Endemic Lagos bat virus infection in Eidolon helvum

Seasonal shedding of coronavirus by straw-colored fruit bats at urban roosts in Africa

The straw-colored fruit bat (Eidolon helvum) is a pteropodid whose conservation is crucial for maintaining functional connectivity of plant populations in tropical Africa. Land conversion has pushed this species to adapt to roosting in urban centers across its range. These colonies often host millions of individuals, creating intensive human-bat contact interfaces that could facilitate the spillover of coronaviruses shed by these bats. A better understanding of coronavirus dynamics in these roosts is needed to identify peak times of exposure risk in order to propose evidence-based management that supports safe human-bat coexistence, as well as the conservation of this chiropteran. We studied the temporal patterns of coronavirus shedding in E. helvum, by testing thousands of longitudinally-collected fecal samples from two spatially distant urban roosts in Ghana and Tanzania. Shedding of coronaviruses peaked during the second part of pup weaning in both roosts. Assuming that coronavirus shedding is directly related to spillover risk, our results indicate that exposure mitigation should target reducing contact between people and E. helvum roosts during the pup "weaning" period. This recommendation can be applied across the many highly-populated urban sites occupied by E. helvum across Africa.

Reduced IFN-ß inhibitory activity of Lagos bat virus phosphoproteins in human compared to Eidolon helvum bat cells

Eidolon helvum bats are reservoir hosts for highly pathogenic lyssaviruses often showing limited disease upon natural infection. An enhanced antiviral interferon (IFN) response combined with reduced inflammation might be linked to the apparent virus tolerance in bats. Lyssavirus phosphoproteins inhibit the IFN response with virus strain-specific efficiency. To date, little is known regarding the lyssavirus P-dependent anti-IFN countermeasures in bats, mainly due to a lack of in vitro tools. By using E. helvum bat cell cultures in a newly established bat-specific IFN-promoter activation assay, we analyzed the IFN-ß inhibitory activity of multiple lyssavirus P in E. helvum compared to human cells. Initial virus infection studies with a recently isolated E. helvum-borne Lagos bat virus street strain from Ghana showed enhanced LBV propagation in an E. helvum lung cell line compared to human A549 lung cells at later time points suggesting effective viral countermeasures against cellular defense mechanisms. A direct comparison of the IFN-ß inhibitory activity of the LBV-GH P protein with other lyssavirus P proteins showed that LBV-GH P and RVP both strongly inhibited the bat IFN-β promotor activation (range 75–90%) in EidLu/20.2 and an E. helvum kidney cell line. Conversely, LBV-GH P blocked the activation of the human IFN-β promoter less efficiently compared to a prototypic Rabies virus P protein (range LBV P 52–68% vs RVP 71–95%) in two different human cell lines (HEK-293T, A549). The same pattern was seen for two prototypic LBV P variants suggesting an overall reduced LBV P IFN-ß inhibitory activity in human cells as compared to E. helvum bat cells. Increased IFN-ß inhibition by lyssavirus P in reservoir host cells might be a result of host-specific adaptation processes towards an enhanced IFN response in bat cells.

Serum Neutralization Profiles of Straw-Colored Fruit Bats (Eidolon helvum) in Makurdi (Nigeria), against Four Lineages of Lagos Bat Lyssavirus

Lagos bat lyssavirus (LBV) comprising four lineages (A, B, C and D) can potentially cause the fatal disease rabies. Although LBV-B was initially isolated in Nigeria in 1956, there is no information on LBV lineages circulating in Nigeria. This study was undertaken for the first time to measure the neutralizing antibodies against four lineages of LBVs in straw-colored fruit bats (Eidolon helvum) in Makurdi, Nigeria. Serum samples (n = 180) collected during two periods (November 2017-March 2018 and November 2018-March 2019) from terminally bled bats captured for human consumption were tested using a modified fluorescent antibody virus neutralization (mFAVN) assay. A high proportion of bat sera (74%) neutralized at least one lineage of LBV (with reciprocal titers from 9 to >420.89) and most of them neutralized LBV-A (63%), followed by LBV-D (49%), LBV-C (45%) and LBV-B (24%). The majority of positive sera (75%, n = 100) neutralized multiple LBV lineages while the remaining 25% (n = 33) neutralized only a single lineage, i.e., LBV-A (n = 23), LBV-D (n = 8) and LBV-C (n = 2). None exclusively neutralized LBV-B. The results suggest that exposure to LBV is common in E. helvum and that LBV-A (but not LBV-B) is likely to be circulating in this region of Nigeria.

Experimental Lagos bat virus infection in straw-colored fruit bats: A suitable model for bat rabies in a natural reservoir species

Rabies is a fatal neurologic disease caused by lyssavirus infection. Bats are important natural reservoir hosts of various lyssaviruses that can be transmitted to people. The epidemiology and pathogenesis of rabies in bats are poorly understood, making it difficult to prevent zoonotic transmission. To further our understanding of lyssavirus pathogenesis in a natural bat host, an experimental model using straw-colored fruit bats (Eidolon helvum) and Lagos bat virus, an endemic lyssavirus in this species, was developed. To determine the lowest viral dose resulting in 100% productive infection, bats in five groups (four bats per group) were inoculated intramuscularly with one of five doses, ranging from 100.1 to 104.1 median tissue culture infectious dose (TCID50). More bats died due to the development of rabies after the middle dose (102.1 TCID50, 4/4 bats) than after lower (101.1, 2/4; 101.1, 2/4) or higher (103.1, 2/4; 104.1, 2/4) doses of virus. In the two highest dose groups, 4/8 bats developed rabies. Of those bats that remained healthy 3/4 bats seroconverted, suggesting that high antigen loads can trigger a strong immune response that abrogates a productive infection. In contrast, in the two lowest dose groups, 3/8 bats developed rabies, 1/8 remained healthy and seroconverted and 4/8 bats remained healthy and did not seroconvert, suggesting these doses are too low to reliably induce infection. The main lesion in all clinically affected bats was meningoencephalitis associated with lyssavirus-positive neurons. Lyssavirus antigen was detected in tongue epithelium (5/11 infected bats) rather than in salivary gland epithelium (0/11), suggesting viral excretion via the tongue. Thus, intramuscular inoculation of 102.1 TCID50 of Lagos bat virus into straw-colored fruit bats is a suitable model for lyssavirus associated bat rabies in a natural reservoir host, and can help with the investigation of lyssavirus infection dynamics in bats.

Bat-borne viruses in Africa: a critical review

In Africa, bat-borne zoonoses emerged in the past few decades resulting in large outbreaks or just sporadic spillovers. In addition, hundreds of more viruses are described without any information on zoonotic potential. We discuss important characteristics of bats including bat biology, evolution, distribution and ecology that not only make them unique among most mammals but also contribute to their potential as viral reservoirs. The detection of a virus in bats does not imply that spillover will occur and several biological, ecological and anthropogenic factors play a role in such an event. We summarize and critically analyse the current knowledge on African bats as reservoirs for corona-, filo-, paramyxo- and lyssaviruses. We highlight that important information on epidemiology, bat biology and ecology is often not available to make informed decisions on zoonotic spillover potential. Even if knowledge gaps exist, it is still important to recognize the role of bats in zoonotic disease outbreaks and implement mitigation strategies to prevent exposure to infectious agents including working safely with bats. Equally important is the crucial role of bats in various ecosystem services. This necessitates a multidisciplinary One Health approach to close knowledge gaps and ensure the development of responsible mitigation strategies to not only minimize risk of infection but also ensure conservation of the species.

Bat Research Networks and Viral Surveillance: Gaps and Opportunities in Western Asia

Bat research networks and viral surveillance are assumed to be at odds due to seemingly conflicting research priorities. Yet human threats that contribute to declines in bat populations globally also lead to increased transmission and spread of bat-associated viruses, which may pose a threat to global health and food security. In this review, we discuss the importance of and opportunities for multidisciplinary collaborations between bat research networks and infectious disease experts to tackle shared threats that jeopardize bat conservation as well as human and animal health. Moreover, we assess research effort on bats and bat-associated viruses globally, and demonstrate that Western Asia has limited published research and represents a gap for coordinated bat research. The lack of bat research in Western Asia severely limits our capacity to identify and mitigate region-specific threats to bat populations and detect interactions between bats and incidental hosts that promote virus spillover. We detail a regional initiative to establish the first bat research network in Western Asia (i.e., the Western Asia Bat Research Network, WAB-Net), with the aim of integrating ecological research on bats with virus surveillance to find “win-win” solutions that promote bat conservation and safeguard public and animal health across the region.

Maternal antibody and the maintenance of a lyssavirus in populations of seasonally breeding African bats

Pathogens causing acute disease and death or lasting immunity require specific spatial or temporal processes to persist in populations. Host traits, such as maternally-derived antibody (MDA) and seasonal birthing affect infection maintenance within populations. Our study objective is to understand how viral and host traits lead to population level infection persistence when the infection can be fatal. We collected data on African fruit bats and a rabies-related virus, Lagos bat virus (LBV), including through captive studies. We incorporate these data into a mechanistic model of LBV transmission to determine how host traits, including MDA and seasonal birthing, and viral traits, such as incubation periods, interact to allow fatal viruses to persist within bat populations. Captive bat studies supported MDA presence estimated from field data. Captive bat infection-derived antibody decayed more slowly than MDA, and while faster than estimates from the field, supports field data that suggest antibody persistence may be lifelong. Unobserved parameters were estimated by particle filtering and suggest only a small proportion of bats die of disease. Pathogen persistence in the population is sensitive to this proportion, along with MDA duration and incubation period. Our analyses suggest MDA produced bats and prolonged virus incubation periods allow viral maintenance in adverse conditions, such as a lethal pathogen or strongly seasonal resource availability for the pathogen in the form of seasonally pulsed birthing.

Pathogenesis of bat rabies in a natural reservoir: Comparative susceptibility of the straw-colored fruit bat (Eidolon helvum) to three strains of Lagos bat virus

Rabies is a fatal neurologic disease caused by lyssavirus infection. People are infected through contact with infected animals. The relative increase of human rabies acquired from bats calls for a better understanding of lyssavirus infections in their natural hosts. So far, there is no experimental model that mimics natural lyssavirus infection in the reservoir bat species. Lagos bat virus is a lyssavirus that is endemic in straw-colored fruit bats (Eidolon helvum) in Africa. Here we compared the susceptibility of these bats to three strains of Lagos bat virus (from Senegal, Nigeria, and Ghana) by intracranial inoculation. To allow comparison between strains, we ensured the same titer of virus was inoculated in the same location of the brain of each bat. All bats (n = 3 per strain) were infected, and developed neurological signs, and fatal meningoencephalitis with lyssavirus antigen expression in neurons. There were three main differences among the groups. First, time to death was substantially shorter in the Senegal and Ghana groups (4 to 6 days) than in the Nigeria group (8 days). Second, each virus strain produced a distinct clinical syndrome. Third, the spread of virus to peripheral tissues, tested by hemi-nested reverse transcriptase PCR, was frequent (3 of 3 bats) and widespread (8 to 10 tissues positive of 11 tissues examined) in the Ghana group, was frequent and less widespread in the Senegal group (3/3 bats, 3 to 6 tissues positive), and was rare and restricted in the Nigeria group (1/3 bats, 2 tissues positive). Centrifugal spread of virus from brain to tissue of excretion in the oral cavity is required to enable lyssavirus transmission. Therefore, the Senegal and Ghana strains seem most suitable for further pathogenesis, and for transmission, studies in the straw-colored fruit bat.

Rabies is a neurologic disease that causes severe suffering and is almost always fatal. The disease is caused by infection with a virus of the genus Lyssavirus, of which 16 species are known. These viruses replicate in neurons, are excreted in the mouth, and are transmitted by bites. Dogs are the most important source of rabies for humans, but recently there is a relative increase in people contracting the disease from bats. To better understand the development of human rabies caused by these bat-acquired viruses, we need to study this disease in its bat host under controlled circumstances. To do so, we chose a naturally occurring lyssavirus–host combination: Lagos bat virus in straw-colored fruit bats. We compared three available strains of Lagos bat virus (all isolated from brains of this bat species) for their ability to mimic a natural infection. We used intracranial inoculation to ensure infection of the brain. All three strains infected brain neurons, resulting in fatal neurologic disease, however only two of the strains showed the ability to reach the site of excretion—the mouth—and were considered a suitable virus to use for further studies of this disease in bats.

Living with Bats: The Case of Ve Golokuati Township in the Volta Region of Ghana

Transmission of zoonotic pathogens from bats to humans through direct and indirect contact with bats raises public apprehension about living close to bats. In the township of Ve Golokuati in Ghana, several "camps" of Epomophorus gambianus roost in fruit trees that provide ecosystems services for residents. This study explored human-bat interaction in the township and the potential risks of disease transmission from bats to humans. Data were derived through questionnaire administration and participatory appraisal approach involving focus group discussions, participatory landscape mapping, and transect walk. The study found that most human activities within the township, such as petty-trading, domestic chores, and children's outdoor recreation, exposed people to bats. Though there have been no reported cases of disease spillover from bats to humans from the perspective of residents and from medical records, respondents whose activities brought them closer to bats within the township were found to be more likely to experience fevers than those who do not interact with bats frequently. The study recommends education of community members about the potential risks involved in human-bat interactions and makes suggestions for reducing the frequent interactions with and exposure to bats by humans.

Sero-Surveillance of Lyssavirus Specific Antibodies in Nigerian Fruit Bats (Eidolon helvum)

The aetiological agent of rabies is a member of the Lyssavirus genus (Rhabdoviridae family, order Mononegavirales). The disease (rabies) is endemic in many parts of Asia and Africa and still remains an important public and veterinary health threat. In Nigeria, there is a dearth of information on the natural infection and/or exposure of bat species to lyssaviruses. Therefore, this study was undertaken to assess the prevalence of rabies virus (RABV) neutralizing antibodies in sera obtained from bats from the central Plateau and North-East Bauchi States in Nigeria. Two hundred serum samples were collected from Nigerian fruit bats from six different locations and tested for anti-RABV antibodies using a commercial blocking ELISA. Of the 200 bat serum samples collected, one batch consisting of 111 samples did not meet the validation criteria and hence was not included in the final analysis. Of the remaining 89, only three (3.4%) contained anti-lyssavirus antibodies, demonstrating a low prevalence of lyssavirus antibodies in the study population. In order to further understand the exposure of bat species to phylogroup II lyssaviruses (Lagos bat virus and Mokola virus), the same panel of samples will be tested for neutralizing antibodies to phylogroup II members, viruses that do not cross-neutralize with members of phylogroup I.

Lagos Bat Virus Infection Dynamics in Free-Ranging Straw-Colored Fruit Bats (Eidolon helvum)

Bats are key species for ecological function, but they are also reservoirs of zoonotic agents, such as lyssaviruses that cause rabies. Little is known about the maintenance and transmission of lyssaviruses in bats, although the observation of clinically sick bats, both in experimental studies and wild bats, has at least demonstrated that lyssaviruses are capable of causing clinical disease in bat species. Despite this, extensive surveillance for diseased bats has not yielded lyssaviruses, whilst serological surveys demonstrate that bats must be exposed to lyssavirus without developing clinical disease. We hypothesize that there is endemic circulation of Lagos bat virus (LBV) in the straw-coloured fruit bat (Eidolon helvum) in Ghana, West Africa. To investigate this further, longitudinal blood sampling was undertaken quarterly between 2012 and 2014 on wild E. helvum at two sites in Ghana. Serum samples were collected and tested for LBV-neutralizing antibodies using a modified flourescent antibody virus neutralisation (FAVN) assay (n = 294) and brains from moribund or dead bats were tested for antigen and viral RNA (n = 55). Overall, 44.7% of the 304 bats sampled had LBV-neutralising antibodies. None of the brain samples from bats contained lyssavirus antigen or RNA. Together with the results of an earlier serological study, our findings demonstrate that LBV is endemic and circulates within E. helvum in Ghana even though the detection of viral infection in dead bats was unsuccessful. Confirmation that LBV infection is endemic in E. helvum in Ghana is an important finding and indicates that the potential public health threats from LBV warrant further investigation.

Seasonal Fluctuations of Astrovirus, But Not Coronavirus Shedding in Bats Inhabiting Human-Modified Tropical Forests

Emerging infectious diseases (EIDs) are considered a major threat to global health. Most EIDs appear to result from increased contact between wildlife and humans, especially when humans encroach into formerly pristine habitats. Habitat deterioration may also negatively affect the physiology and health of wildlife species, which may eventually lead to a higher susceptibility to infectious agents and/or increased shedding of the pathogens causing EIDs. Bats are known to host viruses closely related to important EIDs. Here, we tested in a paleotropical forest with ongoing logging and fragmentation, whether habitat disturbance influences the occurrence of astro- and coronaviruses in eight bat species. In contrast to our hypothesis, anthropogenic habitat disturbance was not associated with corona- and astrovirus detection rates in fecal samples. However, we found that bats infected with either astro- or coronaviruses were likely to be coinfected with the respective other virus. Additionally, we identified two more risk factors influencing astrovirus shedding. First, the detection rate of astroviruses was higher at the beginning of the rainy compared to the dry season. Second, there was a trend that individuals with a poor body condition had a higher probability of shedding astroviruses in their feces. The identification of risk factors for increased viral shedding that may potentially result in increased interspecies transmission is important to prevent viral spillovers from bats to other animals, including humans.

The Recently Discovered Bokeloh Bat Lyssavirus: Insights Into Its Genetic Heterogeneity and Spatial Distribution in Europe and the Population Genetics of Its Primary Host

In 2010, a novel lyssavirus named Bokeloh bat lyssavirus (BBLV) was isolated from a Natterer's bat (Myotis nattereri) in Germany. Two further viruses were isolated in the same country and in France in recent years, all from the same bat species and all found in moribund or dead bats. Here we report the description and the full-length genome sequence of five additional BBLV isolates from Germany (n=4) and France (n=1). Interestingly, all of them were isolated from the Natterer's bat, except one from Germany, which was found in a common Pipistrelle bat (Pipistrellus pipistrellus), a widespread and abundant bat species in Europe. The latter represents the first case of transmission of BBLV to another bat species. Phylogenetic analysis clearly demonstrated the presence of two different lineages among this lyssavirus species: lineages A and B. The spatial distribution of these two lineages remains puzzling, as both of them comprised isolates from France and Germany; although clustering of isolates was observed on a regional scale, especially in Germany. Phylogenetic analysis based on the mitochondrial cytochrome b (CYTB) gene from positive Natterer's bat did not suggest a circulation of the respective BBLV sublineages in specific Natterer's bat subspecies, as all of them were shown to belong to the M. nattereri sensu stricto clade/subspecies and were closely related (German and French positive bats). At the bat host level, we demonstrated that the distribution of BBLV at the late stage of the disease seems large and massive, as viral RNA was detected in many different organs.

Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum

Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) allowed derivation of rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data.

The close genetic relationship of lineage D Betacoronavirus from Nigerian and Kenyan straw-colored fruit bats (Eidolon helvum) is consistent with the existence of a single epidemiological unit across sub-Saharan Africa

Straw-colored fruit bats (Eidolon helvum), which have been identified as natural hosts for several zoonotic pathogens, such as lyssaviruses, henipaviruses, and ebolavirus, are associated with human settlements in Nigeria where they are commonly consumed as a delicacy. However, information on the viruses harbored by these bats is scarce. In this study, coronavirus sequences were detected using a nested RT-PCR targeting 440 bp of the RNA-dependent RNA polymerase (RdRp) in six of 79 fecal samples collected from an urban colony of E. helvum in Ibadan, Nigeria. Phylogenetic analysis revealed that all six sequences were monophyletic and clustered in lineage D of Betacoronavirus. The extension of two fragments allowed us to classify our sequences within the RdRp Group Unit defined for Kenyan Betacoronavirus from the same host species. These findings are consistent with the previous suggestion on the existence of a single epidemiological unit of E. helvum across sub-Saharan Africa. This theory, which is supported by the genetic structure of continental E. helvum, could facilitate viral mixing between different colonies across the continent.

The Role of Bats as Reservoir Hosts of Emerging Neuroviruses

Recent studies have clearly shown that bats are the reservoir hosts of a wide diversity of novel viruses with representatives from most of the known animal virus families. In many respects bats make ideal reservoir hosts for viruses: they are the only mammals that fly, thus assisting in virus dispersal; they roost in large numbers, thus aiding transmission cycles; some bats hibernate over winter, thus providing a mechanism for viruses to persist between seasons; and genetic factors may play a role in the ability of bats to host viruses without resulting in clinical disease. Within the broad diversity of viruses found in bats are some important neurological pathogens, including rabies and other lyssaviruses, and Hendra and Nipah viruses, two recently described viruses that have been placed in a new genus, Henipaviruses in the family Paramyxoviridae. In addition, bats can also act as alternative hosts for the flaviviruses Japanese encephalitis and St Louis encephalitis viruses, two important mosquito-borne encephalitogenic viruses, and bats can assist in the dispersal and over-wintering of these viruses. Bats are also the reservoir hosts of progenitors of SARS and MERS coronaviruses, although other animals act as spillover hosts. This chapter presents the physiological and ecological factors affecting the ability of bats to act as reservoirs of neurotropic viruses, and describes the major transmission cycles leading to human infection.

Biannual birth pulses allow filoviruses to persist in bat populations

Filoviruses Ebolavirus (EBOV) and Marburgvirus (MARV) cause haemorrhagic fevers with high mortality rates, posing significant threats to public health. To understand transmission into human populations, filovirus dynamics within reservoir host populations must be understood. Studies have directly linked filoviruses to bats, but the mechanisms allowing viral persistence within bat populations are poorly understood. Theory suggests seasonal birthing may decrease the probability of pathogen persistence within populations, but data suggest MARV may persist within colonies of seasonally breeding Egyptian fruit bats, Rousettus aegyptiacus. I synthesize available filovirus and bat data in a stochastic compartmental model to explore fundamental questions relating to filovirus ecology: can filoviruses persist within isolated bat colonies; do critical community sizes exist; and how do host-pathogen relationships affect spillover transmission potential? Synchronous annual breeding and shorter incubation periods did not allow filovirus persistence, whereas bi-annual breeding and longer incubation periods, such as reported for Egyptian fruit bats and EBOV in experimental studies, allowed persistence in colony sizes often found in nature. Serological data support the findings, with bats from species with two annual birth pulses more likely to be seropositive (odds ratio (OR) 4.4, 95% confidence interval (CI) 2.5-8.7) than those with one, suggesting that biannual birthing is necessary for filovirus persistence.

Zoonotic Viruses and Conservation of Bats

Many of the recently emerging highly virulent zoonotic diseases have a likely bat origin, for example Hendra, Nipah, Ebola and diseases caused by coronaviruses. Presumably because of their long history of coevolution, most of these viruses remain subclinical in bats, but have the potential to cause severe illnesses in domestic and wildlife animals and also humans. Spillovers from bats to humans either happen directly (via contact with infected bats) or indirectly (via intermediate hosts such as domestic or wildlife animals, by consuming food items contaminated by saliva, faeces or urine of bats, or via other environmental sources). Increasing numbers of breakouts of zoonotic viral diseases among humans and livestock have mainly been accounted to human encroachment into natural habitat, as well as agricultural intensification, deforestation and bushmeat consumption. Persecution of bats, including the destruction of their roosts and culling of whole colonies, has led not only to declines of protected bat species, but also to an increase in virus prevalence in some of these populations. Educational efforts are needed in order to prevent future spillovers of bat-borne viruses to humans and livestock, and to further protect bats from unnecessary and counterproductive culling.

Lagos bat virus transmission in an Eidolon helvum bat colony, Ghana

A brain sample of a straw-coloured fruit bat (Eidolon helvum) from Ghana without evident signs of disease tested positive by generic Lyssavirus RT-PCR and direct antigen staining. Sequence analysis confirmed the presence of a Lagos bat virus belonging to phylogenetic lineage A. Virus neutralization tests using the isolate with sera from the same group of bats yielded neutralizing antibodies in 74% of 567 animals. No cross-neutralization was observed against a different Lagos bat virus (lineage B).

Why we can prevent, control and possibly treat – but will not eradicate – rabies

ABSTRACT 

Rabies is an acute, progressive viral encephalitis. Despite historical recognition, millions still remain exposed annually. Most fatalities are of children, although this zoonosis is a vaccine-preventable disease. All developed countries interrupted canine transmission and increasingly, Asian and African communities recognize what Latin Americans demonstrated – dog rabies can be eliminated – by mass application of veterinary vaccines. Realistically, rabies is not a candidate for eradication. Management is lacking for major reservoirs, such as bats. Increasing pre-exposure immunization of individuals at risk, simplification of postexposure schedules, enhancing vaccine delivery by alternative routes, development of less expensive biologics and antiviral drugs, may lessen its impact if applied strategically in a One Health context.

Antibodies against Duvenhage virus in insectivorous bats in Swaziland

Several rabies-related lyssaviruses have been associated with bat species in southern Africa, the rarest of these being Duvenhage virus (DUVV), for which only five isolations have been made over five decades. Three of these were from human fatalities, and it is not known which bat species acts as reservoir. In studying a population of Nycteris thebaica in the kingdom of Swaziland, a landlocked country bordering Mozambique and South Africa, we found evidence of the circulation of a lyssavirus. Virus-neutralization assays indicated DUVV-neutralizing antibodies in 30% of the sera collected from this population of N. thebaica, providing the first indication of a Duvenhage virus circulating in this particular species and the first evidence of a bat lyssavirus circulating in Swaziland bats.

Bat distribution size or shape as determinant of viral richness in african bats

The rising incidence of emerging infectious diseases (EID) is mostly linked to biodiversity loss, changes in habitat use and increasing habitat fragmentation. Bats are linked to a growing number of EID but few studies have explored the factors of viral richness in bats. These may have implications for role of bats as potential reservoirs. We investigated the determinants of viral richness in 15 species of African bats (8 Pteropodidae and 7 microchiroptera) in Central and West Africa for which we provide new information on virus infection and bat phylogeny. We performed the first comparative analysis testing the correlation of the fragmented geographical distribution (defined as the perimeter to area ratio) with viral richness in bats. Because of their potential effect, sampling effort, host body weight, ecological and behavioural traits such as roosting behaviour, migration and geographical range, were included into the analysis as variables. The results showed that the geographical distribution size, shape and host body weight have significant effects on viral richness in bats. Viral richness was higher in large-bodied bats which had larger and more fragmented distribution areas. Accumulation of viruses may be related to the historical expansion and contraction of bat species distribution range, with potentially strong effects of distribution edges on virus transmission. Two potential explanations may explain these results. A positive distribution edge effect on the abundance or distribution of some bat species could have facilitated host switches. Alternatively, parasitism could play a direct role in shaping the distribution range of hosts through host local extinction by virulent parasites. This study highlights the importance of considering the fragmentation of bat species geographical distribution in order to understand their role in the circulation of viruses in Africa.

Continent-wide panmixia of an African fruit bat facilitates transmission of potentially zoonotic viruses

The straw-coloured fruit bat, Eidolon helvum, is Africa’s most widely distributed and commonly hunted fruit bat, often living in close proximity to human populations. This species has been identified as a reservoir of potentially zoonotic viruses, but uncertainties remain regarding viral transmission dynamics and mechanisms of persistence. Here we combine genetic and serological analyses of populations across Africa, to determine the extent of epidemiological connectivity among E. helvum populations. Multiple markers reveal panmixia across the continental range, at a greater geographical scale than previously recorded for any other mammal, whereas populations on remote islands were genetically distinct. Multiple serological assays reveal antibodies to henipaviruses and Lagos bat virus in all locations, including small isolated island populations, indicating that factors other than population size and connectivity may be responsible for viral persistence. Our findings have potentially important public health implications, and highlight a need to avoid disturbances which may precipitate viral spillover.

Insights into persistence mechanisms of a zoonotic virus in bat colonies using a multispecies metapopulation model

Rabies is a worldwide zoonosis resulting from Lyssavirus infection. In Europe, Eptesicus serotinus is the most frequently reported bat species infected with Lyssavirus, and thus considered to be the reservoir of European bat Lyssavirus type 1 (EBLV-1). To date, the role of other bat species in EBLV-1 epidemiology and persistence remains unknown. Here, we built an EBLV-1−transmission model based on local observations of a three-cave and four-bat species (Myotis capaccinii, Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum) system in the Balearic Islands, for which a 1995–2011 serological dataset indicated the continuous presence of EBLV-1. Eptesicus serotinus was never observed in the system during the 16-year follow-up and therefore was not included in the model. We used the model to explore virus persistence mechanisms and to assess the importance of each bat species in the transmission dynamics. We found that EBLV-1 could not be sustained if transmission between M. schreibersii and other bat species was eliminated, suggesting that this species serves as a regional reservoir. Global sensitivity analysis using Sobol's method revealed that following the rate of autumn−winter infectious contacts, M. schreibersii's incubation- and immune-period durations, but not the infectious period length, were the most relevant factors driving virus persistence.

Viral antibody dynamics in a chiropteran host

Bats host many viruses that are significant for human and domestic animal health, but the dynamics of these infections in their natural reservoir hosts remain poorly elucidated. In these, and other, systems, there is evidence that seasonal life-cycle events drive infection dynamics, directly impacting the risk of exposure to spillover hosts. Understanding these dynamics improves our ability to predict zoonotic spillover from the reservoir hosts. To this end, we followed henipavirus antibody levels of >100 individual E. helvum in a closed, captive, breeding population over a 30-month period, using a powerful novel antibody quantitation method. We demonstrate the presence of maternal antibodies in this system and accurately determine their longevity. We also present evidence of population-level persistence of viral infection and demonstrate periods of increased horizontal virus transmission associated with the pregnancy/lactation period. The novel findings of infection persistence and the effect of pregnancy on viral transmission, as well as an accurate quantitation of chiropteran maternal antiviral antibody half-life, provide fundamental baseline data for the continued study of viral infections in these important reservoir hosts.

Antigenic and genetic characterization of a divergent African virus, Ikoma lyssavirus

In 2009, a novel lyssavirus (subsequently named Ikoma lyssavirus, IKOV) was detected in the brain of an African civet (Civettictis civetta) with clinical rabies in the Serengeti National Park of Tanzania. The degree of nucleotide divergence between the genome of IKOV and those of other lyssaviruses predicted antigenic distinction from, and lack of protection provided by, available rabies vaccines. In addition, the index case was considered likely to be an incidental spillover event, and therefore the true reservoir of IKOV remained to be identified. The advent of sensitive molecular techniques has led to a rapid increase in the discovery of novel viruses. Detecting viral sequence alone, however, only allows for prediction of phenotypic characteristics and not their measurement. In the present study we describe the in vitro and in vivo characterization of IKOV, demonstrating that it is (1) pathogenic by peripheral inoculation in an animal model, (2) antigenically distinct from current rabies vaccine strains and (3) poorly neutralized by sera from humans and animals immunized against rabies. In a laboratory mouse model, no protection was elicited by a licensed rabies vaccine. We also investigated the role of bats as reservoirs of IKOV. We found no evidence for infection among 483 individuals of at least 13 bat species sampled across sites in the Serengeti and Southern Kenya.

Diversity and epidemiology of Mokola virus

Mokola virus (MOKV) appears to be exclusive to Africa. Although the first isolates were from Nigeria and other Congo basin countries, all reports over the past 20 years have been from southern Africa. Previous phylogenetic studies analyzed few isolates or used partial gene sequence for analysis since limited sequence information is available for MOKV and the isolates were distributed among various laboratories. The complete nucleoprotein, phosphoprotein, matrix and glycoprotein genes of 18 MOKV isolates in various laboratories were sequenced either using partial or full genome sequencing using pyrosequencing and a phylogenetic analysis was undertaken. The results indicated that MOKV isolates from the Republic of South Africa, Zimbabwe, Central African Republic and Nigeria clustered according to geographic origin irrespective of the genes used for phylogenetic analysis, similar to that observed with Lagos bat virus. A Bayesian Markov-Chain-Monte-Carlo- (MCMC) analysis revealed the age of the most recent common ancestor (MRCA) of MOKV to be between 279 and 2034 years depending on the genes used. Generally, all MOKV isolates showed a similar pattern at the amino acid sites considered influential for viral properties.

Twenty years of active bat rabies surveillance in Germany: a detailed analysis and future perspectives

In Germany, active bat rabies surveillance was conducted between 1993 and 2012. A total of 4546 oropharyngeal swab samples from 18 bat species were screened for the presence of EBLV-1- , EBLV-2- and BBLV-specific RNA. Overall, 0·15% of oropharyngeal swab samples tested EBLV-1 positive, with the majority originating from Eptesicus serotinus. Interestingly, out of seven RT–PCR-positive oropharyngeal swabs subjected to virus isolation, viable virus was isolated from a single serotine bat (E. serotinus). Additionally, about 1226 blood samples were tested serologically, and varying virus neutralizing antibody titres were found in at least eight different bat species. The detection of viral RNA and seroconversion in repeatedly sampled serotine bats indicates long-term circulation of the virus in a particular bat colony. The limitations of random-based active bat rabies surveillance over passive bat rabies surveillance and its possible application of targeted approaches for future research activities on bat lyssavirus dynamics and maintenance are discussed.

Deciphering serology to understand the ecology of infectious diseases in wildlife

The ecology of infectious disease in wildlife has become a pivotal theme in animal and public health. Studies of infectious disease ecology rely on robust surveillance of pathogens in reservoir hosts, often based on serology, which is the detection of specific antibodies in the blood and is used to infer infection history. However, serological data can be inaccurate for inference to infection history for a variety of reasons. Two major aspects in any serological test can substantially impact results and interpretation of antibody prevalence data: cross-reactivity and cut-off thresholds used to discriminate positive and negative reactions. Given the ubiquitous use of serology as a tool for surveillance and epidemiological modeling of wildlife diseases, it is imperative to consider the strengths and limitations of serological test methodologies and interpretation of results, particularly when using data that may affect management and policy for the prevention and control of infectious diseases in wildlife. Greater consideration of population age structure and cohort representation, serological test suitability and standardized sample collection protocols can ensure that reliable data are obtained for downstream modeling applications to characterize, and evaluate interventions for, wildlife disease systems.

Use of cross-reactive serological assays for detecting novel pathogens in wildlife: assessing an appropriate cutoff for henipavirus assays in African bats

Reservoir hosts of novel pathogens are often identified or suspected as such on the basis of serological assay results, prior to the isolation of the pathogen itself. Serological assays might therefore be used outside of their original, validated scope in order to infer seroprevalences in reservoir host populations, until such time that specific diagnostic assays can be developed. This is particularly the case in wildlife disease research. The absence of positive and negative control samples and gold standard diagnostic assays presents challenges in determining an appropriate threshold, or 'cutoff', for the assay that enables differentiation between seronegative and seropositive individuals. Here, multiple methods were explored to determine an appropriate cutoff for a multiplexed microsphere assay that is used to detect henipavirus antibody binding in fruit bat plasma. These methods included calculating multiples of 'negative' control assay values, receiver operating characteristic curve analyses, and Bayesian mixture models to assess the distribution of assay outputs for classifying seropositive and seronegative individuals within different age classes. As for any diagnostic assay, the most appropriate cutoff determination method and value selected must be made according to the aims of the study. This study is presented as an example for others where reference samples, and assays that have been characterised previously, are absent.

Ecology of zoonotic infectious diseases in bats: current knowledge and future directions

Bats are hosts to a range of zoonotic and potentially zoonotic pathogens. Human activities that increase exposure to bats will likely increase the opportunity for infections to spill over in the future. Ecological drivers of pathogen spillover and emergence in novel hosts, including humans, involve a complex mixture of processes, and understanding these complexities may aid in predicting spillover. In particular, only once the pathogen and host ecologies are known can the impacts of anthropogenic changes be fully appreciated. Cross-disciplinary approaches are required to understand how host and pathogen ecology interact. Bats differ from other sylvatic disease reservoirs because of their unique and diverse lifestyles, including their ability to fly, often highly gregarious social structures, long lifespans and low fecundity rates. We highlight how these traits may affect infection dynamics and how both host and pathogen traits may interact to affect infection dynamics. We identify key questions relating to the ecology of infectious diseases in bats and propose that a combination of field and laboratory studies are needed to create data-driven mechanistic models to elucidate those aspects of bat ecology that are most critical to the dynamics of emerging bat viruses. If commonalities can be found, then predicting the dynamics of newly emerging diseases may be possible. This modelling approach will be particularly important in scenarios when population surveillance data are unavailable and when it is unclear which aspects of host ecology are driving infection dynamics.

A framework for the study of zoonotic disease emergence and its drivers: spillover of bat pathogens as a case study

Many serious emerging zoonotic infections have recently arisen from bats, including Ebola, Marburg, SARS-coronavirus, Hendra, Nipah, and a number of rabies and rabies-related viruses, consistent with the overall observation that wildlife are an important source of emerging zoonoses for the human population. Mechanisms underlying the recognized association between ecosystem health and human health remain poorly understood and responding appropriately to the ecological, social and economic conditions that facilitate disease emergence and transmission represents a substantial societal challenge. In the context of disease emergence from wildlife, wildlife and habitat should be conserved, which in turn will preserve vital ecosystem structure and function, which has broader implications for human wellbeing and environmental sustainability, while simultaneously minimizing the spillover of pathogens from wild animals into human beings. In this review, we propose a novel framework for the holistic and interdisciplinary investigation of zoonotic disease emergence and its drivers, using the spillover of bat pathogens as a case study. This study has been developed to gain a detailed interdisciplinary understanding, and it combines cutting-edge perspectives from both natural and social sciences, linked to policy impacts on public health, land use and conservation.

Bat Rabies

The lyssaviruses are a diverse group of viruses capable of causing rabies, which is an invariably fatal encephalitic disease in both humans and animals. Currently, the lyssavirus genus consists of 12 species with 11 of these distinct species having been isolated from bats. The basis for the apparent geographical segregation of bat lyssavirus infection between the Old and New World is poorly understood. In the New World species of insectivorous, frugivorous, and hematophagous bats, all represent important reservoirs of rabies virus. In contrast, rabies virus has never been detected in Old World bat populations, despite being endemic in terrestrial mammals. Instead, both insectivorous and frugivorous bat species across the Old World appear to act as reservoirs for the non-rabies lyssaviruses. In this chapter, we describe the association of the different lyssaviruses with different bat species across the world, classifying bat species by their feeding behavior.

Model-guided fieldwork: practical guidelines for multidisciplinary research on wildlife ecological and epidemiological dynamics

Infectious disease ecology has recently raised its public profile beyond the scientific community due to the major threats that wildlife infections pose to biological conservation, animal welfare, human health and food security. As we start unravelling the full extent of emerging infectious diseases, there is an urgent need to facilitate multidisciplinary research in this area. Even though research in ecology has always had a strong theoretical component, cultural and technical hurdles often hamper direct collaboration between theoreticians and empiricists. Building upon our collective experience of multidisciplinary research and teaching in this area, we propose practical guidelines to help with effective integration among mathematical modelling, fieldwork and laboratory work. Modelling tools can be used at all steps of a field-based research programme, from the formulation of working hypotheses to field study design and data analysis. We illustrate our model-guided fieldwork framework with two case studies we have been conducting on wildlife infectious diseases: plague transmission in prairie dogs and lyssavirus dynamics in American and African bats. These demonstrate that mechanistic models, if properly integrated in research programmes, can provide a framework for holistic approaches to complex biological systems.