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Current Opinion in Virology Jun 2021Our understanding of the biology and pathogenesis of plant negative-stranded RNA viruses (NSVs) has lagged behind those made with positive-stranded RNA and DNA virus... (Review)
Review
Our understanding of the biology and pathogenesis of plant negative-stranded RNA viruses (NSVs) has lagged behind those made with positive-stranded RNA and DNA virus counterparts. This tardiness is mainly due to the lack of reverse genetics tools for NSV genome engineering for many years. The eventual establishment and application of recombinant systems with diverse plant NSVs has provided renewed momentum for investigations of these important viral pathogens. In this review, we summarize the recent advances in plant NSV reverse genetics systems, highlighting the general principles and the uniqueness of each system and emphasizing important considerations for strategy designing. We also provide a brief overview of the insights about NSV morphogenesis, movement, and virus-host interactions gained from reverse genetics-enabled studies.
Topics: DNA Viruses; Gene Expression Regulation, Viral; Host-Pathogen Interactions; Plant Viruses; Plants; RNA Interference; RNA Viruses; Reverse Genetics; Viral Core Proteins
PubMed: 33774424
DOI: 10.1016/j.coviro.2021.03.003 -
Neoplasma Apr 2023After a decade of human urinary microbiota research, little is known about the composition of the urinary virome and its association with health and disease. This study...
After a decade of human urinary microbiota research, little is known about the composition of the urinary virome and its association with health and disease. This study aimed to investigate the presence of 10 common DNA viruses in human urine and their putative association with bladder cancer (BC). Catheterized urine samples were collected from patients undergoing endoscopic urological procedures under anesthesia. After DNA extraction from the samples, viral DNA sequences were detected using real-time PCR. Viruria rates were compared between BC patients and controls. A total of 106 patients (89 males and 17 females) were included in the study. Fifty-seven (53.8%) were BC patients and 49 (46.2%) had upper urinary tract stones or bladder outlet obstruction. The viruses detected in the urine were human cytomegalovirus (2.0%), Epstein-Barr virus (6.0%), human herpesvirus-6 (12.5%), human papillomavirus (15.2%), BK polyomavirus (15.5%), torque teno virus (44.2%), and JC polyomavirus (47.6%), while no adenoviruses, herpes simplex virus 1 and 2, or parvoviruses were found. There were statistically significant differences in HPV viruria rates between cancer patients and controls (24.5% vs. 4.3%, p=0.032 after adjustment for age and gender). Viruria rates increased from benign to non-muscle-invasive and muscle-invasive tumors. Patients with a history of BC have higher HPV viruria rates than controls. Whether this relationship is a causal one remains to be established by further research.
Topics: Female; Male; Humans; Epstein-Barr Virus Infections; Papillomavirus Infections; Herpesvirus 4, Human; DNA Viruses; Urinary Bladder Neoplasms
PubMed: 37226931
DOI: 10.4149/neo_2023_220703N681 -
Archives of Virology Jun 2021Beekeeping is a widespread activity in Argentina, mainly producing honey that has gained both national and international recognition. There are more than 3,000,000 hives... (Review)
Review
Beekeeping is a widespread activity in Argentina, mainly producing honey that has gained both national and international recognition. There are more than 3,000,000 hives in the country, mainly concentrated in Buenos Aires Province (approximately 1,000,000 hives). In recent decades, worrying rates of hive loss have been observed in many countries around the world. In Latin America, the estimated loss of hives is between 13% (Peru and Ecuador) and 53% (Chile). Argentina had annual losses of 34% for the period of October 1, 2016 to October 1, 2017. The causes of these losses are not clear but probably involve multiple stressors that can act simultaneously. One of the main causes of loss of bee colonies worldwide is infestation by the ectoparasitic mite Varroa destructor in combination with viral infections. To date, 10 viruses have been detected that affect honey bees (Apis mellifera) in Argentina. Of these, deformed wing virus, sacbrood virus, acute bee paralysis virus, chronic bee paralysis virus, and Israeli acute bee paralysis can be transmitted by mites. Deformed wing virus and the AIK complex are the viruses most often associated with loss of hives worldwide. Considering that bee viruses have been detected in Argentina in several hymenopteran and non-hymenopteran insects, these hosts could act as important natural reservoirs for viruses and play an important role in their dispersal in the environment. Further studies to investigate the different mechanisms by which viruses spread in the environment will enable us to develop various strategies for the control of infected colonies and the spread of viruses in the habitat where they are found.
Topics: Animals; Argentina; Bees; DNA Viruses; Host-Pathogen Interactions; RNA Viruses
PubMed: 33683476
DOI: 10.1007/s00705-021-05000-6 -
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 -
Current Opinion in Virology Aug 2017Virophages are satellite DNA viruses that depend for their replication on giant viruses of the family Mimiviridae. An evolutionary relationship exists between the... (Review)
Review
Virophages are satellite DNA viruses that depend for their replication on giant viruses of the family Mimiviridae. An evolutionary relationship exists between the virophages and Polintons, large self-synthesizing transposons that are wide spread in the genomes of diverse eukaryotes. Most of the Polintons encode homologs of major and minor icosahedral virus capsid proteins and accordingly are predicted to form virions. Additionally, metagenome analysis has led to the discovery of an expansive family of Polinton-like viruses (PLV) that are more distantly related to bona fide Polintons and virophages. Another group of giant virus parasites includes small, linear, double-stranded DNA elements called transpovirons. Recent in-depth comparative genomic analysis has yielded evidence of the origin of the PLV and the transpovirons from Polintons. Integration of virophage genomes into genomes of both giant viruses and protists has been demonstrated. Furthermore, in an experimental coinfection system that consisted of a protist host, a giant virus and an associated virophage, the virophage integrated into the host genome and, after activation of its expression by a superinfecting giant virus, served as an agent of adaptive immunity. There is a striking analogy between this mechanism and the CRISPR-Cas system of prokaryotic adaptive immunity. Taken together, these findings show that Polintons, PLV, virophages and transpovirons form a dynamic network of integrating mobile genetic elements that contribute to the cellular antivirus defense and host-virus coevolution.
Topics: CRISPR-Cas Systems; DNA Replication; DNA Transposable Elements; DNA Viruses; DNA, Viral; Eukaryota; Evolution, Molecular; Genome, Viral; Giant Viruses; Host-Pathogen Interactions; Metagenome; Phylogeny; Virion; Virophages
PubMed: 28672161
DOI: 10.1016/j.coviro.2017.06.008 -
Viruses Sep 2022It is well-known that viruses activate various inflammasomes, which can initiate the programmed cell death pathway known as pyroptosis, subsequently leading to cell... (Review)
Review
It is well-known that viruses activate various inflammasomes, which can initiate the programmed cell death pathway known as pyroptosis, subsequently leading to cell lysis and release of inflammatory cytokines IL-1β and IL-18. This pathway can be triggered by various sensors, including, but not limited to, NLRP3, AIM2, IFI16, RIG-I, and NLRC4. Many viruses are known either to activate or inhibit inflammasomes as a part of the innate immune response or as a mechanism of pathogenesis. Early research in the field of virus-induced pyroptosis suggested a dichotomy, with RNA viruses activating the NLRP3 inflammasome and DNA viruses activating the AIM2 inflammasome. More recent research has shown that this dichotomy may not be as distinct as once thought. It seems many viruses activate multiple inflammasome sensors. Here, we detail which viruses fit the dichotomy as well as many that appear to defy this clearly false dichotomy. It seems likely that most, if not all, viruses activate multiple inflammasome sensors, and future research should focus on expanding our understanding of inflammasome activation in a variety of tissue types as well as virus activation of multiple inflammasomes, challenging biases that stemmed from early literature in this field. Here, we review primarily research performed on human viruses but also include details regarding animal viruses whenever possible.
Topics: Animals; Humans; Inflammasomes; Pyroptosis; NLR Family, Pyrin Domain-Containing 3 Protein; Interleukin-18; RNA; Virus Activation; DNA-Binding Proteins; Cytokines; DNA Viruses; Viruses; RNA Viruses
PubMed: 36298668
DOI: 10.3390/v14102113 -
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 -
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 -
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 -
Advances in Experimental Medicine and... 2019Membrane-containing enterobacterial phage PRD1 was isolated from sewage more than 40 years ago. At that time none would have expected the impact that unravelling its... (Review)
Review
Membrane-containing enterobacterial phage PRD1 was isolated from sewage more than 40 years ago. At that time none would have expected the impact that unravelling its biology would have on modern virology and on the way we understand virus assembly, evolution and classification today. PRD1 structural analyses have provided a framework for understanding some aspects of virus evolution-introducing the concept of "viral lineages"-where the three-dimensional structures of virus capsids represent the fingerprint for evolutionary relationship which cannot be traced from the sequence data. In this review we summarise those findings that have led to the notion of viral lineages and the multidisciplinary efforts made in elucidating PRD1 life cycle. These studies have rendered PRD1 a model system not only for the family Tectiviridae to which it belongs, but more generally to complex DNA viruses enclosing a membrane vesicle beneath the capsid shell.
Topics: Animals; Bacteriophage PRD1; DNA Viruses; History, 20th Century; History, 21st Century; Humans; Virology; Virus Assembly
PubMed: 31317497
DOI: 10.1007/978-3-030-14741-9_5