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.

Keywords: Animal surveillance; Epidemiology; Genomic analysis; Mammals; SARS-CoV-2; Viral adaptation; Wildlife; Zoonotic transmission; Zoos.

Fig. 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

Fig. 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

Fig. 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