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 Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

2011 ◽  
Vol 77 (22) ◽  
pp. 8062-8070 ◽  
Author(s):  
Min-Soo Kim ◽  
Eun-Jin Park ◽  
Seong Woon Roh ◽  
Jin-Woo Bae
Keyword(s):  
Capsid Protein ◽  
Protein Sequences ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Content Type ◽  
Double Stranded Dna ◽  
Abundance And Diversity ◽  
Ssdna Viruses ◽  
Virus Abundance ◽  
Large Contigs

ABSTRACTIn this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 108to 109per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400,133 sequences, an average of 86.2% viromes were previously uncharacterized in public databases. Among previously known viruses, double-stranded DNA podophages (52 to 74%), siphophages (11 to 30%), myophages (1 to 4%), and ssDNA microphages (3 to 9%) were major constituents of human fecal viromes. A phylogenetic analysis of 24 large contigs of microphages based on conserved capsid protein sequences revealed five distinct newly discovered evolutionary microphage groups that were distantly related to previously known microphages. Moreover, putative capsid protein sequences of five contigs were closely related to prophage-like sequences in the genomes of threeBacteroidesand threePrevotellastrains, suggesting thatBacteroidesandPrevotellaare the sources of infecting microphages in their hosts.

scholarly journals Discovery of Four Novel Circular Single-Stranded DNA Viruses in Fungus-Farming Termites

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Mason Kerr ◽  
Karyna Rosario ◽  
Christopher C. M. Baker ◽  
Mya Breitbart
Keyword(s):  
Termite Mounds ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Content Type ◽  
The Family

ABSTRACT Here, we describe four novel circular single-stranded DNA viruses discovered in fungus-farming termites ( Odontotermes sp.). The viruses, named termite-associated circular virus 1 (TaCV-1) through TaCV-4, are most similar to members of the family Genomoviridae and were widely detected in African termite mounds.

scholarly journals Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

2008 ◽  
Vol 74 (19) ◽  
pp. 5975-5985 ◽  
Author(s):  
Kyoung-Ho Kim ◽  
Ho-Won Chang ◽  
Young-Do Nam ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Rice Paddy ◽  
Viral Diversity ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Amplification Method ◽  
Metagenome Sequencing ◽  
Biological Entities ◽  
Related Proteins ◽  
Ssdna Viruses

ABSTRACT Viruses are known to be the most numerous biological entities in soil; however, little is known about their diversity in this environment. In order to explore the genetic diversity of soil viruses, we isolated viruses by centrifugation and sequential filtration before performing a metagenomic investigation. We adopted multiple-displacement amplification (MDA), an isothermal whole-genome amplification method with φ29 polymerase and random hexamers, to amplify viral DNA and construct clone libraries for metagenome sequencing. By the MDA method, the diversity of both single-stranded DNA (ssDNA) viruses and double-stranded DNA viruses could be investigated at the same time. On the contrary, by eliminating the denaturing step in the MDA reaction, only ssDNA viral diversity could be explored selectively. Irrespective of the denaturing step, more than 60% of the soil metagenome sequences did not show significant hits (E-value criterion, 0.001) with previously reported viral sequences. Those hits that were considered to be significant were also distantly related to known ssDNA viruses (average amino acid similarity, approximately 34%). Phylogenetic analysis showed that replication-related proteins (which were the most frequently detected proteins) related to those of ssDNA viruses obtained from the metagenomic sequences were diverse and novel. Putative circular genome components of ssDNA viruses that are unrelated to known viruses were assembled from the metagenomic sequences. In conclusion, ssDNA viral diversity in soil is more complex than previously thought. Soil is therefore a rich pool of previously unknown ssDNA viruses.

scholarly journals Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses

2008 ◽  
Vol 83 (6) ◽  
pp. 2697-2707 ◽  
Author(s):  
P. Lefeuvre ◽  
J.-M. Lett ◽  
A. Varsani ◽  
D. P. Martin
Keyword(s):  
Genetic Recombination ◽  
Recombination Breakpoint ◽  
Ssdna Virus ◽  
Structural Protein ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Diverse Range ◽  
Genome Wide ◽  
Virus Genomes ◽  
Recombination Breakpoints

ABSTRACT The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.

scholarly journals Genome Sequences of Two Single-Stranded DNA Viruses Identified in Varroa destructor

2018 ◽  
Vol 6 (9) ◽  
Author(s):  
Simona Kraberger ◽  
Gabriel A. Visnovsky ◽  
Ron F. van Toor ◽  
Maketalena F. Male ◽  
Kara Waits ◽  
...  
Keyword(s):  
New Zealand ◽  
Honey Bee ◽  
Honey Bees ◽  
Varroa Destructor ◽  
Genome Sequences ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Content Type ◽  
Pathogenic Viruses ◽  
Parasitic Mite

ABSTRACT Varroa destructor is a ubiquitous and parasitic mite of honey bees, infecting them with pathogenic viruses having a major impact on apiculture. We identified two novel circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses from V. destructor sampled from a honey bee hive near Christchurch in New Zealand.

scholarly journals Isolation and Characterization of a Single-Stranded DNA Virus Infecting Chaetoceros lorenzianus Grunow

2011 ◽  
Vol 77 (15) ◽  
pp. 5285-5293 ◽  
Author(s):  
Yuji Tomaru ◽  
Yoshitake Takao ◽  
Hidekazu Suzuki ◽  
Tamotsu Nagumo ◽  
Kanae Koike ◽  
...  
Keyword(s):  
Burst Size ◽  
Open Reading Frames ◽  
Dna Virus ◽  
Single Stranded Dna ◽  
Content Type ◽  
Virus Particles ◽  
Isolation And Characterization ◽  
Double Stranded Dna ◽  
Circular Ssdna ◽  
Related Proteins

ABSTRACTDiatoms are one of the most significant primary producers in the ocean, and the importance of viruses as a potential source of mortality for diatoms has recently been recognized. Thus far, eight different diatom viruses infecting the generaRhizosoleniaandChaetoceroshave been isolated and characterized to different extents. We report the isolation of a novel diatom virus (ClorDNAV), which causes the lysis of the bloom-forming speciesChaetoceros lorenzianus, and show its physiological, morphological, and genomic characteristics. The free virion was estimated to be ∼34 nm in diameter. The arrangement of virus particles appearing in cross-section was basically a random aggregation in the nucleus. Occasionally, distinctive formations such as a ring-like array composed of 9 or 10 spherical virions or a centipede-like array composed of rod-shaped particles were also observed. The latent period and the burst size were estimated to be <48 h and 2.2 × 104infectious units per host cell, respectively. ClorDNAV harbors a covalently closed circular single-stranded DNA (ssDNA) genome (5,813 nucleotides [nt]) that includes a partially double-stranded DNA region (979 nt). At least three major open reading frames were identified; one showed a high similarity to putative replicase-related proteins of the other ssDNA diatom viruses,Chaetoceros salsugineumDNA virus (previously reported as CsNIV) andChaetoceros tenuissimusDNA virus. ClorDNAV is the third member of the closed circular ssDNA diatom virus group, the genusBacilladnavirus.

scholarly journals Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2585 ◽  
Author(s):  
Victoria M. Pearson ◽  
S. Brian Caudle ◽  
Darin R. Rokyta
Keyword(s):  
Wastewater Treatment ◽  
Microbial Communities ◽  
Rolling Circle Amplification ◽  
Treatment Plant ◽  
Microbial Pathogens ◽  
Model Organisms ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Depth Analysis ◽  
Ssdna Viruses

Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (CircoviridaeandGeminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such asCircoviridae,Geminiviridae, andMicroviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group.

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 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.

scholarly journals Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Mart Krupovic ◽  
Natalya Yutin ◽  
Eugene Koonin
Keyword(s):  
Glycoside Hydrolase ◽  
Carbohydrate Binding ◽  
Virion Protein ◽  
Gene Encoding ◽  
Dna Viruses ◽  
Virus Particles ◽  
Major Increase ◽  
A Minor ◽  
Particle Shapes ◽  
Icosahedral Capsid

Abstract The diverse viruses in the phylum Nucleocytoviricota (also known as NLCDVs, Nucleo-cytoplasmic Large DNA Viruses) typically possess large icosahedral virions. However, in several families of Nucleocytoviricota, the icosahedral capsid was replaced by irregular particle shapes, most notably, the amphora-like virions of pandoraviruses and pithoviruses, the largest known virus particles in the entire virosphere. Pandoraviruses appear to be the most highly derived viruses in this phylum because their evolution involved not only the change in the virion shape, but also, the actual loss of the gene encoding double-jelly roll major capsid protein (DJR MCP), the main building block of icosahedral capsids in this virus assemblage. Instead, pandoravirus virions are built of unrelated abundant proteins. Here we show that the second most abundant virion protein of pandoraviruses, major virion protein 2 (MVP2), evolved from an inactivated derivative of a bacterial glycoside hydrolase of the GH16 family. The ancestral form of MVP2 was apparently acquired early in the evolution of the Nucleocytoviricota, to become a minor virion protein. After a duplication in the common ancestor of pandoraviruses and molliviruses, one of the paralogs displaces DJR MCP in pandoraviruses, conceivably, opening the way for a major increase in the size of the virion and the genome. Exaptation of a carbohydrate-binding protein for the function of the MVP is a general trend in virus evolution and might underlie the transformation of the virion shape in other groups of the Nucleocytoviricota as well.

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