Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond

Kraberger, Simona; Argüello‐Astorga, Gerardo R.; Greenfield, L. G.; Galilee, Craig; Law, Donald; Martin, Darren P.; Varsani, Arvind

doi:10.1016/j.meegid.2015.01.001

Cited by 81 publications

(84 citation statements)

References 111 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A recent comprehensive metagenomic analysis of thousands of diverse samples has led to the discovery of approximately 125,000 new viral genomes and a 16-fold increase in the number of identified viral genes 24 . Similarly, as technology advances, it is becoming clear that ssDNA and RNA viruses in marine and other ecosystems are far more diverse than currently characterized viruses; however, these new viruses remain understudied despite their ecological importance 11,[25][26][27][28][29][30][31] . Many ssDNA viruses identified in metagenomic data encode an evolutionarily conserved replication-associated protein (Rep), whereas the number, orientation and evolutionary origin of other genes are highly variable in these circular Rep-encoding ssDNA viruses (CRESS-DNA viruses) 32 .…”

Section: Virus Diversitymentioning

confidence: 99%

“…Although some virologists have adopted the term 'associated' as part of the nomenclature of viruses that were identified in metagenomics datasets (for example, human stool-associated circular virus (GQ404856 (REF. 60)); for other examples see REFS 12,13,26,61), it is unnecessary to incorporate this or other such terms that are equivalent to the bacterial term 'Candidatus' into virus taxon names.…”

Section: Proposed Taxonomymentioning

confidence: 99%

See 1 more Smart Citation

Virus taxonomy in the age of metagenomics

et al. 2017

Self Cite

View full text Add to dashboard Cite

| 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 experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV. NATURE REVIEWS | MICROBIOLOGY VOLUME 15 | MARCH 2017 | 161 CONSENSUS STATEMENT © 2 0 1 7 M a c m i l l a n P u b l i s h e r s L i m i t e d , p a r t o f S p r i n g e r N a t u r e . A l l r i g h t s r e s e r v e d .

show abstract

Section: Virus Diversitymentioning

confidence: 99%

Section: Proposed Taxonomymentioning

confidence: 99%

Virus taxonomy in the age of metagenomics

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…It shares with geminiviral proteins two conserved domains, namely geminivirus Rep catalytic domain (Gemini_AL1; PF00799) and geminivirus Rep protein central domain (Gemini_AL1_M; PF08283), with conserved motifs for rolling-circle replication. Notably, similar to some geminiviruses [31], certain SsHADV-1-like viruses also contain introns within their Rep-encoding genes [6,7,12,13,18,19,[26][27][28]30]. However, Rep-based phylogenetic analysis shows that SsHADV-1 and other related putative viruses form a well-supported, monophyletic clade, which branches as a sister group to geminiviruses (Fig.…”

mentioning

confidence: 96%

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

et al. 2016

Self Cite

View full text Add to dashboard Cite

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 family, named Genomoviridae, contains a single genus, Gemycircularvirus, which currently has one recognized virus species, Sclerotinia gemycircularvirus 1. Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) is currently the sole representative isolate of the family; however, a great number of SsHADV-1-like ssDNA virus genomes has been sequenced from various environmental, plant- and animal-associated samples, indicating that members of family Genomoviridae are widespread and abundant in the environment.

show abstract

“…The high prevalence of CRESS DNA genomes in spiders 289 is even more striking considering that most spiders were processed individually ( 341 LfBACM-1 is most similar to a genomic segment from a novel multicomponent CRESS DNA 342 virus discovered in the feces of fruit-eating bats (Male et al 2016). However, the SACM-2 putative 343 capsid protein sequence is most similar to the capsid encoded by a presumably monopartite CRESS 344 DNA virus discovered from a sewage oxidation pond (Kraberger et al 2015). Surprisingly, the 345 remaining two molecules, longjawed orbweaver circular molecule 1 (LjOrbCM-1) and giant house 346 spider associated circular molecule 1 (GhSACM-1), encoded a protein most similar to the large T 347 antigen (LT) encoded by polyomaviruses.…”

mentioning

confidence: 99%

Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates

Rosario

Mettel

Benner

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling towards vertebrates and land plants has limited our understanding of their diversity and evolution. Here we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated virus genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.

show abstract

Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond

Cited by 81 publications

References 111 publications

Virus taxonomy in the age of metagenomics

Virus taxonomy in the age of metagenomics

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

Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates

Contact Info

Product

Resources

About