Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil
Open Access
- 2 August 2019
- Vol. 11 (8), 710
- https://doi.org/10.3390/v11080710
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.Keywords
Funding Information
- Embrapa (internal)
This publication has 68 references indexed in Scilit:
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell SequencingJournal of Computational Biology, 2012
- Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence dataBioinformatics, 2012
- ProtTest 3: fast selection of best-fit models of protein evolutionBioinformatics, 2011
- A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungusProceedings of the National Academy of Sciences of the United States of America, 2010
- New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0Systematic Biology, 2010
- Multiple Diverse Circoviruses Infect Farm Animals and Are Commonly Found in Human and Chimpanzee FecesJournal of Virology, 2010
- Fast and accurate long-read alignment with Burrows–Wheeler transformBioinformatics, 2010
- CD-HIT Suite: a web server for clustering and comparing biological sequencesBioinformatics, 2010
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksGenome Research, 2003