Virus taxonomy in the age of metagenomics

P Simmonds, MJ Adams, M Benkő, M Breitbart… - Nature Reviews …, 2017 - nature.com
The number and diversity of viral sequences that are identified in metagenomic data far
exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of …

Eukaryotic circular rep-encoding single-stranded DNA (CRESS DNA) viruses: ubiquitous viruses with small genomes and a diverse host range

L Zhao, K Rosario, M Breitbart, S Duffy - Advances in virus research, 2019 - Elsevier
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic
architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA …

Discovery of several thousand highly diverse circular DNA viruses

MJ Tisza, DV Pastrana, NL Welch, B Stewart, A Peretti… - elife, 2020 - elifesciences.org
Although millions of distinct virus species likely exist, only approximately 9000 are
catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of …

Reproducible protocols for metagenomic analysis of human faecal phageomes

AN Shkoporov, FJ Ryan, LA Draper, A Forde… - Microbiome, 2018 - Springer
Background Recent studies have demonstrated that the human gut is populated by complex,
highly individual and stable communities of viruses, the majority of which are …

[HTML][HTML] Viral diversity and potential environmental risk in microplastic at watershed scale: Evidence from metagenomic analysis of plastisphere

R Li, L Zhu, L Cui, YG Zhu - Environment international, 2022 - Elsevier
Microplastics (MPs) have been considered as a new vector for the long-distance transport of
pathogens in aquatic ecosystems. However, the composition of viral communities attached …

Genomoviridae: a new family of widespread single-stranded DNA viruses

M Krupovic, SA Ghabrial, D Jiang, A Varsani - Archives of virology, 2016 - Springer
Here, we introduce a new family of eukaryote-infecting single-stranded (ss) DNA viruses that
was created recently by the International Committee on Taxonomy of Viruses (ICTV). The …

Virome comparisons in wild-diseased and healthy captive giant pandas

W Zhang, S Yang, T Shan, R Hou, Z Liu, W Li, L Guo… - Microbiome, 2017 - Springer
Abstract Background The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal
herbivore living wild in central China. Viral infections have become a potential threat to the …

Family Genomoviridae: 2021 taxonomy update

A Varsani, M Krupovic - Archives of virology, 2021 - Springer
Abstract The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order
Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two …

Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae

A Varsani, M Krupovic - Virus evolution, 2017 - academic.oup.com
With the advent of metagenomics approaches, a large diversity of known and unknown
viruses has been identified in various types of environmental, plant, and animal samples …

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics

DA Lima, SP Cibulski, C Tochetto, APM Varela… - Virus research, 2019 - Elsevier
Malabsorption syndrome (MAS) is an economically important disease of young,
commercially reared broilers, characterized by growth retardation, defective feather …