A novel adenovirus isolated from the Egyptian fruit bat in South Africa is closely related to recent isolates from China

A systematic review on current approaches in bat virus discovered between 2018 and 2022

Zoonotic viruses are widely seen as the primary threat for future pandemics. Bats are the most diverse group of mammals, with more than 1400 species distributed across most habitats on Earth. So far, 31 known virus families were associated with bats, although the understanding of most viruses were insufficient. Continuous efforts to discover, understand and monitor these bats viruses, is thereby an area of public health interest. This systematic review was designed to catalogue publications reporting novel bat virus discoveries within PubMed, SCOPUS, and Web of Science databases, within a 5-year period from 2018 to 2022. Various experimental parameters, including sampling locations, methodology, bat species diversity, similarity to known viruses, species demarcation of new viruses, and genomic sequencing strategies, were extracted from 41 publications and analyzed. In total, 72 novel viruses from 19 virus families were identified between 2018 and 2022, particularly from Genomoviridae (DNA viruses) and Coronaviridae (RNA viruses). That said, only a limited number of bat families featured extensively despite noticeable shift towards next generation sequencing methods and metagenomics pipeline for virus identification across different sampling methods. This review aims to provide a comprehensive analysis of the global efforts made over the past five years to identify and characterize emerging viruses in bat species, and to provide a detailed overview of the current technologies and methodologies used in these studies.

Identification of a novel adenovirus in liver tissue sample of the Great Himalayan leaf-nosed bat (Hipposideros armiger)

Bats are important reservoirs for many zoonotic viruses. To explore and monitor potential novel viruses carried by bats, 21 liver samples of bats (Hipposideros armiger) were collected from Yunnan Province in southern China. Only one (4.8%) of all models was detected with adenovirus. The whole genome strain obtained by the viral metagenomics method combined with PCR was temporarily named YN01. The complete genome of YN01 was 37,676 bp, with a G + C content of 55.20% and 28 open reading frames. Phylogenetic analysis indicated that the strain YN01 can be classified as genus Mastadenovirus and was the most similar to the adenovirus isolated from Rhinolophus sinicus in China in 2016. The analysis is needed to verify the possibility of cross-species transmission. This virological investigation has increased our understanding of the ecology of bat-borne viruses in this area and provided a reference for possible future infectious diseases.

Detection and Phylogenetic Characterization of a Novel Adenovirus Found in Lesser Mouse-Eared Bat (Myotis blythii) in South Kazakhstan

Bats are an important natural reservoir of various pathogenic microorganisms, and regular monitoring is necessary to track the situation of zoonotic infections. When examining samples from bats in South Kazakhstan, nucleotide sequences of putative novel bat adenovirus (AdV) species were found. Estimates of amino acid identities of the hexon protein have shown that potentially novel Bat mastadenovirus BatAdV-KZ01 shared higher similarity with monkey Rhesus adenovirus 59 (74.29%) than with Bat AdVs E and H (74.00%). Phylogenetically, BatAdV-KZ01 formed a separate clade, distant from Bat AdVs and other mammalian AdVs. Since adenoviruses are essential pathogens for many mammals, including humans and bats, this finding is of interest from both scientific and epidemiological points of view.

Prevalence of bat viruses associated with land-use change in the Atlantic Forest, Brazil

Introduction

Bats are critical to maintaining healthy ecosystems and many species are threatened primarily due to global habitat loss. Bats are also important hosts of a range of viruses, several of which have had significant impacts on global public health. The emergence of these viruses has been associated with land-use change and decreased host species richness. Yet, few studies have assessed how bat communities and the viruses they host alter with land-use change, particularly in highly biodiverse sites.

Methods

In this study, we investigate the effects of deforestation on bat host species richness and diversity, and viral prevalence and richness across five forested sites and three nearby deforested sites in the interior Atlantic Forest of southern Brazil. Nested-PCR and qPCR were used to amplify and detect viral genetic sequence from six viral families (corona-, adeno-, herpes-, hanta-, paramyxo-, and astro-viridae) in 944 blood, saliva and rectal samples collected from 335 bats.

Results

We found that deforested sites had a less diverse bat community than forested sites, but higher viral prevalence and richness after controlling for confounding factors. Viral detection was more likely in juvenile males located in deforested sites. Interestingly, we also found a significant effect of host bat species on viral prevalence indicating that viral taxa were detected more frequently in some species than others. In particular, viruses from the Coronaviridae family were detected more frequently in generalist species compared to specialist species.

Discussion

Our findings suggest that deforestation may drive changes in the ecosystem which reduce bat host diversity while increasing the abundance of generalist species which host a wider range of viruses.

Myotis fimbriatus Virome, a Window to Virus Diversity and Evolution in the Genus Myotis

Significant efforts have been made to characterize viral diversity in bats from China. Many of these studies were prospective and focused mainly on Rhinolophus bats that could be related to zoonotic events. However, other species of bats that are part of ecosystems identified as virus diversity hotspots have not been studied in-depth. We analyzed the virome of a group of Myotis fimbriatus bats collected from the Yunnan Province during 2020. The virome of M. fimbriatus revealed the presence of families of pathogenic viruses such as Coronavirus, Astrovirus, Mastadenovirus, and Picornavirus, among others. The viral sequences identified in M. fimbriatus were characterized by significant divergence from other known viral sequences of bat origin. Complex phylogenetic landscapes implying a tendency of co-specificity and relationships with viruses from other mammals characterize these groups. The most prevalent and abundant virus in M. fimbriatus individuals was an alphacoronavirus. The genome of this virus shows evidence of recombination and is likely the product of ancestral host-switch. The close phylogenetic and ecological relationship of some species of the Myotis genus in China may have played an important role in the emergence of this alphacoronavirus.

Interaction between Old World fruit bats and humans: From large scale ecosystem services to zoonotic diseases

The Old World tropical and subtropical frugivorous bat genus Rousettus (Pteropodidae) contains species with broad distributions, as well as those occurring in restricted geographical areas, particularly islands. Herein we review the role of Rousettus as a keystone species from a global "One Health" approach and related to ecosystem functioning, zoonotic disease and public health. Rousettus are efficient at dispersing seeds and pollinating flowers; their role in forest regeneration is related to their ability to fly considerable distances during nightly foraging bouts and their relatively small body size, which allows them to access fruits in forested areas with closed vegetation. Rousettus are also reservoirs for various groups of pathogens (viruses, bacteria, fungi, protozoa), which, by definition, are infectious agents causing disease. The study of day roosts of different species of Rousettus and the successful establishment of captive breeding colonies have provided important details related to the infection dynamics of their associated pathogens. Large-scale conversion of forested areas into agricultural landscapes has increased contact between humans and Rousettus, therefore augmenting the chances of infectious agent spillover. Many crucial scientific details are still lacking related to members of this genus, which have direct bearing on the prevention of emerging disease outbreaks, as well as the conservation of these bats. The public should be better informed on the capacity of fruit bats as keystone species for large scale forest regeneration and in spreading pathogens. Precise details on the transmission of zoonotic diseases of public health importance associated with Rousettus should be given high priority.

Genomic characteristics and pathogenicity of a new bat adenoviruses strains that was isolated in at sites along the southeastern coasts of the P. R. of China from 2015 to 2019

Bats are important reservoirs for many kinds of emerging zoonotic viruses. In order to explore potential pathogens carried by bats and trace the source of adenovirus outbreaks on the southeastern coast of China, we took pharyngeal and anal swabs from a total of 552 bats (Rhinolophus pusillus) collected from various areas of Chinese southeastern coast. Adenoviruses were identified in 36 out of the 552 samples (6.5%) . Complete genome sequences of two adenovirus isolations from Vero E6 cells were obtained, which were further validated as identical strains via next-generation sequencing and were named Bat-Advcxc6. The cell culture inoculated with the two samples exhibited remarkable cytopathic changes. The full genome has 37,315 bp and owns 29 open reading frames. Phylogenetic analyses confirmed that Bat-Advcxc6 represented a novel bat adenovirus species in the genus Mastadenovirus. Transmission electron microgram showed clear virus particles. Bat-Advcxc6 shared similar characteristics of G + C contents with Bat mastadenovirus WIV11 (Bat mastadenovirus C) found in China in 2016, but differed from this serotype due to a <75% similarity with DNA polymerase amino acid sequences in WIV11. As it is a newly found adenovirus strain according to the international classification criteria, further analyses of virus dynamics, epithelial invasion, and immunization assays are required to explore its potential threats of cross-species transmission.

Seasonal shedding patterns of diverse henipavirus-related paramyxoviruses in Egyptian rousette bats

Bat-borne viruses in the Henipavirus genus have been associated with zoonotic diseases of high morbidity and mortality in Asia and Australia. In Africa, the Egyptian rousette bat species (Rousettus aegyptiacus) is an important viral host in which Henipavirus-related viral sequences have previously been identified. We expanded these findings by assessing the viral dynamics in a southern African bat population. A longitudinal study of henipavirus diversity and excretion dynamics identified 18 putative viral species circulating in a local population, three with differing seasonal dynamics, and the winter and spring periods posing a higher risk of virus spillover and transmission. The annual peaks in virus excretion are most likely driven by subadults and may be linked to the waning of maternal immunity and recolonization of the roost in early spring. These results provide insightful information into the bat-host relationship that can be extrapolated to other populations across Africa and be communicated to at-risk communities as a part of evidence-based public health education and prevention measures against pathogen spillover threats.

Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats

Hepatitis is a major global health concern. However, the etiology of 10-20% hepatitis cases remains unclear. Some hepatitis-associated viruses, like the hepatitis E virus, are zoonotic pathogens. Rats, shrews, and bats are reservoirs for many zoonotic pathogens. Therefore, understanding the virome in the liver of these animals is important for the investigation of the etiologies of hepatitis and monitoring the emerging zoonotic viruses. In this study, viral metagenomics and PCR methods were used to investigate viral communities in rats, mice, house shrews, and bats livers. Viral metagenomic analysis showed a diverse set of sequences in liver samples, comprising: sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses. Using PCR methods, we first detected hepatovirus sequences in Hipposideros larvatus (3.85%). We also reported the first detection of Zika virus-related sequences in rats and house shrews. Sequences related to influenza A virus and herpesviruses were detected in liver. Higher detection rates of pegivirus sequences were found in liver tissue and serum samples from rats (7.85% and 15.79%, respectively) than from house shrews. Torque teno virus sequences had higher detection rates in the serum samples of rats and house shrews (52.72% and 5.26%, respectively) than in the liver. Near-full length genomes of pegivirus and torque teno virus were amplified. This study is the first to compare the viral communities in the liver of bats, rats, mice, and house shrews. Its findings expand our understanding of the virome in the liver of these animals and provide an insight into hepatitis-related viruses.

Bat virome research: the past, the present and the future

Bats have been increasingly recognised as an exceptional reservoir for emerging zoonotic viruses for the past few decades. Recent studies indicate that the unique bat immune system may be partially responsible for their ability to co-exist with viruses with minimal or no clinical diseases. In this review, we discuss the history and importance of bat virome studies and contrast the vast difference between such studies before and after the introduction of next generation sequencing (NGS) in this area of research. We also discuss the role of discovery serology and high-throughput single cell RNA-seq in future bat virome research.

Adenoviruses across the animal kingdom: a walk in the zoo

Adenoviruses (AdVs) infect representatives of numerous species from almost every major vertebrate class, albeit their incidence shows great variability. AdVs infecting birds, reptiles, and bats are the most common and diverse, whereas only one AdV has been so far isolated both from fish and amphibians. The family Adenoviridae is divided into five genera, each corresponding to an independent evolutionary lineage that supposedly coevolved with its respective vertebrate hosts. Members of genera Mastadenovirus and Aviadenovirus seem to infect exclusively mammals and birds, respectively. The genus Ichtadenovirus includes the single known AdV from fish. The majority of AdVs in the genus Atadenovirus originated from squamate reptiles (lizards and snakes), but also certain mammalian and avian AdVs are classified within this genus. The genus Siadenovirus contains the only AdV isolated from frog, along with numerous avian AdVs. In turtles, members of a sixth AdV lineage have been discovered, pending official recognition as an independent genus. The most likely scenario for AdV evolution includes long-term cospeciation with the hosts, as well as occasional switches between closely or, rarely, more distantly related hosts.

New Adenovirus Groups in Western Palaearctic Bats

In the context of long-term screening for viruses on Western Palaearctic bats, we tested for the presence of adenovirus 1392 oropharyngeal swabs and 325 stool samples taken from 27 bat species. Adenoviruses were detected in 12 species of the Vespertilionidae and the Rhinolophidae families. Fifty positive respiratory and 26 positive stool samples were studied. Phylogenetic analyses of partial hexon protein and partial DNA-dependent DNA polymerase genes indicate that all these bat adenoviruses belong to the genus Mastadenovirus but without constituting a monophyletic cluster. According to genetic identities, the new groups are distinct to the previously described Bat mastadenovirus A and B species and contribute with potentially new members. Our data support that diversity of bat mastadenovirus is host-dependent and increase the knowledge of potentially pathogenic virus from bats. Due to the active role of bats as viral reservoirs, the characterization of these viruses is relevant for Public Health.