Unravelling the Single-Stranded DNA Virome of the New Zealand Blackfly

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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.

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil

Fontenele

Lacorte

Lamas

et al. 2019

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“…Currently, the ICTV recognises 11 families of ssDNA viruses, with several new families discovered recently including the Genomoviridae, Redondoviridae, and Smacoviridae [13,15,33]. Known invertebrate ssDNA viruses include members of the Parvoviridae, Circoviridae, and Bidnaviridae, and recent metagenomic studies have recently identified ssDNA in a variety of invertebrates, including termites [34], pine beetles [35] honey bees [36], dragonflies [6], and a range of marine and terrestrial invertebrates [9,37]. Similarly, CRESS DNA viruses, that contain many ssDNA virus families (including the Genomoviridae, Smacoviridae, Bacilladnaviridae, and Circoviridae), have also been sampled from invertebrates [33], as well as from such diverse environments as oceans and estuaries [38,39] and even poxvirus lesions in tanagers [31].…”

Section: Discussionmentioning

confidence: 99%

Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics

Porter

Shī

Eden

et al. 2019

DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. By incorporating the sequence of a “blank” experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the diversity and evolution of DNA viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.

“…Single-stranded DNA (ssDNA) viruses are currently classified into 13 families ( Anelloviridae, Bacillidnaviridae, Bidnaviridae, Circoviridae, Geminiviridae, Genomoviridae, Inoviridae, Microviridae, Nanoviridae, Parvoviridae, Pleolipoviridae, Smacoviridae and Spiraviridae ) and those that encode replication-associated protein (Rep) are known informally as circular Rep-encoding ssDNA (CRESS) viruses [48,49]. Once thought to be relatively rare, metagenomic studies have more recently revealed that ssDNA viruses in particular are ubiquitous in many environments and infect a diversity of hosts [37,50,51,52,53,54,55,56,57,58,59]. Families of ssDNA viruses, such as Microviridae comprise of bacteriophages, those that have been cultured infect enterobacteria and parasitic bacteria [60].…”

Section: Introductionmentioning

confidence: 99%

Single-Stranded DNA Viruses in Antarctic Cryoconite Holes

Sommers

Fontenele

Kringen

et al. 2019

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Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.