scholarly journals A planarian nidovirus expands the limits of RNA genome size

2018 ◽  
Author(s):  
Amir Saberi ◽  
Anastasia A. Gulyaeva ◽  
John L. Brubacher ◽  
Phillip A. Newmark ◽  
Alexander E. Gorbalenya
Keyword(s):  
Genome Size ◽  
Secretory Cell ◽  
Rna Viruses ◽  
Rna Virus ◽  
Evolutionary Analysis ◽  
Reading Frame ◽  
Autonomous Replication ◽  
Rna Genome ◽  
On The Road ◽  
Cellular Dna

AbstractRNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication (albeit within a permissive environment). A 33.5-kb nidovirus has been considered close to the upper size limit for such entities; conversely, the minimal cellular DNA genome is ~200 kb. This large difference presents a daunting gap for the transition from primordial RNP to contemporary DNA-RNP-based life. Whether or not RNA viruses represent transitional steps on the road to DNA-based life, studies of larger RNA viruses advance our understanding of size constraints on RNP entities. For example, emergence of the largest previously known RNA genomes (20-34 kb in positive-stranded nidoviruses, including coronaviruses) is associated with a proofreading exoribonuclease encoded in the nidoviral open reading frame 1b (ORF1b). However, apparent constraints on the size of ORF1b, which encodes this and other key replicative enzymes, have been hypothesized to limit further expansion of viral RNA genomes. Here, we characterize a novel nidovirus (planarian secretory cell nidovirus; PSCNV) whose disproportionately large ORF1b-like region, and overall 41.1 kb genome, substantially extend the presumed limits on RNA genome size. This genome encodes a predicted 13,556-aa polyprotein in an unconventional single ORF, yet retains canonical nidoviral genome organization and expression, and key replicative domains. Our evolutionary analysis suggests that PSCNV diverged early from multi-ORF nidoviruses, and subsequently acquired additional genes, including those typical of large DNA viruses or hosts. PSCNV’s greatly expanded genome, proteomic complexity, and unique features – impressive in themselves – attest to the likelihood of still-larger RNA genomes awaiting discovery.Significance StatementRNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication. The upper genome size for such entities was assumed to be <35 kb; conversely, the minimal cellular DNA genome is ~200 kb. This large difference presents a daunting gap for the proposed evolution of contemporary DNA-RNP-based life from primordial RNP entities. Here, we describe a nidovirus from planarians, whose 41.1 kb genome is 23% larger than the largest known of RNA virus. The planarian secretory cell nidovirus has broken apparent constraints on the size of the genomic subregion that encodes core replication machinery, and has acquired genes not previously observed in RNA viruses. This virus challenges and advances our understanding of the limits to RNA genome size.

scholarly journals Isolation and Characterization of an Arterivirus Defective Interfering RNA Genome

2000 ◽  
Vol 74 (7) ◽  
pp. 3156-3165 ◽  
Author(s):  
Richard Molenkamp ◽  
Babette C. D. Rozier ◽  
Sophie Greve ◽  
Willy J. M. Spaan ◽  
Eric J. Snijder
Keyword(s):  
Rna Virus ◽  
Equine Arteritis Virus ◽  
Reading Frame ◽  
Isolation And Characterization ◽  
The Family ◽  
Defective Interfering Rna ◽  
Rna Genome ◽  
Interfering Rna ◽  
Discontinuous Transcription

ABSTRACT Equine arteritis virus (EAV), the type member of the family Arteriviridae, is a single-stranded RNA virus with a positive-stranded genome of approximately 13 kb. EAV uses a discontinuous transcription mechanism to produce a nested set of six subgenomic mRNAs from which its structural genes are expressed. We have generated the first documented arterivirus defective interfering (DI) RNAs by serial undiluted passaging of a wild-type EAV stock in BHK-21 cells. A cDNA copy of the smallest DI RNA (5.6 kb) was cloned. Upon transfection into EAV-infected BHK-21 cells, transcripts derived from this clone (pEDI) were replicated and packaged. Sequencing of pEDI revealed that the DI RNA was composed of three segments of the EAV genome (nucleotides 1 to 1057, 1388 to 1684, and 8530 to 12704) which were fused in frame with respect to the replicase reading frame. Remarkably, this DI RNA has retained all of the sequences encoding the structural proteins. By insertion of the chloramphenicol acetyltransferase reporter gene in the DI RNA genome, we were able to delimitate the sequences required for replication/DI-based transcription and packaging of EAV DI RNAs and to reduce the maximal size of a replication-competent EAV DI RNA to approximately 3 kb.

scholarly journals THE HISTORICAL/EVOLUTIONARY CAUSE AND POSSIBLE TREATMENT OF PANDEMIC COVID-19 (SARS-CoV-2, 2019CORONAVIRUS)

2021 ◽  
Author(s):  
Sorush Niknamian
Keyword(s):  
Older Adults ◽  
Natural Selection ◽  
Respiratory Tract ◽  
Genome Size ◽  
Rna Viruses ◽  
Rna Virus ◽  
Influenza Viruses ◽  
Recombinant Viruses ◽  
Lamarckian Evolution ◽  
Tract Infections

Background: A virus is a small infectious agent that replicates only inside the living cells of an organism. Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity in a way analogous to sexual reproduction. Influenza (Including (COVID-19), is an infectious disease caused by an influenza virus. Some viruses especially smallpox, throughout history, has killed between 300-500 million people in its 12,000year existence. As modern humans increased in numbers, new infectious diseases emerged, including SARS-CoV-2. We have two groups of virus, RNA and DNA viruses. The most brutal viruses are RNA ones like COVID-19 (Sars-CoV-2 [1] Introduction: Coronaviruses are a group of viruses that cause diseases in mammals and birds. In humans, coronaviruses cause respiratory tract infections that are typically mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), though rarer forms can be lethal, such as SARS, MERS, and COVID-19. Symptoms vary in other species: in chickens, they cause an upper respiratory tract disease, while in cows and pigs they cause diarrhea. Coronaviruses constitute the subfamily Orthocoronavirinae, The genome size, coronaviruses ranges from approximately 27 to 34 kilobases, the largest among known RNA viruses. Discussions and Results: We have researched from the first virus in the planet to the last mutated version which is SARS-COV-2. We have collected many informative data in tables and figures to reach the main cause of 2019Coronavirus and calculated the probability and estimated deaths in the current time. We have discussed about the possible treatment and prevention of the virus and did algebraic calculations on the epidemiology, the size and even the future of this pandemic. The only era which any virus had not been epidemic, were through world war 2, were the German scientists had found the way to fight any viral infections which is very important and can help scientists to reach the main treatment of the new 2019-Coronavirus. We have sorted the deadly and non-deadly coronaviruses and explained how this epidemic had begun through Evolutionary Medicine (EM). The result of the article is that 16% of the whole population in the world has been contaminated which is 1248000000 of 7.8 billion people world-wide. SARS-CoV-2 is an RNA Virus. its nucleic acid is 2 single-stranded RNA (ssRNA). The polarity of this virus is positive-sense ((+) ssRNA). Positivesense viral RNA is similar to mRNA and thus can be immediately translated by the host cell. Recombination in RNA viruses appears to be an adaptation for coping with genome damage. Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans. RNA viruses have very high mutation rates This is one reason why it is difficult to make effective vaccines to prevent diseases caused by RNA viruses. The resulting recombinant viruses causes an outbreak of infection in humans. Conclusion: In conclusion, the mutation of the SARSCoV and influenza viruses through Drift and Reassortment is the main cause of SARS-CoV-2 through natural selection, Lamarckian Evolution and coevolution which caused this RNA virus so powerful, unpredicted and different in the genome size and nations worldwide. The first Pandemic of Influenza was first detected in 1732 and this virus evolved through natural selection till 2019 which caused the worldwide pandemic of SARS-CoV-2. Based on many studies, inhalation of Ozone plus Sulfur Dioxide, increasing the amounts of L-Glutathione (Which is low in children and older adults and this is the main reason why older adults and children die from this disease.) plus Viral Phage Therapy (VPT) which we discussed fully in this article can be the possible prime treatment of SARS-CoV-2 infection. The seasonal temperature cannot be useful in controlling/reducing the pandemic of this virus since the natural selection, Lamarckian Evolution and high mutation of the virus helps its survival. No antiviral drugs will be useful against SARSCoV-2 because of high rate of mutation and primarily adaptation of the virus to the drugs and even the environmental Temperature.

scholarly journals Chemogenetic ON and OFF switches for RNA virus replication

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
E. Heilmann ◽  
J. Kimpel ◽  
B. Hofer ◽  
A. Rössler ◽  
I. Blaas ◽  
...  
Keyword(s):  
Protease Inhibitor ◽  
Rna Viruses ◽  
Rna Virus ◽  
Hiv Protease ◽  
Hiv Protease Inhibitors ◽  
Dependent Manner ◽  
Reading Frame ◽  
Virus Activity ◽  
Gene Vectors ◽  
Or Gene

AbstractTherapeutic application of RNA viruses as oncolytic agents or gene vectors requires a tight control of virus activity if toxicity is a concern. Here we present a regulator switch for RNA viruses using a conditional protease approach, in which the function of at least one viral protein essential for transcription and replication is linked to autocatalytical, exogenous human immunodeficiency virus (HIV) protease activity. Virus activity can be en- or disabled by various HIV protease inhibitors. Incorporating the HIV protease dimer in the genome of vesicular stomatitis virus (VSV) into the open reading frame of either the P- or L-protein resulted in an ON switch. Here, virus activity depends on co-application of protease inhibitor in a dose-dependent manner. Conversely, an N-terminal VSV polymerase tag with the HIV protease dimer constitutes an OFF switch, as application of protease inhibitor stops virus activity. This technology may also be applicable to other potentially therapeutic RNA viruses.

scholarly journals A new lineage of segmented RNA viruses infecting animals

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Darren J Obbard ◽  
Mang Shi ◽  
Katherine E Roberts ◽  
Ben Longdon ◽  
Alice B Dennis
Keyword(s):  
Small Rnas ◽  
Rna Viruses ◽  
Rna Virus ◽  
Close Relative ◽  
Metagenomic Sequencing ◽  
Reading Frame ◽  
Virus Identification ◽  
Conserved Sequence ◽  
Virus Diversity ◽  
Close Relatives

Abstract Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.

scholarly journals Engineering RNA Virus Interference via the CRISPR/Cas13 Machinery in Arabidopsis

Viruses ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 732 ◽  
Author(s):  
Rashid Aman ◽  
Ahmed Mahas ◽  
Haroon Butt ◽  
Fatimah Aljedaani ◽  
Magdy Mahfouz
Keyword(s):  
Genome Engineering ◽  
Rna Viruses ◽  
Rna Virus ◽  
Basic Research ◽  
Dna Viruses ◽  
Eukaryotic Species ◽  
Exciting Potential ◽  
Rna Genome ◽  
Target Rna ◽  
Rna And Dna

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are key immune mechanisms helping prokaryotic species fend off RNA and DNA viruses. CRISPR/Cas9 has broad applications in basic research and biotechnology and has been widely used across eukaryotic species for genome engineering and functional analysis of genes. The recently developed CRISPR/Cas13 systems target RNA rather than DNA and thus offer new potential for transcriptome engineering and combatting RNA viruses. Here, we used CRISPR/LshCas13a to stably engineer Arabidopsis thaliana for interference against the RNA genome of Turnip mosaic virus (TuMV). Our data demonstrate that CRISPR RNAs (crRNAs) guiding Cas13a to the sequences encoding helper component proteinase silencing suppressor (HC-Pro) or GFP target 2 (GFP-T2) provide better interference compared to crRNAs targeting other regions of the TuMV RNA genome. This work demonstrates the exciting potential of CRISPR/Cas13 to be used as an antiviral strategy to obstruct RNA viruses, and encourages the search for more robust and effective Cas13 variants or CRISPR systems that can target RNA.

scholarly journals Regulation of RNA Virus Processes by Viral Genome Structure

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 68
Author(s):  
K. Andrew White
Keyword(s):  
Viral Genome ◽  
Rna Viruses ◽  
Rna Virus ◽  
Genome Structure ◽  
Viral Proteins ◽  
Viral Rna ◽  
Rna Sequences ◽  
Virus Reproduction ◽  
The Family ◽  
Rna Genome

The genomes of RNA viruses contain a variety of RNA sequences and structures that regulate different steps in virus reproduction. Events that are controlled by RNA elements include (i) the translation of viral proteins, (ii) the replication of viral RNA genomes, and (iii) the transcription of viral subgenomic mRNAs. Studies of members of the family Tombusviridae, which possess plus-strand RNA genomes, have revealed novel ways in which the RNA genome structure is utilized to control different viral processes. Recent advances in our understanding of RNA-based viral regulation in select tombusvirids will be presented.

scholarly journals Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dongbin Park ◽  
Yoonsoo Hahn
Keyword(s):  
Amino Acid ◽  
Large Scale ◽  
Rna Viruses ◽  
Rna Virus ◽  
Phylogenetic Analyses ◽  
Sequence Evolution ◽  
Protein Coding ◽  
Coding Sequences ◽  
Reading Frame ◽  
Nucleotide Insertions

Abstract Background RNA viruses possess remarkable evolutionary versatility driven by the high mutability of their genomes. Frameshifting nucleotide insertions or deletions (indels), which cause the premature termination of proteins, are frequently observed in the coding sequences of various viral genomes. When a secondary indel occurs near the primary indel site, the open reading frame can be restored to produce functional proteins, a phenomenon known as the compensatory frameshift. Results In this study, we systematically analyzed publicly available viral genome sequences and identified compensatory frameshift events in hundreds of viral protein-coding sequences. Compensatory frameshift events resulted in large-scale amino acid differences between the compensatory frameshift form and the wild type even though their nucleotide sequences were almost identical. Phylogenetic analyses revealed that the evolutionary distance between proteins with and without a compensatory frameshift were significantly overestimated because amino acid mismatches caused by compensatory frameshifts were counted as substitutions. Further, this could cause compensatory frameshift forms to branch in different locations in the protein and nucleotide trees, which may obscure the correct interpretation of phylogenetic relationships between variant viruses. Conclusions Our results imply that the compensatory frameshift is one of the mechanisms driving the rapid protein evolution of RNA viruses and potentially assisting their host-range expansion and adaptation.

scholarly journals A new lineage of segmented RNA viruses infecting animals

2019 ◽  
Author(s):  
Darren J. Obbard ◽  
Mang Shi ◽  
Katherine E. Roberts ◽  
Ben Longdon ◽  
Alice B. Dennis
Keyword(s):  
Small Rnas ◽  
Rna Viruses ◽  
Rna Virus ◽  
Close Relative ◽  
Metagenomic Sequencing ◽  
Reading Frame ◽  
Virus Identification ◽  
Conserved Sequence ◽  
Virus Diversity ◽  
Close Relatives

AbstractMetagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.

scholarly journals Mapping RNA-capsid interactions and RNA secondary structure within authentic virus particles using next-generation sequencing

2019 ◽  
Author(s):  
Yiyang Zhou ◽  
Andrew Routh
Keyword(s):  
Next Generation Sequencing ◽  
High Resolution ◽  
Virus Replication ◽  
Binding Sites ◽  
Rna Viruses ◽  
Rna Virus ◽  
Genomic Rna ◽  
Virus Particles ◽  
Rna Genome ◽  
Generation Sequencing

AbstractTo characterize RNA-capsid binding sites genome-wide within mature RNA virus particles, we have developed a Next-Generation Sequencing (NGS) platform: Photo-Activatable Ribonucleoside Cross-Linking (PAR-CL). In PAR-CL, 4-thiouracil is incorporated into the encapsidated genomes of authentic virus particles and subsequently UV-crosslinked to adjacent capsid proteins. We demonstrate that PAR-CL can readily and reliably identify capsid binding sites in genomic viral RNA by detecting crosslink-specific uridine to cytidine transitions in NGS data. Using Flock House virus (FHV) as a model system, we identified highly consistent and significant PAR-CL signals across virus RNA genome indicating a clear tropism of the encapsidated RNA genome. Certain interaction sites correlate to previously identified FHV RNA motifs. We additionally performed dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to generate a high-resolution profile of single-stranded genomic RNA inside viral particles. Combining PAR-CL and DMS-MaPseq reveals that the predominant RNA-capsid sites favor double-stranded RNA regions. We disrupted secondary structures associated with PAR-CL sites using synonymous mutations, resulting in varied effects to virus replication, propagation, and packaging. Certain mutations showed substantial deficiency in virus replication, suggesting these RNA-capsid sites are multifunctional. These provide further evidence to support that FHV packaging and replication are highly coordinated and inter-dependent events.ImportanceIcosahedral RNA viruses must package their genetic cargo into the restrictive and tight confines of the protected virions. High resolution structures of RNA viruses have been solved by Cryo-EM and crystallography, but the encapsidated RNA often eluded visualization due to the icosahedral averaging imposed during image reconstruction. Asymmetrical reconstructions of some icosahedral RNA virus particles have revealed that the encapsidated RNAs conform to specific structures, which may be related to programmed assembly pathway or an energy-minima for RNA folding during or after encapsidation. Despite these advances, determining whether encapsidated RNA genomes conform to a single structure and determining what regions of the viral RNA genome interact with the inner surface of the capsid shell remains challenging. Furthermore, it remains to be determined whether there exists a single RNA structure with conserved topology in RNA virus particles or an ensemble of genomic RNA structures. This is important as resolving these features will inform the elusive structures of the asymmetrically encapsidated genomic material and how virus particles are assembled.

scholarly journals Structure Unveils Relationships between RNA Virus Polymerases

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 313
Author(s):  
Heli A. M. Mönttinen ◽  
Janne J. Ravantti ◽  
Minna M. Poranen
Keyword(s):  
Phylogenetic Tree ◽  
Rna Viruses ◽  
Rna Virus ◽  
Sequence Similarity ◽  
Protein Structures ◽  
Structural Similarity ◽  
Functional Differentiation ◽  
Comparison Method ◽  
Homologous Structure ◽  
Biological Entities

RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.

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