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Viruses Jan 2024Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent,...
Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.
Topics: DNA, Viral; Brassicaceae; Virome; DNA Viruses; Viruses; Phylogeny; Genome, Viral
PubMed: 38400004
DOI: 10.3390/v16020228 -
Journal of Clinical Virology : the... Oct 2020Redondovirus (ReDoV) is a recently discovered circular, Rep-encoding single-stranded DNA (CRESS-DNA) virus in humans. Its pathogenesis and clinical associations are...
BACKGROUND
Redondovirus (ReDoV) is a recently discovered circular, Rep-encoding single-stranded DNA (CRESS-DNA) virus in humans. Its pathogenesis and clinical associations are still completely unknown.
METHODS
The presence of ReDoV DNA was investigated in biological specimens of 543 Italian subjects by in-house developed PCR assays.
RESULTS
The overall ReDoV prevalence was about 4% (23 of 543 samples). The virus was detected in 22 of 209 (11 %) respiratory samples. One stool sample was also ReDoV positive. Viral DNA was not found in blood samples from immunocompetent and immunosuppressed subjects and cerebrospinal fluids from patients with neurological diseases. Genomic nucleotide differences were detected among the ReDoV isolates by sequencing a 582-nucleotide fragment of the capsid gene of the viral genome.
CONCLUSIONS
The results demonstrate that ReDoV is mainly present in the respiratory tract of infected people. Further investigations are needed to reveal possible clinical implications of this new CRESS-DNA virus in humans.
Topics: Adult; Aged; Capsid Proteins; DNA Virus Infections; DNA Viruses; DNA, Viral; Feces; Female; Genetic Variation; Genome, Viral; Humans; Italy; Male; Middle Aged; Phylogeny; Prevalence; Respiratory Tract Infections; Retrospective Studies; Sequence Analysis, DNA
PubMed: 32841923
DOI: 10.1016/j.jcv.2020.104586 -
Proceedings of the National Academy of... Mar 2016Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with...
Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Here, we describe a filamentous hyperthermophilic archaeal virus, Pyrobaculum filamentous virus 1 (PFV1), with a type of virion organization not previously observed in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an envelope and an inner core consisting of two structural units: a rod-shaped helical nucleocapsid formed of two 14-kDa major virion proteins and a nucleocapsid-encompassing protein sheath composed of a single major virion protein of 18 kDa. The virion organization of PFV1 is superficially similar to that of negative-sense RNA viruses of the family Filoviridae, including Ebola virus and Marburg virus. The linear dsDNA of PFV1 carries 17,714 bp, including 60-bp-long terminal inverted repeats, and contains 39 predicted ORFs, most of which do not show similarities to sequences in public databases. PFV1 is a lytic virus that completely disrupts the host cell membrane at the end of the infection cycle.
Topics: Archaea; DNA Viruses; Genome, Viral; Host-Pathogen Interactions; Microscopy, Electron, Transmission
PubMed: 26884161
DOI: 10.1073/pnas.1518929113 -
ACS Chemical Biology Aug 2023The constant and the sudden emergence of zoonotic human and animal viruses is a significant threat to human health, the world economy, and the world food supply. This...
The constant and the sudden emergence of zoonotic human and animal viruses is a significant threat to human health, the world economy, and the world food supply. This has necessitated the development of broad-spectrum therapeutic strategies to combat these emerging pathogens. Mechanisms that are essential for viral replication and propagation have been successfully targeted in the past to develop broad-spectrum therapeutics that can be readily repurposed to combat new zoonotic pathogens. Because of the importance of viral RNA capping enzymes to viral replication and pathogenesis, as well as their presence in both DNA and RNA viruses, these viral proteins have been a long-standing therapeutic target. Here, we use genome sequencing information and yeast-based platforms (YeRC0M) to identify, characterize, and target viral genome-encoded essential RNA capping enzymes from emerging strains of DNA viruses, i.e., Monkeypox virus and African Swine Fever Virus, which are a significant threat to human and domestic animal health. We first identified and biochemically characterized these viral RNA capping enzymes and their necessary protein domains. We observed significant differences in functional protein domains and organization for RNA capping enzymes from emerging DNA viruses in comparison to emerging RNA viruses. We also observed several differences in the biochemical properties of these viral RNA capping enzymes using our phenotypic yeast-based approaches (YeRC0M) as compared to the previous in vitro studies. Further, using directed evolution, we were able to identify inactivation and attenuation mutations in these essential viral RNA capping enzymes; these data could have implications on virus biocontainment as well as live attenuated vaccine development. We also developed methods that would facilitate high-throughput phenotypic screening to identify broad-spectrum inhibitors that selectively target viral RNA capping enzymes over host RNA capping enzymes. As demonstrated here, our approaches to identify, characterize, and target viral genome-encoded essential RNA capping enzymes are highly modular and can be readily adapted for targeting emerging viral pathogens as well as their variants that emerge in the future.
Topics: Animals; Humans; Swine; Saccharomyces cerevisiae; African Swine Fever Virus; Viruses; RNA, Viral; Virus Replication; DNA Viruses
PubMed: 37498174
DOI: 10.1021/acschembio.3c00243 -
Biochemical Pharmacology Apr 2020Innate sensing of viruses by cytosolic nucleic acid sensors is a key feature of anti-viral immunity against these pathogens. The DNA sensing pathway through the sensor... (Review)
Review
Innate sensing of viruses by cytosolic nucleic acid sensors is a key feature of anti-viral immunity against these pathogens. The DNA sensing pathway through the sensor cyclic GMP-AMP synthase (cGAS) and its downstream effector stimulator of interferon genes (STING) has emerged in recent years as a key, front-line means of driving interferons and pro-inflammatory cytokines in response to DNA virus infection in vertebrates. Unsurprisingly, many DNA viruses have evolved effective inhibitors of this signalling system which target at a wide variety of points from sensing all the way down to the activation of Interferon Regulatory Factor (IRF)-family and Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB)-family transcription factors which drive a program of pro-inflammatory and anti-viral gene expression. Here we review DNA viruses that have been shown to inhibit this pathway and the inhibitors they have evolved to do it.
Topics: Animals; DNA Viruses; DNA, Viral; Gene Targeting; Humans; Immunity, Innate; Inflammation Mediators; Membrane Proteins; Nucleotidyltransferases
PubMed: 32004549
DOI: 10.1016/j.bcp.2020.113831 -
ELife Oct 2020Hosts and viruses are constantly evolving in response to each other: as a host attempts to suppress a virus, the virus attempts to evade and suppress the host's immune...
Hosts and viruses are constantly evolving in response to each other: as a host attempts to suppress a virus, the virus attempts to evade and suppress the host's immune system. Here, we describe the recurrent evolution of a virulent strain of a DNA virus, which infects multiple Drosophila species. Specifically, we identified two distinct viral types that differ 100-fold in viral titer in infected individuals, with similar differences observed in multiple species. Our analysis suggests that one of the viral types recurrently evolved at least four times in the past ~30,000 years, three times in Arizona and once in another geographically distinct species. This recurrent evolution may be facilitated by an effective mutation rate which increases as each prior mutation increases viral titer and effective population size. The higher titer viral type suppresses the host-immune system and an increased virulence compared to the low viral titer type.
Topics: Animals; Biological Evolution; DNA Virus Infections; DNA Viruses; Drosophila; Female; Humans; Male; Virulence
PubMed: 33112738
DOI: 10.7554/eLife.58931 -
The Journal of General Virology Nov 2021It is widely recognized that pathogens can be transmitted across the placenta from mother to foetus. Recent re-evaluation of metagenomic studies indicates that the...
It is widely recognized that pathogens can be transmitted across the placenta from mother to foetus. Recent re-evaluation of metagenomic studies indicates that the placenta has no unique microbiome of commensal bacteria. However, viral transmission across the placenta, including transmission of DNA viruses such as the human herpesviruses, is possible. A fuller understanding of which DNA virus sequence can be found in the placenta is required. We employed a metagenomic analysis to identify viral DNA sequences in placental metagenomes from full-term births (20 births), pre-term births (13 births), births from pregnancies associated with antenatal infections (12 births) or pre-term births with antenatal infections (three births). Our analysis found only a small number of DNA sequences corresponding to the genomes of human herpesviruses in four of the 48 metagenomes analysed. Therefore, our data suggest that DNA virus infection of the placenta is rare and support the concept that the placenta is largely free of pathogen infection.
Topics: DNA Virus Infections; DNA Viruses; Female; Genome, Viral; Humans; Infant, Newborn; Male; Metagenome; Placenta; Pregnancy; Pregnancy Complications; Premature Birth; Term Birth
PubMed: 34723784
DOI: 10.1099/jgv.0.001677 -
Journal of Cellular Physiology Oct 1969
Topics: Carbon Isotopes; Centrifugation, Density Gradient; Coliphages; Culture Techniques; DNA Replication; DNA Viruses; DNA, Viral; Electrophoresis; Microscopy, Electron; Models, Biological; RNA Viruses; RNA, Viral; Tritium; Viral Proteins; Virus Replication
PubMed: 5361232
DOI: 10.1002/jcp.1040740404 -
Protein & Cell Jan 2013The innate immune system acts as the first line of defense against pathogens, which is also essential for initiation of adaptive immunity. Innate immune responses are... (Review)
Review
The innate immune system acts as the first line of defense against pathogens, which is also essential for initiation of adaptive immunity. Innate immune responses are initiated by pattern-recognition receptors (PRRs), which recognize conserved molecular structures of pathogens called pathogen-associated molecular patterns (PAMPs). The infection of virus triggers a series of signaling events leading to transcriptional induction of type I interferons (IFNs) and proinflammatory cytokines. In recent years, the mechanisms of viral RNA recognition and RNA virus-triggered signaling pathways have been well studied. However, it remains unclear on how DNA virus infection is sensed by host cells and triggers the host antiviral defense. Although ten potential viral DNA sensors have been reported, none of them is validated as a generally used sensor for distinct DNA viruses in divergent cell types and animals. Here, we provide a summary and perspective on recent advances in innate immune responses to DNA viruses.
Topics: Animals; DNA Viruses; Humans; Immunity, Innate; Proteins
PubMed: 23307778
DOI: 10.1007/s13238-012-2122-6 -
Viruses Jan 2020DNA viruses that replicate in the nucleus encompass a range of ubiquitous and clinically important viruses, from acute pathogens to persistent tumor viruses. These... (Review)
Review
DNA viruses that replicate in the nucleus encompass a range of ubiquitous and clinically important viruses, from acute pathogens to persistent tumor viruses. These viruses must co-opt nuclear processes for the benefit of the virus, whilst evading host processes that would otherwise attenuate viral replication. Accordingly, DNA viruses induce the formation of membraneless assemblies termed viral replication compartments (VRCs). These compartments facilitate the spatial organization of viral processes and regulate virus-host interactions. Here, we review advances in our understanding of VRCs. We cover their initiation and formation, their function as the sites of viral processes, and aspects of their composition and organization. In doing so, we highlight ongoing and emerging areas of research highly pertinent to our understanding of nuclear-replicating DNA viruses.
Topics: Cell Nucleus; DNA Viruses; Host Microbial Interactions; Humans; Viral Proteins; Viral Replication Compartments; Virus Replication
PubMed: 32013091
DOI: 10.3390/v12020151