Viral diversity in wild rodents in the regions of Canaã de Carajás and Curionopólis, State of Pará, Brazil

Abstract

Wild rodents serve as crucial reservoirs for zoonotic viruses. Anthropogenic and environmental disruptions, particularly those induced by mining activities, can destabilize rodent populations and facilitate the emergence of viral agents. In the Canaã dos Carajás and Curionópolis regions of Brazil, significant environmental changes have occurred due to mining expansion, potentially creating conditions conducive to the emergence of rodent-associated viral diseases. This study aimed to investigate the viral diversity in wild rodents captured in Canaã dos Carajás and Curionópolis, Pará, between 2017 and 2019. A total of 102 rodent samples were taxonomically identified through karyotyping and screened for anti-Orthohantavirus antibodies using the ELISA method. Subsequently, nucleotide sequencing and bioinformatics analyses were conducted on 14 selected samples to characterize the virome. This selection was based on the most commonly associated rodent genera as reservoirs of Orthohantavirus and Mammarenavirus. Of the 102 samples tested via ELISA, 100 were negative, and two showed optical density at the cutoff point. Sequencing of the 14 samples generated approximately 520 million reads, with 409 million retained after quality control. These reads were categorized into 53 viral families, including both DNA and RNA viruses, with Retroviridae, Baculoviridae, and Microviridae being the most abundant. Viral contigs were identified, including one fragment related to Arenaviridae and three to Filoviridae. Metagenomic analysis revealed high viral diversity in the sampled rodents, with the presence of viral families of public health concern, such as Arenaviridae and Filoviridae. The findings suggest that increased human activities associated with mining may contribute to the emergence of these viruses, underscoring the need for ongoing surveillance to prevent potential outbreaks.

Keywords: Arenaviridae; Filoviridae; epidemiologic vigilance; metagenomics; rodent.

Figure 1

Map showing the location of rodent capture sites in the municipalities of Canaã dos Carajás and Curionópolis, State of Pará, Brazil. The figure was created using QGIS v.3.10.4 software (available at https://qgis.org/pt_BR/site), in conjunction with the IBGE 2022 database (available at: https://www.ibge.gov.br/).

Figure 2

Heatmap of viral reads, normalized on a log₁₀ scale, showing 53 viral families detected across the evaluated samples. The clusters indicate groupings based on abundance levels. The samples are displayed on the x-axis, and the potentially detected viral families are displayed on the y-axis. Samples from the regions of Canaã dos Carajás and Curionópolis are highlighted in blue and red, respectively.

Figure 3

(A) Representation of the functional domains of the Arenaviridae glycoprotein region, comparing the identified contig with other members of the viral family. (B) Representation of the functional domains of the Filoviridae nucleoprotein region, comparing the identified contigs with other members of the viral family (BioProject PRJNA1157879).

Figure 4

(A) Phylogenetic reconstruction using the Maximum Likelihood method based on amino acid sequences from the glycoprotein region of New and Old World Arenaviruses, including the identified contig highlighted in red. (B) Maximum likelihood mapping diagram showing the quality of the phylogenetic signal from the quartet analysis, with 90.2% of quartets resolved. (C) Heatmap of nucleotide (lower triangle) and amino acid (upper triangle) identities between representatives of clades (A, C) of New World Arenaviridae, including the identified contig (BioProject PRJNA1157879).

Figure 5

(A) Phylogenetic reconstruction using the Maximum Likelihood method based on amino acid sequences of Filoviridae. (B) Maximum Likelihood mapping diagram showing the quality of the phylogenetic signal from the quartet analysis, with 64.8% of quartets resolved. (C) Heatmap of nucleotide (lower triangle) and amino acid (upper triangle) identities between the identified contigs and representatives of the genera Orthoebolavirus, Cuevavirus, Orthomarbugvirus, and Dianlovirus (BioProject PRJNA1157879).