Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community

Phylogeographic Aspects of Bat Lyssaviruses in Europe: A Review

During the last few decades, bat lyssaviruses have become the topic of intensive molecular and epidemiological investigations. Since ancient times, rhabdoviruses have caused fatal encephalitis in humans which has led to research into effective strategies for their eradication. Modelling of potential future cross-species virus transmissions forms a substantial component of the recent infection biology of rabies. In this article, we summarise the available data on the phylogeography of both bats and lyssaviruses in Europe and the adjacent reg ions, especially in the contact zone between the Palearctic and Ethiopian realms. Within these zones, three bat families are present with high potential for cross-species transmission and the spread of lyssaviruses in Phylogroup II to Europe (part of the western Palearctic). The lack of effective therapies for rabies viruses in Phylogroup II and the most divergent lyssaviruses generates impetus for additional phylogenetic and virological research within this geographical region.

Geographic Distribution of Common Vampire Bat Desmodus rotundus (Chiroptera: Phyllostomidae) Shelters: Implications for the Spread of Rabies Virus to Cattle in Southeastern Brazil

Desmodus rotundus bats show a complex social structure and developed adaptive characteristics, considered key features of a pathogen disseminator, such as the rabies virus, among bats and other mammals, including cattle and humans. Our aim was to understand the correlation between the environment and the ecological features of these bats in bovine rabies outbreaks. Geostatistical analyses were performed, covering 104 cattle positives for rabies, between 2016 and 2018, in 25 municipalities, in addition to the characteristics of D. rotundus colonies mapped during this period in the state of São Paulo, Brazil. Data from the shelters showed that 86.15% were artificial, mainly abandoned houses (36.10%) and manholes (23.87%), in addition to demonstrating a correlation between these shelters and a higher concentration of bovine rabies cases. Due to their adaptive capacity, these bats choose shelters close to the food source, such as livestock. In Brazil, D. rotundus is the main transmitter of rabies and the cause of outbreaks in cattle and deaths in humans, considering the advance of humans in previously preserved ecosystems. There seems to be a correlation between the impact of anthropic changes on the environment, mainly for the expansion of pasture for cattle and the outbreaks of bovine rabies in this area.

A mixed-methods approach to understanding domestic dog health and disease transmission risk in an indigenous reserve in Guyana, South America

Domestic dogs (Canis lupus familiaris) can transmit a variety of pathogens due to their ubiquitousness in urban, rural and natural environments, and their close interactions with wildlife and humans. In this study, we used a mixed-methods approach to assess the role of domestic dogs as potential intermediaries of disease transmission from wildlife to humans among indigenous Waiwai in the Konashen Community Owned Conservation Area, Guyana. To address these objectives we 1) performed physical examinations and collected biological samples to assess Waiwai domestic dog health, and 2) administered questionnaires to characterize the role of dogs in the community and identify potential transmission pathways between wildlife, dogs, and humans. We observed ectoparasites on all dogs (n = 20), including: fleas (100%), ticks (15%), botflies (30%), and jigger flea lesions (Tunga penetrans) (80%). Ten percent of dogs were seropositive for Ehrlichia canis/ewingii, 10% were positive for Dirofilaria immitis, and one dog was seropositive for Leishmania infantum. All dogs (n = 20) were seronegative for: canine distemper virus, Brucella canis, Leptospira serovars, Trypanosoma cruzi, Anaplasma phagocytophilum/platys and Borrelia burgdorferi. Our questionnaire data revealed that the Waiwai remove ectoparasites from their dogs, clean up dog feces, and administer traditional and/or Western medicine to their dogs. White blood cell, strongyle-type ova, and eosinophil counts were lower in dogs that were not frequently used for hunting, dogs that did receive traditional and/or western medicine, and dogs that were frequently kept in elevated dog houses, although differences were not statistically significant. While our results suggest that the Waiwai have developed cultural practices that may promote dog health and/or prevent zoonotic disease transmission, more research is necessary to determine the efficacy of these practices. Our study provides important data on the health of dogs and the potential for disease transmission to humans in a zoonotic hotspot.

Domestic dogs are found throughout the world and interact closely with both wildlife and humans. Dogs can harbor numerous diseases that can be transmitted to other domestic and wildlife species, and human populations. They can serve as bridges, moving diseases between unconnected populations. Additionally, dogs can help in the early detection of wildlife and human diseases. Therefore, understanding what pathogens domestic dogs harbor can inform both wildlife and human health. In this study, we performed physical examinations, collected biological samples, and administered questionnaires to assess dog health and understand the role of dogs as potential bridges of disease transmission from wildlife to humans among indigenous Waiwai in the Konashen Community Owned Conservation Area, Guyana. On physical exam, we observed ectoparasites on all dogs, however, few pathogens were detected with diagnostic screening. Our questionnaire data revealed that the Waiwai engage in husbandry practices that may promote Waiwai dog health.

The New Face of Human Rabies in Mexico, What's Next After Eradicating Rabies in Dogs

In pre-Hispanic Mexico, dogs were not identified as an important source of rabies. We know from codexes and chronicles of the conquerors that at that time, rabies cases in humans and domestic animals were caused by local wildlife species such as bats. Canine-rabies virus variant seems to have arrived with Europeans. The first documented case of canine rabies in the Americas is found in Mexico in the Annals of the Holy Inquisition (16th century). During Mexico's independence, cases were frequently reported. In the 19th century the first attempts to control human rabies were made through sanitary measures such as elimination of rabid dogs and applying postexposure vaccination. During the first half of the 20th century, the efficacy of canine vaccination to prevent human rabies was established. However, in Mexico, despite reports of numerous human cases (>70/year), canine vaccination did not have enough coverage. It was only during the 1990s that Mexico made a serious commitment to eliminate dog-transmitted human rabies. Since the beginning, vaccination campaigns have been free and massive. Coverage increased from 7,100,000 doses in 1990 to more than 18,000,000 since 2017. This culminated in the elimination of dog-mediated human rabies cases since 2006. Subsequently, the epidemiology of rabies had changed. Nowadays, it is wildlife species (mainly bats and skunks) that are the source of human rabies. As a mega-biodiverse country Mexico has numerous wildlife species with potential to transmit rabies virus. Thus it is paramount to remain vigilant with respect to canine vaccination campaigns and to promote rabies research in wildlife.

Serological Surveillance of Rabies in Free-Range and Captive Common Vampire Bats Desmodus rotundus

The control of vampire bat rabies (VBR) in Brazil is based on the culling of Desmodus rotundus and the surveillance of outbreaks caused by D. rotundus in cattle and humans in addition to vaccination of susceptible livestock. The detection of anti-rabies antibodies in vampire bats indicates exposure to the rabies virus, and several studies have reported an increase of these antibodies following experimental infection. However, the dynamics of anti-rabies antibodies in natural populations of D. rotundus remains poorly understood. In this study, we took advantage of recent outbreaks of VBR among livestock in the Sao Paulo region of Brazil to test whether seroprevalence in D. rotundus reflects the incidence of rabies in nearby livestock populations. Sixty-four D. rotundus were captured during and after outbreaks from roost located in municipalities belonging to three regions with different incidences of rabies in herbivores. Sixteen seropositive bats were then kept in captivity for up to 120 days, and their antibodies and virus levels were quantified at different time points using the rapid fluorescent focus inhibition test (RFFIT). Antibody titers were associated with the occurrence of ongoing outbreak, with a higher proportion of bats showing titer >0.5 IU/ml in the region with a recent outbreak. However, low titers were still detected in bats from regions reporting the last outbreak of rabies at least 3 years prior to sampling. This study suggests that serological surveillance of rabies in vampire bats can be used as a tool to evaluate risk of outbreaks in at risk populations of cattle and human.

Ecology, evolution, and epidemiology of zoonotic and vector-borne infectious diseases in French Guiana: Transdisciplinarity does matter to tackle new emerging threats

French Guiana is a European ultraperipheric region located on the northern Atlantic coast of South America. It constitutes an important forested region for biological conservation in the Neotropics. Although very sparsely populated, with its inhabitants mainly concentrated on the Atlantic coastal strip and along the two main rivers, it is marked by the presence and development of old and new epidemic disease outbreaks, both research and health priorities. In this review paper, we synthetize 15 years of multidisciplinary and integrative research at the interface between wildlife, ecosystem modification, human activities and sociodemographic development, and human health. This study reveals a complex epidemiological landscape marked by important transitional changes, facilitated by increased interconnections between wildlife, land-use change and human occupation and activity, human and trade transportation, demography with substantial immigration, and identified vector and parasite pharmacological resistance. Among other French Guianese characteristics, we demonstrate herein the existence of more complex multi-host disease life cycles than previously described for several disease systems in Central and South America, which clearly indicates that today the greater promiscuity between wildlife and humans due to demographic and economic pressures may offer novel settings for microbes and their hosts to circulate and spread. French Guiana is a microcosm that crystallizes all the current global environmental, demographic and socioeconomic change conditions, which may favor the development of ancient and future infectious diseases.

Paramyxovirus circulation in bat species from French Guiana

Bats are recognized as reservoirs of numerous viruses. Among them, paramyxoviruses, for example, Hendra and Nipah viruses, are highly pathogenic to humans. Nothing is known regarding the circulation of this viral family in bats from French Guiana. To search for the presence of paramyxoviruses in this territory, 103 bats of seven different species were sampled and screened using a molecular approach. Four distinct paramyxovirus sequences were detected from three bat species (Desmodus rotundus, Carollia perspicillata, and Pteronotus alitonus) at high prevalence rates. In D. rotundus, two types of paramyxovirus co-circulate, with most of the bats co-infected. The phylogenetic analysis of these sequences revealed that three of them were closely related to previously characterized sequences from D. rotundus, C. perspicillata, and P. parnellii from Brazil and Costa Rica. The fourth sequence, identified in D. rotundus, was closely related to the one detected in P. alitonus in French Guiana and to previously described sequences detected in P. parnellii in Costa Rica. All paramyxovirus sequences detected in this study are close to the Jeilongvirus genus. Altogether, our results and those of previous studies indicate a wide geographical distribution of these paramyxoviruses (from Central to South America) and suggest potential cross-species transmissions of paramyxoviruses between two different bat families: Mormoopidae (P. alitonus) and Phyllostomidae (D. rotundus). In addition, their closeness to paramyxoviruses identified in rodents emphasizes the need to investigate the role of these animals as potential reservoirs or incidental hosts. Finally, the high prevalence rates of some paramyxoviruses in certain bat species, associated with the presence of large bat colonies and, in some cases, their potential proximity with humans are all parameters that can contribute to the risk of cross-species transmission between bat species and to the emergence of new paramyxoviruses in humans, a risk that deserves further investigation.

Characterization of Novel Rhabdoviruses in Chinese Bats

Bats, the second largest order of mammals worldwide, harbor specific characteristics such as sustaining flight, a special immune system, unique habits, and ecological niches. In addition, they are the natural reservoirs of a variety of emerging or re-emerging zoonotic pathogens. Rhabdoviridae is one of the most diverse families of RNA viruses, which consists of 20 ecologically diverse genera, infecting plants, mammals, birds, reptiles, and fish. To date, three bat-related genera are described, named Lyssavirus, Vesiculovirus, and Ledantevirus. However, the prevalence and the distribution of these bat-related rhabdoviruses remain largely unknown, especially in China. To fill this gap, we performed a large molecular retrospective study based on the real-time reverse transcription polymerase chain reaction (RT-qPCR) detection of lyssavirus in bat samples (1044 brain and 3532 saliva samples, from 63 different bat species) originating from 21 provinces of China during 2006–2018. None of them were positive for lyssavirus, but six bat brains (0.6%) of Rhinolophus bat species, originating from Hubei and Hainan provinces, were positive for vesiculoviruses or ledanteviruses. Based on complete genomes, these viruses were phylogenetically classified into three putative new species, tentatively named Yinshui bat virus (YSBV), Taiyi bat virus (TYBV), and Qiongzhong bat virus (QZBV). These results indicate the novel rhabdoviruses circulated in different Chinese bat populations.

Update on lyssaviruses and rabies: will past progress play as prologue in the near term towards future elimination?

Rabies is an ancient, much-feared, and neglected infectious disease. Caused by pathogens in the family Rhabdoviridae, genus Lyssavirus, and distributed globally, this viral zoonosis results in tens of thousands of human fatalities and millions of exposures annually. All mammals are believed susceptible, but only certain taxa act as reservoirs. Dependence upon direct routing to, replication within, and passage from the central nervous system serves as a basic viral strategy for perpetuation. By a combination of stealth and subversion, lyssaviruses are quintessential neurotropic agents and cause an acute, progressive encephalitis. No treatment exists, so prevention is the key. Although not a disease considered for eradication, something of a modern rebirth has been occurring within the field as of late with regard to detection, prevention, and management as well as applied research. For example, within the past decade, new lyssaviruses have been characterized; sensitive and specific diagnostics have been optimized; pure, potent, safe, and efficacious human biologics have improved human prophylaxis; regional efforts have controlled canine rabies by mass immunization; wildlife rabies has been controlled by oral rabies vaccination over large geographic areas in Europe and North America; and debate has resumed over the controversial topic of therapy. Based upon such progress to date, there are certain expectations for the next 10 years. These include pathogen discovery, to uncover additional lyssaviruses in the Old World; laboratory-based surveillance enhancement by simplified, rapid testing; anti-viral drug appearance, based upon an improved appreciation of viral pathobiology and host response; and improvements to canine rabies elimination regionally throughout Africa, Asia, and the Americas by application of the best technical, organizational, economic, and socio-political practices. Significantly, anticipated Gavi support will enable improved access of human rabies vaccines in lesser developed countries at a national level, with integrated bite management, dose-sparing regimens, and a 1 week vaccination schedule.

Predicting the presence and titre of rabies virus-neutralizing antibodies from low-volume serum samples in low-containment facilities

Serology is a core component of the surveillance and management of viral zoonoses. Virus neutralization tests are a gold standard serological diagnostic, but requirements for large volumes of serum and high biosafety containment can limit widespread use. Here, focusing on Rabies lyssavirus, a globally important zoonosis, we developed a pseudotype micro-neutralization rapid fluorescent focus inhibition test (pmRFFIT) that overcomes these limitations. Specifically, we adapted an existing micro-neutralization test to use a green fluorescent protein-tagged murine leukaemia virus pseudotype in lieu of pathogenic rabies virus, reducing the need for specialized reagents for antigen detection and enabling use in low-containment laboratories. We further used statistical models to generate rapid, quantitative predictions of the probability and titre of rabies virus-neutralizing antibodies from microscopic imaging of neutralization outcomes. Using 47 serum samples from domestic dogs with neutralizing antibody titres estimated using the fluorescent antibody virus neutralization test (FAVN), pmRFFIT showed moderate sensitivity (78.79%) and high specificity (84.62%). Despite small conflicts, titre predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93) and in a second data set of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. Our test uses a starting volume of 3.5 µl of serum, estimates titres from a single dilution of serum rather than requiring multiple dilutions and end point titration, and may be adapted to target neutralizing antibodies against alternative lyssavirus species. The pmRFFIT enables high-throughput detection of rabies virus-neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained.

Defining New Pathways to Manage the Ongoing Emergence of Bat Rabies in Latin America

Rabies transmitted by common vampire bats (Desmodus rotundus) has been known since the early 1900s but continues to expand geographically and in the range of species and environments affected. In this review, we present current knowledge of the epidemiology and management of rabies in D. rotundus and argue that it can be reasonably considered an emerging public health threat. We identify knowledge gaps related to the landscape determinants of the bat reservoir, reduction in bites on humans and livestock, and social barriers to prevention. We discuss how new technologies including autonomously-spreading vaccines and reproductive suppressants targeting bats might manage both rabies and undesirable growth of D. rotundus populations. Finally, we highlight widespread under-reporting of human and animal mortality and the scarcity of studies that quantify the efficacy of control measures such as bat culling. Collaborations between researchers and managers will be crucial to implement the next generation of rabies management in Latin America.

Synergistic Effects of Grassland Fragmentation and Temperature on Bovine Rabies Emergence

In 2007, common vampire bats were the source of the first outbreak of paralytic bovine rabies in Uruguay. The outbreak coincided in space and time with the fragmentation of native grasslands for monospecific forestry for wood and cellulose production. Using spatial analyses, we show that the increase in grassland fragmentation, together with the minimum temperature in the winter, accounts for the spatial pattern of outbreaks in the country. We propose that fragmentation may increase the connectivity of vampire bat colonies by promoting the sharing of feeding areas, while temperature modulates their home range plasticity. While a recent introduction of the virus from neighboring Brazil could have had an effect on outbreak occurrence, we show here that the distribution of rabies cases is unlikely to be explained by only an invasion process from Brazil. In accordance with previous modeling efforts, an increase in connectivity may promote spatial persistence of rabies virus within vampire bat populations. Our results suggest that land use planning might help to reduce grassland fragmentation and thus reduce risk of rabies transmission to livestock. This will be especially important in the context of climatic changes and increasing minimum temperatures in the winter.

Novel herpesviruses in neotropical bats and their relationship with other members of the Herpesviridae family

In the past decade, a large number of studies have detected herpesvirus sequences from many bat species around the world. Nevertheless, the discovery of bat herpesviruses is geographically uneven. Of the various bat species tested to date, only a few were from the New World. Seeking to investigate the distribution and diversity of herpesviruses circulating in neotropical bats, we carried out molecular screening of 195 blood DNA samples from 11 species of three bat families (Phyllostomidae, Mormoopidae, and Molossidae). Using polymerase chain reaction amplification, with degenerate consensus primers targeting highly conserved amino acid motifs of the herpesvirus DNA polymerase and Glycoprotein B genes, we characterized novel viral sequences from all tested species. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, as well as phylogenetic analyses confirmed that they all belonged to the Herpesviridae family, of the Beta- and Gammaherpesvirinae subfamilies. Fourteen partial DNA polymerase gene sequences, of which three beta- and 11 gamma-herpesviruses, were detected. A total of 12 partial Glycoprotein B gene sequences, all gamma-herpesviruses, were characterized. Every sequence was specific to a bat species and in some species (Desmodus rotundus, Carollia perspicillata, and Pteronotus rubiginosus) multiple viruses were found. Phylogenetic analyses of beta- and gammaherpesvirus sequences led to the identification of bat-specific clades. Those composed of sequences obtained from different bat species belonging to distinct subfamilies follow the taxonomy of bats. This study confirms the astonishing diversity of bat herpesviruses and broadens our knowledge of their host range. Nevertheless, it also emphasizes the fact that, to better appreciate the evolutionary history of these viruses, much remains to be done at various taxonomic levels.

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Molecular screening was carried out on 11 bat species from French Guiana and Martinique (French West Indies).

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Partial DNA polymerase gene sequences of 14 viruses were characterized as well as 12 Glycoprotein B sequences.

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Genetic characterization of these sequences reveals a high degree of genetic divergence.

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Phylogenetically, most of the newly discovered sequences fall within bat-specific clades well correlated with the taxonomy of their hosts.

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This study is the largest conducted to date in terms of species diversity from the New World.

Leukocyte Profiles Reflect Geographic Range Limits in a Widespread Neotropical Bat

Quantifying how the environment shapes host immune defense is important for understanding which wild populations may be more susceptible or resistant to pathogens. Spatial variation in parasite risk, food and predator abundance, and abiotic conditions can each affect immunity, and these factors can also manifest at both local and biogeographic scales. Yet identifying predictors and the spatial scale of their effects is limited by the rarity of studies that measure immunity across many populations of broadly distributed species. We analyzed leukocyte profiles from 39 wild populations of the common vampire bat (Desmodus rotundus) across its wide geographic range throughout the Neotropics. White blood cell differentials varied spatially, with proportions of neutrophils and lymphocytes varying up to six-fold across sites. Leukocyte profiles were spatially autocorrelated at small and very large distances, suggesting that local environment and large-scale biogeographic factors influence cellular immunity. Generalized additive models showed that bat populations closer to the northern and southern limits of the species range had more neutrophils, monocytes, and basophils, but fewer lymphocytes and eosinophils, than bats sampled at the core of their distribution. Habitats with access to more livestock also showed similar patterns in leukocyte profiles, but large-scale patterns were partly confounded by time between capture and sampling across sites. Our findings suggest that populations at the edge of their range experience physiologically limiting conditions that predict higher chronic stress and greater investment in cellular innate immunity. High food abundance in livestock-dense habitats may exacerbate such conditions by increasing bat density or diet homogenization, although future spatially and temporally coordinated field studies with common protocols are needed to limit sampling artifacts. Systematically assessing immune function and response over space will elucidate how environmental conditions influence traits relevant to epidemiology and help predict disease risks with anthropogenic disturbance, land conversion, and climate change.

The Serological Prevalence of Rabies Virus-Neutralizing Antibodies in the Bat Population on the Caribbean Island of Trinidad

: Rabies virus (RABV) is the only lyssavirus known to be present within the Caribbean. The island of Trinidad, is richly diverse in chiropteran fauna and endemic for bat-transmitted rabies with low RABV isolation rates observed in this population. We aimed to determine the seroprevalence of rabies virus neutralizing antibodies (RVNA) in light of spatio-temporal and bat demographic factors to infer the extent of natural exposure to RABV in the Trinidadian bat population. RVNA titers were determined by the RABV micro-neutralization test on 383 bat samples representing 21 species, comprising 30.9% of local bat diversity, from 31 locations across the island over 5 years. RVNA was positively detected in 33 samples (8.6%) representing 6 bat species (mainly frugivorous) with titers ranging from 0.1 to 19 IU/mL (mean 1.66 IU/mL). The analyses based on a multivariable binomial generalised linear mixed-effects model showed that bat age and year of capture were significant predictors of seropositivity. Thus, juvenile bats were more likely to be seropositive when compared to adults (estimate 1.13; p = 0.04) which may suggest early exposure to the RABV with possible implications for viral amplification in this population. Temporal variation in rabies seropositivity, 2012-2014 versus 2015-2017 (estimate 1.07; p = 0.03) may have been related to the prevailing rabies epizootic situation. Regarding other factors investigated, RVNA was found in bats from both rural and non-rural areas, as well as in both hematophagous and non-hematophagous bat species. The most common seropositive species, Artibeusjamaicensisplanirostris is ubiquitous throughout the island which may potentially facilitate human exposure. The findings of this study should be factored into public health assessments on the potential for rabies transmission by non-hematophagous bats in Trinidad.

Unravelling virus community ecology in bats through the integration of metagenomics and community ecology

The spillover of viruses from wildlife into agricultural animals or humans has profound socioeconomic and public health impact. Vampire bats, found throughout South America, feed directly on humans and other animals and are an important reservoir for zoonotic viruses, including rabies virus. This has resulted in considerable effort in understanding both the ecology of bat-borne viruses and the composition and associated correlates of the structure of entire virus communities in wildlife, particularly in the context of disease control interventions. In a From the Cover article in this issue of Molecular Ecology, Bergner et al. (2019) set out to reveal virus community dynamics in vampire bats by interrogating factors that affect the structure, diversity and richness of these communities. Due to the linkage of metagenomic sequence data with community ecology, this study represents an important advance in the field of virus ecology.

Demographic and environmental drivers of metagenomic viral diversity in vampire bats

Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. Here we test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities that was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile-biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.

Rabies virus monitoring in bat populations in Rondônia state, Brazil

INTRODUCTION

The Jirau hydroelectric power plant built in Rondônia state has environmental impacts that could be relevant to rabies outbreaks.

METHODS

Bat populations were monitored for rabies by fluorescent antibody testing and simplified fluorescent inhibition microtesting between 2010 and 2015.

RESULTS

All 1,183 bats tested negative for rabies. The prevalence of rabies antibodies was 17.5% in 1,049 bats.

CONCLUSIONS

The rabies antibody dosage was not reactive in samples collected before the environmental changes, and there was a progressive increase in subsequent collections that could indicate an increase in rabies virus circulation among bats and risk of a rabies outbreak.

The shift in rabies epidemiology in France: time to adjust rabies post-exposure risk assessment

The epidemiology of rabies in France and western Europe has changed during the past 22 years. In France, rabies in non-flying terrestrial mammals was declared to be eliminated in 2001, and the risk of rabies is now limited to contact with bats, rabid animals illegally imported from rabies-enzootic countries and traveller exposure in enzootic areas. We analysed the epidemiology of rabies in France from 1995 to 2016, describing and analysing data on human rabies surveillance as well as data on post-exposure prophylaxis (PEP) collected from the network of French antirabies clinics. Over the study period, seven individuals were diagnosed with rabies in France, all of whom were infected outside mainland France. PEP data analysis revealed an expected overall decrease in PEP administration for individuals exposed in mainland France, but there was still overuse of anti-rabies drugs, given the very low epidemiological risk. On the other hand, a significant increase in PEP delivered to individuals exposed abroad was evidenced. These epidemiological trends indicate that clear guidelines should be provided to support physicians' efforts to adjust rabies risk assessment to the evolution of the epidemiological situation.

Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats

Bartonella spp. are globally distributed bacteria that cause endocarditis in humans and domestic animals. Recent work has suggested bats as zoonotic reservoirs of some human Bartonella infections; however, the ecological and spatiotemporal patterns of infection in bats remain largely unknown. Here we studied the genetic diversity, prevalence of infection across seasons and years, individual risk factors, and possible transmission routes of Bartonella in populations of common vampire bats (Desmodus rotundus) in Peru and Belize, for which high infection prevalence has previously been reported. Phylogenetic analysis of the gltA gene for a subset of PCR-positive blood samples revealed sequences that were related to Bartonella described from vampire bats from Mexico, other Neotropical bat species, and streblid bat flies. Sequences associated with vampire bats clustered significantly by country but commonly spanned Central and South America, implying limited spatial structure. Stable and nonzero Bartonella prevalence between years supported endemic transmission in all sites. The odds of Bartonella infection for individual bats was unrelated to the intensity of bat flies ectoparasitism, but nearly all infected bats were infested, which precluded conclusive assessment of support for vector-borne transmission. While metagenomic sequencing found no strong evidence of Bartonella DNA in pooled bat saliva and fecal samples, we detected PCR positivity in individual saliva and feces, suggesting the potential for bacterial transmission through both direct contact (i.e., biting) and environmental (i.e., fecal) exposures. Further investigating the relative contributions of direct contact, environmental, and vector-borne transmission for bat Bartonella is an important next step to predict infection dynamics within bats and the risks of human and livestock exposures.

The spread and evolution of rabies virus: conquering new frontiers

Rabies is a lethal zoonotic disease that is caused by lyssaviruses, most often rabies virus. Despite control efforts, sporadic outbreaks in wildlife populations are largely unpredictable, underscoring our incomplete knowledge of what governs viral transmission and spread in reservoir hosts. Furthermore, the evolutionary history of rabies virus and related lyssaviruses remains largely unclear. Robust surveillance efforts combined with diagnostics and disease modelling are now providing insights into the epidemiology and evolution of rabies virus. The immune status of the host, the nature of exposure and strain differences all clearly influence infection and transmission dynamics. In this Review, we focus on rabies virus infections in the wildlife and synthesize current knowledge in the rapidly advancing fields of rabies virus epidemiology and evolution, and advocate for multidisciplinary approaches to advance our understanding of this disease.

Development of molecular and cellular tools to decipher the type I IFN pathway of the common vampire bat

Though the common vampire bat, Desmodus rotundus, is known as the main rabies virus reservoir in Latin America, no tools are available to investigate its antiviral innate immune system. To characterize the IFN-I pathway, we established an immortalized cell line from a D. rotundus fetal lung named FLuDero. Then we molecularly characterized some of the Toll-like receptors (TLR3, 7, 8 and 9), the three RIG-I-like receptor members, as well as IFNα1 and IFNβ. Challenging the FLuDero cell line with poly (I:C) resulted in an up-regulation of both IFNα1 and IFNβ and the induction of expression of the different pattern recognition receptors characterized. These findings provide evidence of the intact dsRNA recognition machinery and the IFN-I signaling pathway in our cellular model. Herein, we generated a sum of insightful specific molecular and cellular tools that will serve as a useful model to study virus-host interactions of the common vampire bat.

Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics

Rabies is an important zoonotic disease distributed worldwide. A key question in rabies epidemiology is the identification of factors that impact virus dispersion. Here we apply new analytical methods, based on phylogeographic reconstructions of viral lineage movement, to undertake a comparative evolutionary-epidemiological study of the spatial dynamics of rabies virus (RABV) epidemics in different hosts and habitats. We compiled RABV data sets from skunk, raccoon, bat and domestic dog populations in order to investigate the viral diffusivity of different RABV epidemics, and to detect and compare the environmental factors that impact the velocity of viral spread in continuous spatial landscapes. We build on a recently developed statistical framework that uses spatially- and temporally-referenced phylogenies. We estimate several spatial statistics of virus spread, which reveal a higher diffusivity of RABV in domestic dogs compared with RABV in other mammals. This finding is explained by subsequent analyses of environmental heterogeneity, which indicate that factors relating to human geography play a significant role in RABV dispersion in domestic dogs. More generally, our results suggest that human-related factors are important worldwide in explaining RABV dispersion in terrestrial host species. Our study shows that phylogenetically informed viral movements can be used to elucidate the factors that impact virus dispersal, opening new opportunities for a better understanding of the impact of host species and environmental conditions on the spatial dynamics of rapidly evolving populations.

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana

Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensification, urbanization) contribute to an increasing risk of cross-species transmission of microorganisms and to disease outbreaks due to changing ecosystems of reservoir hosts. Although Amazonia encompasses the greatest diversity of reservoir species, the outsized viral population diversity (virome) has yet to be investigated. Here, through a metagenomic approach, we identified 10,991 viral sequences in the saliva and feces of two bat species, Desmodus rotundus (hematophagous), trapped in two different caves surrounded by primary lowland forest, and Molossus molossus (insectivorous), trapped in forest and urban habitats. These sequences are related to 51 viral families known to infect a wide range of hosts (i.e., bacteria, plants, insects and vertebrates). Most viruses detected reflected the diet of bat species, with a high proportion of plant and insect-related viral families for M. molossus and a high proportion of vertebrate-related viral families for D. rotundus, highlighting its influence in shaping the viral diversity of bats. Lastly, we reconstructed the phylogenetic relationships for five vertebrate-related viral families (Nairoviridae, Circoviridae, Retroviridae, Herpesviridae, Papillomaviridae). The results showed highly supported clustering with other viral sequences of the same viral family hosted by other bat species, highlighting the potential association of viral diversity with the host’s diet. These findings provide significant insight into viral bat diversity in French Guiana belonging to the Amazonian biome and emphasize that habitats and the host’s dietary ecology may drive the viral diversity in the bat communities investigated.

Experimental infection of Artibeus intermedius with a vampire bat rabies virus

Experimental infection of Artibeus intermedius, the great fruit-eating bat, was performed with vampire bat rabies isolates. Bats (n=35) were captured in the wild and quarantined prior to experimental infection. No rabies antibodies were detected by rapid fluorescent focus inhibition test (RFFIT) prior to infection. Three doses of rabies virus (RV) and three different routes of infection were used. One out of 35 bats died without showing any clinical signs at day 14 and was positive for rabies. None of the 34 other bats showed clinical signs for rabies, but high antibody titers were detected post-inoculation, suggesting either innate immune response to the vampire bat rabies virus or possible pre-exposure to RV and inoculation leading to a booster effect. Rabies virus was detected by hemi-nested RT-PCR (hnRT-PCR) in the brain (n=3), stomach (n=1) of bats that were negative by immunofluorescence and that survived rabies infection. The bat that died on day 14 was positive by hnRT-PCR on the brain, heart and liver. These results suggest that either previous non-lethal exposure to RV or natural low susceptibility to vampire bat viruses somehow protected Artibeus intermedius from clinical rabies infection leading to a marginal lethality effect on this bats species population in the wild.

Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species

Background

Although bats are natural reservoirs of many pathogens, few studies have been conducted on the genetic variation and detection of selection in major histocompatibility complex (MHC) genes. These genes are critical for resistance and susceptibility to diseases, and host–pathogen interactions are major determinants of their extensive polymorphism. Here we examined spatial patterns of diversity of the expressed MHC class II DRB gene of three sympatric Neotropical bats, Carollia perspicillata and Desmodus rotundus (Phyllostomidae), and Molossus molossus (Molossidae), all of which use the same environments (e.g., forests, edge habitats, urban areas). Comparison with neutral marker (mtDNA D-loop) diversity was performed at the same time.

Results

Twenty-three DRB alleles were identified in 19 C. perspicillata, 30 alleles in 35 D. rotundus and 20 alleles in 28 M. molossus. The occurrence of multiple DRB loci was found for the two Phyllostomidae species. The DRB polymorphism was high in all sampling sites and different signatures of positive selection were detected depending on the environment. The patterns of DRB diversity were similar to those of neutral markers for C. perspicillata and M. molossus. In contrast, these patterns were different for D. rotundus for which a geographical structure was highlighted. A heterozygote advantage was also identified for this species. No recombination or gene conversion event was found and phylogenetic relationships showed a trans-species mode of evolution in the Phyllostomids.

Conclusions

This study of MHC diversity demonstrated the strength of the environment and contrasting pathogen pressures in shaping DRB diversity. Differences between positively selected sites identified in bat species highlighted the potential role of gut microbiota in shaping immune responses. Furthermore, multiple geographic origins and/or population admixtures observed in C. perspicillata and M. molossus populations acted as an additional force in shaping DRB diversity. In contrast, DRB diversity of D. rotundus was shaped by environment rather than demographic history.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0802-1) contains supplementary material, which is available to authorized users.

Complete Genome Sequence of a Vampire Bat Rabies Virus from French Guiana

A rabies virus was detected in a common vampire bat (Desmodus rotundus) in French Guiana. Its genomic sequence was obtained and found to be closely related to other hematophagous bat-related viruses that widely circulate in the northern Amazon region. This virus is named AT6.