Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil

Abstract

Capybaras (Hydrochoerus hydrochaeris), the world’s largest rodents, are distributed throughout South America. These wild herbivores are commonly found near water bodies and are well adapted to rural and urban areas. There is limited information on the viruses circulating through capybaras. This study aimed to expand the knowledge on the viral diversity associated with capybaras by sampling their faeces. Using a viral metagenomics approach, we identified diverse single-stranded DNA viruses in the capybara faeces sampled in the Distrito Federal, Brazil. A total of 148 complete genomes of viruses in the Microviridae family were identified. In addition, 14 genomoviruses (family Genomoviridae), a novel cyclovirus (family Circoviridae), and a smacovirus (family Smacoviridae) were identified. Also, 37 diverse viruses that cannot be assigned to known families and more broadly referred to as unclassified circular replication associated protein encoding single-stranded (CRESS) DNA viruses were identified. This study provides a snapshot of the viral diversity associated with capybaras that may be infectious to these animals or associated with their microbiota or diet.

Metagenomics of Neotropical Single-Stranded DNA Viruses in Tomato Cultivars with and without the Ty-1 Gene

“…Both isolates were collected in Leopoldo de Bulhões, Goiás (GO) State in 2004. These isolates displayed 98% identity to Capybara genomovirus 9 isolate cap1_561 (MK483081.1) from Brazil [ 56 ]. The gemycircularviruses have ssDNA, and some species of this genus have been reported in association with plants [ 57 , 58 , 59 ].…”

Novel Circoviruses Detected in Feces of Sonoran Felids

“…Fecal viral metagenomics 5g of the fecal sample were homogenized in SM buffer and the homogenate was centrifuged at 6,000 × g for 10mins. The supernatant was sequentially filtered through 0.45μm and 0.2μm syringe filters and viral particles in the filtrate were precipitated with 15% (w/v) PEG-8000 with overnight incubation at 4°C followed by centrifugation at 10,000 × g as described in Fontenele et al [26].…”

“…Genomes from several families of circular rep-encoding single-stranded DNA viruses (CRESS-DNA viruses, which contain a gene for the rolling circle replication associated protein (Rep)) are part of the phylum Cressdnaviricota [22] and have been identified in fecal viral metagenomic studies of other mammals, including domestic cats [23,24], bobcats, African lions [25], capybaras [26], and Tasmanian devils [27]. Circoviridae is one of the families in the Cressdnaviricota phylum and is composed of the genera Circovirus and Cyclovirus.…”

Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer

“…These are widely found in various environments [12,13], plant samples [14][15][16][17], dragonflies and damselflies [18][19][20][21], mosquitoes [22], rats [23], bats [24], duck [25], cattle [26], pigs [27,28], dogs [29], human [30][31][32][33], and turkey [34]. CRESS-DNA genomes typically encode a replication initiator protein (Rep) and a capsid protein (Cap) [35].…”