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

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 532 ◽  
Author(s):  
Simona Kraberger ◽  
Kara Schmidlin ◽  
Rafaela S. Fontenele ◽  
Matthew Walters ◽  
Arvind Varsani
Keyword(s):  
New Zealand ◽  
Viral Metagenomics ◽  
Dna Viruses ◽  
Rep Protein ◽  
Viral Genomes ◽  
Rich Diversity ◽  
Protein Encoding ◽  
Ssdna Viruses ◽  
Virus Genomes ◽  
Flying Fox

Over the last decade, arthropods have been shown to harbour a rich diversity of viruses. Through viral metagenomics a large diversity of single-stranded (ss) DNA viruses have been identified. Here we examine the ssDNA virome of the hematophagous New Zealand blackfly using viral metagenomics. Our investigation reveals a plethora of novel ssDNA viral genomes, some of which cluster in the viral families Genomoviridae (n = 9), Circoviridae (n = 1), and Microviridae (n = 108), others in putative families that, at present, remain unclassified (n = 20) and one DNA molecule that only encodes a replication associated protein. Among these novel viruses, two putative multi-component virus genomes were recovered, and these are most closely related to a Tongan flying fox faeces-associated multi-component virus. Given that the only other known multi-component circular replication-associated (Rep) protein encoding single-stranded (CRESS) DNA viruses infecting plants are in the families Geminiviridae (members of the genus Begomovirus) and Nanoviridae, it appears these are likely a new multi-component virus group which may be associated with animals. This study reiterates the diversity of ssDNA viruses in nature and in particular with the New Zealand blackflies.

A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs

2021 ◽  
Vol 102 (12) ◽  
Author(s):  
Caroline Tochetto ◽  
Samuel Paulo Cibulski ◽  
Ana Paula Muterle Varela ◽  
Cristine Cerva ◽  
Diane Alves de Lima ◽  
...  
Keyword(s):  
Potential Role ◽  
Clinical Signs ◽  
Viral Metagenomics ◽  
Dna Viruses ◽  
Circular Dna ◽  
Viral Genomes ◽  
The Family ◽  
Circular Ssdna ◽  
Ssdna Viruses ◽  
Targeted Approach

Over the last decade, viral metagenomics has been established as a non-targeted approach for identifying viruses in stock animals, including pigs. This has led to the identification of a vast diversity of small circular ssDNA viruses. The present study focuses on the investigation of eukaryotic circular Rep-encoding single-stranded (CRESS) DNA viral genomes present in serum of commercially reared pigs from southern Brazil. Several CRESS DNA viral genomes were detected, including representatives of the families Smacoviridae (n=5), Genomoviridae (n=3), Redondoviridae (n=1), Nenyaviridae (n=1) and other yet unclassified genomes (n=9), plus a circular DNA molecule, which probably belongs to the phylum Cressdnaviricota. A novel genus within the family Smacoviridae, tentatively named ‘Suismacovirus’, comprising 21 potential new species, is proposed. Although the reported genomes were recovered from pigs with clinical signs of respiratory disease, further studies should examine their potential role as pathogens. Nonetheless, these findings highlight the diversity of circular ssDNA viruses in serum of domestic pigs, expand the knowledge on CRESS DNA viruses’ genetic diversity and distribution and contribute to the global picture of the virome of commercially reared pigs.

scholarly journals Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta)

2012 ◽  
Vol 93 (12) ◽  
pp. 2668-2681 ◽  
Author(s):  
Karyna Rosario ◽  
Anisha Dayaram ◽  
Milen Marinov ◽  
Jessica Ware ◽  
Simona Kraberger ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Molecular Techniques ◽  
Limited Information ◽  
Dna Viruses ◽  
Rolling Circle ◽  
Viral Genomes ◽  
Initiator Protein ◽  
Circular Ssdna ◽  
Insect Populations ◽  
Ssdna Viruses

Viruses with circular ssDNA genomes that encode a replication initiator protein (Rep) are among the smallest viruses known to infect both eukaryotic and prokaryotic organisms. In the past few years an overwhelming diversity of novel circular Rep-encoding ssDNA (CRESS-DNA) viruses has been unearthed from various hosts and environmental sources. Since there is limited information regarding CRESS-DNA viruses in invertebrates, this study explored the diversity of CRESS-DNA viruses circulating among insect populations by targeting dragonflies (Epiprocta), top insect predators that accumulate viruses from their insect prey over space and time. Using degenerate PCR and rolling circle amplification coupled with restriction digestion, 17 CRESS-DNA viral genomes were recovered from eight different dragonfly species collected in tropical and temperate regions. Nine of the genomes are similar to cycloviruses and represent five species within this genus, suggesting that cycloviruses are commonly associated with insects. Three of the CRESS-DNA viruses share conserved genomic features with recently described viruses similar to the mycovirus Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1, leading to the proposal of the genus Gemycircularvirus. The remaining viruses are divergent species representing four novel CRESS-DNA viral genera, including a gokushovirus-like prokaryotic virus (microphage) and three eukaryotic viruses with Reps similar to circoviruses. The novelty of CRESS-DNA viruses identified in dragonflies using simple molecular techniques indicates that there is an unprecedented diversity of ssDNA viruses among insect populations.

Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand

2016 ◽  
Vol 43 ◽  
pp. 151-164 ◽  
Author(s):  
Olivia Steel ◽  
Simona Kraberger ◽  
Alyssa Sikorski ◽  
Laura M. Young ◽  
Ryan J. Catchpole ◽  
...  
Keyword(s):  
New Zealand ◽  
Dna Viruses ◽  
Faecal Matter ◽  
Protein Encoding

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

2018 ◽  
Author(s):  
Karyna Rosario ◽  
Kaitlin A Mettel ◽  
Bayleigh E Benner ◽  
Ryan Johnson ◽  
Catherine Scott ◽  
...  
Keyword(s):  
Land Plants ◽  
Biased Sampling ◽  
Agricultural Crops ◽  
Virus Discovery ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Terrestrial Arthropods ◽  
Eukaryotic Organisms ◽  
Virus Genomes ◽  
Viral Sequences

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.

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

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5761 ◽  
Author(s):  
Karyna Rosario ◽  
Kaitlin A. Mettel ◽  
Bayleigh E. Benner ◽  
Ryan Johnson ◽  
Catherine Scott ◽  
...  
Keyword(s):  
Land Plants ◽  
Biased Sampling ◽  
Agricultural Crops ◽  
Virus Discovery ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Terrestrial Arthropods ◽  
Eukaryotic Organisms ◽  
Virus Genomes ◽  
Viral Sequences

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 toward 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 viral 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.

scholarly journals Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

2015 ◽  
Vol 81 (12) ◽  
pp. 3934-3945 ◽  
Author(s):  
Brian Reavy ◽  
Maud M. Swanson ◽  
Peter J. A. Cock ◽  
Lorna Dawson ◽  
Thomas E. Freitag ◽  
...  
Keyword(s):  
Soil Types ◽  
Metagenomic Sequencing ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Unique Type ◽  
Content Type ◽  
Virus Particles ◽  
Intracellular Parasites ◽  
Ssdna Viruses ◽  
Virus Genomes

ABSTRACTThe potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the familyMicroviridae(icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis ofMicroviridaemajor coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamilyGokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar familyCircoviridaein BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in theCircoviridaeshowed that they are a novel clade ofCircoviridae-related CRESS-DNA viruses distinct from knownCircoviridaegenera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.

scholarly journals Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 604
Author(s):  
Mohd Faiz Mat Saad ◽  
Aziz Ramlee Sau ◽  
Muhamad Afiq Akbar ◽  
Syarul Nataqain Baharum ◽  
Ahmad Bazli Ramzi ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Potential Threat ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Agriculture Sector ◽  
Infectious Clones ◽  
And Function ◽  
Virus Genomes ◽  
Considerable Loss

Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique’s impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.

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

2018 ◽  
Author(s):  
Karyna Rosario ◽  
Kaitlin A Mettel ◽  
Bayleigh E Benner ◽  
Ryan Johnson ◽  
Catherine Scott ◽  
...  
Keyword(s):  
Land Plants ◽  
Biased Sampling ◽  
Agricultural Crops ◽  
Virus Discovery ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Terrestrial Arthropods ◽  
Eukaryotic Organisms ◽  
Virus Genomes ◽  
Viral Sequences

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.

scholarly journals Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2777 ◽  
Author(s):  
Simon Roux ◽  
Natalie E. Solonenko ◽  
Vinh T. Dang ◽  
Bonnie T. Poulos ◽  
Sarah M. Schwenck ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Ecosystem Functions ◽  
Library Preparation ◽  
Single Stranded Dna ◽  
Preparation Methods ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Sequencing Library ◽  
Dsdna Viruses ◽  
Ssdna Viruses

BackgroundViruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation).MethodsHere we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses.ResultsMock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from theMicroviridaefamily, can be among the most abundant viral genomes in a sample.DiscussionTogether these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.

scholarly journals Latest Advances of Virology Research Using CRISPR/Cas9-Based Gene-Editing Technology and Its Application to Vaccine Development

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 779
Author(s):  
Man Teng ◽  
Yongxiu Yao ◽  
Venugopal Nair ◽  
Jun Luo
Keyword(s):  
Biological Sciences ◽  
Gene Therapy ◽  
Genetic Engineering ◽  
Gene Function ◽  
Viral Genome ◽  
Gene Editing ◽  
Vaccine Development ◽  
Future Prospects ◽  
Dna Viruses ◽  
Viral Genomes

In recent years, the CRISPR/Cas9-based gene-editing techniques have been well developed and applied widely in several aspects of research in the biological sciences, in many species, including humans, animals, plants, and even in viruses. Modification of the viral genome is crucial for revealing gene function, virus pathogenesis, gene therapy, genetic engineering, and vaccine development. Herein, we have provided a brief review of the different technologies for the modification of the viral genomes. Particularly, we have focused on the recently developed CRISPR/Cas9-based gene-editing system, detailing its origin, functional principles, and touching on its latest achievements in virology research and applications in vaccine development, especially in large DNA viruses of humans and animals. Future prospects of CRISPR/Cas9-based gene-editing technology in virology research, including the potential shortcomings, are also discussed.

Sign in / Sign up

Export Citation Format

Share Document