Next Article in Journal
Transcriptomic Analysis Provides New Insights into Oocyte Growth and Maturation in Greater Amberjack (Seriola dumerili)
Previous Article in Journal
A Review of the Monitoring Techniques Used to Detect Oestrus in Sows
Previous Article in Special Issue
Ovarian Sex Cord Stromal Tumor in a Free-Ranging Brown Bear (Ursus arctos)
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Animals
Volume 15
Issue 3
10.3390/ani15030332
animals-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations

by
Thays Figueiroa
1,
Marina Galvão Bueno
2,*,
Patricia Emilia Bento Moura
2,
Marcione Brito de Oliveira
3,
José Luís Passos Cordeiro
4,5,
Nádia Santos-Cavalcante
6,7,
Giovanny A. Camacho Antevere Mazzarotto
8,
Gabriel Luz Wallau
9,10,
Leonardo Corrêa da Silva Junior
1,
Paola Cristina Resende
1,
Marilda M. Mendonça Siqueira
1 and
Maria Ogrzewalska
1,*
1
Fundação Oswaldo Cruz, IOC, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro 21040-900, RJ, Brazil
2
Fundação Oswaldo Cruz, IOC, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro 21040-900, RJ, Brazil
3
Museu Nacional, Departamento de Vertebrados, Setor de Mastozoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, RJ, Brazil
4
Fundação Oswaldo Cruz, Unidade do Ceará, Área de Saúde e Ambiente, Eusébio, Ceará 61773-270, CE, Brazil
5
Plataforma Internacional para Ciência, Tecnologia e Inovação em Saúde (PICTIS), Via do Conhecimento, Edifício Central, 3830-352 Ílhavo, Portugal
6
Museu de História Natural do Ceará Prof. Dias da Rocha, Universidade Estadual do Ceará, Pacoti, Ceará 62770-000, CE, Brazil
7
Fundação Oswaldo Cruz, Instituto Lêonidas and Maria Deane (ILDM), Unidade da Amazônia, Manaus 69057-070, AM, Brazil
8
Fundação Oswaldo Cruz, Unidade do Ceará, Laboratório Analítico de Competências Moleculares e Epidemiológicas, Plataforma de Camelídeos e Produção de Nanocorpos, Eusébio, Ceará 61773-270, CE, Brazil
9
Fundação Oswaldo Cruz, Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães (IAM), Cidade Universitária, Recife 50740-465, PE, Brazil
10
Department of Arbovirology and Entomology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, 20359 Hamburg, Germany
*
Authors to whom correspondence should be addressed.
Animals 2025, 15(3), 332; https://doi.org/10.3390/ani15030332
Submission received: 10 April 2024 / Revised: 19 June 2024 / Accepted: 16 July 2024 / Published: 24 January 2025
(This article belongs to the Special Issue Disease and Health in Free-Ranging and Captive Wildlife)
Browse Figures
Review Reports Versions Notes

Abstract

:

Simple Summary

Our world is facing an urgent challenge with the rise of zoonotic viral diseases like COVID-19, emphasizing the critical need to understand viruses in wildlife. Bats, comprising about 20% of mammalian species globally, are known reservoirs for many pathogens, including coronaviruses. This study focused on investigating the presence and variety of coronaviruses in bat populations from northeastern Brazil, particularly in Ceará, where bat pathogen research is scarce. Over a year, we collected oral and rectal swabs from 298 bats across three municipalities. Our molecular analyses unveiled alphacoronaviruses in several bat species, and we identified a new type of Betacoronavirus in Artibeus planirostris, broadening our understanding of the coronavirus diversity in Brazilian bats. Furthermore, our findings suggest that closely related coronavirus strains can infect various bat species in distant Brazilian regions and habitats. While we did not find SARS-CoV-2 or influenza A viruses in the sampled bats, our study emphasizes the need for ongoing surveillance to detect and track zoonotic viruses circulating in wildlife populations, which is crucial for preventing future pandemics.

Abstract

The emergence of zoonotic viral diseases, notably exemplified by the recent coronavirus disease pandemic in 2019 (COVID-19), underscores the critical need to understand the dynamics of viruses circulating in wildlife populations. This study aimed to investigate the diversity of coronaviruses in bat populations from northeastern Brazil, particularly in the state of Ceará, where little research on bat pathogens has been conducted previously. Bat sampling was performed between March 2021 and March 2022 across three municipalities, resulting in the collection of oral and rectal swabs from 298 captured individuals. Molecular analyses revealed alphacoronaviruses in multiple bat species. Additionally, a novel Betacoronavirus was identified in Artibeus planirostris, which did not fall within an established subgenus. Phylogenetic placement of these new coronavirus sequences suggests that closely related coronavirus lineages can infect a wide range of bat species sampled in distantly related Brazilian states and biomes. No SARS-CoV-2 and influenza A viruses were found in the sampled bats. These findings expand our understanding of coronavirus diversity in Brazilian bats. The detection of coronaviruses in various bat species underscores the importance of bats as reservoirs for these viruses. The absence of SARS-CoV-2 in the sampled bats indicates a lack of spillback events from human or environmental sources. However, the potential for future transmission events underscores the importance of ongoing surveillance and transmission mitigation protocols in wildlife management practices.

Graphical Abstract

1. Introduction

Bats, as other vertebrate species (non-human primates, rodents, ungulates, and birds), are highly diverse and motile taxa of great relevance in the One Health context of multi-host pathogens. They represent approximately 20% of the global mammal population [1], comprising around 1474 known species [2]. Approximately 450 of these species are found in the neotropical region but they have a broad geographic distribution, with specimens found on all continents except Antarctica [3,4]. Additionally, bats exhibit a high diversity of diets [5] and generally display gregarious behavior, often forming large colonies either to promote thermoregulation or for protection against predators [6]. The flight adaptation in chiropterans has likely selected a distinct and innate immune response in these animals, associated with genes in the oxidative phosphorylation pathway responsible for supplying energy during sustained flight [7]. Furthermore, they are generally capable of expressing Toll-like receptors associated with the action of pro-inflammatory and antiviral cytokines, inhibiting viral replication or even inducing apoptosis of infected cells [8]. At the same time, the risk of a generalized inflammatory response due to the constitutive expression of interferon-alpha is neutralized through attenuation of NLRP3 inflammasome activation in primary immune cells. Thus, bats are well adapted to viral infections and are considered competent hosts or even reservoirs for different viral agents with the potential to threaten human health, as seen with Hendra, Nipah, Marburg, Rabies, and various coronaviruses, including those responsible for MERS, SARS, and probably SARS-CoV-2 [9,10,11,12].
Coronaviruses are single-stranded positive-sense RNA viruses with genomes of 16 to 31 kb [13]. Members of the family Coronaviridae (realm, Riboviria; kingdom, Orthornavirae; phylum, Pisoniviricetes; order, Nidovirales; suborder, Cornidovirineae) can infect a wide range of animals and are generally associated with respiratory and/or digestive illness [13,14]. Research into coronaviruses and the potential spillover from bat species has become more important since the 2002 epidemic of SARS-CoV, which was presumably transmitted from masked palm civets (Paguma larvata) to human populations, although its origin might be traced back mainly to horseshoe bats (Rhinolophus species) from Asia [12,15,16,17,18,19]. Subsequent studies unveiled a diverse range of novel bat coronaviruses from Alpha and Betacoronavirus genera circulating in bats worldwide [20], but their global diversity and distribution is non-random and driven by variation in the biogeography of bats, and their richness is estimated to be much higher than previously appreciated [21].
In South America, particularly in Brazil, there is a noticeable scarcity of studies on pathogens associated with wild animals, including bats and coronaviruses [22]. Notably, none of these studies have been conducted in the state of Ceará, located in the northeastern region of Brazil. The study area, Serra de Baturité, constitutes one of the most important enclaves of moist forest in Ceará [23]. The mountain forests within these areas are recognized as ecological disjunctions of the Atlantic Forest, making them remnants of high biodiversity [24]. Additionally, the regions are considered ecotourism sites with the potential for human interaction [25].
Considering this, we tested bats sampled in the state of Ceará for coronaviruses encompassing SARS-CoV-2 and other related coronavirus species, as well as for the influenza A virus. This initiative commenced in March 2021, over a year after the first autochthonous case of COVID-19 was detected in Brazil [26]. The aim was to shed light on the presence and potential transmission of these viruses among animal populations, contributing to a more comprehensive understanding of the dynamics and risks associated with respiratory pathogens in both wildlife and human contexts.

2. Materials and Methods

2.1. Study Area and Capture Sites

Bat captures were conducted between March 2021 and March 2022 in the northeast region of Brazil, which is predominantly characterized as semi-arid and primarily covered by caatinga vegetation [27]. Bat sampling was carried out in three municipalities in the state of Ceará, located in northeastern Brazil: Guaramiranga, Pacoti, and Eusébio. Within these municipalities, six sampling sites were selected. In Guaramiranga, the chosen sites were Sítio Nova Olinda (4°14′48.11″ S, 38°56′29.38″ W) and Sítio Riacho Fundo (4°15′40.37″ S, 38°55′5.41″ W). In Pacoti, sampling occurred at the headquarters of the Natural History Museum of Ceará Prof. Dias da Rocha (4°13’38.87″ S, 38°55’21.25″ W), Sítio São João (4°13′33.21″ S, 38°54′50.09″ W), and Sítio Boa Vista (4°13′6.85″ S, 38°54′7.00″ W). In Eusébio, a municipality that is part of the metropolitan region of Fortaleza, the capital of Ceará, sampling was conducted at the headquarters of Fiocruz Ceará, close to Lagoa da Precabura (3°50′11.89″ S, 38°26′41.93″ W) (Figure 1).

2.2. Bat Sampling

Each site was sampled for two consecutive nights using eight mist nets, measuring 9 × 3 m, installed at ground level in clearings, trails, near rivers, or residences. The nets were opened at 6:00 PM and maintained for 6 h, with checks every 15 min. Specimens captured were placed in cloth bags, sorted, and identified using keys available in the literature [28,29]. For each individual, the species name, date and time of capture, forearm length (mm), body mass (g), sex, and age category were recorded. Age category was determined by examining the epiphyses of the phalanges, classifying individuals as young, subadults, or adults [30]. The reproductive status of females was visually or palpably assessed, then categorized as inactive, pregnant, lactating, or post-lactating. Captured individuals without indications of trauma or stress, as well as pregnant or lactating females, were released after recording relevant data. Nomenclature followed [31]. The collected specimens were accessioned into the mammal collection of the Museu de História Natural do Ceará Prof. Dias da Rocha.
Oral and rectal swabs were collected from all captured individuals. Rectal samples were gathered using sterile Ultra-Thin Minitip Size Nylon® Flocked Swabs (Copan Italia, Brescia, Italy), while oral swabs were employed with regular rayon swabs. All samples were collected and preserved in 1 mL RNAlater™ Stabilization Solution (Invitrogen™, Waltham, MA, USA).

2.3. Viral RNA Extraction and Virus Detection

To extract viral RNA, 140 µL of the sample was utilized. The QIAamp® Viral RNA Mini Kit (Qiagen, Hilden, Germany) was used for the extraction process, following the manufacturer’s instructions. The elution buffer was used to elute the viral RNA, resulting in a final volume of 60 µL. The extracted RNA was promptly stored at −80 °C until molecular analysis. Negative controls, using RNAse/DNAse-free water, were included in each extraction procedure. Following the extraction, genetic material from the collected biological samples underwent analysis with RT-PCR, real-time RT-PCR, and partial genome sequencing to examine the selected viral panel.
For the detection of SARS-CoV-2 and influenza A virus in animals, a real-time RT-PCR assay was employed. The extracted RNA underwent screening through a SARS-CoV-2 and InfA (for all influenza A subtypes) real-time RT-PCR utilizing the SARS-CoV-2 detection Molecular InfA/E/RP Kit (Biomanguinhos, Rio de Janeiro, Brazil), following the methodology outlined by [32]. Both reverse transcription and amplification procedures were conducted without duplication on the ABI7500 platform (Thermo Fisher Scientific, Waltham, MA, USA). Samples exhibiting a cycle threshold (Ct) value below 38 were considered positive. Each run incorporated a negative control (RNAse/DNAse-free water) and positive control RNA templates (synthetized genblock provided by Molecular InfA/E/RP Kit) for validation and quality assurance.
Screening for other coronaviruses (CoVs) was conducted using conventional panco-ronavirus RT-PCR. All samples underwent pancoronavirus RT-PCR, specifically targeting the RNA-dependent RNA polymerase (RdRp) gene, following the procedure outlined by [33,34]. In brief, cDNA was synthesized and amplified in a first-round PCR using the One-Step RT-PCR Enzyme Mix Kit (Qiagen, Hilden, Germany). The primers used in the first round were RdRp S1 (5′-GGKTGGGAYTAYCCKAARTG-3′) and RdRp R1 (5′-TGYTGTSWRCARAAYTCRTG-3′) [32], generating an expected product size of 602 base pairs (bps). Reactions were conducted in a Veriti Thermo Cycler (Applied Biosystems, Waltham, MA, USA) with the following conditions: reverse transcription (50 °C, 30 min), reverse transcriptase inactivation, and DNA polymerase activation (95 °C, 15 min), followed by 40 cycles of DNA denaturation (94 °C, 45 s), annealing (52 °C, 45 s), and extension (72 °C, 45 s), concluding with a final extension step (72 °C, 10 min). Subsequently, nested PCR was carried out using the Phusion RT-PCR Enzyme Mix Kit (Sigma-Aldrich, San Luis, MO, EUA), along with primers Bat1F (5′-GGTTGGGACTATCCTAAGTGTGA-3′) and Bat1R (5′-CCATCATCAGATAGAATCATCAT-3′) [34]. One microliter of the amplified product from the first round was used as a template in the nested PCR, conducted under the following conditions: denaturation (98 °C, 30 s), followed by 35 cycles of DNA denaturation (98 °C, 15 s), annealing (52 °C, 15 s), extension (72 °C, 30 s), and a final extension step (72 °C, 5 min). The RdRp amplicons, approximately 440 bps in size, were visualized on 1.5% agarose gels using SYBR™ Safe DNA Gel Stain (Thermo Fisher Scientific, Waltham, MA, USA). The positive controls utilized for PCR consisted of RNA samples of SARS-CoV-2 extracted from an isolated virus, following the same procedures outlined for animal samples.
For Sanger sequencing, the DNA of RdRp amplicons (440 bps) was purified using the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) following the manufacturer’s recommendations. The Sanger sequencing reaction was prepared utilizing the BigDye Terminator v3.1 Cycle Sequencing Kit (Life Technologies, Carlsbad, CA, EUA) with primers Bat1F and Bat1R at a concentration of 3.2 pmoles. Sequencing was executed on the ABI 3730 DNA Analyzer (Applied Biosystems, Waltham, MA, USA) following the protocols established by [35]. Reads were assembled and were evaluated using Sequencher 5.1 (GeneCodes, Ann Arbor, MI, USA) to obtain the final consensus, which was uploaded to the National Center for Biotechnology Information (NCBI) GenBank database.

2.4. Coronaviridae Sequence Data Recovery and Phylogenetic Analysis

To determine from which Coronavirus genus the obtained sequences belong to, we first performed the amino acid translation of the fragments obtained in this study using ORFinder (https://www.ncbi.nlm.nih.gov/orffinder/, accessed on 14 February 2023—any sense codon option) and aligned the amino acid sequence from the largest reading frame to the full RdRp region of reference Coronaviridae genomes (Table S1) using MAFFT v7.0 [36] online (https://mafft.cbrc.jp/alignment/server/index.html, accessed on 14 February 2023) with default parameters. No trimming was performed. We then performed a maximum likelihood phylogenetic reconstruction using IQTREE 2.0 [37] using the GECV01031551.1_MLeV as an outgroup. Amino acid substitution models were selected according to the best model suggested by ModelFinder, then implemented within IQTREE 2.0 as reported in each figure legend.
To gain further insights and a higher phylogenetic understanding of the sequences generated in this study, we then performed homologous sequence retrieval from the non-redundant NCBI database based on BLAST searches of all partial RdRp obtained in this study. Up to the 100 first best hits were recovered based on the highly similar sequence option (megablast). Due to the high nucleotide divergence between Coronavirus genera at the nucleotide level, we performed a within genus partial RdRp nucleotide alignment and included one outgroup sequence from the most closely related genus (full trees can be accessed in the Supplementary Material, Nexus file S1–S3). Nucleotide alignments were performed with MAFFT v7.0 online (https://mafft.cbrc.jp/alignment/server/index.html, accessed on 20 June 2023) with the --add option and --keeplength option based on the highly curated initial alignment of the reference genomes (reference genomes accession numbers can be found at Table S1). In order to evaluate the phylogenetic clustering of the sequences at the subgenus level, we also included sequences with curated subgenus metadata associated with the ICTV (https://ictv.global/report/chapter/coronaviridae/coronaviridae/alphacoronavirus, https://ictv.global/report/chapter/coronaviridae/coronaviridae/betacoronavirus, accessed on 20 June 2023).
Maximum likelihood phylogenetic analyses were performed using IQTREE 2.0 [37] at the amino acid and nucleotide levels. Substitution models were selected with ModelFinder [38] and implemented within IQTREE. Branch support was evaluated with an approximate likelihood ratio test (aLRT) [39] and ultrafast bootstrap (UFBOOT = 1000) [40].

3. Results

A total of 298 bats from six sampling sites within three municipalities were analyzed in the present study (Table 1 and Table S2). This diverse collection exhibited a rich array of biodiversity, encompassing 16 genera, 22 species, and five families: Emballonuridae, Molossidae, Noctilionidae, Phyllostomidae, and Vespertilionidae (Table 1 and Table S2). The most frequently sampled bats in the present study were Carollia perspicillata (N = 76), Glossophaga soricina (N = 48), Artibeus planirostris (N = 37), Phyllostomus discolor (N = 33), and Sturnira lilium (N = 32). Most of the sampled species (19) were only represented by less than ten individuals (Table 1).
All oral and rectal swabs tested from these captured bats returned negative results for influenza A and SARS-CoV-2. However, 21 bats yielded positive results in RT-PCR for Coronavirus and after sequencing and comparison with the sequences available in GenBank, Alphacoronavirus RNA was detected in 20 (6.7%) of the tested bats, all of which were from the Phyllostomidae family, encompassing seven different species: C. perspicillata (7/76, 9.2%), G. soricina (3/48, 6.2%), Lonchorhina aurita (2/4, 50%), Platyrrhinus lineatus (1/9, 11.1%), Platyrrhinus recifinus (1/7, 14.2%), P. discolor (5/33, 15.1%), and S. lilium (1/32, 3.1%). In one male A. planirostris from the Pacoti municipality, a Betacoronavirus was detected (1/37, 3.7%). All positive samples except two were from rectal swabs (Table 2). High quality consensus sequences, based on the alignment of forward and reverse Sanger reads, with an expected size of 400–420 bps, were successfully obtained from 17 samples and deposited in GenBank (Table 2). None of the sampled bats exhibited any clinical signs of disease.
Phylogenetic reconstruction including the known diversity of Coronavirus genera confirmed that 16 out of 17 sequences were clustered with high branch support within the Alphacoronavirus genus (Figure 2A, Supplementary Material S1 and S3).
The single sequence from the Betacoronavirus genus detected in A. planirostris did not cluster within known Betacoronavirus subgenera (Figure 2A). At the higher resolution phylogenetic analysis, the novel Betacoronavirus sequence clustered with high node support to two other coronavirus sequences recovered from the Artibeus species (A. planirostris and Artibeus lituratus) sampled in 2011 and 2012, which are not members of known Betacoronavirus subgenera (Figure 2B, Supplementary Material S2).
Nine out of sixteen Alphacoronavirus sequences clustered into the Amalacovirus subgenus (Figure 3A). These sequences are grouped with other characterized viruses from P. discolor, sampled in different regions of Brazil (Pernambuco state also in Northeast Brazil) as well as in Colombia and Panamá (Figure 3A). On the other hand, five sequences from C. perspicillata (4) and P. lineatus (1) clustered in a monophyletic clade that is a sister to Amalacovirus subgenus, but lacks a subgenus classification (Figure 3B, Supplementary Material S3). These sequences clustered with high node support to other Coronavirus sequences recovered from Brazilian bats between 2012 and 2021, such as from other populations of C. perspicillata and A. planirostris (Figure 3B). One sequence from S. lilium clustered with other sequences recovered from different populations of the same species sampled between 2012 and 2021 in Brazil in a sister clade (with no known subgenus) of the subgenus Tegacovirus and Minacovirus (Figure 4A). Lastly, one sequence obtained from P. recifinus clustered with sequences from A. lituratus and Artibeus jamaicensis sampled in Brazil, Colombia, and Panama, forming a sister clade (with no known subgenus) of the subgenus Decacovirus (Figure 4B).

4. Discussion

The 298 bats analyzed belong to 22 species from the Emballonuridae, Molossidae, Noctilionidae, Phyllostomidae, and Vespertilionidae families. A total of 20 individuals from the Phyllostomidae family were found to be carrying several alphacoronaviruses from the Amalacovirus subgenus and alphacoronaviruses that clustered in monophyletic clades with no known subgenera, but were sister clades to the Amalacovirus, Tegacovirus, Minacovirus, and Decacovirus subgenera. One A. planirostris was found to be infected with a novel Betacoronavirus. This study represents the first detection and classification of coronaviruses from bats sampled in the Brazilian state Ceará.
In Brazil, Bat-CoVs have been identified in over 29 bat species spanning the Phyllostomidae, Molossidae, and Vespertilionidae families, exhibiting diverse dietary preferences, including omnivory, frugivory, nectarivory, insectivory, and hematophagy [41,42,43,44,45,46,47,48]. The 7% prevalence of CoVs we observed falls within the range reported in other studies of neotropical bats. Detection rates in these studies varied widely, from as low as 0–1% [49,50] to around 2.7–3.7% [42,45,51], reaching as high as 12.9–17.2% [43,48]. However, it is important to highlight that differences in detection rates can be attributed to many factors such as seasonality, increased numbers of certain species being included in different studies [41,46,47], or different types of samples tested [50,52].
Most Bat-CoVs sequences identified in Brazil fall within the Alphacoronavirus genus [41,42,43,45,46,47,48,52], a trend which is consistent with our own findings. Our data further reveal that the sequences generated in this study are linked to various distinct subclades of alphacoronaviruses. We observed that coronaviruses from hosts of the same species are closely related. For example, sequences of CoV (Amalacovirus) obtained from P. discolor were grouped with other viruses characterized from P. discolor samples recovered in different regions of South and Central America. Similarly, CoV recovered from S. lilium in the present study clustered with other sequences recovered from different populations of the same species sampled in southern Brazil (Sao Paulo state). However, some CoVs recovered here also clustered in the same clade with CoVs recovered from distantly related bat species belonging to different genera. For instance, Amalacovirus from P. discolor clustered together with CoVs recovered in C. perspicillata and S. lilium. In another case, CoVs found in C. perspicillata were closely related to the CoVs detected in P. lineatus. These bat genera visit the same fruits, which could facilitate viral cross-species transmission. Although sporadic observations of closely related coronaviruses in different bat species and even families have been reported among neotropical bats [43,48,53], it appears that host-switching events are less common in Latin America compared to bats in Africa and Asia [21]. It was suggested that coronaviruses sampled from Latin American bats still undergo host-switching, but they tend to move between closely related species whereas, in Africa and Asia, viruses are more likely to cross the species barrier between more distantly related species [21]. The mechanism underlying these differences is not yet fully understood, but it may reflect regional variations in the risk of disease emergence. This could be one of the factors contributing to the emergence of highly pathogenic coronaviruses such as MERS-CoV and SARS-CoV in Asia rather than in South America [21].
Only a few sequences from the Betacoronavirus genus have been detected in Brazil [44,45]. Thus, our most important finding is the Betacoronavirus genus detected in A. planirostris. This CoV did not cluster within a known Betacoronavirus subgenus and at the higher resolution phylogenetic analysis, it clustered with high node support to other two coronavirus sequences within a non-defined subgenus recovered from the Artibeus species (A. planirostris and A. lituratus) sampled over decade ago in the Atlantic rainforest, southern Brazil.
Regions with higher bat diversity are likely to harbor a greater variety of viruses [21]. Therefore, it is anticipated that Brazilian bats, with their rich diversity, host a high diversity of coronaviruses. However, our current understanding remains limited, and ongoing research is expected to uncover more coronaviruses [22]. It has been estimated that sampling up to 400 individuals from each bat species would be necessary to capture the full diversity of coronaviruses [21]. Therefore, increased temporal and population sampling is warranted to further uncover more divergent coronaviruses in Brazil.
The higher prevalence of positive rectal samples compared to oral swabs is consistent with the findings of previous studies [12,21,53,54,55]. While feces serve as the primary source for CoV detection in bats, it is worth noting that detection in oral swabs has also been demonstrated, although less frequently [53,56]. Additionally, the study by [43], which identified CoVs not only in the intestines but also in the lungs and liver, underscores the multiple organ/tissue tropism of coronaviruses in bats, as has already been observed for other mammal species [57].
The captured bats showed no visible signs of disease, including those infected with CoVs, which is in line with the findings from previous studies [49,55,58]. This observation suggests that, despite the presence of CoVs within bat populations, individual bats may only experience transient infections with CoVs without displaying noticeable illness. In another study, it was noted that no bat remained persistently positive for CoV RNA after six weeks [59], providing additional evidence that CoV infections in bats may have a short duration and be self-limiting. This corresponds to the concept that bats have evolved mechanisms to coexist with coronaviruses, and these viruses may establish a more symbiotic relationship with their natural hosts compared to the severe outcomes observed in other species, such as humans.
The urgency and amplification of coronavirus research have significantly intensified since the emergence of the COVID-19 pandemic, attributed to the SARS-CoV-2 virus. Analogous to its predecessor, SARS-CoV, SARS-CoV-2 was presumed to have originated in Rhinolophus spp. in Asia [60,61,62], although the exact spillover mechanism remains yet undetermined. SARS-CoV-2 presents a potential threat to New World bat populations if bats encounter the virus through interspecies contact, if the virus can subsequently establish infection and propagate within bat populations, or if it engenders morbidity or mortality in bats. Furthermore, the establishment of SARS-CoV-2 within bat reservoirs could serve as a reservoir for secondary transmission to humans, domestic animals, or other wildlife species [63,64,65]. However, at present, SARS-CoV-2 has not been detected in wild New World bat populations, suggesting a lack of spillover from human sources [65,66], consistent with the outcomes of our investigations, which indicate that the virus is either not present or that it persists in undetectable levels in bat populations in this region. These findings offer encouraging prospects from both conservation and public health standpoints. Nonetheless, spillover events are contingent upon the level of exposure, and wildlife practitioners engaged in bat-related activities are urged to adhere strictly to transmission mitigation protocols [67,68].
Brazil does not harbor Old World Rhinolophidae and Hipposideridae bats, which are natural reservoirs of SARS-related coronaviruses. Consequently, the absence of SARS-CoV-2 in phyllostomid, molossid, and vespertilionid bats in the present study aligns with expectations, although it cannot be discarded in the future. It is also known that susceptibility to SARS-like viruses varies among bat species and families. SARS-like betacoronaviruses have been identified not only in horseshoe bats, but also in molossid bats (Chaerephon plicatus) in China [69] and in guano samples from vespertilionid and molossid bats in Europe [70]. Moreover, experimental studies involving neotropical bat species, such as Eptesicus fuscus (Vespertilionidae) [71] and the Tadarida brasiliensis (Molossidae) [72], suggest that these species exhibit minimal competence as hosts for SARS-CoV-2.
In the current investigation, we did not detect influenza A viruses. Influenza viruses have been identified in terrestrial, flying, and aquatic mammals, as well as in a wide variety of wild aquatic birds, which are considered natural reservoirs for avian influenza viruses (AIVs) [73]. Ten years ago, the new subtypes H17N10 and H18N11 were observed in fruit bats in Guatemala, Peru [74,75] and, more recently, in Brazil [76]. These discoveries suggest that neotropical bats may serve as a potentially significant and likely ancient reservoir for a diverse range of influenza viruses. However, these avian-associated influenza A viruses, which are phylogenetically highly divergent in their hemagglutinin (HA) and neuraminidase (NA) genes, have thus far only been detected in six individual bat specimens from the S. lilium (N = 4) and A. planirostris (N = 2) species [74,75,76]. The absence of this virus in our study may be attributed to its low prevalence, as observed in previous studies on neotropical bats (0% [50], 0.4% [76], 0.9% [75], and 1.0% [74]). Moreover, in 2017, a novel IAV A(H9N2)-like virus was isolated from Egyptian fruit bats (Rousettus aegyptiacus) [77] that has features associated with an increased risk to humans. This emphasizes the need for continued surveillance of influenza A among South American bats [77,78].
Bat fauna sampling was conducted using mist nets, a method commonly employed in the neotropical region. Although they are efficient in capturing bats of the Phyllostomidae family, especially frugivorous species, their effectiveness is reduced for insectivorous bats as these species tend to fly at higher altitudes and avoid mist nets by using echolocation [79,80]. However, the recent documentation of the first sightings of Myotis ruber and Molossus pretiosus species in the same region as the present study, Ceará [81], captured using mist nets, plays a crucial role in expanding our knowledge of bat biodiversity. These new records represent a valuable contribution to the list of known species in the region [82], providing a more robust foundation for future research and conservation initiatives aimed at protecting bat diversity in the region. Therefore, this study can contribute to the understanding of bat biodiversity and offer valuable insights for research related to the ecology and epidemiology of diseases with the potential for transmission by bats.
We are aware of the limitations of our study. Ideally, isolating the virus would have been optimal; however, due to the remote locations where samples were collected, preservation in RNAlater™ Stabilization Solution was necessary, precluding attempts to isolate the virus. Another limitation is that some species were not well represented in our sample set through the use mist nets for sampling, as discussed above. Additionally, we only obtained short fragments of the genome, which limited our analyses. Ideally, having the complete genome would provide a more comprehensive understanding of the viruses present.

5. Conclusions

Our study provides valuable insights into the prevalence and diversity of coronaviruses in bat populations in northeastern Brazil. The detection of alphacoronaviruses in various bat species underscores the importance of bats as reservoirs for these viruses. Additionally, a single Betacoronavirus was detected in A. planirostris which does not fall within established genera. Higher resolution phylogenetic analysis indicated that it is closely related to two other coronavirus sequences which had been recovered from A. planirostris and A. lituratus bats captured in southern Brazil over a decade ago. The absence of SARS-CoV-2 in the sampled bats indicates a lack of spillback events from human or environmental sources. However, the potential for future transmission events underscores the importance of ongoing surveillance and transmission mitigation protocols in wildlife management practices. Continued research into bat pathogens and their interactions with humans and other animals is essential for developing comprehensive strategies to promote public health. Understanding these dynamics is crucial for effectively mitigating the risks of zoonotic diseases.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ani15030332/s1, Table S1. List of accession numbers of the reference genomes used in Figure 2A. Table S2. List of all bat species sampled in the present study. Supplementary file S1. Nexus file of the whole phylogenetic tree of detected coronaviruses in the present study with reference sequences. Supplementary file S2. Nexus file of the whole phylogenetic tree of detected Betacoronavirus in the present study. Supplementary file S3. Nexus file of the whole phylogenetic tree of detected Alphacoronavirus in the present study.

Author Contributions

Conceptualization: M.O., M.G.B. and J.L.P.C.; Methodology: M.O., P.C.R., M.B.d.O., J.L.P.C. and G.L.W. Formal Analysis: G.L.W., T.F. and L.C.d.S.J.; Investigation: G.A.C.A.M., N.S.-C., M.B.d.O., P.E.B.M., T.F. and L.C.d.S.J.; Resources: M.M.M.S. and J.L.P.C.; Data Curation: M.B.d.O., P.E.B.M., T.F., M.O., T.F. and N.S.-C.; Writing—Original Draft Preparation: M.O., G.L.W., T.F. and M.B.d.O.; Writing—Review and Editing: M.B.d.O., P.C.R., M.G.B., P.E.B.M., N.S.-C., G.A.C.A.M. and M.M.M.S. Visualization: P.E.B.M. and J.L.P.C.; Supervision: M.O. and J.L.P.C.; Project Administration: M.O. and J.L.P.C.; Funding Acquisition: J.L.P.C., M.M.M.S. and P.C.R. All authors have read and agreed to the published version of the manuscript.

Funding

This study was founded by Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico (FUNCAP, no 06347980/2020), with scholarship to PM, and partly funded by Reference laboratories from Oswaldo Cruz Foundation (CVSLR/FIOCRUZ), Oswaldo Cruz Institute.

Institutional Review Board Statement

Fieldwork followed national guidelines and provisions of the ‘Sistema de Autorização e Informação em Biodiversidade’ (SISBIO, License numbers 60058 and 84226). All animal procedures and veterinary assistance were in accordance with the ‘Conselho Nacional de Controle de Experimentação Animal’ (CONCEA, 2013), and approved by the ‘Comissão de Ética no Uso de Animais’ (CEUA 10802574/2021) of the Universidade Estadual do Ceará (UECE). The individuals collected as vouchers were deposited in the Coleção de Mamíferos do Museu de História Natural do Ceará Professor Dias da Rocha (MHNCE/UECE), Pacoti, Ceará, Brazil, and registered in the ‘Sistema Nacional de Gestão do Patrimônio Genético e do Conhecimento Tradicional Associado’ (SisGen A344FB0 and A03F9E2).

Informed Consent Statement

Not applicable.

Data Availability Statement

Sequence data have been deposited in GenBank, records are as follows: OR805808–OR805824.

Acknowledgments

We thank the Platform of Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil, and Genomic Platform—DNA Sequencing—RPT01A (Rede de Plataformas Tecnologicas Fiocruz). To the curator of the mammal collection at the MHNCE Aldo Caccavo de Araújo. To the owners of the locations where we carried out the fields, as well as everyone who helped during this period: Adria Teles, Artur Júnior, Beatriz Almeida, Clarissa Nobre, Claudia Velasquez, Felipe Pessoa, Hugo Fernandes, Igor Gutierrez, Karlla Morgana, Luiz Carlos, Marco Crozariol, Mateus Duarte, Roberio Freire, Rodrigo Gonzalez, Sheila Fernandes, and Thabata Cavalcante.

Conflicts of Interest

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

References

  1. Teeling, E.C.; Springer, M.S.; Madsen, O.; Bates, P.; O’Brien, S.J.; Murphy, W.J. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 2005, 307, 580–584. [Google Scholar] [CrossRef] [PubMed]
  2. Simmons, N.B.; Cirranello, A.L. Bat Species of the World: A Taxonomic and Geographic Database. Version 1.5. 2024. Available online: https://batnames.org/home.html (accessed on 5 March 2024).
  3. Díaz, M.M.; Solari, S.; Gregorin, R.; Aguirre, L.F.; Barquez, R.M. Clave de Identificación de los Murciélagos Neotropicales; Programa de Conservación de los Murciélagos de Argentina: Tucumán, Argentina, 2021. [Google Scholar]
  4. Gorbunova, V.; Seluanov, A.; Kennedy, B.K. The World Goes Bats: Living Longer and Tolerating Viruses. Cell Metab. 2020, 31, 31–43. [Google Scholar] [CrossRef] [PubMed]
  5. Potter, J.H.T.; Davies, K.T.J.; Yohe, L.R.; Sanchez, M.K.R.; Rengifo, E.M.; Struebig, M.; Warren, K.; Tsagkogeorga, G.; Lim, B.K.; dos Reis, M.; et al. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol. Biol. Evol. 2021, 38, 3864–3883. [Google Scholar] [CrossRef] [PubMed]
  6. Kerth, G. Causes and Consequences of Sociality in Bats. BioScience 2008, 58, 737–746. [Google Scholar] [CrossRef]
  7. Zhang, G.; Cowled, C.; Shi, Z.; Huang, Z.; Bishop-Lilly, K.A.; Fang, X.; Wynne, J.W.; Xiong, Z.; Baker, M.L.; Zhao, W.; et al. Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science 2013, 339, 456–460. [Google Scholar] [CrossRef]
  8. Ahn, M.A.-O.; Anderson, D.A.-O.; Zhang, Q.; Tan, C.W.; Lim, B.L.; Luko, K.; Wen, M.; Chia, W.N.; Mani, S.; Wang, L.C.; et al. Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host. Nat. Microbiol. 2019, 4, 789–799. [Google Scholar] [CrossRef]
  9. Calisher, C.H.; Childs, J.E.; Field, H.E.; Holmes, K.V.; Schountz, T. Bats: Important reservoir hosts of emerging viruses. Clin. Microbiol. Rev. 2006, 19, 531–545. [Google Scholar] [CrossRef] [PubMed]
  10. Chen, L.; Liu, B.; Yang, J.; Jin, Q. DBatVir: The database of bat-associated viruses. Database 2014, 2014, bau021. [Google Scholar] [CrossRef]
  11. Chua, K.B.; Bellini, W.J.; Rota, P.A.; Harcourt, B.H.; Tamin, A.; Lam, S.K.; Ksiazek, T.G.; Rollin, P.E.; Zaki, S.R.; Shieh, W.; et al. Nipah virus: A recently emergent deadly paramyxovirus. Science 2000, 288, 1432–1435. [Google Scholar] [CrossRef]
  12. Li, W.; Shi, Z.; Yu, M.; Ren, W.; Smith, C.; Epstein, J.H.; Wang, H.; Crameri, G.; Hu, Z.; Zhang, H.; et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 2005, 310, 676–679. [Google Scholar] [CrossRef]
  13. Woo, P.C.Y.; de Groot, R.J.; Haagmans, B.; Lau, S.K.P.; Neuman, B.W.; Perlman, S.; Sola, I.; van der Hoek, L.; Wong, A.C.P.; Yeh, S.H. ICTV Virus Taxonomy Profile: Coronaviridae 2023. J. Gen. Virol. 2023, 104, 001843. [Google Scholar] [CrossRef] [PubMed]
  14. Cui, J.; Li, F.; Shi, Z.L. Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 2019, 17, 181–192. [Google Scholar] [CrossRef] [PubMed]
  15. Ge, X.Y.; Wang, N.; Zhang, W.; Hu, B.; Li, B.; Zhang, Y.Z.; Zhou, J.H.; Luo, C.M.; Yang, X.L.; Wu, L.J.; et al. Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virol. Sin. 2016, 31, 31–40. [Google Scholar] [CrossRef] [PubMed]
  16. Guan, Y.; Zheng, B.J.; He, Y.Q.; Liu, X.L.; Zhuang, Z.X.; Cheung, C.L.; Luo, S.W.; Li, P.H.; Zhang, L.J.; Guan, Y.J.; et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 2003, 302, 276–278. [Google Scholar] [CrossRef] [PubMed]
  17. Hu, B.; Zeng, L.P.; Yang, X.L.; Ge, X.Y.; Zhang, W.; Li, B.; Xie, J.Z.; Shen, X.R.; Zhang, Y.Z.; Wang, N.; et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 2017, 13, e1006698. [Google Scholar] [CrossRef]
  18. Poon, L.L.; Chu, D.K.; Chan, K.H.; Wong, O.K.; Ellis, T.M.; Leung, Y.H.; Lau, S.K.; Woo, P.C.; Suen, K.Y.; Yuen, K.Y.; et al. Identification of a novel coronavirus in bats. J. Virol. 2005, 79, 2001–2009. [Google Scholar] [CrossRef] [PubMed]
  19. Shi, Z.; Hu, Z. A review of studies on animal reservoirs of the SARS coronavirus. Virus Res. 2008, 133, 74–87. [Google Scholar] [CrossRef] [PubMed]
  20. Banerjee, A.; Kulcsar, K.; Misra, V.; Frieman, M.; Mossman, K. Bats and Coronaviruses. Viruses 2019, 11, 41. [Google Scholar] [CrossRef] [PubMed]
  21. Anthony, S.J.; Johnson, C.K.; Greig, D.J.; Kramer, S.; Che, X.; Wells, H.; Hicks, A.L.; Joly, D.O.; Wolfe, N.D.; Daszak, P.; et al. Global patterns in coronavirus diversity. Virus Evol. 2017, 3, vex012. [Google Scholar] [CrossRef]
  22. Wallau, G.L.; Barbier, E.; Tomazatos, A.; Schmidt-Chanasit, J.; Bernard, E. The Virome of Bats Inhabiting Brazilian Biomes: Knowledge Gaps and Biases towards Zoonotic Viruses. Microbiol. Spectr. 2023, 11, e0407722. [Google Scholar] [CrossRef] [PubMed]
  23. Bétard, F. Spatial variations of soil weathering processes in a tropical mountain environment: The Baturité massif and its piedmont (Ceará, NE Brazil). CATENA 2012, 93, 18–28. [Google Scholar] [CrossRef]
  24. Pôrto, K.C.; Cabral, J.J.; Tabarelli, M. Brejos de altitude em Pernambuco e Paraíba. História Natural, Ecologia e Conservação. Brasília, Ministério do Meio Ambiente; Brasília Ministério Do Meio Ambiente: Brasília Brazil, 2004. [Google Scholar]
  25. do Nascimento, F.R.; de Souza, M.J.N.; da Cruz, M.L.B. Diagnóstico Socioeconômico da Área de Proteção Ambiental da Serra de Baturité–Ceará. RAEGA-O Espaço Geográfico Em Análise 2010, 20, 19–33. [Google Scholar] [CrossRef]
  26. ANVISA. Nota Técnica GVIMS/GGTES/ANVISA No 04/2020; ANVISA: Brasilia, Brazil, 2020; p. 118. [Google Scholar]
  27. De Souza Gois, L.S.; De Barros-Corrêa, A.C.; de Araújo Monteiro, A. Análise Integrada dos Brejos de Altitude do Nordeste do Brasil a partir de Atributos Fisiográficos/Integrated Analysis of Highland Humid Brejos in Northeast Brazil Based on Physiographic Attributes. Espaço Aberto 2019, 9, 77–98. [Google Scholar] [CrossRef]
  28. Gardner, A.L. (Ed.) Mammals of South America: Marsupials, Xenarthrans, Shrews, and Bats; University of Chicago Press: Chicago, IL, USA, 2008; Volume 1. [Google Scholar]
  29. Reis, N.R.; Peracchi, A.L.; Batista, C.B.; Lima, I.; Pereira, A. História Natural dos Morcegos Brasileiros: Chave de Identificação de Espécies; Technical Books Editora Ltda.: Rio de Janeiro, Brazil, 2017. [Google Scholar]
  30. Anthony, E.L.P. Age determination in bats. In Behavioral Methods for the Study of Bats; Kunz, T.H., Parsons, S., Eds.; Smithsonian Institution Press: Washington, DC, USA; London, UK, 1988; pp. 47–58. [Google Scholar]
  31. Garbino, G.S.T.; Gregorin, R.; Lima, I.P.; Loureiro, L.; Moras, L.; Moratelli, R.; Nogueira, M.R.; Pavan, A.C.; Tavares, V.C.; Nascimento, M.C.; et al. Updated Checklist of Brazilian Bats: Versão 2020. 2022. Available online: https://www.sbeq.net/lista-de-especies (accessed on 5 March 2024).
  32. Corman, V.M.; Landt, O.; Kaiser, M.; Molenkamp, R.; Meijer, A.; Chu, D.K.; Bleicker, T.; Brunink, S.; Schneider, J.; Schmidt, M.L.; et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020, 25, 2000045. [Google Scholar] [CrossRef]
  33. Chu, D.K.; Leung, C.Y.; Gilbert, M.; Joyner, P.H.; Ng, E.M.; Tse, T.M.; Guan, Y.; Peiris, J.S.; Poon, L.L. Avian coronavirus in wild aquatic birds. J. Virol. 2011, 85, 12815–12820. [Google Scholar] [CrossRef] [PubMed]
  34. Woo, P.C.; Lau, S.K.; Chu, C.M.; Chan, K.H.; Tsoi, H.W.; Huang, Y.; Wong, B.H.; Poon, R.W.; Cai, J.J.; Luk, W.K.; et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 2005, 79, 884–895. [Google Scholar] [CrossRef] [PubMed]
  35. Otto, T.D.; Vasconcellos, E.A.; Gomes, L.H.; Moreira, A.S.; Degrave, W.M.; Mendonca-Lima, L.; Alves-Ferreira, M. ChromaPipe: A pipeline for analysis, quality control and management for a DNA sequencing facility. Genet. Mol. Res. 2008, 7, 861–871. [Google Scholar] [CrossRef]
  36. Katoh, K.; Rozewicki, J.; Yamada, K.D. MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization. Brief. Bioinform. 2019, 20, 1160–1166. [Google Scholar] [CrossRef]
  37. Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef]
  38. Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.K.F.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods 2017, 14, 587–589. [Google Scholar] [CrossRef]
  39. Anisimova, M.; Gascuel, O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 2006, 55, 539–552. [Google Scholar] [CrossRef] [PubMed]
  40. Hoang, D.T.; Chernomor, O.; von Haeseler, A.; Minh, B.Q.; Vinh, L.S. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol. Biol. Evol. 2018, 35, 518–522. [Google Scholar] [CrossRef]
  41. Alves, R.S.; do Canto Olegario, J.; Weber, M.N.; da Silva, M.S.; Canova, R.; Sauthier, J.T.; Baumbach, L.F.; Witt, A.A.; Varela, A.P.M.; Mayer, F.Q.; et al. Detection of coronavirus in vampire bats (Desmodus rotundus) in southern Brazil. Transbound. Emerg. Dis. 2021, 69, 2384–2389. [Google Scholar] [CrossRef] [PubMed]
  42. Asano, K.M.; Hora, A.S.; Scheffer, K.C.; Fahl, W.O.; Iamamoto, K.; Mori, E.; Brandao, P.E. Alphacoronavirus in urban Molossidae and Phyllostomidae bats, Brazil. Virol. J. 2016, 13, 110. [Google Scholar] [CrossRef] [PubMed]
  43. Bittar, C.; Machado, R.R.G.; Comelis, M.T.; Bueno, L.M.; Beguelini, M.R.; Morielle-Versute, E.; Nogueira, M.L.; Rahal, P. Alphacoronavirus Detection in Lungs, Liver, and Intestines of Bats from Brazil. Microb. Ecol. 2020, 79, 203–212. [Google Scholar] [CrossRef] [PubMed]
  44. Brandao, P.E.; Scheffer, K.; Villarreal, L.Y.; Achkar, S.; Oliveira Rde, N.; Fahl Wde, O.; Castilho, J.G.; Kotait, I.; Richtzenhain, L.J. A coronavirus detected in the vampire bat Desmodus rotundus. Braz. J. Infect. Dis. 2008, 12, 466–468. [Google Scholar] [CrossRef] [PubMed]
  45. Goes, L.G.B.; Campos, A.C.A.; Carvalho, C.; Ambar, G.; Queiroz, L.H.; Cruz-Neto, A.P.; Munir, M.; Durigon, E.L. Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil. Infect. Genet. Evol. 2016, 44, 510–513. [Google Scholar] [CrossRef]
  46. Lima, F.E.; Campos, F.S.; Kunert Filho, H.C.; Batista, H.B.; Carnielli, P., Jr.; Cibulski, S.P.; Spilki, F.R.; Roehe, P.M.; Franco, A.C. Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil. Virus Genes. 2013, 47, 164–167. [Google Scholar] [CrossRef]
  47. Simas, P.V.; Barnabe, A.C.; Duraes-Carvalho, R.; Neto, D.F.; Caserta, L.C.; Artacho, L.; Jacomassa, F.A.; Martini, M.C.; Bianchi Dos Santos, M.M.; Felippe, P.A.; et al. Bat coronavirus in Brazil related to appalachian ridge and porcine epidemic diarrhea viruses. Emerg. Infect. Dis. 2015, 21, 729–731. [Google Scholar] [CrossRef]
  48. Bueno, L.M.; Rizotto, L.S.; Viana, A.O.; Silva, L.M.N.; de Moraes, M.; Benassi, J.C.; Scagion, G.P.; Dorlass, E.G.; Lopes, B.L.T.; Cunha, I.N.; et al. High genetic diversity of alphacoronaviruses in bat species (Mammalia: Chiroptera) from the Atlantic Forest in Brazil. Transbound. Emerg. Dis. 2022, 69, e2863–e2875. [Google Scholar] [CrossRef]
  49. Moreira-Soto, A.; Taylor-Castillo, L.; Vargas-Vargas, N.; Rodriguez-Herrera, B.; Jimenez, C.; Corrales-Aguilar, E. Neotropical Bats from Costa Rica harbour Diverse Coronaviruses. Zoonoses Public Health 2015, 62, 501–505. [Google Scholar] [CrossRef]
  50. Violet-Lozano, L.; Haach, V.; Barboza, C.M.; Dos Santos, J.; Gomes, B.F.; de Cassia Pardo de Souza, T.; Junior, P.C.; Arns, C.W.; de Carvalho Ruthner Batista, H.B.; Roehe, P.M.; et al. No molecular evidence for influenza A virus and coronavirus in bats belonging to the families Phyllostomidae, Vespertilionidae, and Molossidae in the state of Sao Paulo, Brazil. Braz. J. Microbiol. 2023, 54, 523–529. [Google Scholar] [CrossRef]
  51. Corman, V.M.; Rasche, A.; Diallo, T.D.; Cottontail, V.M.; Stocker, A.; Souza, B.; Correa, J.I.; Carneiro, A.J.B.; Franke, C.R.; Nagy, M.; et al. Highly diversified coronaviruses in neotropical bats. J. Gen. Virol. 2013, 94, 1984–1994. [Google Scholar] [CrossRef]
  52. Cerri, A.; Bolatti, E.M.; Zorec, T.M.; Montani, M.E.; Rimondi, A.; Hosnjak, L.; Casal, P.E.; Di Domenica, V.; Barquez, R.M.; Poljak, M.; et al. Identification and characterization of novel alphacoronaviruses in Tadarida brasiliensis (Chiroptera, Molossidae) from Argentina: Insights into recombination as a mechanism favoring bat coronavirus cross-species transmission. Microbiol. Spectr. 2023, 11, e0204723. [Google Scholar] [CrossRef]
  53. Anthony, S.J.; Ojeda-Flores, R.; Rico-Chavez, O.; Navarrete-Macias, I.; Zambrana-Torrelio, C.M.; Rostal, M.K.; Epstein, J.H.; Tipps, T.; Liang, E.; Sanchez-Leon, M.; et al. Coronaviruses in bats from Mexico. J. Gen. Virol. 2013, 94, 1028–1038. [Google Scholar] [CrossRef]
  54. Lau, S.K.; Woo, P.C.; Li, K.S.; Huang, Y.; Tsoi, H.W.; Wong, B.H.; Wong, S.S.; Leung, S.Y.; Chan, K.H.; Yuen, K.Y. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc. Natl. Acad. Sci. USA 2005, 102, 14040–14045. [Google Scholar] [CrossRef]
  55. Tang, X.C.; Zhang, J.X.; Zhang, S.Y.; Wang, P.; Fan, X.H.; Li, L.F.; Li, G.; Dong, B.Q.; Liu, W.; Cheung, C.L.; et al. Prevalence and genetic diversity of coronaviruses in bats from China. J. Virol. 2006, 80, 7481–7490. [Google Scholar] [CrossRef]
  56. Carrington, C.V.; Foster, J.E.; Zhu, H.C.; Zhang, J.X.; Smith, G.J.; Thompson, N.; Auguste, A.J.; Ramkissoon, V.; Adesiyun, A.A.; Guan, Y. Detection and phylogenetic analysis of group 1 coronaviruses in South American bats. Emerg. Infect. Dis. 2008, 14, 1890–1893. [Google Scholar] [CrossRef]
  57. Zhang, G.; Li, B.; Yoo, D.; Qin, T.; Zhang, X.; Jia, Y.; Cui, S. Animal coronaviruses and SARS-CoV-2. Transbound. Emerg. Dis. 2021, 68, 1097–1110. [Google Scholar] [CrossRef]
  58. Dominguez, S.R.; O’Shea, T.J.; Oko, L.M.; Holmes, K.V. Detection of group 1 coronaviruses in bats in North America. Emerg. Infect. Dis. 2007, 13, 1295–1300. [Google Scholar] [CrossRef]
  59. Osborne, C.; Cryan, P.M.; O’Shea, T.J.; Oko, L.M.; Ndaluka, C.; Calisher, C.H.; Berglund, A.D.; Klavetter, M.L.; Bowen, R.A.; Holmes, K.V.; et al. Alphacoronaviruses in New World bats: Prevalence, persistence, phylogeny, and potential for interaction with humans. PLoS ONE 2011, 6, e19156. [Google Scholar] [CrossRef]
  60. Boni, M.F.; Lemey, P.; Jiang, X.; Lam, T.T.; Perry, B.W.; Castoe, T.A.; Rambaut, A.; Robertson, D.L. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat. Microbiol. 2020, 5, 1408–1417. [Google Scholar] [CrossRef]
  61. Temmam, S.; Vongphayloth, K.; Baquero, E.; Munier, S.; Bonomi, M.; Regnault, B.; Douangboubpha, B.; Karami, Y.; Chrétien, D.; Sanamxay, D.; et al. Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature 2022, 604, 330–336. [Google Scholar] [CrossRef]
  62. Zhou, P.; Yang, X.L.; Wang, X.G.; Hu, B.; Zhang, L.; Zhang, W.; Si, H.R.; Zhu, Y.; Li, B.; Huang, C.L.; et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020, 579, 270–273. [Google Scholar] [CrossRef]
  63. Cibulski, S.; de Lima, F.E.S.; Roehe, P.M. Coronaviruses in Brazilian bats: A matter of concern? PLoS Negl. Trop. Dis. 2020, 14, e0008820. [Google Scholar] [CrossRef]
  64. Olival, K.J.; Cryan, P.M.; Amman, B.R.; Baric, R.S.; Blehert, D.S.; Brook, C.E.; Calisher, C.H.; Castle, K.T.; Coleman, J.T.H.; Daszak, P.; et al. Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: A case study of bats. PLoS Pathog. 2020, 16, e1008758. [Google Scholar] [CrossRef]
  65. Zeliff, H.; Ellis, J.C.; Turner, G.; Salvo, A.D.; Barnard, A.; Anis, E. Surveillance of Bats in the United States for SARS-Cov-2 and Other Coronaviruses. J. Zoo. Wildl. Med. 2023, 53, 811–816. [Google Scholar] [CrossRef] [PubMed]
  66. Moran, M.L.; Boyd, W.; De La Cruz, J.L.; Bertke, A.S.; Ford, W.M. Oral Sampling of Little Brown Bat (Myotis lucifugus) Maternity Colonies for SARS-CoV-2 in the Northeast and Mid-Atlantic, USA. Animal 2023, 13, 550. [Google Scholar] [CrossRef] [PubMed]
  67. Cook, J.A.-O.; Campbell Grant, E.A.-O.; Coleman, J.A.-O.X.; Sleeman, J.A.-O.; Runge, M.A.-O.X. Evaluating the risk of SARS-CoV-2 transmission to bats in the context of wildlife research, rehabilitation, and control. Wildl. Soc. Bull. 2022, 46, e1262. [Google Scholar] [CrossRef]
  68. Nuñez, G.B.; Cunningham, A.; Fils, E.M.B.; Frick, W.; Islam, M.N.; Jolliffe, T.; Kading, R.; Kepel, A.; Kingston, T.; Leopardi, S.; et al. IUCN SSC Bat Specialist Group (BSG) Recommended Strategy for Researchers to Reduce the Risk of Transmission of SARS-CoV-2 from Humans to Bats–MAP: Minimize, Assess, Protect; Bat Specialist Group–MAP to Prevent Human-Bat Transmission of SARS-CoV-2 2020. Available online: https://www.sbeq.net/_files/ugd/053d6e_3e05932181d44101ac96c4058ad3235d.pdf (accessed on 20 March 2021).
  69. Yang, L.; Wu, Z.; Ren, X.; Yang, F.; He, G.; Zhang, J.; Dong, J.; Sun, L.; Zhu, Y.; Du, J.; et al. Novel SARS-like betacoronaviruses in bats, China, 2011. Emerg. Infect. Dis. 2013, 19, 989–991. [Google Scholar] [CrossRef]
  70. Lecis, R.; Mucedda, M.; Pidinchedda, E.; Pittau, M.; Alberti, A. Molecular identification of Betacoronavirus in bats from Sardinia (Italy): First detection and phylogeny. Virus Genes 2019, 55, 60–67. [Google Scholar] [CrossRef] [PubMed]
  71. Hall, J.S.; Knowles, S.; Nashold, S.W.; Ip, H.S.; Leon, A.E.; Rocke, T.; Keller, S.; Carossino, M.; Balasuriya, U.; Hofmeister, E. Experimental challenge of a North American bat species, big brown bat (Eptesicus fuscus), with SARS-CoV-2. Transbound. Emerg. Dis. 2021, 68, 3443–3452. [Google Scholar] [CrossRef] [PubMed]
  72. Bosco-Lauth, A.M.; Porter, S.M.; Fox, K.A.; Wood, M.E.; Neubaum, D.; Quilici, M. Experimental Infection of Brazilian Free-Tailed Bats (Tadarida brasiliensis) with Two Strains of SARS-CoV-2. Viruses 2022, 14, 1809. [Google Scholar] [CrossRef] [PubMed]
  73. Webster, R.G.; Bean, W.J.; Gorman, O.T.; Chambers, T.M.; Kawaoka, Y. Evolution and ecology of influenza A viruses. Microbiol. Rev. 1992, 56, 152–179. [Google Scholar] [CrossRef] [PubMed]
  74. Tong, S.; Li, Y.; Rivailler, P.; Conrardy, C.; Castillo, D.A.; Chen, L.M.; Recuenco, S.; Ellison, J.A.; Davis, C.T.; York, I.A.; et al. A distinct lineage of influenza A virus from bats. Proc. Natl. Acad. Sci. USA 2012, 109, 4269–4274. [Google Scholar] [CrossRef]
  75. Tong, S.; Zhu, X.; Li, Y.; Shi, M.; Zhang, J.; Bourgeois, M.; Yang, H.; Chen, X.; Recuenco, S.; Gomez, J.; et al. New world bats harbor diverse influenza A viruses. PLoS Pathog. 2013, 9, e1003657. [Google Scholar] [CrossRef] [PubMed]
  76. Campos, A.C.A.; Goes, L.G.B.; Moreira-Soto, A.; de Carvalho, C.; Ambar, G.; Sander, A.L.; Fischer, C.; Ruckert da Rosa, A.; Cardoso de Oliveira, D.; Kataoka, A.P.G.; et al. Bat Influenza A(HL18NL11) Virus in Fruit Bats, Brazil. Emerg. Infect. Dis. 2019, 25, 333–337. [Google Scholar] [CrossRef]
  77. Kandeil, A.; Gomaa, M.R.; Shehata, M.M.; El Taweel, A.N.; Mahmoud, S.H.; Bagato, O.; Moatasim, Y.; Kutkat, O.; Kayed, A.S.; Dawson, P.; et al. Isolation and Characterization of a Distinct Influenza A Virus from Egyptian Bats. J. Virol. 2019, 93, 1–10. [Google Scholar] [CrossRef]
  78. El-Shesheny, R.; Franks, J.; Kandeil, A.; Badra, R.; Turner, J.; Seiler, P.; Marathe, B.M.; Jeevan, T.; Kercher, L.; Hu, M.; et al. Cross-species spill-over potential of the H9N2 bat influenza A virus. Nat. Commun. 2024, 15, 3449. [Google Scholar] [CrossRef]
  79. Fleming, T.H. Opportunism versus specialization: The evolution of feeding strategies in frugivorous bats. In Frugivores and Seed Dispersal; Estrada, A., Fleming, T.H., Eds.; Springer: Dordrecht, The Netherlands, 1986; pp. 105–118. [Google Scholar]
  80. Kurta, A.; Kunz, T.H. Capture Methods and Holding Devices. Ecological and Behavioral Methods for the Study of Bats; Kunz, T.H., Ed.; Smithsonian Institution Press: Washington, DC, USA, 1988; pp. 1–30. [Google Scholar]
  81. Santos-Cavalcante, N.; Passos Cordeiro, J.L.; Fernandes-Ferreira, H.; Mazzarotto, G.; Caccavo, A.; de Oliveira, M.B. First records of Myotis ruber and Molossus pretiosus for the state of Ceará, Northeast Brazil. Therya Notes 2024, 5, 60–68. [Google Scholar] [CrossRef]
  82. Fernandes-Ferreira, H.; Paise, G.; Gurgel-Filho, N.M.; Menezes, F.H.; Guerra, T.S.L.; Rodrigues, A.K.; Becker, R.G.; Feijó, J.A. Lista de Mamíferos Continentais do Ceará. 2021. Available online: https://www.sema.ce.gov.br/fauna-do-ceara/mamiferos (accessed on 3 May 2024).
Animals 15 00332 g001
Figure 1. Sampling points of bats in the state of Ceará, located in Guaramiranga, Pacoti, and Eusébio municipalities.
Figure 1. Sampling points of bats in the state of Ceará, located in Guaramiranga, Pacoti, and Eusébio municipalities.
Animals 15 00332 g001
Animals 15 00332 g002
Figure 2. Maximum likelihood phylogenetic reconstructions with reference genomes covering the known diversity of genera from the Coronaviridae family. (A) Phylogenetic tree reconstructed based on the full RdRp amino acid sequences of reference Coronavirus genomes plus the RdRp fragments recovered in this study using the best amino acid substitution model Q.insect+I+I+R5-, Coronavirus genera coded by color and the subgenera of the genus Betacoronavirus. Tips with blue circles denote the sequences generated in this study (partial RdRp). Branch support of key nodes are shown (aLTR/UFBOOT). (B) Pruned tree of the nucleotide-based phylogenetic reconstruction of the Betacoronavirus genus including RdRp partial sequences from the reference genomes (part A) and 440 bps of the 70 best blast hits against the non-redundant NCBI database, plus the sequence recovered in this study using the nucleotide substitution model GTR+F+I+G4. Blue tip and name denote the nucleotide sequence generated in this study, branch lengths are amino acid and nucleotide substitutions per site. Tip name abbreviations are related to the bat genus as follows: Art, Artibeus; Car, Carollia. Nexus files in the Supplementary Materials S1 and S2.
Figure 2. Maximum likelihood phylogenetic reconstructions with reference genomes covering the known diversity of genera from the Coronaviridae family. (A) Phylogenetic tree reconstructed based on the full RdRp amino acid sequences of reference Coronavirus genomes plus the RdRp fragments recovered in this study using the best amino acid substitution model Q.insect+I+I+R5-, Coronavirus genera coded by color and the subgenera of the genus Betacoronavirus. Tips with blue circles denote the sequences generated in this study (partial RdRp). Branch support of key nodes are shown (aLTR/UFBOOT). (B) Pruned tree of the nucleotide-based phylogenetic reconstruction of the Betacoronavirus genus including RdRp partial sequences from the reference genomes (part A) and 440 bps of the 70 best blast hits against the non-redundant NCBI database, plus the sequence recovered in this study using the nucleotide substitution model GTR+F+I+G4. Blue tip and name denote the nucleotide sequence generated in this study, branch lengths are amino acid and nucleotide substitutions per site. Tip name abbreviations are related to the bat genus as follows: Art, Artibeus; Car, Carollia. Nexus files in the Supplementary Materials S1 and S2.
Animals 15 00332 g002
Animals 15 00332 g003
Figure 3. Maximum likelihood pruned trees focusing on Amalacovirus and a sister non defined subgenus of the whole Alphacoronavirus tree (Supplementary Material S3) reconstructed using the best nucleotide substitution model GTR+F+I+I+R5. (A)—Phylogenetic tree excerpt showing nine sequences obtained in this study clustered within the Amalacovirus subgenus and (B)—a sister monophyletic clade with five sequences with no known Alphacoronavirus subgenus (dark pink clade). Branch lengths are nucleotide substitutions per site. Art, Artibeus; Car, Carollia; Phy, Phyllostomus; Stu, Sturnira; Des, Desmodus; Myo, Myotis; Dip, Diphylla; Glo, Glossophaga; Lic, Lichonycteris; Lon, Lonchorhina; Ano, Anoura; Pla, Platyrrhinus; Mol, Molossus; Gar, Gardnerycteris. The highlighted in blue circles represent the sequences generated in the present study.
Figure 3. Maximum likelihood pruned trees focusing on Amalacovirus and a sister non defined subgenus of the whole Alphacoronavirus tree (Supplementary Material S3) reconstructed using the best nucleotide substitution model GTR+F+I+I+R5. (A)—Phylogenetic tree excerpt showing nine sequences obtained in this study clustered within the Amalacovirus subgenus and (B)—a sister monophyletic clade with five sequences with no known Alphacoronavirus subgenus (dark pink clade). Branch lengths are nucleotide substitutions per site. Art, Artibeus; Car, Carollia; Phy, Phyllostomus; Stu, Sturnira; Des, Desmodus; Myo, Myotis; Dip, Diphylla; Glo, Glossophaga; Lic, Lichonycteris; Lon, Lonchorhina; Ano, Anoura; Pla, Platyrrhinus; Mol, Molossus; Gar, Gardnerycteris. The highlighted in blue circles represent the sequences generated in the present study.
Animals 15 00332 g003
Animals 15 00332 g004
Figure 4. Maximum likelihood pruned trees of non-defined subgenera. These genera are phylogenetically related to the subgenera Tegacovirus, Minacovirus, and Decacovirus from the whole Alphacoronavirus tree (Supplementary Material S3) reconstructed using the best nucleotide substitution model GTR+F+I+I+R5. (A) A single sequence obtained in this study showing well-supported clustering into another clade with no known Alphacoronavirus subgenus association (pinkish square). (B) Phylogenetic tree excerpt showing a sequence obtained in this study clustered within a monophyletic clade with no known Alphacoronavirus subgenus associated, which is a sister clade of Decacovirus subgenus. Branch support is aLRT/UFBOOT, sequences obtained in this study are highlighted in blue, and branch lengths are nucleotide substitutions per site. Art, Artibeus; Car, Carollia; Stu, Sturnira; Glo, Glossophaga; Pla, Platyrrhinus; Phy, Phyllostomus; Uro, Uroderma.
Figure 4. Maximum likelihood pruned trees of non-defined subgenera. These genera are phylogenetically related to the subgenera Tegacovirus, Minacovirus, and Decacovirus from the whole Alphacoronavirus tree (Supplementary Material S3) reconstructed using the best nucleotide substitution model GTR+F+I+I+R5. (A) A single sequence obtained in this study showing well-supported clustering into another clade with no known Alphacoronavirus subgenus association (pinkish square). (B) Phylogenetic tree excerpt showing a sequence obtained in this study clustered within a monophyletic clade with no known Alphacoronavirus subgenus associated, which is a sister clade of Decacovirus subgenus. Branch support is aLRT/UFBOOT, sequences obtained in this study are highlighted in blue, and branch lengths are nucleotide substitutions per site. Art, Artibeus; Car, Carollia; Stu, Sturnira; Glo, Glossophaga; Pla, Platyrrhinus; Phy, Phyllostomus; Uro, Uroderma.
Animals 15 00332 g004
Table 1. Bats infected with CoVs across three municipalities in Ceará, Brazil.
Table 1. Bats infected with CoVs across three municipalities in Ceará, Brazil.
FamilySpeciesNo of Bats Captured/No of Bats Infected with CoVs
EusebioGuaramirangaPacoti
MaleFemaleMaleFemaleMaleFemale
EmballonuridaeSaccopteryx leptura0/00/00/00/00/01/0
NoctilionidaeNoctilio leporinus0/03/03/01/00/00/0
Molossidae Molossus molossus1/01/00/00/00/01/0
PhyllostomidaeArtibeus cinereus1/01/03/02/03/04/0
Artibeus fimbriatus0/00/00/00/01/00/0
Artibeus lituratus1/01/00/00/00/00/0
Artibeus obscurus0/00/00/00/00/01/0
Artibeus planirostris11/014/00/00/010/12/0
Artibeus spp.0/00/00/01/01/01/0
Carollia perspicillata4/02/015/213/228/114/2
Glossophaga soricina2/01/00/00/021/124/2
Lonchophylla mordax0/00/00/00/01/00/0
Lonchorhina aurita0/00/00/00/02/02/2
Lophostoma brasiliense0/00/00/00/00/01/0
Micronycteris minuta0/00/00/00/01/00/0
Phyllostomus discolor2/15/04/16/19/17/1
Phyllostomus hastatus1/01/00/00/00/00/0
Phyllostomus spp.0/00/01/01/00/01/0
Platyrrhinus lineatus1/00/02/14/02/00/0
Platyrrhinus recifinus0/00/01/01/03/02/1
Sturnira lilium4/03/03/02/013/17/0
Sturnira tildae0/01/00/00/02/00/0
Vespertilionidae Eptesicus furinalis0/00/00/00/01/01/0
Myotis lavali1/02/00/00/01/02/0
Myotis spp.0/00/02/00/01/00/0
Total30/132/034/431/3100/571/8
Table 2. Positive samples for CoVs from bats collected in the state of Ceará, Brazil, and analyzed in the present study.
Table 2. Positive samples for CoVs from bats collected in the state of Ceará, Brazil, and analyzed in the present study.
Bat IDSample TypeLocalityBat SpeciesSexCoVVirus NameGenBank Accession Number
MBO477 R 1 EusebioPhyllostomus discolor♂AlfaBatCoV/Phyllostomus_discolor/Brazil/CE/FIOCRUZ-A211186/2021OR805808
NAC14 R GuaramirangaCarollia perspicillata♀AlfaBatCoV/Carollia_perspicillata/Brazil/CE/FIOCRUZ-A220424/2022OR805809
NAC28 R GuaramirangaCarollia perspicillata♀AlfaBatCoV/Carollia_perspicillata/Brazil/CE/FIOCRUZ-A220428/2022OR805810
PC118 R GuaramirangaPhyllostomus discolor♀AlfaBatCoV/Phyllostomus_discolor/Brazil/CE/FIOCRUZ-A220484/2022OR805811
PC122 R GuaramirangaPhyllostomus discolor♂AlfaBatCoV/Phyllostomus_discolor/Brazil/CE/FIOCRUZ-A220488/2022OR805812
ACA102 R GuaramirangaPlatyrrhinus lineatus♂AlfaBatCoV/Platyrrhinus_lineatus/Brazil/CE/FIOCRUZ-A220364/2022OR805813
NAC36R GuaramirangaCarollia perspicillata♂AlfaLow quality sequence (279 bps)not deposited
NAC32O 2 GuaramirangaCarollia perspicillata♂AlfaLow quality sequence (157 bps)not deposited
MBO497 RPacotiCarollia perspicillata♂AlfaBatCoV/Carollia_perspicillata/Brazil/CE/FIOCRUZ-A211329/2021OR805814
PC19 RPacotiSturnira lilium♂AlfaBatCoV/Sturnira_lilium/Brazil/CE/FIOCRUZ-A211383/2021OR805815
MBO514 RPacotiLonchorhina aurita♀AlfaBatCoV/Lonchorhina_aurita/Brazil/CE/FIOCRUZ-A211491/2021OR805816
PC108 RPacotiPlatyrrhinus recifinus♀AlfaBatCoV/Platyrrhinus_recifinus/Brazil/CE/FIOCRUZ-A220474/2022OR805817
PC112 RPacotiGlossophaga soricina♂AlfaBatCoV/Glossophaga_sorcina/Brazil/CE/FIOCRUZ-A220478/2022OR805818
PC156 RPacotiGlossophaga soricina♀AlfaBatCoV/Glossophaga_sorcina/Brazil/CE/FIOCRUZ-A220507/2022OR805819
PC158 RPacotiCarollia perspicillata♀AlfaBatCoV/Carollia_perspicillata/Brazil/CE/FIOCRUZ-A220509/2022OR805820
PC68 RPacotiCarollia perspicillata♀AlfaBatCoV/Carollia_perspicillata/Brazil/CE/FIOCRUZ-A220513/2022OR805821
PC111RPacotiPhyllostomus discolor♂AlfaBatCoV/Phyllostomus discolor/Brazil/CE/FIOCRUZ-A220477/2022OR805822
NAC60RPacoti Lonchorhina aurita♀ AlfaBatCoV/Lonchorhina_aurita/Brazil/CE/FIOCRUZ-A220460/2022OR805823
O
NAC39 RPacotiArtibeus planirostris♂BetaBatCoV/Artibeus_planirostris/Brazil/CE/FIOCRUZ-A220439/2022OR805824
ACA49 RPacotiPhyllostomus discolor♀AlfaLow quality sequence (207 bps)not deposited
PC05 RPacotiGlossophaga soricina♀AlfaLow quality sequence (170 bps)not deposited
1 R—rectal swab, 2 O—oral swab.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Figueiroa, T.; Galvão Bueno, M.; Bento Moura, P.E.; de Oliveira, M.B.; Passos Cordeiro, J.L.; Santos-Cavalcante, N.; Camacho Antevere Mazzarotto, G.A.; Wallau, G.L.; Corrêa da Silva Junior, L.; Resende, P.C.; et al. Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations. Animals 2025, 15, 332. https://doi.org/10.3390/ani15030332

AMA Style

Figueiroa T, Galvão Bueno M, Bento Moura PE, de Oliveira MB, Passos Cordeiro JL, Santos-Cavalcante N, Camacho Antevere Mazzarotto GA, Wallau GL, Corrêa da Silva Junior L, Resende PC, et al. Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations. Animals. 2025; 15(3):332. https://doi.org/10.3390/ani15030332

Chicago/Turabian Style

Figueiroa, Thays, Marina Galvão Bueno, Patricia Emilia Bento Moura, Marcione Brito de Oliveira, José Luís Passos Cordeiro, Nádia Santos-Cavalcante, Giovanny A. Camacho Antevere Mazzarotto, Gabriel Luz Wallau, Leonardo Corrêa da Silva Junior, Paola Cristina Resende, and et al. 2025. "Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations" Animals 15, no. 3: 332. https://doi.org/10.3390/ani15030332

APA Style

Figueiroa, T., Galvão Bueno, M., Bento Moura, P. E., de Oliveira, M. B., Passos Cordeiro, J. L., Santos-Cavalcante, N., Camacho Antevere Mazzarotto, G. A., Wallau, G. L., Corrêa da Silva Junior, L., Resende, P. C., Siqueira, M. M. M., & Ogrzewalska, M. (2025). Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations. Animals, 15(3), 332. https://doi.org/10.3390/ani15030332

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop