Faecal Virome Analysis of Wild Animals from Brazil

Abstract

The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal’s susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. Based on this scenario, high-throughput sequencing contributes a robust tool for the identification of known and unknown virus species in this environment. In the present study, faeces samples from cerrado birds (Psittacara leucophthalmus, Amazona aestiva, and Sicalis flaveola) and mammals (Didelphis albiventris, Sapajus libidinosus, and Galictis cuja) were collected at the Veterinary Hospital, University of Brasília. Viral nucleic acid was extracted, submitted to random amplification, and sequenced by Illumina HiSeq platform. The reads were de novo assembled, and the identities of the contigs were evaluated by Blastn and tblastx searches. Most viral contigs analyzed were closely related to bacteriophages. Novel archaeal viruses of the Smacoviridae family were detected. Moreover, sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families were identified. Complete and nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses were obtained, as well as putative novel species. We demonstrate that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna.

Adenoviruses across the animal kingdom: a walk in the zoo

“…Type 1 was found to occur in Senegal parrot, red‐fronted parrot, and red‐breasted parakeet, whereas PsAdV‐4 originated from red‐bellied parrot . Additional aviadenovirus sequences, obtained from Meyer’s parrot, white‐eyed parakeet , four different falcon species (Aplomado falcon, American kestrel, orange‐breasted falcon, Teita falcon), gull, and Humboldt penguin , as well as neotropic cormorant were also published. Metagenomics study of crane fecal samples revealed almost the complete genome sequence of a new aviadenovirus with a surprisingly low (34%) G+C content .…”

Special Issue “Emerging Viruses: Surveillance, Prevention, Evolution, and Control”

“…Moutelíková et al [34] show the emergence of rare bovine-human reassortant DS-1-Like rotavirus A strains in human patients in the Czech Republic. Duarte et al [35] present the virome of different wild birds and mammals from Brazilian cerrado, showing sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families, complete or nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses, as well as putative novel species.…”

A Novel and Divergent Gyrovirus with Unusual Genomic Features Detected in Wild Passerine Birds from a Remote Rainforest in French Guiana

“…However, our study shows that GyV11 can be dispersed by the faeces of, at least, two different avian species (Myrmeciza ferruginea and Pithys albifrons) and is likely circulating among different bird species within the same community. In fact, in a closer area such as Brazil, the circulation of a phylogenetically close genotype (GyV4) has been detected in chickens and three other gyroviruses (CAV, GyV2, and GyV3) have been found in the fecal virome of wild birds [3,36].…”

“…In recent years, numerous novel viruses and virus variants have been discovered by virus metatranscriptomics and metagenomics in different bird species, mainly in wild birds [1][2][3]. Nevertheless, there is still very little known about viruses that circulate in wild birds, especially…”