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SARS-CoV-2 surveillance in captive animals at the belo horizonte zoo, Minas Gerais, Brazil

Abstract

Background

The pandemic caused by SARS-CoV-2 has not only affected humans but also raised concerns about its transmission to wild animals, potentially creating natural reservoirs. Understanding these dynamics is critical for preventing future pandemics and developing control strategies. This study aims to investigate the presence of SARS-CoV-2 in wild mammals at the Belo Horizonte Zoo in Brazil, analyzing the virus's evolution and zoonotic potential.

Methods

The study was conducted at the Belo Horizonte Zoo, Minas Gerais, Brazil, covering a diverse population of mammals. Oropharyngeal, rectal, and nasal swabs were collected from 47 captive animals between November 2021 and March 2023. SARS-CoV-2 presence was determined using RT-PCR, and positive samples were sequenced for phylogenetic analysis. Consensus genomes were classified using Pangolin and NextClade tools, and a maximum likelihood phylogeny was inferred using IQ-Tree.

Results

Of the 47 animals tested, nine (19.1%) were positive for SARS-CoV-2. Positive samples included rectal, oropharyngeal, and nasal swabs, with the highest positivity in rectal samples. Three genomes were successfully sequenced, revealing two variants: VOC Alpha in a maned wolf (Chrysocyon brachyurus) and a fallow deer (Dama dama), and VOC Omicron in a western lowland gorilla (Gorilla gorilla gorilla). Phylogenetic analysis indicated potential human-to-animal transmission, with animal genomes clustering close to human samples from the same region.

Conclusions

This study highlights the presence of SARS-CoV-2 in various wild mammal species at the Belo Horizonte Zoo, emphasizing the virus's zoonotic potential and the complexity of interspecies transmission. The detection of different variants suggests ongoing viral evolution and adaptation in new hosts. Continuous monitoring and genomic surveillance of SARS-CoV-2 in wildlife are essential for understanding its transmission dynamics and preventing future zoonotic outbreaks. These findings underscore the need for integrated public health strategies that include wildlife monitoring to mitigate the risks posed by emerging infectious diseases.

Introduction

The pandemic caused by SARS-CoV-2 has been a major global challenge in terms of public health and economy. Since its discovery in December 2019, the virus has rapidly spread worldwide, infecting millions of people and causing thousands of deaths [1]. Human-to-human transmission of the virus is well known, but the possibility of transmission from humans to wild animals has raised concerns about the potential formation of natural reservoirs of the virus and its risks to public health [2].

Recent studies have shown that SARS-CoV-2 infection can occur in wild, domestic and zoo animals. In various regions of the world, wild animals such as tigers, lions, monkeys, and minks have been found to be infected with SARS-CoV-2 [3, 4]. This highlights the importance of understanding the spillover mechanism and the zoonotic potential of the disease. Furthermore, comparative analysis of virus sequencing and phylogenetic assembly in humans and wild animals can provide valuable insights into the virus's evolution and its transmission between different species [5, 6].

The Belo Horizonte Zoo, located in Minas Gerais (MG), Brazil, is a site of great interest for studying SARS-CoV-2 infection in wild animals, as it has had cases of infection in some of its species. Genomic studies conducted on samples from infected animals at the zoo and in other regions of the world have shown that wild animal virus sequences differ from human virus sequences, suggesting the existence of different viral lineages circulating in different species. Additionally, indicate adaptation of the virus to the host, highlighting the complexity of the virus-host interaction [7, 8].

Understanding the dynamics of SARS-CoV-2 transmission in different species is crucial for preventing future pandemics and developing effective disease control strategies [9]. Therefore, studying SARS-CoV-2 infection in wild animals at the Belo Horizonte Zoo is highly relevant to public health and biodiversity conservation, as well as contributing to the advancement of knowledge about the relationship between SARS-CoV-2 and wild animals, and the formulation of public policies and management strategies for pandemic prevention and control.

This study aims to review the current evidence of SARS-CoV-2 infection in wild mammals at the Belo Horizonte Zoo, highlighting the zoonotic potential of the disease and the risks of natural reservoir formation in forests and wilderness areas [10, 11]. Additionally, it seeks to analyze the virus's evolution through phylogenetic and comparative sequence analysis to understand better the spillover mechanism and implications for public health [12, 13].

Materials and methods

Ethical statement

The samples used in this study were collected as part of the service provided by the Federal University of Minas Gerais (UFMG) to the Municipal Park and Zoobotanical Foundation of Belo Horizonte (FPMZB), under extension code Siex-UFMG 302557. All procedures related to animal handling, including capture and restraint, were conducted by veterinarians from the FPMZB staff, ensuring adherence to the protocols established for extension activities by UFMG.

Study area and sampling information

The present study was conducted at the FPMZB, which covers a total area of 10.7 million square meters. This foundation hosts, within its Zoo, more than 3,500 individuals, representing over 235 species, with approximately 36 species of mammals totaling 117 individuals. Among these species, over 40 are at risk of extinction, spanning reptiles, birds, fish, amphibians, and mammals from all five continents. It's worth noting that the Zoo's infrastructure includes a veterinary hospital [14].

FPMZB has a well-established history of preserving biodiversity and managing environmental protection areas in Belo Horizonte (MG) (-19.857889841, -44.0075113912). Its foundation was established through Decree 16,684 on August 31, 2017, which merged the former Municipal Parks Foundations and the Zoo-Botanical Foundation. In the context of Belo Horizonte, FPMZB plays a significant role in the conservation of local ecosystems and the research of various mammal species present in its parks and botanical gardens. Remarkably, these spaces house a variety of over a thousand species, representing the Cerrado and Atlantic Forest, biomes found in different regions of Brazil [15].

The relevance of FPMZB as a research site lies in the diversity of mammal species found in its parks, including the marsh deer (Blastocerus dichotomus), the black tufted marmoset (Callithrix penicillata), and the maned wolf (Chrysocyon brachyurus), which may serve as important potential reservoirs for zoonotic pathogens, such as SARS-CoV-2 [16]. Given the global concern about interspecies transmission of the virus between humans and animals, the study investigated the role of these species in the transmission chain and sought a better understanding of the pandemic's dynamics to develop effective prevention strategies. FPMZB is the second-largest public green area in Belo Horizonte and receives over one million visitors annually.

Sample collection

Oropharyngeal, rectal, and nasal swabs were collected from 47 captive animals of the class Mammalia between November 2021 to March 2023, with the aim of investigating SARS-CoV-2 infection in captive animals with no prior knowledge of virus exposure.

Capture and containment of the animals were carried out by the veterinary team at the FPMZB Zoo, who possess the necessary experience and knowledge to ensure the well-being and safety of the animals during the collection process, which was done after the physical and/or chemical restraint of the animals. This was done in accordance with the zoo's management schedule, and whenever containment was necessary for obtaining biological samples.

Laboratories responsible for the analysis in this study provided 1.5 ml Eppendorf tubes containing DNA/RNA Shield™ (2X Concentrate) 125 ml (ZymoResearch) for the collection of animal samples. Each collected sample was properly identified with the animal's microchip number, ensuring data traceability. After collection, the samples were stored in transport containers and subsequently in -80 °C freezers at the Laboratory of Integrative Biology (ICB/UFMG) to maintain their integrity and viability.

Real-time PCR

Viral RNA was extracted from swab samples (rectal, oropharyngeal, and nasal) using the PureLink™ RNA Mini Kit (Invitrogen™, MA, USA), following the manufacturer's protocol.

RNA samples were tested for the presence of SARS-CoV-2 using the CDC 2019-Novel Coronavirus Real-Time RT-PCR Diagnostic Panel (N1, N2) [17]. These tests were performed using the iTaq™ Universal Probes One-Step (Bio-RAD™, CA, USA), following the manufacturer's instructions. The diagnosis was carried out by RT-PCR following the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel protocol.

Sequencing and assembly of SARS-CoV-2 genomes

The samples underwent a concentration and purification process using the RNA Clean & Concentrator™-5 kit (Zymo Research™, CA, USA) to concentrate the amount of viral RNA and eliminate potential contaminants. The cDNA was synthesized using the SuperScript™ IV First-Strand Synthesis System (Thermo Fisher Scientific™, MA, USA).

Sequencing libraries were prepared using the xGen™ SARSCoV-2 Amplicon Panel xGen SARS-CoV-2 S Gene Amplicon Panel (Integrated DNA Technologies™, San Diego, CA, USA) following the manufacturer's instructions. Multiplex PCR was used to enrich the target sequences, as the samples had a Ct > 30.

After library preparation, samples were quantified using the Invitrogen™ Qubit™ 4 Fluorometer (Thermo Fisher Scientific™, MA, USA), and 10 samples were selected to continue the sequencing process. The genomes were sequenced on the MiSeq platform (Illumina™, San Diego, CA, USA) with v3 cartridges (600 cycles) following the manufacturer's instructions. After sequencing, the raw data were used to a custom pipeline optimized for viral genome assembly, following the same protocol described in Moreira et al., 2021 [18].

Briefly, the reads were filtered by quality Phred > 30, the remaining reads were aligned to the reference genome of SARS-CoV-2 (GenBank accession number NC_045512.2) using Bowtie2 [19], and consensus sequences were generated using BEDtools [20] and BCFtools [21]. Sequences that had the expected sequencing quality parameters (coverage greater than or equal to 60% of the genome) were used in our study.

Lineage classification and phylogenetic analysis

The consensus genomes generated were classified using the Pangolin tools [22] and the NextClade web application v2.8.1 [23]. After classification, we constructed a dataset based on human sequences for each of the VOCs (Alpha—190, Beta—13, Zeta—150, Gamma—40, Delta—116, and Omicron—150) from Belo Horizonte (MG) and animal genomes (n = 220; identified all around the world) publicly available in public databases, plus the genomes generated in the study (n = 03). The dataset was aligned using the minimap2 program v.2.2.24 [24] and then used to infer a maximum likelihood phylogeny using the program IQ-Tree v2.0.3 and the evolutionary model GTR + F + I + G4 [25]. Shimodaira-Hasegawa-like approximate likelihood ratio test (SH-aLRT) was used to calculate the branch uncertainty in the phylogeny.

Results

Characteristics of the study population

Total group studied exhibited heterogeneity, with representation from animals of different orders and families. The most common and representative categories were as follows: 48.9% (23/47) from the Primate order, 14.89% (7/47) from the Artiodactyla order, in which 71.43% (5/7) from the Cervidae family and 34% (16/47) from the Carnivora order, such as 43.75% (7/16) from the Canidae family and 50% (8/16) from the Felidae family. Most of the animals were adults—95,7% (45/47) and 4,3% (2/47) were cubs, with 18 females (38.2%) and 29 males (61.8%) (Fig. 1).

Fig. 1
figure 1

Map of the Belo Horizonte Zoo. Black dots denote the locations of the cages, each identified with the lowest taxonomic classification among the individuals housed within. Red circles mark cages where animals tested positive for RT-PCR, while blue points indicate successfully sequenced animals

Detection of SARS-CoV-2 infection

Out of the 47 mammals examined, the presence of SARS-CoV-2 RNA was identified in nine of them, resulting in a positivity rate of 19.1%. Among the 147 collected swab samples, SARS-CoV-2 RNA was found in five rectal samples (10.6%), three oropharyngeal samples (6.3%), and two nasal samples (5.8%). One animal (AZ16) tested positive for rectal and nasal swabs. However, during the period of March 2020 to January 2022, the zoo found itself with different levels of capacity restrictions due to security measures against the COVID-19 pandemic. During this period of time, seven animals were sampled and three animals were positive for SARS-CoV-2 (Fig. 2) (Appendix 1).

Fig. 2
figure 2

Timeline of samples collected at the Belo Horizonte Zoo from November 2021 to March 2023. Blue dots represent the number and moment of sample collection from November 2021 to January 2022 when the zoo reduced visitor entry. Black dots represent the number and moment of sample collection from February 2022 to March 2023 when the zoo was open for visitors. Black bars represent the positive samples found in each collection, with one positive sample on 04/11/2021, two on 22/11/2021, two on 02/08/2022, one on 10/03/2022, three on 16/05/2022, and one on 27/05/2022

All positive samples were subjected to sequencing, but only three of them were successfully sequenced (AZ13, AZ16 nasal, and AZ17), with the sequence being detected only in the nasal swab of the fallow deer (Dama dama)—AZ16, the rectal swab of the maned wolves (Chrysocyon brachyurus)—AZ13, and the oropharyngeal swab of the swab of the western lowland gorilla (Gorilla gorilla gorilla)AZ17 (Table 1).

Table 1 Summary of results for SARS-CoV-2 in captive animals at the Belo Horizonte Zoo, Minas Gerais, Brazil

Genomic characterization of positive SARS-CoV-2 samples

The three genomes sequenced in our study showed an average of 71% genome coverage. Two samples (AZ13—maned wolf and AZ16—fallow deer) were classified as VOC Alpha, while sample AZ17 (western lowland gorilla) was classified as VOC Omicron by strain classification softwares. All sequencing metrics, lineage classification, and all genomes deposited in the GISAID EpiCoV database are available in Appendix 2. To corroborate the classification, we performed a phylogenetic tree with the main variants described around the world. The result of the analysis corroborates the classification of the samples (Fig. 3). The AZ17 sample (western lowland gorilla), classified as VOC omicron, in the phylogeny is represented almost as an outgroup. This occurred since the genome coverage was less than 50%. Samples AZ13 (maned wolf) and AZ16 (fallow deer), classified as VOC Alpha, were grouped together, indicating possible local transmission between animals. Moreover, in the phylogenetic analysis, deer sequences from other regions of the globe were included; however, the samples were grouped closer to human samples collected in the same state, suggesting that there was possibly a transmission from humans to animals.

Fig. 3
figure 3

Phylogenetic analysis inferred by maximum likelihood method. The tree presents three new SARS-CoV-2 animal genomes, generated in our study (AZ13, AZ16 and AZ17), 220 SARS-CoV-2 animal genomes and 530 SARS-CoV-2 human genomes public available on GISAID EpiCoV database. Each branch is filled according to the host from which it was isolated. Gray lines indicate human genomes. Purple circles represent the genomes generated in our study. Bootstrap values for the most important branches are exhibited with the lineage classification

Discussion

Zoos are unique in terms of the epidemiology of human-animal interactions. They shelter multiple species of wildlife from a wide range of taxonomic groups in relative proximity, and interactions between animals and humans are frequent, especially for animal caregivers. Therefore, the COVID-19 pandemic has triggered research for data collection and surveillance of suspected cases of SARS-CoV-2 infection in zoo animals [26]. During the initial months of this study (November 2021 to January 2022), the zoo operated with limited capacity and restricted visitor access as a pandemic control measure. Despite these precautions, three animals tested positive for the virus during this period, suggesting that infection could have occurred through contact with zookeepers [3, 7]. However, starting in February 2022, when the zoo reopened to visitors, there was an observed increase in the detection of SARS-CoV-2-positive animals. This trend raises the possibility that increased human traffic may have heightened the risk of transmission to the keepers, who then potentially transmitted the virus to the animals via direct contact or aerosol exposure [5, 8]. Nevertheless, the limitations of our study prevent us from definitively identifying the route of infection, and further research is necessary to confirm these observations.

We detected SARS-CoV-2 RNA in nine (19.1%) of captive mammals at the zoo in Belo Horizonte, MG, Brazil, who showed no clinical signs of infection. Our results are in contrast to the findings of a study conducted in zoos in Belgium, where no presence of SARS-CoV-2 was observed in fecal samples from a wide range of mammal species, despite systematic surveillance and specific monitoring following a known infection in hippos in December 2021 [27]. This difference in results can be attributed to various factors, including the virus's dynamics in the region, animal management practices, or differences in sample collection and detection methods [28]. Additionally, the specific dates and conditions of our study may have influenced the outcomes. This discrepancy underscores the need for more comprehensive and long-term studies to gain a better understanding of SARS-CoV-2 transmission between humans and animals, both in captivity and in the wild.

In the present study, we report natural SARS-CoV-2 infection in three western lowland gorillas (Gorilla gorilla gorilla), two maned wolves (Chrysocyon brachyurus), one pampas cat (Leopardus braccatus), one brown brocket deer (Subulo gouazoubira), one red deer (Cervus elaphus) and one fallow deer (Dama dama). The detected infection in these animals is consistent with previous reports of non-domestic species infected with SARS-CoV-2 in both wild, captive, and experimental settings: gorillas [29], wild canids [30], wild felids [8, 31,32,33,34] and white-tailed deer (Odocoileus virginianus) [35,36,37].

It is noteworthy that some of the species investigated in our study had previously been described as susceptible to SARS-CoV-2 infection, according to the World Organization for Animal Health (WOAH) [38]. For instance, gorillas (Gorilla gorilla) have demonstrated high susceptibility to natural infection. Furthermore, species like the white-tailed deer (Odocoileus virginianus) exhibited high susceptibility in experimental infections [35]. In other studies, red foxes (Vulpes vulpes) were found to become infected and shed infectious virus after experimental inoculation [30].

In the context of infections in felids, although the majority of case reports of SARS-CoV-2 infection pertain to domestic cats [39], several cases in wild felids have been reported in different parts of the world. This includes members of the Panthera genus, such as tigers, lions, and snow leopards, as well as members of the Puma genus, like the puma (Puma concolor) [40].

Although nine animals tested positive for SARS-CoV-2, we were able to sequence samples from only three animals due to issues with the quantity and quality of the sample. Our results indicate the circulation of two variants in the studied zoo, VOCs Omicron and Alpha. The detection of positive samples classified as Alpha was described in recent studies on deer in Canada and the United States, in which they observed both human-to-animal transmission [37, 41]. Furthermore, it was observed that despite being classified as Alpha, the genomes contain certain mutations that are specific to deer. This suggests the evolution of the virus to a different host: the deer [36,37,38]. The persistence of VOC Alpha in deer may be due to the long-term spread of the variant in the animal, which could lead to the emergence of new mutations [42].

In our phylogenetic analysis, it was possible to observe that two samples AZ13 (maned wolf) and AZ16 (fallow deer) were grouped together and close to samples from human hosts, suggesting that the infection was transferred from humans to animals, possibly to the caretakers of the zoo animals. Nevertheless, we did not examine SARS-CoV-2 infection in animal caretakers, which represents a limitation of the study, as it did not allow for the identification of the source of infection. Our main hypothesis suggests close-contact transmission between animals and their caretakers. Historically, all instances of natural infection in zoo animals have been linked to initial transmission from humans to the animals in their care [8, 31, 43, 44].

Zoonotic infections are common hazards for humans involved in animal welfare management, including veterinarians, zoo and reserve workers, breeders, and farmers [44]. Zoonoses represent a significant concern for public health. According to studies, approximately 60% of emerging pathogens that affect humans have their origins in animals. Furthermore, over 71% of these pathogens originate from wildlife. These pathogens have the capacity to adapt and switch hosts, acquiring new genetic combinations that can enhance their pathogenic potential. Changes in the behavior, socioeconomic, environmental, or ecological characteristics of hosts can also play a role in the transmission of these diseases [45]]. Thus, the monitoring of SARS-CoV-2 infection in wild and domestic animals is important for tracking the appearance of new mutations, possible adaptation of the virus to new hosts and emergence of new lineages in circulation in that area.

Conclusions

The findings of this study underscore the significant risk posed by interspecies transmission of SARS-CoV-2, particularly in environments where humans and a diverse range of animal species are in close proximity, such as zoos. The detection of SARS-CoV-2 RNA in 19.1% of the tested mammals at the Belo Horizonte Zoo and the successful sequencing of three animal samples highlight the virus's ability to infect multiple species, potentially creating new reservoirs and facilitating viral evolution.

This research provides critical insights into the dynamics of SARS-CoV-2 transmission between humans and animals, suggesting that close contact between zoo animals and their caretakers is a likely route of infection. The identification of different viral lineages, such as the Alpha and Omicron variants, in the zoo animals further emphasizes the importance of ongoing surveillance to understand the virus's adaptation and evolution in new hosts.

Given the zoonotic nature of many emerging infectious diseases, these findings are crucial for public health, biodiversity conservation, and the development of effective disease control strategies. Continuous monitoring and genomic analysis of SARS-CoV-2 in both wild and domestic animals are essential to track new mutations, understand the virus's host adaptation, and prevent the emergence of new variants that could pose additional risks to human health.

Overall, this study provides valuable data for the global understanding of SARS-CoV-2 and reinforces the need for comprehensive surveillance systems to mitigate the impact of future pandemics and safeguard both human and animal health.

Availability of data and materials

Data and materials are available upon request to the corresponding author.

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Acknowledgements

Special thanks are extended to all employees of the laboratory PROTOVET, Residents in Public Health with emphasis on human and wildlife health interface, to the mammal management team at the Fundação de Parques Municipais e Zoobotânica – FPMZB de Belo Horizonte.

Funding

This work was supported by grants from UFMG – Universidade Federal de Minas Gerais, CAPES – Coordenação de Aperfeiçoamento de Pessoal de Nível Superior and CNPq – Conselho Nacional de Desenvolvimento Científico e Tecnológico, for the PQ fellowship. We acknowledge support from FAPEMIG (BPD-00820-22), Rede Corona-ômica BR MCTI/FINEP affiliated with RedeVírus/MCTI (1227/21); Instituto Todos pela Saúde—ITpS (Chamada 01/2021-C1294); CNPq (315592/2021-4, INCT-One CNPq 405786/2022-0); FINEP (0494/20 01.20.0026.00); CAPES (Finance Code 001).

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Authors

Contributions

Anisleidy Pérez Castillo: Conceptualization, investigation, methodology, analysis, formal analysis, data curation, writing–original draft, writing, reviewing, and editing, Joao Victor Oliveira Miranda: Methodology, formal analysis, data curation, writing – original draft, review and editing, Paula Luize Camargos Fonseca: Methodology, formal analysis, data curation, visualization, writing – original draft, writing, review, and editing, Rennan Garcias Moreira: Methodology, formal analysis, and data curation, Luiza Campos Guerra de Araújo e Santos: Methodology. Daniel Costa Queiroz: Methodology. Diego Menezes Bonfim: Methodology, original draft. Carlyle Mendes Coelho: Methodology, Investigation. Paula Cristina Senra Lima: Methodology, Investigation. Rafael Otávio Cançado Motta: Methodology, Investigation. Herlandes Penha Tinoco: Methodology, Investigation. Júlia Angélica Gonçalves da Silveira: Conceptualization, resources, investigation, supervision, funding acquisition, review, and editing, Renato Santana de Aguiar: Conceptualization, resources, review, editing, investigation, supervision, funding acquisition and editing. All the authors have read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Júlia Angélica Gonçalves da Silveira or Renato Santana Aguiar.

Ethics declarations

Ethics approval and consent to participate:

The samples were collected as part of a UFMG service to the Belo Horizonte Zoo (FPMZB) under extension code Siex-UFMG 302557. No ethical approval was needed, and written consent was obtained from the zoo administration for the animals' participation.

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Not applicable.

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The authors declare no competing interests.

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Castillo, A.P., Miranda, J.V.O., Fonseca, P.L.C. et al. SARS-CoV-2 surveillance in captive animals at the belo horizonte zoo, Minas Gerais, Brazil. Virol J 21, 297 (2024). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12985-024-02505-9

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