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The Journal of General Virology Mar 2021is a family of enveloped viruses with a linear dsDNA genome. The virions are ellipsoidal, and contain a multi-layered spool-like capsid. The viral genome is presumably...
is a family of enveloped viruses with a linear dsDNA genome. The virions are ellipsoidal, and contain a multi-layered spool-like capsid. The viral genome is presumably replicated through protein priming by a putative DNA polymerase encoded by the virus. Progeny virions are released through hexagonal openings resulting from the rupture of virus-associated pyramids formed on the surface of infected cells. The only known host is a hyperthermophilic archaeon of the genus . This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family which is available at ictv.global/report/ovaliviridae.
Topics: Archaeal Viruses; Capsid; DNA Viruses; Genome, Viral; Sulfolobus; Virion; Virus Replication
PubMed: 33331812
DOI: 10.1099/jgv.0.001546 -
Proceedings of the National Academy of... Apr 2023Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are...
Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be "genomic fossils." Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses. These EVEs, composed of virophages, Polinton-like viruses, and related entities, have remained hitherto hidden owing to poor sequence conservation between virus groups and their repetitive nature that precluded accurate short-read assembly. We show that long-read sequencing technology is ideal for resolving virus insertions. Many protist EVEs appear intact, and most encode integrases, which suggests that they have actively colonized hosts across the tree of eukaryotes. We also found evidence for gene expression in host transcriptomes and that closely related virophage and Polinton-like virus genomes are abundant in viral metagenomes, indicating that many EVEs are probably functional viruses.
Topics: Animals; Eukaryota; DNA Viruses; Viruses; Virophages; Genome, Viral; Phylogeny
PubMed: 37036967
DOI: 10.1073/pnas.2300465120 -
ELife Sep 2023The relative positions of viral DNA genomes to the host intranuclear environment play critical roles in determining virus fate. Recent advances in the application of...
The relative positions of viral DNA genomes to the host intranuclear environment play critical roles in determining virus fate. Recent advances in the application of chromosome conformation capture-based sequencing analysis (3 C technologies) have revealed valuable aspects of the spatiotemporal interplay of viral genomes with host chromosomes. However, to elucidate the causal relationship between the subnuclear localization of viral genomes and the pathogenic outcome of an infection, manipulative tools are needed. Rapid repositioning of viral DNAs to specific subnuclear compartments amid infection is a powerful approach to synchronize and interrogate this dynamically changing process in space and time. Herein, we report an inducible CRISPR-based two-component platform that relocates extrachromosomal DNA pieces (5 kb to 170 kb) to the clear eriphery minutes (CRISPR-nuPin). Based on this strategy, investigations of herpes simplex virus 1 (HSV-1), a prototypical member of the human herpesvirus family, revealed unprecedently reported insights into the early intranuclear life of the pathogen: (I) Viral genomes tethered to the nuclear periphery upon entry, compared with those freely infecting the nucleus, were wrapped around histones with increased suppressive modifications and subjected to stronger transcriptional silencing and prominent growth inhibition. (II) Relocating HSV-1 genomes at 1 hr post infection significantly promoted the transcription of viral genes, termed an 'Escaping' effect. (III) Early accumulation of ICP0 was a sufficient but not necessary condition for 'Escaping'. (IV) Subnuclear localization was only critical during early infection. Importantly, the CRISPR-nuPin tactic, in principle, is applicable to many other DNA viruses.
Topics: Humans; Herpesvirus 1, Human; Drug Repositioning; DNA, Viral; Cell Nucleus; Cytoplasm
PubMed: 37702383
DOI: 10.7554/eLife.85412 -
Viruses Sep 2021In aquaculture, disease management and pathogen control are key for a successful fish farming industry. In past years, European catfish farming has been flourishing.... (Review)
Review
In aquaculture, disease management and pathogen control are key for a successful fish farming industry. In past years, European catfish farming has been flourishing. However, devastating fish pathogens including limiting fish viruses are considered a big threat to further expanding of the industry. Even though mainly the ranavirus () and circovirus () infections are considered well- described in European catfish, more other agents including herpes-, rhabdo or papillomaviruses are also observed in the tissues of catfish with or without any symptoms. The etiological role of these viruses has been unclear until now. Hence, there is a requisite for more detailed information about the latter and the development of preventive and therapeutic approaches to complete them. In this review, we summarize recent knowledge about viruses that affect the European catfish and describe their origin, distribution, molecular characterisation, and phylogenetic classification. We also highlight the knowledge gaps, which need more in-depth investigations in the future.
Topics: Animals; Catfishes; Circoviridae Infections; Circovirus; DNA Virus Infections; Fish Diseases; Herpesviridae; Herpesviridae Infections; Iridoviridae; Papillomaviridae; Papillomavirus Infections; Rhabdoviridae; Rhabdoviridae Infections
PubMed: 34578446
DOI: 10.3390/v13091865 -
The Journal of General Virology Aug 2021African swine fever is a devastating disease of domestic swine and wild boar caused by a large double-stranded DNA virus that encodes for more than 150 open reading...
African swine fever is a devastating disease of domestic swine and wild boar caused by a large double-stranded DNA virus that encodes for more than 150 open reading frames. There is no licensed vaccine for the disease and the most promising current candidates are modified live viruses that have been attenuated by deletion of virulence factors. Like many viruses African swine fever virus significantly alters the host cell machinery to benefit its replication and viral genes that modify host pathways represent promising targets for development of gene deleted vaccines. Autophagy is an important cellular pathway that is involved in cellular homeostasis, innate and adaptive immunity and therefore is manipulated by a number of different viruses. Autophagy is regulated by a complex protein cascade and here we show that African swine fever virus can block formation of autophagosomes, a critical functional step of the autophagy pathway through at least two different mechanisms. Interestingly this does not require the gene that has been shown to interact with Beclin-1, an important autophagy regulator.
Topics: African Swine Fever; African Swine Fever Virus; Animals; Autophagy; Chlorocebus aethiops; Swine; Vero Cells; Viral Proteins; Virulence
PubMed: 34406116
DOI: 10.1099/jgv.0.001637 -
Current Opinion in Insect Science Feb 2022We provide an overview of the currently known diversity of viral sequences integrated into insect genomes. Such endogenous viral elements (EVE) have so far been... (Review)
Review
We provide an overview of the currently known diversity of viral sequences integrated into insect genomes. Such endogenous viral elements (EVE) have so far been annotated in at least eight insect orders and can be assigned to at least three families of large double-stranded (ds) DNA viruses, at least 22 families of RNA viruses, and three families of single-stranded DNA viruses. The study of these EVE has already produced important insights into insect-virus interactions, including the discovery of a new form of adaptive antiviral immunity. Insect EVE diversity will continue to increase as new insect genomes and exogenous viruses are sequenced, which will continue to make paleovirology a vibrant research field in this group of animals in the years to come.
Topics: Animals; DNA Viruses; Genome, Insect; Insecta; RNA Viruses; Viruses
PubMed: 34839030
DOI: 10.1016/j.cois.2021.11.007 -
Current Opinion in Virology Feb 2022The genome sequence is the only characteristic readily obtainable for all known viruses, underlying the growing role of comparative genomics in organizing knowledge... (Review)
Review
The genome sequence is the only characteristic readily obtainable for all known viruses, underlying the growing role of comparative genomics in organizing knowledge about viruses in a systematic evolution-aware way, known as virus taxonomy. Overseen by the International Committee on Taxonomy of Viruses (ICTV), development of virus taxonomy involves taxa demarcation at 15 ranks of a hierarchical classification, often in host-specific manner. Outside the ICTV remit, researchers assess fitting numerous unclassified viruses into the established taxa. They employ different metrics of virus clustering, basing on conserved domain(s), separation of viruses in rooted phylogenetic trees and pair-wise distance space. Computational approaches differ further in respect to methodology, number of ranks considered, sensitivity to uneven virus sampling, and visualization of results. Advancing and using computational tools will be critical for improving taxa demarcation across the virosphere and resolving rank origins in research that may also inform experimental virology.
Topics: Computational Biology; DNA Viruses; Genome, Viral; Phylogeny; Viruses; Viruses, Unclassified
PubMed: 34883443
DOI: 10.1016/j.coviro.2021.11.003 -
MBio Sep 2020The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of...
The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.
Topics: Capsid Proteins; DNA Viruses; Data Mining; Genome, Viral; Metagenome; Metagenomics; RNA Viruses; Tombusviridae
PubMed: 32873755
DOI: 10.1128/mBio.01410-20 -
PLoS Computational Biology Nov 2022The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy,...
The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5,000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe the challenges faced with interpreting the barcode sequences obtained from the library. Our Illumina NextSeq sequencing recalled much greater variation in barcode sequencing reads than the expected 5,000 barcodes-necessarily stemming from the Illumina library processing and sequencing error. Using data from defined control virus genomes cloned into plasmid backbones we develop a vetted post-sequencing method to cluster the erroneous reads around the true virus genome barcodes. These findings may foreshadow problems with randomized barcodes in other microbial systems and provide a useful approach for future work utilizing nucleic acid barcoded pathogens.
Topics: Mice; Animals; DNA Viruses; Nucleic Acids
PubMed: 36413582
DOI: 10.1371/journal.pcbi.1010131 -
World Journal of Gastroenterology Apr 2020The review presents the data accumulated for more than 20 years of research of torque teno virus (TTV). Its molecular genetic structure, immunobiology, epidemiology,... (Review)
Review
The review presents the data accumulated for more than 20 years of research of torque teno virus (TTV). Its molecular genetic structure, immunobiology, epidemiology, diagnostic methods, possible replication sites, and pathogenicity factors are described. TTV is a virus that is frequently detectable in patients with different viral hepatitides, in cases of hepatitis without an obvious viral agent, as well as in a healthy population. There is evidence suggesting that biochemical and histological changes occur in liver tissue and bile duct epithelium in TTV monoinfection. There are sufficient histological signs of liver damage, which confirm that the virus can undergo a replicative cycle in hepatocytes. Along with this, cytological hybridization in TTV-infected cells has shown no substantial cytopathic (cell-damaging) effects that are characteristic of pathogenic hepatotropic viruses. Studying TTV has led to the evolution of views on its role in the development of human pathology. The first ideas about the hepatotropism of the virus were gradually reformed as new data became available on the prevalence of the virus and its co-infection with other viruses, including the viruses of the known types of hepatitides. The high prevalence of TTV in the human population indicates its persistence in the body as a virome and a non-pathogenic virus. It has recently been proposed that the level of TTV DNA in the blood of patients undergoing organ transplantation should be used as an endogenous marker of the body's immune status. The available data show the polytropism of the virus and deny the fact that TTV can be assigned exclusively to hepatitis viruses. Fortunately, the rare detection of the damaging effect of TTV on hepatic and bile duct epithelial cells may be indirect evidence of its conditionally pathogenic properties. The ubiquity of the virus and the variability of its existence in humans cannot put an end to its study.
Topics: Bile Ducts; DNA Virus Infections; DNA, Viral; Epithelium; Hepatitis, Viral, Human; Hepatocytes; Humans; Liver; Prevalence; Torque teno virus; Viral Load; Virome
PubMed: 32351287
DOI: 10.3748/wjg.v26.i15.1691