Journal Article
Fecal virome of paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) in Rio de Janeiro, Brazil
Thamiris dos Santos Miranda; Matheus Augusto Calvano Cosentino; Filipe Romero Rebello Moreira; Francine Bittencourt Schiffler; Amanda Coimbra; Ricardo Mouta; Gabriel Medeiros; Déa Luiza Girardi; Victor Wanderkoke; Monique Lima; Thiago Henrique de Oliveira; Talitha Mayumi Francisco; Flávio Landim Soffiati; Suelen Sanches Ferreira; Carlos Ramon Ruiz-Miranda; Marcelo Alves Soares; Mirela D’arc; André Felipe Andrade dos Santos
Brazilian Journal of Microbiology · Vol. 57, Issue 1 · 2026
Abstract
The Paraguayan hairy dwarf porcupine ( Coendou spinosus , Cuvier, 1823) is a rodent species (Rodentia, Erethizontidae) widely distributed in the Brazilian Atlantic forest. However, little is known about their viral diversity. In this study, we aimed to evaluate, using high-throughput sequencing (HTS), the virome of the feces of seven healthy adult free-living porcupines from Silva Jardim, Rio de Janeiro, Brazil. Total viral nucleic acid was extracted and used for the library preparation for HTS using the Illumina MiSeq platform. The bioinformatics pipeline included quality control, with taxonomic assignments by Kraken2 and Diamond. Unclassified RNA viruses were investigated for viral genome characterization. A total of 41 viral families were classified, of which only seven were validated by both taxonomic analysis tools, including bacteriophages, vertebrate viruses, and unclassified RNA viruses. The most abundant bacterial reads identified belonged to the phylum Proteobacteria. In addition, in-depth analyses of RNA viruses revealed the presence of the Tombusviridae family, a group of plant-infecting viruses possibly associated with the host’s diet. This study provides new insights into the fecal virome of Paraguayan hairy dwarf porcupines, contributing to the knowledge of microbial diversity in Erethizontidae and supporting non-invasive virome studies in wildlife.