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.

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 Genetic diversity of novel circular ssDNA viruses in bats in China

2011 ◽  
Vol 92 (11) ◽  
pp. 2646-2653 ◽  
Author(s):  
Xingyi Ge ◽  
Jialu Li ◽  
Cheng Peng ◽  
Lijun Wu ◽  
Xinglou Yang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Full Length ◽  
Inverse Pcr ◽  
Sequencing Data ◽  
Stem Loop ◽  
Amplification Method ◽  
Loop Region ◽  
The Family ◽  
Circular Ssdna ◽  
Ssdna Viruses

Novel circular ssDNA genomes have recently been detected in animals and in the environment using metagenomic and high-throughput sequencing approaches. In this study, five full-length circular ssDNA genomes were recovered from bat faecal samples using inverse PCR with sequences designed based on circovirus-related sequences obtained from Solexa sequencing data derived from a random amplification method. These five sequences shared a similar genomic organization to circovirus or the recently proposed cyclovirus of the family Circoviridae. The newly obtained circovirus/cyclovirus-like genomes ranged from 1741 to 2177 bp, and each consisted of two major ORFs, ORF1 and ORF2, encoding putative replicase (Rep) and capsid (Cap) proteins, respectively. The potential stem–loop region was predicted in all five genomes, and three of them had the typical conserved nonanucleotide motif of cycloviruses. A set of primers targeting the conserved Rep region was designed and used to detect the prevalence of circovirus/cyclovirus sequences in individual bats. Among 199 samples tested, 47 were positive (23.6 %) for the circovirus genome and two (1.0 %) were positive for the cyclovirus genome. In total, 48 partial Rep sequences plus the five full-length genomes were obtained in this study. Detailed analysis indicated that these sequences are distantly related to known circovirus/cyclovirus genomes and may represent 22 novel species that belong to the family Circoviridae.

scholarly journals Discovery of several thousand highly diverse circular DNA viruses

2019 ◽  
Author(s):  
Michael J. Tisza ◽  
Diana V. Pastrana ◽  
Nicole L. Welch ◽  
Brittany Stewart ◽  
Alberto Peretti ◽  
...  
Keyword(s):  
Viral Capsid ◽  
Soil Nematodes ◽  
Viral Sequence ◽  
Bioinformatics Pipeline ◽  
Dna Viruses ◽  
Circular Dna ◽  
Dna Elements ◽  
Tissue Specimens ◽  
Ssdna Viruses ◽  
Viral Capsid Proteins

SummaryAlthough it is suspected that there are millions of distinct viral species, fewer than 9,000 are catalogued in GenBank’s RefSeq database. We selectively enriched for and amplified the genomes of circular DNA viruses in over 70 animal samples, ranging from cultured soil nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2,500 circular genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA viruses and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these “dark matter” sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.

scholarly journals Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera)

2011 ◽  
Vol 92 (6) ◽  
pp. 1302-1308 ◽  
Author(s):  
Karyna Rosario ◽  
Milen Marinov ◽  
Daisy Stainton ◽  
Simona Kraberger ◽  
Elizabeth J. Wiltshire ◽  
...  
Keyword(s):  
Viral Metagenomics ◽  
Nucleotide Identity ◽  
Ssdna Virus ◽  
Single Strain ◽  
Genome Wide ◽  
Faecal Samples ◽  
The Family ◽  
Circular Ssdna ◽  
A New Species ◽  
Dragonfly Species

Dragonfly cyclovirus (DfCyV), a new species of ssDNA virus discovered using viral metagenomics in dragonflies (family Libellulidae) from the Kingdom of Tonga. Metagenomic sequences of DfCyV were similar to viruses of the recently proposed genus Cyclovirus within the family Circoviridae. Specific PCRs resulted in the recovery of 21 DfCyV genomes from three dragonfly species (Pantala flavescens, Tholymis tillarga and Diplacodes bipunctata). The 1741 nt DfCyV genomes share >95 % nucleotide identity and are classified into 11 subtypes representing a single strain. The DfCyV genomes share 48–63 % genome-wide nucleotide identity with cycloviruses identified in human faecal samples. Recombination analysis revealed three recombinant DfCyV genomes, suggesting that recombination plays an important role in cyclovirus evolution. To our knowledge, this is the first report of a circular ssDNA virus identified in insects, and the data may help elucidate evolutionary links among novel Circoviridae recently identified in animals and environmental samples.

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 Identification of a novel single-stranded, circular DNA virus from bovine stool

2012 ◽  
Vol 93 (3) ◽  
pp. 635-639 ◽  
Author(s):  
Hye Kwon Kim ◽  
Seong Jun Park ◽  
Van Giap Nguyen ◽  
Dae Sub Song ◽  
Hyoung Joon Moon ◽  
...  
Keyword(s):  
Capsid Proteins ◽  
Putative Orfs ◽  
Dna Virus ◽  
Stem Loop ◽  
Dna Viruses ◽  
Circular Dna ◽  
Stem Loop Structure ◽  
A Genome ◽  
Circular Ssdna ◽  
Circular Dna Virus

We report the identification of a novel single-stranded, circular DNA virus isolated from bovine stool. The virus, named bovine stool-associated circular DNA virus (BoSCV), has a genome comprising 2600 bases of circular ssDNA, with two putative ORFs encoding replicase and capsid proteins, arranged inversely. The stem–loop structure was located between the 3′ ends of the two putative ORFs, as in chimpanzee stool-associated circular virus (ChimpSCV) and unlike other circular DNA viruses, including members of the families Circoviridae, Nanoviridae and Geminiviridae. BoSCV was also genetically similar to ChimpSCV, with approximately 30 % identity in the replicase and capsid proteins. A phylogenetic analysis based on the replicase protein showed that BoSCV and ChimpSCV are in the same clade. A field survey using BoSCV-specific PCRs targeting ORF1 detected BoSCV and BoSCV-like sequences in bovine and porcine stool samples. BoSCV appears to belong to a new genus of circular DNA viruses.

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.

scholarly journals Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Amy Gaye ◽  
Tolla Ndiaye ◽  
Mouhamad Sy ◽  
Awa B. Deme ◽  
Alphonse B. Thiaw ◽  
...  
Keyword(s):  
West Africa ◽  
Dengue Virus ◽  
Clinical Signs ◽  
Health Concern ◽  
Public Health Concern ◽  
Local Circulation ◽  
Viral Genomes ◽  
Genomic Characterization ◽  
The City

AbstractDengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we report complete viral genomes from 17 previously undetected DENV cases from the city of Thiès. In total we identified 19 cases of DENV in a cohort of 198 individuals with fever collected in October and November 2018. We detected 3 co-circulating serotypes; DENV 3 was the most frequent accounting for 11/17 sequences (65%), 4 (23%) were DENV2 and 2 (12%) were DENV1. Sequences were most similar to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.

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.

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