Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses

Oncogenic viruses, like viruses in general, can be divided into two classes, those that contain deoxyribonucleic acid (DNA) and those that contain ribonucleic acid (RNA). The RNA viruses have been recovered readily from the tumors which they cause whereas, the DNA-virus induced tumors have not yielded the virus. Since DNA viruses cannot be recovered, the bulk of present day investigations have been concerned with RNA viruses.The Lucké renal adenocarcinoma is a spontaneous tumor which occurs in northern leopard frogs (Rana pipiens) and has received increased attention in recent years because of its probable viral etiology. This hypothesis was first advanced by Lucké after he observed intranuclear inclusions in some of the tumor cells. Tumors with inclusions were examined at the fine structural level by Fawcett who showed that they contained immature and mature virus˗like particles.The use of this system in the study of oncogenic tumors offers several unique features, the virus has been shown to contain DNA and it can be recovered from the tumor, also, it is temperature sensitive. This latter feature is of importance because the virus can be transformed from a latent to a vegetative state by lowering or elevating the environmental temperature.

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Faculty Opinions recommendation of Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1032149.373802 ◽

2006 ◽

Author(s):

Lynn Enquist

Keyword(s):

Rna Viruses ◽

Dna Viruses ◽

Double Stranded Rna ◽

Positive Strand ◽

Negative Strand ◽

Positive Strand Rna

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Faculty Opinions recommendation of Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1032149.372810 ◽

2006 ◽

Author(s):

Grant McFadden

Keyword(s):

Rna Viruses ◽

Dna Viruses ◽

Double Stranded Rna ◽

Positive Strand ◽

Negative Strand ◽

Positive Strand Rna

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Intercellular Transmission of Naked Viruses through Extracellular Vesicles: Focus on Polyomaviruses

Viruses ◽

10.3390/v12101086 ◽

2020 ◽

Vol 12 (10) ◽

pp. 1086

Author(s):

Francois Helle ◽

Lynda Handala ◽

Marine Bentz ◽

Gilles Duverlie ◽

Etienne Brochot

Keyword(s):

Immune System ◽

Extracellular Vesicles ◽

Rna Viruses ◽

Viral Transmission ◽

Viral Fitness ◽

Host Cells ◽

Dna Viruses ◽

Recent Advances ◽

Viral Particles ◽

Similar Strategy

Extracellular vesicles have recently emerged as a novel mode of viral transmission exploited by naked viruses to exit host cells through a nonlytic pathway. Extracellular vesicles can allow multiple viral particles to collectively traffic in and out of cells, thus enhancing the viral fitness and diversifying the transmission routes while evading the immune system. This has been shown for several RNA viruses that belong to the Picornaviridae, Hepeviridae, Reoviridae, and Caliciviridae families; however, recent studies also demonstrated that the BK and JC viruses, two DNA viruses that belong to the Polyomaviridae family, use a similar strategy. In this review, we provide an update on recent advances in understanding the mechanisms used by naked viruses to hijack extracellular vesicles, and we discuss the implications for the biology of polyomaviruses.

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VirusTaxo: Taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment

10.1101/2021.04.29.442004 ◽

2021 ◽

Author(s):

Rajan Saha Raju ◽

Abdullah Al Nahid ◽

Preonath Shuvo ◽

Rashedul Islam

Keyword(s):

Genome Sequence ◽

Rna Viruses ◽

Hierarchical Classification ◽

Classification Problem ◽

Virus Genome ◽

Taxonomic Classification ◽

Dna Viruses ◽

Dna And Rna ◽

Full Length Genome

AbstractTaxonomic classification of viruses is a multi-class hierarchical classification problem, as taxonomic ranks (e.g., order, family and genus) of viruses are hierarchically structured and have multiple classes in each rank. Classification of biological sequences which are hierarchically structured with multiple classes is challenging. Here we developed a machine learning architecture, VirusTaxo, using a multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach and accurately assigns the order, family and genus of a virus from the genome sequence. The average accuracies of VirusTaxo for DNA viruses are 99% (order), 98% (family) and 95% (genus) and for RNA viruses 97% (order), 96% (family) and 82% (genus). VirusTaxo can be used to detect taxonomy of novel viruses using full length genome or contig sequences.AvailabilityOnline version of VirusTaxo is available at https://omics-lab.com/virustaxo/.

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Viral Mutation Rates

Journal of Virology ◽

10.1128/jvi.00694-10 ◽

2010 ◽

Vol 84 (19) ◽

pp. 9733-9748 ◽

Cited By ~ 634

Author(s):

Rafael Sanjuán ◽

Miguel R. Nebot ◽

Nicola Chirico ◽

Louis M. Mansky ◽

Robert Belshaw

Keyword(s):

Mutation Rate ◽

Rna Viruses ◽

Experimental Testing ◽

Mutation Rates ◽

Cell Infection ◽

Nucleotide Substitutions ◽

Data Set ◽

Dna Viruses ◽

Double Stranded Dna ◽

Viral Mutation

ABSTRACT Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10−8 to10−6 s/n/c for DNA viruses and from 10−6 to 10−4 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut .

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Unveiling Crucivirus Diversity by Mining Metagenomic Data

mBio ◽

10.1128/mbio.01410-20 ◽

2020 ◽

Vol 11 (5) ◽

Cited By ~ 1

Author(s):

Ignacio de la Higuera ◽

George W. Kasun ◽

Ellis L. Torrance ◽

Alyssa A. Pratt ◽

Amberlee Maluenda ◽

...

Keyword(s):

De Novo ◽

Rna Viruses ◽

Sequence Data ◽

Ecosystem Dynamics ◽

Capsid Proteins ◽

Metagenomic Data ◽

Dna Viruses ◽

Rep Protein ◽

Dna And Rna ◽

Core Proteins

ABSTRACT 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 Tombusviridae. 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 de novo 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. IMPORTANCE 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.

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Double-Stranded RNA Is Produced by Positive-Strand RNA Viruses and DNA Viruses but Not in Detectable Amounts by Negative-Strand RNA Viruses

Journal of Virology ◽

10.1128/jvi.80.10.5059-5064.2006 ◽

2006 ◽

Vol 80 (10) ◽

pp. 5059-5064 ◽

Cited By ~ 578

Author(s):

Friedemann Weber ◽

Valentina Wagner ◽

Simon B. Rasmussen ◽

Rune Hartmann ◽

Søren R. Paludan

Keyword(s):

Viral Infections ◽

Rna Viruses ◽

Innate Immune ◽

Genome Replication ◽

Dna Viruses ◽

Double Stranded Rna ◽

Positive Strand ◽

Negative Strand ◽

A Genome ◽

Positive Strand Rna

ABSTRACT Double-stranded RNA (dsRNA) longer than 30 bp is a key activator of the innate immune response against viral infections. It is widely assumed that the generation of dsRNA during genome replication is a trait shared by all viruses. However, to our knowledge, no study exists in which the production of dsRNA by different viruses is systematically investigated. Here, we investigated the presence and localization of dsRNA in cells infected with a range of viruses, employing a dsRNA-specific antibody for immunofluorescence analysis. Our data revealed that, as predicted, significant amounts of dsRNA can be detected for viruses with a genome consisting of positive-strand RNA, dsRNA, or DNA. Surprisingly, however, no dsRNA signals were detected for negative-strand RNA viruses. Thus, dsRNA is indeed a general feature of most virus groups, but negative-strand RNA viruses appear to be an exception to that rule.

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The ATP-Dependent RNA Helicase DDX3X Modulates Herpes Simplex Virus 1 Gene Expression

Journal of Virology ◽

10.1128/jvi.02411-16 ◽

2017 ◽

Vol 91 (8) ◽

Cited By ~ 17

Author(s):

Bita Khadivjam ◽

Camille Stegen ◽

Marc-Aurèle Hogue-Racine ◽

Nabil El Bilali ◽

Katinka Döhner ◽

...

Keyword(s):

Gene Expression ◽

Herpes Simplex ◽

Rna Viruses ◽

Rna Helicase ◽

Viral Gene ◽

Herpes Simplex Virus 1 ◽

Dna Viruses ◽

Viral Particles ◽

Simplex Virus ◽

Hsv 1

ABSTRACT The human protein DDX3X is a DEAD box ATP-dependent RNA helicase that regulates transcription, mRNA maturation, and mRNA export and translation. DDX3X concomitantly modulates the replication of several RNA viruses and promotes innate immunity. We previously showed that herpes simplex virus 1 (HSV-1), a human DNA virus, incorporates DDX3X into its mature particles and that DDX3X is required for optimal HSV-1 infectivity. Here, we show that viral gene expression, replication, and propagation depend on optimal DDX3X protein levels. Surprisingly, DDX3X from incoming viral particles was not required for the early stages of the HSV-1 infection, but, rather, the protein controlled the assembly of new viral particles. This was independent of the previously reported ability of DDX3X to stimulate interferon type I production. Instead, both the lack and overexpression of DDX3X disturbed viral gene transcription and thus subsequent genome replication. This suggests that in addition to its effect on RNA viruses, DDX3X impacts DNA viruses such as HSV-1 by an interferon-independent pathway. IMPORTANCE Viruses interact with a variety of cellular proteins to complete their life cycle. Among them is DDX3X, an RNA helicase that participates in most aspects of RNA biology, including transcription, splicing, nuclear export, and translation. Several RNA viruses and a limited number of DNA viruses are known to manipulate DDX3X for their own benefit. In contrast, DDX3X is also known to promote interferon production to limit viral propagation. Here, we show that DDX3X, which we previously identified in mature HSV-1 virions, stimulates HSV-1 gene expression and, consequently, virion assembly by a process that is independent of its ability to promote the interferon pathway.

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Why genes overlap in viruses

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.1052 ◽

2010 ◽

Vol 277 (1701) ◽

pp. 3809-3817 ◽

Cited By ~ 79

Author(s):

Nicola Chirico ◽

Alberto Vianelli ◽

Robert Belshaw

Keyword(s):

Rna Viruses ◽

Harmful Effect ◽

Negative Relationship ◽

Mutation Rates ◽

Virus Species ◽

Overlapping Genes ◽

Genome Length ◽

Dna Viruses ◽

The Relationship ◽

Gene Overlap

The genomes of most virus species have overlapping genes—two or more proteins coded for by the same nucleotide sequence. Several explanations have been proposed for the evolution of this phenomenon, and we test these by comparing the amount of gene overlap in all known virus species. We conclude that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length. However, we do find a negative relationship between overlap proportion and genome length among viruses with icosahedral capsids, but not among those with other capsid types that we consider easier to enlarge in size. Our interpretation is that a physical constraint on genome length by the capsid has led to gene overlap evolving as a mechanism for producing more proteins from the same genome length. We consider that these patterns cannot be explained by other factors, namely the possible roles of overlap in transcription regulation, generating more divergent proteins and the relationship between gene length and genome length.

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