from 2001 to 2006, we radiotracked adult female long-legged myotis (n = 153) to day roosts (n = 395) across 6 watersheds in Washington, Oregon, and Idaho, USA, and compared characteristics associated with roosting sites to those of random snags (n = 260) sampled in the same watersheds using use-availability logistic regression and an information-theoretic approach. Model rankings varied among geographic locations, with quantity of stem surface for roosting the best model for explaining roost-site selection of long-legged myotis in both Washington and Oregon. Model rankings for populations of bats in Idaho found stand- and landscape-scale features to be important in roost-site selection, with a habitat fragmentation model and a foraging habitat quality model both demonstrating strong support as best model. Choice of day roosts by long-legged myotis was associated with snags that were taller, intact at the top of the stem, possessing a greater amount of exfoliating bark, in stands with a larger basal area of dead stems, and in landscapes that were unfragmented (i.e., supporting lesser amounts of edge). Results indicate that roost-site selection of bats in western coniferous forests, particularly long-legged myotis, is likely to be region-specific. We encourage land managers to consider importance of geographic variation in intraspecific habitat use in forest-dwelling bats when implementing silvicultural systems to promote biological diversity in actively managed forests of the Pacific Northwest region.     

Distribution and population densities of seven species of bat in northern England

Distribution and minimum population densities for seven UK bat species known to be resident in northern England were calculated in an area covering 2500 km². The species present were pipistrelle ( Pipistrellus pipistrellus ), brown long-eared ( Plecotus auritus ), Daubenton's ( Myotis daubentonii ), whiskered ( Myotis mystacinus ), Natterer's (Myotis nattereri) , noctule ( Nyctalus noctula ) and Brandt's (Myotis brandtii). Data were collected primarily from counts at summer roosts over the period 1983 to 1990. A total of 310 bat roosts were discovered within the study area. Of the 256 roosts at which the species present was identified, the majority, 127 (49.6%) were P. pipistrellus , with a mean maternity roost size of 69.6 bats. A minimum population density of 12.6 batskm⁻² was estimated for P. pipistrellus , based on summer (maternity) roosts. The minimum population density estimate was higher than previous studies in northern England but substantially lower than those reported in Scotland (18.2 bats km-⁻²). The combined density of M. mystacinus, M. brandtii, and P. pipistrellus , which have similar foraging styles (15.8 bats km⁻²), is comparable to Scottish P. pipistrellus densities. The density of M. duubentonii was also lower than in Scotland, although the density of P. auritus was comparable. The majority of summer roosts for all species were found in buildings, except N. noctula and M. duubentonii which used bridges/tunnels or trees.     

Variability in Seroprevalence of Rabies Virus Neutralizing Antibodies and Associated Factors in a Colorado Population of Big Brown Bats (Eptesicus fuscus)

In 2001–2005 we sampled permanently marked big brown bats (Eptesicus fuscus) at summer roosts in buildings at Fort Collins, Colorado, for rabies virus neutralizing antibodies (RVNA). Seroprevalence was higher in adult females (17.9%, n = 2,332) than males (9.4%, n = 128; P = 0.007) or volant juveniles (10.2%, n = 738; P<0.0001). Seroprevalence was lowest in a drought year with local insecticide use and highest in the year with normal conditions, suggesting that environmental stress may suppress RVNA production in big brown bats. Seroprevalence also increased with age of bat, and varied from 6.2 to 26.7% among adult females at five roosts sampled each year for five years. Seroprevalence of adult females at 17 other roosts sampled for 1 to 4 years ranged from 0.0 to 47.1%. Using logistic regression, the only ranking model in our candidate set of explanatory variables for serological status at first sampling included year, day of season, and a year by day of season interaction that varied with relative drought conditions. The presence or absence of antibodies in individual bats showed temporal variability. Year alone provided the best model to explain the likelihood of adult female bats showing a transition to seronegative from a previously seropositive state. Day of the season was the only competitive model to explain the likelihood of a transition from seronegative to seropositive, which increased as the season progressed. We found no rabies viral RNA in oropharyngeal secretions of 261 seropositive bats or in organs of 13 euthanized seropositive bats. Survival of seropositive and seronegative bats did not differ. The presence of RVNA in serum of bats should not be interpreted as evidence for ongoing rabies infection.     

Scale-Dependent Effects of Landscape Structure and Composition on Diurnal Roost Selection by Forest Bats

Abstract: Forest management affects the quality and availability of roost sites for forest-dwelling bats, but information on roost selection beyond the scale of individual forest stands is limited. We evaluated effects of topography (elevation, slope, and proximity of roads and streams), forest habitat class, and landscape patch configuration on selection of summer diurnal roosts by 6 species of forest-dwelling bats in a diverse forested landscape of the Ouachita Mountains, Arkansas, USA. Our objectives were to identify landscape attributes that potentially affect roost placement, determine whether commonalities exist among species in their response to landscape attributes, and evaluate the effects of scale. We modeled roost selection at 2 spatial scales (250- and 1,000-m radius around each roost). For each species, parameters included in models differed between the 2 scales, and there were no shared parameters for 2 species. Average coefficients of determination (R²) for small-scale models were generally higher than for large-scale models. Abundance of certain forest habitat classes were included more often than patch configuration or topography in differentiating roost from random locations, regardless of scale, and most species were more likely to roost in areas containing abundant thinned forest. Among topographic metrics, big brown bats (Eptesicus fuscus) were more likely to roost at higher elevations; roosts of big brown bats, northern long-eared bats (Myotis septentrionalis), and Seminole bats (Lasiurus seminolus) were influenced by slope; and big brown bats, evening bats (Nycticeius humeralis), and Seminole bats were more likely to roost closer to water than random. Northern long-eared bats and red bats (Lasiurus borealis) were more likely to roost closer to roads, whereas eastern pipistrelles (Perimyotis subflavus) were more likely to roost further from roads than random. Common parameters in most models included 1) positive associations with group selection (5 of 6 species) and thinned mature forest (4 species) at the small scale; 2) negative associations with unmanaged mixed pine-hardwood forest 50–99 years old at the large scale (4 species); 3) negative association with stands of immature pine 15–29 years old at the small scale (3 species); and 4) a positive association with largest patch index at the large scale (3 species). Our results suggest that, in a completely forested landscape, a variety of stand types, seral stages, and management conditions, varying in size and topographic location throughout the landscape, would likely provide the landscape components for roosting required to maintain a diverse community of forest bats in the Ouachita Mountains.     

Bat Rabies in Guatemala

Rabies in bats is considered enzootic throughout the New World, but few comparative data are available for most countries in the region. As part of a larger pathogen detection program, enhanced bat rabies surveillance was conducted in Guatemala, between 2009 and 2011. A total of 672 bats of 31 species were sampled and tested for rabies. The prevalence of rabies virus (RABV) detection among all collected bats was low (0.3%). Viral antigens were detected and infectious virus was isolated from the brains of two common vampire bats (Desmodus rotundus). RABV was also isolated from oral swabs, lungs and kidneys of both bats, whereas viral RNA was detected in all of the tissues examined by hemi-nested RT-PCR except for the liver of one bat. Sequencing of the nucleoprotein gene showed that both viruses were 100% identical, whereas sequencing of the glycoprotein gene revealed one non-synonymous substitution (302_T,S). The two vampire bat RABV isolates in this study were phylogenetically related to viruses associated with vampire bats in the eastern states of Mexico and El Salvador. Additionally, 7% of sera collected from 398 bats demonstrated RABV neutralizing antibody. The proportion of seropositive bats varied significantly across trophic guilds, suggestive of complex intraspecific compartmentalization of RABV perpetuation.     

Bat rabies in Illinois: 1965 to 1986

From 1968 to 1986, Illinois (USA) citizens and agencies submitted 4,272 bats to the Illinois Department of Public Health for rabies testing. Of this number, 6% tested positive, a rate comparable to similar studies from other parts of North America. Due to sampling biases, the true infection rate among bats in Illinois is probably lower than 6%. Additional analysis relied on a subsample (n = 2,433) of the specimens collected from 1965 to 1986. Prevalences were significantly different among years, but no linear trends were found over the study period. Evidence for a local outbreak of bat rabies was found. Prevalences for the species with sample sizes adequate for statistical analysis were, from high to low: hoary bat (Lasiurus cinereus), 11%; red bat (L. borealis), 5%; silver-haired bat (Lasionycteris noctivagans), 4%; little brown bat (Myotis lucifugus), 4%; big brown bat (Eptesicus fuscus), 3%; Keen's bat (Myotis keenii), 2%; and evening bat (Nycticeius humeralis), 2%. The higher prevalences found among the non-colonial species (hoary, red and silver-haired bats) were consistent with similar studies. Considerable annual variation in prevalences was found within species, and the prevalence rankings of the species varied over the study period. Prevalences were significantly higher in females (6%) than in males (4%) when species were pooled, but no significant differences between sexes were found within species. In contrast to the other species analyzed, all of which had sex ratios favoring females, the big brown bat sample had a large majority of males. Prevalences were significantly higher in adults (6%) than in juveniles (3%) when species were pooled. Within individual species, significant differences between age groups were found only for hoary and red bats; in two species, juveniles had higher prevalences. Above average prevalences were observed in May and August to November. Southern Illinois had the highest prevalences; prevalences were intermediate in the north and lowest in the central region. Overall, the patterns of rabies prevalence among bats submitted by the public in Illinois from 1965 to 1986 were similar to those reported from other parts of North America.     

Ectoparasites in an urban population of big brown bats (Eptesicus fuscus) in Colorado

Ectoparasites of an urban population of big brown bats (Eptesicus fuscus) in Fort Collins, Colorado, were investigated during summers 2002, 2003, and 2004. Eleven species of ectoparasites were found (the macronyssid mite Steatonyssus occidentalis, the wing mite Spinturnix bakeri, the myobiid mites Acanthophthirius caudata and Pteracarus aculeus, the chirodiscid mite Alabidocarpus eptesicus, the demodicid mite Demodex sp., the chigger Leptotrombidium myotis, the soft tick Carios kelleyi, the batfly Basilia forcipata, the batbug Cimex pilosellus, and the flea Myodopsylla borealis). Five species were analyzed by prevalence and intensity (C. pilosellus, M. borealis, L. myotis, S. bakeri, and S. occidentalis) based on 2161 counts of 1702 marked individual bats over the 3 summer study periods. We investigated 4 factors potentially influencing prevalence and intensity: age class of the host, reproductive status of adult female hosts, roosts in which the hosts were found, and abiotic conditions during the year sampled. The macronyssid mite, S. occidentalis, was the most prevalent and abundant ectoparasite. Adult big brown bats had more ectoparasites than volant juveniles for most of the species analyzed. In a sample of known age bats at 1 large colony, bats of 4 yr of age or greater had higher ectoparasite loads of S. occidentalis and S. bakeri when compared with younger bats. Lactating female bats had the highest prevalence and intensities of most ectoparasites. Annual differences in ectoparasite prevalence and intensity were related to temperature and humidity, which can affect the nidicolous species of ectoparasites. Residents of 2 buildings sprayed insecticides in response to Cimex sp., and this appeared to reduce ectoparasitism of S. occidentalis and C. pilosellus present at these buildings. Intensity of S. occidentalis had no influence on annual survival of big brown bats.     

Calls in the Forest: A Comparative Approach to How Bats Find Tree Cavities

Although tree cavities are a particularly critical resource for forest bats, how bats search for and find new roosts is still poorly known. Building on a recent study on the sensory basis of roost finding in the noctule (Ruczynski et al. 2007), here we take a comparative approach to how bats find roosts. We tested the hypothesis that species' flight abilities and echolocation call characteristics play important roles in how well and by which cues bats find new tree roosts. We used the very manoeuvrable, faintly echolocating brown long-eared bat ( Plecotus auritus ) and the less manoeuvrable, louder Daubenton's bat ( Myotis daubentonii ) as study species. The species are sympatric in European temperate forests and both roost in tree cavities. We trained bats in short-term captivity to find entrances to tree cavities and experimentally manipulated the sensory cues available to them. In both species, cue type influenced the search time for successful cavity detection. Visual, olfactory and temperature cues did not improve the bats' performance over the performance by echolocation alone. Eavesdropping on conspecific echolocation calls played back from inside the cavity decreased search time in Daubenton's bat ( M. daubentonii ), underlining the double function of echolocation signals – orientation and communication. This was not so in the brown long-eared bat ( P. auritus ) that has low call amplitudes. The highly manoeuvrable P. auritus found cavities typically from flight and the less manoeuvrable M. daubentonii found more entrances during crawling. Comparison with the noctule data from Ruczyński et al. (2007) indicates that manoeuvrability predicts the mode of cavity search. It further highlights the importance of call amplitude for eavesdropping and cavity detection in bats.     

West nile virus antibodies in bats from New Jersey and New York

Eighty-three serum samples were obtained from big brown (Eptesicus fuscus), little brown (Myotis lucifugus), and northern long-eared (Myotis septentriotalis) bats (Chiroptera: Vespertilionidae), from New Jersey and New York (USA) between July and October 2002. Samples were analyzed for neutralizing antibodies to West Nile virus (WNV) and St. Louis encephalitis (SLE) virus. One little brown bat and one northern long-eared bat tested positive for WNV neutralizing antibodies. No bats had antibodies to SLE virus. This was the first large-scale investigation of WNV infection in bats in New Jersey. Additional work is needed to determine the effects of WNV on bat populations.     

Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses,caliciviruses and rotaviruses

This is the first country-wide surveillance of bat-borne viruses in Kenya spanning from 2012–2015covering sites perceived to have medium to high level bat-human interaction. The objective of this surveillance study was to apply a non-invasive approach using fresh feces to detect viruses circulating within the diverse species of Kenyan bats. We screened for both DNA and RNA viruses;specifically, astroviruses(AstVs), adenoviruses(ADVs), caliciviruses(CalVs), coronaviruses(CoVs), flaviviruses, filoviruses, paramyxoviruses(PMVs), polyomaviruses(PYVs) and rotaviruses.We used family-specific primers, amplicon sequencing and further characterization by phylogenetic analysis. Except for filoviruses, eight virus families were detected with varying distributions and positive rates across the five regions(former provinces) studied. AstVs(12.83%), CoVs(3.97%), PMV(2.4%), ADV(2.26%), PYV(1.65%), CalVs(0.29%), rotavirus(0.19%) and flavivirus(0.19%). Novel CalVs were detected in Rousettus aegyptiacus and Mops condylurus while novel Rotavirus-A-related viruses were detected in Taphozous bats and R. aegyptiacus. The two Rotavirus A(RVA) strains detected were highly related to human strains with VP6 genotypes I2 and I16. Genotype I16 has previously been assigned to human RVA-strain B10 from Kenya only, which raises public health concern, particularly considering increased human-bat interaction.Additionally, 229E-like bat CoVs were detected in samples originating from Hipposideros bats roosting in sites with high human activity. Our findings confirm the presence of diverse viruses in Kenyan bats while providing extended knowledge on bat virus distribution. The detection of viruses highly related to human strains and hence of public health concern, underscores the importance of continuous surveillance.     

Temporal dynamics of roost snags of long-legged myotis in the Pacific Northwest,USA

Snags are used as roosting sites by many bats living in coniferous forests of western North America. Thus, providing sufficient numbers of snags both spatially and temporally in forested landscapes is critical to sustaining populations of these species. One aspect that remains poorly understood is length of time that roost snags persist on the landscape in a form suitable for use by bats. This information is critical for forest-planning efforts in ensuring long-term availability of snag resources on forested landscapes. We monitored condition of 339 snags used as roosting sites by long-legged myotis (Myotis volans) 1–5 years post-discovery from 2001 to 2006 across 6 watersheds in Washington, Oregon, and Idaho, USA. Persistence rates (i.e., probability a snag remains standing from year x to x + 1) of roost snags declined with year post-discovery in all study areas. Fir snags (Abies spp.) exhibited lower persistence rates than other conifer species. Data for the Washington area indicated only 4.3% of roost snags likely remain standing 10 years post-discovery, with half-lives of all snag species <3 roost-years. Model ranking of habitat models predicting fall year of roost snags revealed that snag condition models were the most parsimonious in all geographic locations. Roost snags larger in diameter, shorter in height, and with fewer branches on the bole were likely to persist for more years. These data indicate that snags used as roosts by long-legged myotis are suitable as roosting sites for only a few years before falling. We recommend management policies for coniferous forests in the Pacific Northwest, USA, that promote sufficient leave-trees in set-aside areas to provide for future suitable, large-diameter snags for bats in managed, forested landscapes. © 2012 The Wildlife Society.     

Disease‐related population declines in bats demonstrate non‐exchangeability in generalist predators

The extent to which persisting species may fill the functional role of extirpated or declining species has profound implications for the structure of biological communities and ecosystem functioning. In North America, arthropodivorous bats are threatened on a continent‐wide scale by the spread of white‐nose syndrome (WNS), a disease caused by the fungus Pseudogymnoascus destructans. We tested whether bat species that display lower mortality from this disease can partially fill the functional role of other bat species experiencing population declines. Specifically, we performed high‐throughput amplicon sequencing of guano from two generalist predators: the little brown bat (Myotis lucifugus) and big brown bat (Eptesicus fuscus). We then compared changes in prey consumption before versus after population declines related to WNS. Dietary niches contracted for both species after large and abrupt declines in little brown bats and smaller declines in big brown bats, but interspecific dietary overlap did not change. Furthermore, the incidence and taxonomic richness of agricultural pest taxa detected in diet samples decreased following bat population declines. Our results suggest that persisting generalist predators do not necessarily expand their dietary niches following population declines in other predators, providing further evidence that the functional roles of different generalist predators are ecologically distinct.