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Viruses Jul 2015A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double stranded DNA...
A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double stranded DNA molecule of approximately 498,500 nucleotides with a GC content of 50.8%. It encompasses 247 non-overlapping open reading frames (ORFs), equally distributed on both strands, which cover 65% of the genome. While most of the ORFs lacked threshold sequence alignments to reference protein databases, twenty-eight were found to display significant homologies with proteins present in other large double stranded DNA viruses. Remarkably, 13 ORFs had strong similarity with typical baculovirus domains such as PIFs (per os infectivity factor genes: pif-1, pif-2, pif-3 and p74) and BRO (Baculovirus Repeated Open Reading Frame). The putative AmFV DNA polymerase is of type B, but is only distantly related to those of the baculoviruses. The ORFs encoding proteins involved in nucleotide metabolism had the highest percent identity to viral proteins in GenBank. Other notable features include the presence of several collagen-like, chitin-binding, kinesin and pacifastin domains. Due to the large size of the AmFV genome and the inconsistent affiliation with other large double stranded DNA virus families infecting invertebrates, AmFV may belong to a new virus family.
Topics: Animals; Bees; DNA Viruses; Genome, Viral; Molecular Sequence Data; Open Reading Frames; Phylogeny; Sequence Alignment; Viral Proteins
PubMed: 26184284
DOI: 10.3390/v7072798 -
Virus Research May 2019En Bloc transmission of viruses allow multiple genomes to collectivelly penetrate and initiate infection in the same cell, often resulting in enhanced infectivity. Given... (Review)
Review
En Bloc transmission of viruses allow multiple genomes to collectivelly penetrate and initiate infection in the same cell, often resulting in enhanced infectivity. Given the quasispecies (mutant cloud) nature of RNA viruses and many DNA viruses, en bloc transmission of multiple genomes provides different starting points in sequence space to initiate adaptive walks, and has implications for modulation of viral fitness and for the response of viral populations to lethal mutagenesis. Mechanisms that can enable multiple viral genomes to be transported en bloc among hosts has only recently been gaining attention. A growing body of research suggests that extracellular vesicles (EV) are highly prevalent and robust vehicles for en bloc delivery of viral particles and naked infectious genomes among organisms. Both RNA and DNA viruses appear to exploit these vesicles to increase their multiplicity of infection and enhance virulence.
Topics: Animals; DNA Viruses; Extracellular Vesicles; Genome, Viral; Humans; Membrane Lipids; Mice; Quasispecies; RNA Viruses; Virion; Virus Diseases; Virus Replication; Viruses
PubMed: 30928427
DOI: 10.1016/j.virusres.2019.03.023 -
Journal of Evolutionary Biology Dec 2021Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the...
Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientists have identified and annotated copious numbers of novel CRESS DNA viruses - many without known hosts but which have been found in association with eukaryotes. Similar advances in cellular genomics have revealed that many eukaryotes have endogenous sequences homologous to viral Reps, which not only provide 'fossil records' to reconstruct the evolutionary history of CRESS DNA viruses but also reveal potential host species for viruses known by their sequences alone. The Rep protein is a conserved protein that all CRESS DNA viruses use to assist rolling-circle replication that is known to be endogenized in a few eukaryotic species (notably tobacco and water yam). A systematic search for endogenous Rep-like sequences in GenBank's non-redundant eukaryotic database was performed using tBLASTn. We utilized relaxed search criteria for the capture of integrated Rep sequence within eukaryotic genomes, identifying 93 unique species with an endogenized fragment of Rep in their nuclear, plasmid (one species), mitochondrial (six species) or chloroplast (eight species) genomes. These species come from 19 different phyla, scattered across the eukaryotic tree of life. Exogenous and endogenous CRESS DNA viral Rep tree topology suggested potential hosts for one family of uncharacterized viruses and supports a primarily fungal host range for genomoviruses.
Topics: Brassicaceae; DNA Viruses; DNA, Single-Stranded; Eukaryota; Genome, Viral; Phylogeny
PubMed: 34498333
DOI: 10.1111/jeb.13927 -
Intervirology 2000Although recent studies indicate a high prevalence (12-92%) of TT virus (TTV) DNA in sera of healthy Japanese individuals, there is a paucity of information regarding...
Although recent studies indicate a high prevalence (12-92%) of TT virus (TTV) DNA in sera of healthy Japanese individuals, there is a paucity of information regarding the route of transmission of this virus. Analyzing the nucleotide sequences of the existing polymerase chain reaction (PCR) primers of TTV DNA, we developed a set of noble primers (HM-1) and looked for the prevalence of TTV DNA in sera from 39 normal healthy Japanese individuals using PCR. The existence of TTV DNA was also checked in saliva, urine, sweat, stool, and tears from 11 and in semen from 10 serum TTV-positive normal subjects. TTV DNA was detected in sera from 23 of 39 (59.0%) normal subjects. TTV DNA was also detected in saliva, stool, semen and tears from all cases with TTV-DNA-positive serum, but not in body fluids from subjects with TTV-DNA-negative serum. TTV DNA remained undetected in urine and sweat from all cases. Data from these experiments showing the existence of TTV DNA in different body fluids suggest that the high rates of prevalence of TTV among normal healthy subjects might be due to a possible fecal-oral, droplet, or sexual route of transmission of TTV.
Topics: Adult; Blood; Body Fluids; DNA Primers; DNA Virus Infections; DNA Viruses; DNA, Viral; Feces; Female; Humans; Japan; Male; Saliva; Semen; Sweat; Tears; Urine; Viremia
PubMed: 10773733
DOI: 10.1159/000025018 -
Advances in Virus Research 2019While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA... (Review)
Review
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
Topics: Animals; Biological Evolution; Capsid Proteins; DNA Viruses; DNA, Single-Stranded; DNA, Viral; Eukaryotic Cells; Genetic Variation; Genome, Viral; Host Specificity; Plant Diseases; Recombination, Genetic
PubMed: 30635078
DOI: 10.1016/bs.aivir.2018.10.001 -
Viruses Nov 2019DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest...
DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the , and families of single-stranded DNA virus families, and six double-stranded DNA virus species from the , , and , for which few invertebrate viruses have been identified to date. By incorporating the sequence of a "blank" experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the diversity and evolution of DNA viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.
Topics: Animals; Biological Evolution; DNA Viruses; Genetic Variation; Genome, Viral; Genomics; Host Specificity; Invertebrates; Phylogeny
PubMed: 31775324
DOI: 10.3390/v11121092 -
Pathologie-biologie Mar 2009Unlike other recent viral emergences, which were in majority caused by RNA viruses, the monkeypox results from infection by a DNA virus, an orthopoxvirus closely related... (Review)
Review
Unlike other recent viral emergences, which were in majority caused by RNA viruses, the monkeypox results from infection by a DNA virus, an orthopoxvirus closely related to both vaccine and smallpox viruses and whose two genomic variants are known. Unexpectedly isolated from captive Asiatic monkeys and first considered as an laboratory curiosity, this virus was recognised in 1970 as an human pathogen in tropical Africa. Here it was responsible for sporadic cases following intrusions (for hunting) into tropical rain forests or rare outbreak with human-to-human transmission as observed in 1996 in Democratic Republic of Congo. As monkeypox in humans is not distinguishable from smallpox (a disease globally eradicated in 1977) it was only subjected to vigilant epidemiological surveillance and not considered as a potential threat outside Africa. This point of view radically changed in 2003 when monkeypox was introduced in the USA by African wild rodents and spread to 11 different states of this country. Responsible for 82 infections in American children and adults, this outbreak led to realize the sanitary hazards resulting from international trade of exotic animals and scientific investigations increasing extensively our knowledge of this zoonosis.
Topics: Adult; Animals; Child; DNA Viruses; Democratic Republic of the Congo; Disease Outbreaks; Humans; Mpox (monkeypox); Monkeypox virus; RNA Viruses; RNA, Viral; Rodentia
PubMed: 18394820
DOI: 10.1016/j.patbio.2008.02.006 -
FEBS Letters Aug 2006A large DNA virus, designated koi herpes virus (KHV), carp interstitial nephritis gill necrosis virus (CNGV) and Cyprinid herpes virus-3 (CyHV-3), causes massive...
A large DNA virus, designated koi herpes virus (KHV), carp interstitial nephritis gill necrosis virus (CNGV) and Cyprinid herpes virus-3 (CyHV-3), causes massive mortality of carp. Morphologically, the virus resembles herpes viruses, but it contains a genome of ca 295 kbp, larger than that of any Herpesviridae member. Interestingly, three CyHV-3 genes, thymidylate monophosphate kinase (TmpK), ribonucleotide reductase and thymidine kinase, which are involved in deoxynucleotide tri-phosphate synthesis, resemble those of pox viruses. In addition to the TmpK gene, which is nonexistent in the genome of herpes viruses, CyHV-3 contains a B22R-like gene, exclusively expressed by pox viruses. These results raise questions on the phylogenic origin of CyHV-3.
Topics: Amino Acid Sequence; Animals; Carps; Cell Line; Genes, Viral; Genome, Viral; Herpesviridae; Molecular Sequence Data; Phylogeny; Poxviridae; Sequence Alignment; Viral Proteins
PubMed: 16860321
DOI: 10.1016/j.febslet.2006.07.013 -
Advances in Experimental Medicine and... 2017Viruses have evolved elaborate means to regulate diverse cellular pathways in order to create a cellular environment that facilitates viral survival and reproduction.... (Review)
Review
Viruses have evolved elaborate means to regulate diverse cellular pathways in order to create a cellular environment that facilitates viral survival and reproduction. This includes enhancing viral macromolecular synthesis and assembly, as well as preventing antiviral responses, including intrinsic, innate, and adaptive immunity. There are numerous mechanisms by which viruses mediate their effects on the host cell, and this includes targeting various cellular post-translational modification systems, including sumoylation. The wide-ranging impact of sumoylation on cellular processes such as transcriptional regulation, apoptosis, stress response, and cell cycle control makes it an attractive target for viral dysregulation. To date, proteins from both RNA and DNA virus families have been shown to be modified by SUMO conjugation, and this modification appears critical for viral protein function. More interestingly, members of the several viral families have been shown to modulate sumoylation, including papillomaviruses, adenoviruses , herpesviruses, orthomyxoviruses, filoviruses , and picornaviruses . This chapter will focus on mechanisms by which sumoylation both impacts human viruses and is used by viruses to promote viral infection and disease.
Topics: Animals; DNA Viruses; Gene Expression Regulation, Viral; Host-Pathogen Interactions; Humans; RNA Viruses; Signal Transduction; Small Ubiquitin-Related Modifier Proteins; Sumoylation; Ubiquitin-Protein Ligases; Viral Proteins; Virus Diseases
PubMed: 28197923
DOI: 10.1007/978-3-319-50044-7_21 -
Viruses Jan 2019Viruses manipulate numerous host factors and cellular pathways to facilitate the replication of viral genomes and the production of infectious progeny. One way in which... (Review)
Review
Viruses manipulate numerous host factors and cellular pathways to facilitate the replication of viral genomes and the production of infectious progeny. One way in which viruses interact with cells is through the utilization and exploitation of the host lipid metabolism. While it is likely that most-if not all-viruses require lipids or intermediates of lipid synthesis to replicate, many viruses also actively induce lipid metabolic pathways to sustain a favorable replication environment. From the formation of membranous replication compartments, to the generation of ATP or protein modifications, viruses exhibit differing requirements for host lipids. Thus, while the exploitation of lipid metabolism is a common replication strategy, diverse viruses employ a plethora of mechanisms to co-opt these critical cellular pathways. Here, we review recent literature regarding the exploitation of host lipids and lipid metabolism specifically by DNA viruses. Importantly, furthering the understanding of the viral requirements for host lipids may offer new targets for antiviral therapeutics and provide opportunities to repurpose the numerous FDA-approved compounds targeting lipid metabolic pathways as antiviral agents.
Topics: Animals; DNA Viruses; Genome, Viral; Host Microbial Interactions; Humans; Lipid Metabolism; Metabolic Networks and Pathways; Mice; Rhadinovirus; Virus Replication
PubMed: 30699959
DOI: 10.3390/v11020119