Kanyawara Virus: A Novel Rhabdovirus Infecting Newly Discovered Nycteribiid Bat Flies Infesting Previously Unknown Pteropodid Bats in Uganda

High frequencies of nonviral colds and respiratory bacteria colonization among children in rural Western Uganda

Introduction

Respiratory illness is the most common childhood disease globally, especially in developing countries. Previous studies have detected viruses in approximately 70-80% of respiratory illnesses.

Methods

In a prospective cohort study of 234 young children (ages 3-11 years) and 30 adults (ages 22-51 years) in rural Western Uganda sampled monthly from May 2019 to August 2021, only 24.2% of nasopharyngeal swabs collected during symptomatic disease had viruses detectable by multiplex PCR diagnostics and metagenomic sequencing. In the remaining 75.8% of swabs from symptomatic participants, we measured detection rates of respiratory bacteria Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae by quantitative PCR.

Results

100% of children tested positive for at least one bacterial species. Detection rates were 87.2%, 96.8%, and 77.6% in children and 10.0%, 36.7%, and 13.3% for adults for H. influenzae, M. catarrhalis, and S. pneumoniae, respectively. In children, 20.8% and 70.4% were coinfected with two and three pathogens, respectively, and in adults 6.7% were coinfected with three pathogens but none were coinfected with two. Detection of any of the three pathogens was not associated with season or respiratory symptoms severity, although parsing detection status by symptoms was challenged by children experiencing symptoms in 80.3% of monthly samplings, whereas adults only reported symptoms 26.6% of the time. Pathobiont colonization in children in Western Uganda was significantly more frequent than in children living in high-income countries, including in a study of age-matched US children that utilized identical diagnostic methods. Detection rates were, however, comparable to rates in children living in other Sub-Saharan African countries.

Discussion

Overall, our results demonstrate that nonviral colds contribute significantly to respiratory disease burden among children in rural Uganda and that high rates of respiratory pathobiont colonization may play a role. These conclusions have implications for respiratory health interventions in the area, such as increasing childhood immunization rates and decreasing air pollutant exposure.

Virome profiling of fig wasps (Ceratosolen spp.) reveals virus diversity spanning four realms

We investigated the virome of agaonid fig wasps (Ceratosolen spp.) inside syconia ("fruits") of various Ficus trees fed upon by frugivores such as pteropodid bats in Sub-Saharan Africa. This virome includes representatives of viral families spanning four realms and includes near-complete genome sequences of three novel viruses and fragments of five additional potentially novel viruses evolutionarily associated with insects, fungi, plants, and vertebrates. Our study provides evidence that frugivorous animals are exposed to a plethora of viruses by coincidental consumption of fig wasps, which are obligate pollinators of figs worldwide.

Tick-borne viruses and their risk to public health in the Caribbean: Spotlight on bats as reservoirs in Cuba

In recent decades, tick-borne diseases (TBDs) have surged and expanded globally due to factors like changes in human activities, land use patterns, and climate change, and it have been associated with the emergence of zoonotic diseases. Cuba faces the impact of ticks on human health and the economy. Although Cuba has studied TBDs extensively for the past 50 years, focus on tick-borne viral pathogens affecting humans remains scant. Despite TBDs not currently being a major health concern in Cuba, factors like inadequate clinician awareness, climate conditions, global tick emergence, and evidence of zoonotic pathogens in ticks underscore the importance of enhanced TBD surveillance in the country. Here we revised the available information on ticks as vectors of pathogenic viruses to humans, spotlighting bats as potential reservoirs of tick-borne viruses (TBVs). Ticks on bats have gained interest as potential reservoirs of pathogenic viruses to humans in Cuba and worldwide. Understanding their role in maintaining viruses and their potential transmission to humans is crucial for the implementation of surveillance and control programs to reduce the risk of tick-borne viral diseases and public health management.

Virome characterization and identification of a putative parvovirus and poxvirus in bat ectoparasites of Yunnan Province, China

Ectoparasites found on bats are known to contain important microbes. However, the viruses hosted by these obligate parasites are understudied. This has led to the near oversight of the potential role of these ectoparasites in virus maintenance and transmission from bats to other interacting species and the environment. Here, we sampled bat ectoparasites parasitizing a diverse selection of bat species in the families Rhinolophidae, Vespertilionidae, Megadermatidae, Hipposideridae and Pteropodidae in Yunnan Province, China. We show that the ectoparasite prevalence was generally higher in male compared to female bats. Most ectoparasites were found to fall within the Nycteribiidae, Spinturnicidae and Streblidae bat ectoparasite families. We subsequently applied a non-biased sequencing of libraries prepared from the pooled ectoparasites, followed by an in-silico virus-centric analysis of the resultant reads. We show that ectoparasites hosted by the sampled families of bats are found to carry, in addition to a diverse set of phages, vertebrate and insect viruses in the families Aliusviridae, Ascoviridae, Chuviridae, Circoviridae, Flaviviridae, Hepadnaviridae, Hepeviridae, Herpesviridae, Iridoviridae, Marseilleviridae, Nairoviridae, Orthomyxoviridae, Parvoviridae, Poxviridae, Reoviridae, Retroviridae, and Rhabdoviridae. We further report a partial Parvovirus VP1/VP2 gene and partial Poxvirus ubiquitin-like gene predicted by two independent next generation sequencing data analysis pipelines. This study describes the natural virome of bat ectoparasites, providing a platform for understanding the role these ectoparasites play in the maintenance and spread of viruses to other animals.

Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria

We investigated ectoparasite diversity, interspecific infestation rates and host preference in roosting fruit bats, Eidolon helvum, from Bowen University, Southwest Nigeria. Fur of captured E. helvum were sampled monthly for ectoparasites from January 2021 to June 2022. We examined a total of 231 E. helvum and observed a significant female to male adult sex ratio (0.22:1); with 53.9% ectoparasitic infestation rate. We identified and enumerated the ectoparasite; and subjected its Cytochrome c oxidase subunit I (COI) gene to phylogenetic analysis with other nycteribiids. COI gene sequences obtained formed a distinct clade with other C. greeffi sequences. We recovered a total of 319 (149 female and 170 male) ectoparasites and observed a balanced C. greeffi female to male adult sex ratio of 0.88:1. Ectoparasitic sex distribution had no association with host sex and season. Prevalence was significantly higher during the wet season, but not between sexes of E. helvum. The intensity of infestation, 3.7 ± 0.4 individuals per fruit bat, was significantly higher during the wet season with a bimodal seasonal distribution. The strongly male-biased host adult sex ratio had no significant influence on C. greeffi metapopulation adult sex ratio.

Emerging Rhabdoviruses and Human Infection

Rhabdoviridae is a large viral family, with members infecting a diverse range of hosts including, vertebrate species, arthropods, and plants. The predominant human pathogen within the family is Rabies lyssavirus, the main cause of human rabies. While rabies is itself a neglected disease, there are other, less well studied, rhabdoviruses known to cause human infection. The increasing application of next-generation sequencing technology to clinical samples has led to the detection of several novel or rarely detected rhabdoviruses associated with febrile illness. Many of these viruses have been detected in low- and middle-income countries where the extent of human infection and the burden of disease remain largely unquantified. This review describes the rhabdoviruses other than Rabies lyssavirus that have been associated with human infection. The discovery of the Bas Congo virus and Ekpoma virus is discussed, as is the re-emergence of species such as Le Dantec virus, which has recently been detected in Africa 40 years after its initial isolation. Chandipura virus and the lyssaviruses that are known to cause human rabies are also described. Given their association with human disease, the viruses described in this review should be prioritised for further study.

Viral Hyperparasitism in Bat Ectoparasites: Implications for Pathogen Maintenance and Transmission

Humans continue to encroach on the habitats of wild animals, potentially bringing different species into contact that would not typically encounter each other under natural circumstances, and forcing them into stressful, suboptimal conditions. Stressors from unsustainable human land use changes are suspected to dramatically exacerbate the probability of zoonotic spillover of pathogens from their natural reservoir hosts to humans, both by increasing viral load (and shedding) and the interface between wildlife with livestock, pets and humans. Given their known role as reservoir hosts, bats continue to be investigated for their possible role as the origins of many viral outbreaks. However, the participation of bat-associated ectoparasites in the spread of potential pathogens requires further work to establish. Here, we conducted a comprehensive review of viruses, viral genes and other viral sequences obtained from bat ectoparasites from studies over the last four decades. This review summarizes research findings of the seven virus families in which these studies have been performed, including Paramyxoviridae, Reoviridae, Flaviviridae, Peribunyaviridae, Nairoviridae, Rhabdoviridae and Filoviridae. We highlight that bat ectoparasites, including dipterans and ticks, are often found to have medically important viruses and may have a role in the maintenance of these pathogens within bat populations.

Viruses associated with ill health in wild chimpanzees

Viral infection is a major cause of ill health in wild chimpanzees (Pan troglodytes), but most evidence to date has come from conspicuous disease outbreaks with high morbidity and mortality. To examine the relationship between viral infection and ill health during periods not associated with disease outbreaks, we conducted a longitudinal study of wild eastern chimpanzees (P. t. schweinfurthii) in the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We collected standardized, observational health data for 4 years and then used metagenomics to characterize gastrointestinal viromes (i.e., all viruses recovered from fecal samples) in individual chimpanzees before and during episodes of clinical disease. We restricted our analyses to viruses thought to infect mammals or primarily associated with mammals, discarding viruses associated with nonmammalian hosts. We found 18 viruses (nine of which were previously identified in this population) from at least five viral families. Viral richness (number of viruses per sample) did not vary by health status. By contrast, total viral load (normalized proportion of sequences mapping to viruses) was significantly higher in ill individuals compared with healthy individuals. Furthermore, when ill, Kanyawara chimpanzees exhibited higher viral loads than Ngogo chimpanzees, and males, but not females, exhibited higher infection rates with certain viruses and higher total viral loads as they aged. Post-hoc analyses, including the use of a machine-learning classification method, indicated that one virus, salivirus (Picornaviridae), was the main contributor to health-related and community-level variation in viral loads. Another virus, chimpanzee stool-associated virus (chisavirus; unclassified Picornavirales), was associated with ill health at Ngogo but not at Kanyawara. Chisavirus, chimpanzee adenovirus (Adenoviridae), and bufavirus (Parvoviridae) were also associated with increased age in males. Associations with sex and age are consistent with the hypothesis that nonlethal viral infections cumulatively reflect or contribute to senescence in long-lived species such as chimpanzees.

Vector Competence of Eucampsipoda africana (Diptera: Nycteribiidae) for Marburg Virus Transmission in Rousettus aegyptiacus (Chiroptera: Pteropodidae)

This study aimed to determine the vector competence of bat-associated nycteribiid flies (Eucamsipoda africana) for Marburg virus (MARV) in the Egyptian Rousette Bat (ERB), Rousettus aegyptiacus. In flies fed on subcutaneously infected ERBs and tested from 3 to 43 days post infection (dpi), MARV was detected only in those that took blood during the peak of viremia, 5-7 dpi. Seroconversion did not occur in control bats in contact with MARV-infected bats infested with bat flies up to 43 days post exposure. In flies inoculated intra-coelomically with MARV and tested on days 0-29 post inoculation, only those assayed on day 0 and day 7 after inoculation were positive by q-RT-PCR, but the virus concentration was consistent with that of the inoculum. Bats remained MARV-seronegative up to 38 days after infestation and exposure to inoculated flies. The first filial generation pupae and flies collected at different times during the experiments were all negative by q-RT-PCR. Of 1693 nycteribiid flies collected from a wild ERB colony in Mahune Cave, South Africa where the enzootic transmission of MARV occurs, only one (0.06%) tested positive for the presence of MARV RNA. Our findings seem to demonstrate that bat flies do not play a significant role in the transmission and enzootic maintenance of MARV. However, ERBs eat nycteribiid flies; thus, the mechanical transmission of the virus through the exposure of damaged mucous membranes and/or skin to flies engorged with contaminated blood cannot be ruled out.

Virome of bat-infesting arthropods: highly divergent viruses in different vectors

Bats are reservoirs of important zoonotic viruses like Nipah and SARS viruses. However, whether the blood-sucking arthropods on the body surface of bats also carry these viruses, and the relationship between viruses carried by the blood-sucking arthropods and viruses carried by bats, have not been reported. This study collected 686 blood-sucking arthropods on the body surface of bats from Yunnan Province, China between 2012 and 2015, and they included wingless bat flies, bat flies, ticks, mites, and fleas. The viruses carried by these arthropods were analyzed using meta-transcriptomic approach, and 144 highly diverse positive-sense single-stranded RNA, negative-sense single-stranded RNA, and double-stranded RNA viruses were found, of which 138 were potentially new viruses. These viruses were classified into 14 different virus families or orders, including Bunyavirales, Mononegavirales, Reoviridae, and Picornavirales. Further analyses found that Bunyavirales were the most abundant virus group (84% of total virus RNA) in ticks, whereas narnaviruses were the most abundant (52-92%) in the bat flies and wingless bat flies libraries, followed by solemoviruses (1-29%) and reoviruses (0-43%). These viruses were highly structured based on the arthropod types. It is worth noting that no bat-borne zoonotic viruses were found in the virome of bat-infesting arthropod, seemly not supporting that bat surface arthropods are vectors of zoonotic viruses carried by bats. IMPORTANCE Bats are reservoir of many important viral pathogens. To evaluate whether bat-parasitic blood-sucking arthropods participate in the circulation of these important viruses, it is necessary to conduct unbiased virome studies on these arthropods. We evaluated five types of blood-sucking parasitic arthropods on the surface of bats in Yunnan, China and identified a variety of viruses, some of which had high prevalence and abundance level, although there is limited overlap in virome between distant arthropods. While most of the virome discovered here are potentially arthropod-specific viruses, we identified three possible arboviruses, including one orthobunyavirus and two vesiculoviruses (family Rhabdoviridae), suggesting bat-parasitic arthropods carry viruses with risk of spillage, which warrants further study.

Associations between Afrotropical bats, eukaryotic parasites, and microbial symbionts

Skin is the largest mammalian organ and the first defensive barrier against the external environment. The skin and fur of mammals can host a wide variety of ectoparasites, many of which are phylogenetically diverse, specialized, and specifically adapted to their hosts. Among hematophagous dipteran parasites, volatile organic compounds (VOCs) are known to serve as important attractants, leading parasites to compatible sources of blood meals. VOCs have been hypothesized to be mediated by host‐associated bacteria, which may thereby indirectly influence parasitism. Host‐associated bacteria may also influence parasitism directly, as has been observed in interactions between animal gut microbiota and malarial parasites. Hypotheses relating bacterial symbionts and eukaryotic parasitism have rarely been tested among humans and domestic animals, and to our knowledge have not been tested in wild vertebrates. In this study, we used Afrotropical bats, hematophagous ectoparasitic bat flies, and haemosporidian (malarial) parasites vectored by bat flies as a model to test the hypothesis that the vertebrate host microbiome is linked to parasitism in a wild system. We identified significant correlations between bacterial community composition of the skin and dipteran ectoparasite prevalence across four major bat lineages, as well as striking differences in skin microbial network characteristics between ectoparasitized and nonectoparasitized bats. We also identified links between the oral microbiome and presence of malarial parasites among miniopterid bats. Our results support the hypothesis that microbial symbionts may serve as indirect mediators of parasitism among eukaryotic hosts and parasites.

see also the Perspective by Kelly A. Speer

Bat Flies of the Family Streblidae (Diptera: Hippoboscoidea) Host Relatives of Medically and Agriculturally Important "Bat-Associated" Viruses

Bat flies (Hippoboscoidea: Nycteribiidae and Streblidae) are obligate hematophagous ectoparasites of bats. We collected streblid bat flies from the New World (México) and the Old World (Uganda), and used metagenomics to identify their viruses. In México, we found méjal virus (Rhabdoviridae; Vesiculovirus), Amate virus (Reoviridae: Orbivirus), and two unclassified viruses of invertebrates. Méjal virus is related to emerging zoonotic encephalitis viruses and to the agriculturally important vesicular stomatitis viruses (VSV). Amate virus and its sister taxon from a bat are most closely related to mosquito- and tick-borne orbiviruses, suggesting a previously unrecognized orbivirus transmission cycle involving bats and bat flies. In Uganda, we found mamucuso virus (Peribunyaviridae: Orthobunyavirus) and two unclassified viruses (a rhabdovirus and an invertebrate virus). Mamucuso virus is related to encephalitic viruses of mammals and to viruses from nycteribiid bat flies and louse flies, suggesting a previously unrecognized orthobunyavirus transmission cycle involving hippoboscoid insects. Bat fly virus transmission may be neither strictly vector-borne nor strictly vertical, with opportunistic feeding by bat flies occasionally leading to zoonotic transmission. Many "bat-associated" viruses, which are ecologically and epidemiologically associated with bats but rarely or never found in bats themselves, may actually be viruses of bat flies or other bat ectoparasites.

Isolation of a Novel Bat Rhabdovirus with Evidence of Human Exposure in China

Bats are well-recognized reservoirs of zoonotic viruses. Several spillover events from bats to humans have been reported, causing severe epidemic or endemic diseases including severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), SARS-CoV, Middle East respiratory syndrome-CoV (MERS-CoV), henipaviruses, and filoviruses. In this study, a novel rhabdovirus species, provisionally named Rhinolophus rhabdovirus DPuer (DPRV), was identified from the horseshoe bat (Rhinolophus affinis) in Yunnan province, China, using next-generation sequencing. DPRV shedding in the spleen, liver, lung, and intestinal contents of wild bats with high viral loads was detected by real-time quantitative PCR, indicating that DPRV has tropism for multiple host tissues. Furthermore, DPRV can replicate in vitro in multiple mammalian cell lines, including BHK-21, A549, and MA104 cells, with the highest efficiency in hamster kidney cell line BHK-21, suggesting infectivity of DPRV in these cell line-derived hosts. Ultrastructure analysis revealed a characteristic bullet-shaped morphology and tightly clustered distribution of DPRV particles in the intracellular space. DPRV replicated efficiently in suckling mouse brains and caused death of suckling mice; death rates increased with passaging of DPRV in suckling mice. Moreover, 421 serum samples were collected from individuals who lived near the bat collection site and had fever symptoms within 1 year. DPRV-specific antibodies were detected in 20 (4.75%) human serum samples by indirect immunofluorescence assay. Furthermore, 10 (2.38%) serum samples were DPRV positive according to plaque reduction neutralization assay, which revealed potential transmission of DPRV from bats to humans and highlighted the potential public health risk. Potential vector association with DPRV was not found with negative viral RNA in bloodsucking arthropods. IMPORTANCE We identified a novel rhabdovirus from the horseshoe bat (Rhinolophus thomasi) in China with probable infectivity in humans. DPRV was isolated in vitro from several mammalian cell lines, indicating wide host tropism, excluding bats, of DPRV. DPRV replicated in the brains of suckling mice, and the death rate of suckling mice increased with passaging of DPRV in vivo. Serological tests indicated the possible infectivity of DPRV in humans and the potential transmission to humans. The present findings provide preliminary evidence for the potential risk of DPRV to public health. Additional studies with active surveillance are needed to address interspecies transmission and determine the pathogenicity of DPRV in humans.

A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone

Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease of unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which we have named "epizootic neurologic and gastroenteric syndrome" (ENGS), is characterized by neurologic and gastrointestinal signs and results in death of the animals, even after medical treatment. Using a case-control study design, we show that ENGS is strongly associated with Sarcina infection. The microorganism is distinct from Sarcina ventriculi and other known members of its genus, based on bacterial morphology and growth characteristics. Whole-genome sequencing confirms this distinction and reveals the presence of genetic features that may account for the unusual virulence of the bacterium. Therefore, we propose that this organism be considered the representative of a new species, named "Candidatus Sarcina troglodytae". Our results suggest that a heretofore unrecognized complex of related sarcinae likely exists, some of which may be highly virulent. However, the potential role of "Ca. S. troglodytae" in the etiology of ENGS, alone or in combination with other factors, remains a topic for future research.

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.

Host conservation through their parasites: molecular surveillance of vector-borne microorganisms in bats using ectoparasitic bat flies

Most vertebrates host a wide variety of haematophagous parasites, which may play an important role in the transmission of vector-borne microorganisms to hosts. Surveillance is usually performed by collecting blood and/or tissue samples from vertebrate hosts. There are multiple methods to obtain samples, which can be stored for decades if properly kept. However, blood sampling is considered an invasive method and may possibly be harmful to the sampled individual. In this study, we investigated the use of ectoparasites as a tool to acquire molecular information about the presence and diversity of infectious microorganism in host populations. We tested the presence of three distinct vector-borne microorganisms in both bat blood and bat flies: Bartonella bacteria, malaria-like Polychromophilus sp. (Apicomplexa), and Trypanosoma sp. (Kinetoplastea). We detected the presence of these microorganisms both in bats and in their bat flies, with the exception of Trypanosoma sp. in South African bat flies. Additionally, we found Bartonella sp. in bat flies from one population in Spain, suggesting its presence in the host population even if not detected in bats. Bartonella and Polychromophilus infection showed the highest prevalence in both bat and bat fly populations. Single, co- and triple infections were also frequently present in both. We highlight the use of haematophagous ectoparasites to study the presence of infectious microorganism in host blood and its use as an alternative, less invasive sampling method.

Novel and Diverse Non-Rabies Rhabdoviruses Identified in Bats with Human Exposure, South Dakota, USA

Bats are a host and reservoir for a large number of viruses, many of which are zoonotic. In North America, the big brown bat (Eptesicus fuscus) is widely distributed and common. Big brown bats are a known reservoir for rabies virus, which, combined with their propensity to roost in human structures, necessitates testing for rabies virus following human exposure. The current pandemic caused by severe acute respiratory syndrome coronavirus 2, likely of bat origin, illustrates the need for continued surveillance of wildlife and bats for potentially emerging zoonotic viruses. Viral metagenomic sequencing was performed on 39 big brown bats and one hoary bat submitted for rabies testing due to human exposure in South Dakota. A new genotype of American bat vesiculovirus was identified in seven of 17 (41%) heart and lung homogenates at high levels in addition to two of 23 viscera pools. A second rhabdovirus, Sodak rhabdovirus 1 (SDRV1), was identified in four of 23 (17%) viscera pools. Phylogenetic analysis placed SDRV1 in the genus Alphanemrhavirus, which includes two recognized species that were identified in nematodes. Finally, a highly divergent rhabdovirus, Sodak rhabdovirus 2 (SDRV2), was identified in two of 23 (8.7%) big brown bats. Phylogenetic analysis placed SDRV2 as ancestral to the dimarhabdovirus supergroup and Lyssavirus. Intracranial inoculation of mouse pups with rhabdovirus-positive tissue homogenates failed to elicit clinical disease. Further research is needed to determine the zoonotic potential of these non-rabies rhabdoviruses.

Demography, life-history trade-offs, and the gastrointestinal virome of wild chimpanzees

In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates-even in our closest living relatives, chimpanzees and bonobos (Pan troglodytes and P. paniscus)-are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees (P. t. schweinfurthii), using metagenomics to characterize viromes (full viral communities) in the faeces of 42 sexually mature chimpanzees (22 males, 20 females) from the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We identified 12 viruses from at least four viral families possessing genomes of both single-stranded RNA and single-stranded DNA. Faecal viromes of both sexes varied with chimpanzee age, but viral richness increased with age only in males. This effect was largely due to three viruses, salivirus, porprismacovirus and chimpanzee stool-associated RNA virus (chisavirus), which occurred most frequently in samples from older males. This finding is consistent with the hypothesis that selection on males for early-life reproduction compromises investment in somatic maintenance, which has delayed consequences for health later in life, in this case reflected in viral infection and/or shedding. Faecal viromes are therefore useful for studying processes related to the divergent reproductive strategies of males and females, ageing, and sex differences in longevity. This article is part of the theme issue 'Evolution of the primate ageing process'.

Diversity, Transmission, and Cophylogeny of Ledanteviruses (Rhabdoviridae: Ledantevirus) and Nycteribiid Bat Flies Parasitizing Angolan Soft-Furred Fruit Bats in Bundibugyo District, Uganda

Obligate hematophagous ectoparasitic flies of the superfamily Hippoboscoidea are distributed worldwide, but their role as vectors and reservoirs of viruses remains understudied. We examined hippoboscoid bat flies (family Nycteribiidae) parasitizing Angolan soft-furred fruit bats (Lissonycteris angolensis ruwenzorii) from Bundibugyo District, Uganda. Using metagenomic methods, we detected 21 variants of the rhabdovirid genus Ledantevirus, which contains medically important "bat-associated" viruses. These 21 viruses, representing at least two divergent viral lineages, infected 26 bat flies from 8 bats in a single roost. Cophylogenetic analyses of viruses and bat flies resulted in strong evidence of virus-host codivergence, indicating vertical transmission of bat fly ledanteviruses. Examination of oral swabs from bats revealed ledantevirus RNA in the saliva of 1 out of 11 bats, with no evidence of insect genetic material in the mouth of this bat. These data demonstrate that bat flies can harbor diverse ledanteviruses even in a single roost and that the predominant mode of transmission is likely vertical (among bat flies), but that bats can become infected and shed viruses orally. In conclusion, bat flies may serve as ectoparasitic reservoirs of "bat-associated" viruses that only transiently or sporadically infect bats.

The Coevolution Effect as a Driver of Spillover

Global habitat fragmentation is associated with the emergence of infectious diseases of wildlife origins in human populations. Despite this well-accepted narrative, the underlying mechanisms driving this association remain unclear. We introduce a nuanced hypothesis, the 'coevolution effect'. The central concept is that the subdivision of host populations which occurs with habitat fragmentation causes localized coevolution of hosts, obligate parasites, and pathogens which act as 'coevolutionary engines' within each fragment, accelerating pathogen diversification, and increasing pathogen diversity across the landscape. When combined with a mechanism to exit a fragment (e.g., mosquitoes), pathogen variants will spill over into human communities. Through this combined ecoevolutionary approach we may be able to understand the fine-scale mechanisms that drive disease emergence in the Anthropocene.

Bat Flies and Their Microparasites: Current Knowledge and Distribution

Bats are the second most diverse mammalian group, playing keystone roles in ecosystems but also act as reservoir hosts for numerous pathogens. Due to their colonial habits which implies close contacts between individuals, bats are often parasitized by multiple species of micro- and macroparasites. The particular ecology, behavior, and environment of bat species may shape patterns of intra- and interspecific pathogen transmission, as well as the presence of specific vectorial organisms. This review synthetizes information on a multi-level parasitic system: bats, bat flies and their microparasites. Bat flies (Diptera: Nycteribiidae and Streblidae) are obligate, hematophagous ectoparasites of bats consisting of ~500 described species. Diverse parasitic organisms have been detected in bat flies including bacteria, blood parasites, fungi, and viruses, which suggest their vectorial potential. We discuss the ecological epidemiology of microparasites, their potential physiological effects on both bats and bat flies, and potential research perspectives in the domain of bat pathogens. For simplicity, we use the term microparasite throughout this review, yet it remains unclear whether some bacteria are parasites or symbionts of their bat fly hosts.

Genetic diversity of the Yokose virus, XYBX1332, isolated from bats (Myotis daubentonii) in China

BACKGROUND

Yokose virus was first isolated from bats (Miniopterus fuliginosus) collected in Yokosuka, Japan, in 1971, and is a new member of the family Flaviviridae, genus Flavivirus. In this study, we isolated a Yokose virus from a serum sample of Myotis daubentonii (order Chiroptera, family Vespertilionidae) collected in Yunnan province, China in 2013.

METHODS

The serum specimens of bat were used to inoculate in BHK-21 and Vero E6 cells for virus isolation. Then the viral complete genome sequence was obtained and was used for phylogenetic analysis performed by BEAST software package.

RESULTS

The virus was shown to have cytopathic effects in mammalian cells (BHK-21 and Vero E6). Genome sequencing indicated that it has a single open reading frame (ORF), with a genome of 10,785 nucleotides in total. Phylogenetic analysis of the viral genome suggests that XYBX1332 is a Yokose virus (YOKV) of the genus Flavivirus. Nucleotide and amino acid homology levels of the ORF of XYBX1332 and Oita-36, the original strain of YOKV, were 72 and 82%, respectively. The ORFs of XYBX1332 and Oita-36 encode 3422 and 3425 amino acids, respectively. In addition, the non-coding regions (5'- and 3'-untranslated regions [UTRs]) of these two strains differ in length and the homology of the 5'- and 3'-UTRs was 81.5 and 78.3%, respectively.

CONCLUSION

The isolation of YOKV (XYBX1332) from inland China thousands of kilometers from Yokosuka, Japan, suggests that the geographical distribution of YOKV is not limited to the islands of Japan and that it can also exist in the inland areas of Asia. However, there are large differences between the Chinese and Japanese YOKV strains in viral genome.

Diverse RNA viruses of arthropod origin in the blood of fruit bats suggest a link between bat and arthropod viromes

Bats host diverse viruses due to their unique ecology, behavior, and immunology. However, the role of other organisms with which bats interact in nature is understudied as a contributor to bat viral diversity. We discovered five viruses in the blood of fruit bats (Hypsignathus monstrosus) from the Republic of Congo. Of these five viruses, four have phylogenetic and genomic features suggesting an arthropod origin (a dicistrovirus, a nodavirus, and two tombus-like viruses), while the fifth (a hepadnavirus) is clearly of mammalian origin. We also report the parallel discovery of related tombus-like viruses in fig wasps and primitive crane flies from bat habitats, as well as high infection rates of bats with haemosporidian parasites (Hepatocystis sp.). These findings suggest transmission between arthropods and bats, perhaps through ingestion or hyperparasitism (viral infection of bat parasites). Some "bat-associated" viruses may be epidemiologically linked to bats through their ecological associations with invertebrates.

Isolation and Identification of a Highly Divergent Kaeng Khoi Virus from Bat Flies (Eucampsipoda sundaica) in China

BACKGROUND

Kaeng Khoi virus (KKV), which belongs to the genus Orthobunyavirus, family Perbunyaviridae, was originally isolated from the brain tissue of bats and may cause infection in humans. In this study, the KKV strain WDBC1403 was isolated from bat flies (Eucampsipoda sundaica), ectoparasites of the bat Rousettus leschenaultia, collected from Yunnan Province of China at the Sino-Burmese border.

METHODS AND RESULTS

The bat fly specimens were ground and inoculated in culture cells. The WDBC1403 strain was shown to induce cytopathic effects in Vero, baby hamster kidney (BHK-21), and Tb1Lu cells, but not in C6/36 cells; however, viral gene amplification was detected in the supernatants of C6/36 cells. Using electron microscopy, the virus was determined to be spherical, enveloped, and 80-90 nm in diameter; it was also shown to form plaques in BHK-21 cells and the titer reached 1 × 10^6.57 plaque-forming units/mL 24 h after infection. The phylogenetic analysis showed that WDBC1403 is a KKV strain, but is independent of the original KKV strain (PSC-19). Viral genome analysis revealed that the nucleotide and amino acid sequence identities of the S, M, and L segments of WDBC1403 with PSC-19 were 88.2% and 96.1%, 76.7% and 85.0%, and 78.3% and 88.9%, respectively. Two amino acids were removed at the end of the open reading frame of the M segment, and 47 nucleotides were removed in the 3'-untranslated region of the M segment of the WDBC1403 strain compared with the PSC-19 strain.

CONCLUSIONS

The WDBC1403 strain is a highly divergent KKV strain, suggesting that there are a variety of KKV strains that exhibit molecular differences. Moreover, because of the large variations in nucleotide and amino acid sequence in the M segment, which encodes an important membrane protein, further research on antigenicity and pathogenicity in humans and animals is needed.

Ectoparasites are unlikely to be a primary cause of population declines of bent-winged bats in south-eastern Australia

While bats carry a diverse range of ectoparasites, little research has been conducted on the effects these organisms may have on bat populations. The southern bent-winged bat (Miniopterus orianae bassanii) is a critically endangered subspecies endemic to south-eastern Australia, whose numbers have declined over the past 50 years for unknown reasons. As part of a larger study to investigate the potential role of disease in these declines, southern bent-winged bats from four locations were captured and examined for the presence of bat flies, mites, ticks and the nematode Riouxgolvania beveridgei (previously associated with skin nodules in bent-winged bats). Results were compared with those obtained from the more common eastern bent-winged bat (Miniopterus orianae oceanensis), sampling animals from three different locations. All four types of parasite were found on both subspecies. There was no correlation between the presence of ectoparasites, body weight or any signs of disease. However, prevalence of tick and R. beveridgei infections were greater in Victorian southern bent-winged bats than South Australian southern bent-winged bats and eastern bent-winged bats, possibly indicative of some type of chronic stress impacting the immune system of this subspecies.

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Ectoparasites not associated with ill health in bent-winged bats.

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Greater prevalence of ticks and R. beveridgei infections on Victorian southern bent-winged bats.

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Bat flies and mites more common in summer. Ticks more common in spring. R. beveridgei more common in winter and spring.

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Mites more common on juvenile bats.

Taxonomy of the order Mononegavirales: update 2018

In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

Rates of hematophagous ectoparasite consumption during grooming by an endemic Madagascar fruit bat

BACKGROUND

Few details are available on the consumption of ectoparasites, specifically bat flies (Diptera: Nycteribiidae and Streblidae), by their chiropteran hosts while grooming. Such details are important to document consumption rates of ectoparasites by their bat host provide details on the dynamics of host-parasite interactions. We present data on ectoparasite consumption rates for an endemic Malagasy fruit bat (Pteropodidae: Rousettus madagascariensis) occupying a cave day roost colony in northern Madagascar. Using quantified behavioral analyses, grooming and associated ingestion rates were measured from infrared videos taken in close proximity to day-roosting bats. The recorded individual bats could be visually identified to age (adult, juvenile) and sex (male, female), allowing analyses of the proportion of time these different classes allocated to consuming ectoparasites via auto-grooming (self) or allo-grooming (intraspecific) per 10 min video recording session. These figures could then be extrapolated to estimates of individual daily consumption rates.

RESULTS

Based on video recordings, adults spent significantly more time auto-grooming and allo-grooming than juveniles. The latter group was not observed consuming ectoparasites. Grooming rates and the average number of ectoparasites consumed per day did not differ between adult males and females. The mean extrapolated number consumed on a daily basis for individual adults was 37 ectoparasites. When these figures are overlaid on the estimated number of adult Rousettus occurring at the roost site during the dry season, the projected daily consumption rate was 57,905 ectoparasites.

CONCLUSIONS

The details presented here represent the first quantified data on bat consumption rates of their ectoparasites, specifically dipterans. These results provide new insights in host-parasite predation dynamics. More research is needed to explore the mechanism zoonotic diseases isolated from bat flies might be transmitted to their bat hosts, specifically those pathogens that can be communicated via an oral route.

Isolation of a novel Rhabdovirus from an insectivorous bat (Pipistrellus kuhlii) in Italy

Background

Rhabdoviridae is one of the most ecologically diverse families of RNA viruses which can infect a wide range of vertebrates and invertebrates. Bats, among mammals, are pointed to harbor a significantly higher proportion of unknown or emerging viruses with zoonotic potential. Herein, we report the isolation of a novel rhabdovirus, detected in the framework of a virological survey on bats implemented in North Italy.

Methods

Virus isolation and identification were performed on samples of 635 bats by using cell cultures, negative staining electron microscopy and PCRs for different viruses. NGS was commonly performed on cell culture supernatants showing cytopathic effect or in case of samples resulted positive by at least one of the PCRs included in the diagnostic protocol.

Results

A rhabdovirus was isolated from different organs of a Pipistrellus kuhlii. Virus identification was obtained by electron microscopy and NGS sequencing. The complete genome size was 11,774 nt comprised 5 genes, encoding the canonical rhabdovirus structural proteins, and an additional transcriptional unit (U1) encoding a hypothetical small protein (157aa) (3’-N-P-M-G-U1-L-5′). The genome organization and phylogenetic analysis suggest that the new virus, named Vaprio virus (VAPV), belongs to the recently established genus Ledantevirus (subgroup B) and it is highly divergent to its closest known relative, Le Dantec virus (LDV) (human, 1965 Senegal). A specific RT-PCR amplifying a 350 bp fragment of the ORF 6 gene, encoding for L protein, was developed and used to test retrospectively a subset of 76 bats coming from the same area and period, revealing two more VAPV positive bats.

Conclusions

VAPV is a novel isolate of chiropteran rhabdovirus. Genome organization and phylogenetic analyses demonstrated that VAPV should be considered a novel species within the genus Ledantevirus for which viral ecology and disease associations should be investigated.