Detection and phylogenetic characterization of astroviruses in insectivorous bats from Central-Southern Italy

Molecular Surveillance for Potential Zoonotic Pathogens in Troglophilus Bats: Detection and Molecular Characterization of Bat Coronaviruses in Southern Italy

The recent COVID-19 pandemic has renewed interest in bats, as they are natural hosts for numerous viruses, some of which have crossed species boundaries. Despite continued efforts in the past, the ecology of bat-related viruses in a significant part of national territories, such as Italy, remains largely unexplored. Herein, we describe the detection and molecular characterization of bat coronaviruses, identified during a viral survey on selected potential zoonotic pathogens (lyssavirus and coronaviruses) carried out in Sicily, southern Italy. A total number of 330 samples were collected from 149 bats in a period (November 2020-April 2023) overlapping the COVID-19 pandemic. All samples tested negative for lyssavirus and SARS-CoV-2, while 12 bats (8.05%) tested positive to a pan-coronavirus assay. Both alphacoronaviruses and betacoronaviruses were identified in samples from three species (Miniopterus schreibersii, Rhinolophus ferrumequinum, and Rhinolophus hipposideros). Strain sequences were related to coronaviruses detected in the last decade in northern Italy as well as in other countries bordering the Mediterranean basin, suggesting a widespread diffusion of these strains. This study supports the need for further monitoring efforts and early detection of circulating coronavirus genotypes, particularly for those which have been repeatedly emerging as zoonotic spillovers.

Monitoring of Astroviruses, Brno-Hantaviruses, Coronaviruses, Influenza Viruses, Bornaviruses, Morbilliviruses, Lyssaviruses and Pestiviruses in Austrian Bats

Here, we report the results of a monitoring study of bat viruses in Austria to strengthen the knowledge of circulating viruses in Austrian bat populations. In this study, we analyzed 618 oropharyngeal and rectal swab samples from 309 bats and 155 pooled tissue samples from dead bats. Samples were collected from 18 different bat species from multiple locations in Austria, from November 2015 to April 2018, and examined for astroviruses, bornaviruses, coronaviruses, hantaviruses, morbilliviruses, orthomyxoviruses (influenza A/C/D viruses), pestiviruses and rhabdoviruses (lyssaviruses) using molecular techniques and sequencing. Using RT-qPCR, 36 samples revealed positive or suspicious results for astroviruses, Brno-hantaviruses, and coronaviruses in nine different bat species. Further sequencing revealed correspondent sequences in five samples. In contrast, none of the tested samples was positive for influenza viruses A/C/D, bornaviruses, morbilliviruses, lyssaviruses, or pestiviruses.

Viral Co-Infection in Bats: A Systematic Review

Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.

Identification of new astroviruses in synanthropic squamates

Astroviruses have been identified in a wide variety of animal species and are associated with gastro-intestinal disease in humans. Pathologies due to extra-intestinal localization are known in different hosts. We report the detection of astroviruses in synanthropic squamate reptile species (Podercis siculus and Tarentola mauritanica). Fecal samples were collected from 100 squamates from urban and peri-urban areas of three regions in South Italy and tested for the presence of astroviruses using a broadly reactive (pan-astrovirus) RT-PCR protocol targeting the RNA-dependent RNA polymerase. Astrovirus RNA was detected in 11% of the samples and for six strains a 3 kb-long fragment at the 3' end of the genome was sequenced, obtaining information on the complete capsid-encoding ORF2 sequence. Viral RNA was also detected in the brain of one of the positive animals. The sequences generated from the astrovirus strains shared low nucleotide identities in the ORF2 (< 43.7%) with other known reptilian astrovirus sequences, hinting to the massive genetic diversity of members of this viral family. Based on the partial RdRp gene of the sequenced strains, however, we observed species-specific patterns, regardless of the geographic origin of the animals, and we also identified a possible inter-species transmission event between geckoes and lizards.

A First Assessment of SARS-CoV-2 Circulation in Bats of Central-Southern Italy

One serious concern associated with the SARS-CoV-2 pandemic is that the virus might spill back from humans to wildlife, which would render some animal species reservoirs of the human virus. We assessed the potential circulation of SARS-CoV-2 caused by reverse infection from humans to bats, by performing bat surveillance from different sites in Central-Southern Italy. We restricted our survey to sampling techniques that are minimally invasive and can therefore be broadly applied by non-medical operators such as bat workers. We collected 240 droppings or saliva from 129 bats and tested them using specific and general primers for SARS-CoV-2 and coronaviruses, respectively. All samples (127 nasal swabs and 113 faecal droppings) were negative for SARS-CoV-2, and these results were confirmed by testing the samples with the Droplet Digital PCR. Additionally, pancoronavirus end-point RT-PCR was performed, and no sample showed specific bands. This outcome is a first step towards a better understanding of the reverse transmission of this virus to bats. Although the occurrence of a reverse zoonotic pattern can only be fully established by serological testing, the latter might represent an in-depth follow-up to a broad-scale preliminary assessment performed with our approach. We encourage the systematic surveillance of bats to help prevent reverse zoonotic episodes that would jeopardize human health, as well as biodiversity conservation and management.

Update on Potentially Zoonotic Viruses of European Bats

Bats have been increasingly gaining attention as potential reservoir hosts of some of the most virulent viruses known. Numerous review articles summarize bats as potential reservoir hosts of human-pathogenic zoonotic viruses. For European bats, just one review article is available that we published in 2014. The present review provides an update on the earlier article and summarizes the most important viruses found in European bats and their possible implications for Public Health. We identify the research gaps and recommend monitoring of these viruses.

First Detection of Bat Astroviruses (BtAstVs) among Bats in Poland: The Genetic BtAstVs Diversity Reveals Multiple Co-Infection of Bats with Different Strains

Background: Astroviruses (AstVs) are common pathogens of a wide range of animal hosts, including mammals and avians, causing gastrointestinal diseases, mainly gastroenteritis and diarrhea. They prompt a significant health problem in newborns and young children and economic losses in the poultry sector and mink farms. Recent studies revealed a growing number of bat species carrying astroviruses with a noticeable prevalence and diversity. Here, we demonstrate the first detection of bat astroviruses (BtAstVs) circulating in the population of insectivorous bats in the territory of Poland. Results: Genetically diverse BtAstVs (n = 18) were found with a varying degree of bat species specificity in five out of 15 bat species in Poland previously recognized as BtAstV hosts. Astroviral RNA was found in 12 out of 98 (12.2%, 95% CI 7.1–20.2) bat intestines, six bat kidneys (6.1%, 95% CI 2.8–12.7) and two bat livers (2.0%, 95% CI 0.4–7.1). Deep sequencing of the astroviral RNA-dependent RNA polymerase (RdRp) region revealed co-infections in five single bat individuals with highly distinct astrovirus strains. Conclusions: The detection of highly distinct bat astroviruses in Polish bats favors virus recombination and the generation of novel divergent AstVs and creates a potential risk of virus transmission to domestic animals and humans in the country. These findings provide a new insight into molecular epidemiology, prevalence of astroviruses in European bat populations and the risk of interspecies transmission to other animals including humans.

Interface between Bats and Pigs in Heavy Pig Production

Bats are often claimed to be a major source for future viral epidemics, as they are associated with several viruses with zoonotic potential. Here we describe the presence and biodiversity of bats associated with intensive pig farms devoted to the production of heavy pigs in northern Italy. Since chiropters or signs of their presence were not found within animal shelters in our study area, we suggest that fecal viruses with high environmental resistance have the highest likelihood for spillover through indirect transmission. In turn, we investigated the circulation of mammalian orthoreoviruses (MRVs), coronaviruses (CoVs) and astroviruses (AstVs) in pigs and bats sharing the same environment. Results of our preliminary study did not show any bat virus in pigs suggesting that spillover from these animals is rare. However, several AstVs, CoVs and MRVs circulated undetected in pigs. Among those, one MRV was a reassortant strain carrying viral genes likely acquired from bats. On the other hand, we found a swine AstV and a MRV strain carrying swine genes in bat guano, indicating that viral exchange at the bat–pig interface might occur more frequently from pigs to bats rather than the other way around. Considering the indoor farming system as the most common system in the European Union (EU), preventive measures should focus on biosecurity rather than displacement of bats, which are protected throughout the EU and provide critical ecosystem services for rural settings.

Analysis of astrovirus transmission pathways in a free-ranging fission-fusion colony of Natterer’s bats (Myotis nattereri)

Abstract

Bats are a diverse and widespread order of mammals. They fulfill critical ecosystem roles but may also act as reservoirs and spreaders for zoonotic agents. Consequently, many recent studies have focused on the potential of bats to spread diseases to other animals and to humans. However, virus transmission networks within bat colonies remain largely unexplored. We studied the detection rate and transmission pathway of astroviruses in a free-ranging Natterer’s bat colony (Myotis nattereri) that exhibits a high fission-fusion dynamic. Based on automatic roost monitoring data of radio-frequency identification tagged bats, we assessed the impact of the strength of an individual’s roosting associations with all other colony members (weighted degree), and the number of roost sites (bat boxes) an individual used—both being proxies for individual exposure risk—on the detected presence of astrovirus-related nucleic acid in individual swab samples. Moreover, we tested to which degree astrovirus sequence types were shared between individuals that frequently roosted together, as proxy for direct transmission risk, and between bats sharing the same roost sites in close temporal succession, as proxy for indirect transmission risk. Neither roosting associations nor the number of different roost sites had an effect on detected virus presence in individual bats. Transmission network data suggest that astroviruses are transmitted both via direct and indirect contact, implying that roost sites pose a risk of astrovirus infection for several days after the bats leave them. Our study offers novel insights in the presence and transmission of viruses within social networks of bat colonies.

Significance statement

Bats provide many ecosystem services but have moved into the focus of virological research as potential carriers of zoonotic disease agents. However, the sparse information available about virus transmission within bat colonies is solely based on simulated transmission data. In this field study, we examined the daily roosting behavior in a wild bat colony in relation to the presence of viruses in individual colony members. Our findings suggest that astroviruses are transmitted by direct contact and via contaminated roost sites. Bats typically defecate in their roost sites, and astroviruses can remain infectious in feces for several days. The here observed virus diversity and roosting behavior suggest that bats can contract astroviruses even if they use contaminated roost sites days after infected individuals have left. This study provides first-time insights in the transmission of astroviruses within bat colonies in the wild.

Diversity of Astroviruses Circulating in Humans, Bats, and Wild Birds in Egypt

Astroviruses belong to Astroviridae family which includes two main genera: Mamastroviruses that infect mammals, and Avastroviruses that infect avian hosts. Bats and wild birds are considered among the natural reservoirs for astroviruses. Infections in humans are associated with severe gastroenteritis, especially among children. We conducted surveillance for astroviruses in bats, wild birds, and humans in Egypt. Our results indicated relatively high prevalence of astroviruses in those hosts. Phylogenetic analysis revealed diversity of these viruses within hosts. Detected human viruses showed similarity with classic and variant human astroviruses, as well as similarity with animal-origin viruses. Viruses in bats were dispersed, with similarities to other bat viruses as well as other mammalian, including human, viruses. Wild bird viruses varied and were related to other avastroviruses, as well as human astroviruses. Our results indicate that astroviruses are common in bats, wild birds, and humans in Egypt, with a wide gene pool. Potential cross-species transmission may be occurring but should be verified by further surveillance and molecular studies.

Hypsugopoxvirus: A Novel Poxvirus Isolated from Hypsugo savii in Italy

Interest in bat-related viruses has increased considerably during the last decade, leading to the discovery of a rising number of new viruses in several bat species. Poxviridae are a large, diverse family of DNA viruses that can infect a wide range of vertebrates and invertebrates. To date, only a few documented detections of poxviruses have been described in bat populations on three different continents (America, Africa, and Australia). These viruses are phylogenetically dissimilar and have diverse clinical impacts on their hosts. Herein, we report the isolation, nearly complete genome sequencing, and annotation of a novel poxvirus detected from an insectivorous bat (Hypsugo savii) in Northern Italy. The virus is tentatively named Hypsugopoxvirus (HYPV) after the bat species from which it was isolated. The nearly complete genome size is 166,600 nt and it encodes 161 genes. Genome analyses suggest that HYPV belongs to the Chordopoxvirinae subfamily, with the highest nucleotide identity (85%) to Eptesipoxvirus (EPTV) detected from a microbat Eptesicus fuscus in WA, USA, in 2011. To date, HYPV represents the first poxvirus detected in bats in Europe; thus, its viral ecology and disease associations should be investigated further.

Molecular identification of Betacoronavirus in bats from Sardinia (Italy): first detection and phylogeny

Bats may be natural reservoirs for a large variety of emerging viruses, including mammalian coronaviruses (CoV). The recent emergence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) in humans, with evidence that these viruses may have their ancestry in bats, highlights the importance of virus surveillance in bat populations. Here, we report the identification and molecular characterization of a bat β-Coronavirus, detected during a viral survey carried out on different bat species in the island of Sardinia (Italy). Cutaneous, oral swabs, and faecal samples were collected from 46 bats, belonging to 15 different species, and tested for viral presence. Coronavirus RNA was detected in faecal samples from three different species: the greater horseshoe bat (Rhinolophus ferrumequinum), the brown long-eared bat (Plecotus auritus), and the European free-tailed bat (Tadarida teniotis). Phylogenetic analyses based on RNA-dependent RNA polymerase (RdRp) sequences assigned the detected CoV to clade 2b within betacoronaviruses, clustering with SARS-like bat CoVs previously reported. These findings point to the need for continued surveillance of bat CoV circulating in Sardinian bats, and extend the current knowledge on CoV ecology with novel sequences detected in bat species not previously described as β-Coronavirus hosts.

Detection and phylogenetic characterization of astroviruses in insectivorous bats from Central-Southern Italy

In recent years, bats have been found to harbour many viruses, raising several questions about their role as reservoirs and potential disseminators of zoonotic viruses. We investigated the presence of six virus families in bats in three regions of Central‐Southern Italy. Astroviruses were identified in seven of 13 bat species. Sequence analysis revealed marked genetic heterogeneity among the astroviruses identified, with nucleotide identity ranging between 60.26% and 87.62%. Astrovirus diversity was not associated with the bat species, the geographic areas or the bat colony, suggesting the circulation of several astrovirus strains in Italian ecosystems. Genetic diversification and interspecies transmission appear common in bat astroviruses and could provide, potentially, the bases for transmission to humans and other mammals. Yet overemphasizing this risk might have detrimental consequences for bat conservation and preservation of the important ecosystem services bats provide.