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Journal of Virological Methods Apr 2020The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined...
The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined its performance for environmental viromes. Here we seeded one RNA virus bacteriophage MS2 and one DNA virus bacteriophage PhiX174 into 10 L well water at three levels ranging from 1 to 21,100 plaque-forming units (PFU)/mL. Two workflows were established to maximize the number of sequencing reads of RNA and DNA viruses using MinION™. With dead-end ultrafiltration, PEG precipitation, and random amplification, MinION™ was capable of detecting MS2 at 155 PFU/mL and PhiX174 at 1-2 PFU/mL. While the DNA workflow only detected PhiX174, the RNA workflow detected both MS2 and PhiX174. The virus concentration, or relative abundance of viral nucleic acids in total nucleic acids, is critical to the proportion of viral reads in sequencing results. Our findings also highlight the importance of including control samples in sequencing runs for environmental water samples with low virus abundance.
Topics: Bacteriophages; DNA Viruses; Nanopore Sequencing; RNA Viruses; Sensitivity and Specificity; Sequence Analysis, DNA; Water Microbiology
PubMed: 31891731
DOI: 10.1016/j.jviromet.2019.113805 -
Diseases of Aquatic Organisms Apr 2011In 2000, a pathogenic virus was discovered in juvenile Caribbean spiny lobsters Panulirus argus from the Florida Keys, U.S.A. Panulirus argus virus 1 (PaV1) is the first... (Review)
Review
In 2000, a pathogenic virus was discovered in juvenile Caribbean spiny lobsters Panulirus argus from the Florida Keys, U.S.A. Panulirus argus virus 1 (PaV1) is the first naturally occurring pathogenic virus reported from lobsters, and it profoundly affects their ecology and physiology. PaV1 is widespread in the Caribbean with infections reported in Florida (U.S.A.), St. Croix, St. Kitts, Yucatan (Mexico), Belize, and Cuba. It is most prevalent and nearly always lethal in the smallest juvenile lobsters, but this declines with increasing lobster size; adults harbor the virus, but do not present the characteristic signs of the disease. No other PaV1 hosts are known. The prevalence of PaV1 in juvenile lobsters from the Florida Keys has been stable since 1999, but has risen to nearly 11% in the eastern Yucatan since 2001. Heavily infected lobsters become sedentary, cease feeding, and die of metabolic exhaustion. Experimental routes of viral transmission include ingestion, contact, and for newly settled juveniles, free virus particles in seawater. Prior to infectiousness, healthy lobsters tend to avoid diseased lobsters and so infected juvenile lobsters mostly dwell alone, which appears to reduce disease transmission. However, avoidance of diseased individuals may result in increased shelter competition between healthy and diseased lobsters, and greater predation on infected lobsters. Little is known about PaV1 outside of Mexico and the USA, but it poses a potential threat to P. argus fisheries throughout the Caribbean.
Topics: Animals; DNA Viruses; In Situ Hybridization, Fluorescence; Palinuridae
PubMed: 21648244
DOI: 10.3354/dao02326 -
Proceedings of the National Academy of... Jan 2022Type I interferons (IFNs) are the first frontline of the host innate immune response against invading pathogens. Herein, we characterized an unknown protein encoded by...
Type I interferons (IFNs) are the first frontline of the host innate immune response against invading pathogens. Herein, we characterized an unknown protein encoded by phospholipase A2 inhibitor and LY6/PLAUR domain-containing (PINLYP) gene that interacted with TBK1 and induced type I IFN in a TBK1- and IRF3-dependent manner. Loss of PINLYP impaired the activation of IRF3 and production of IFN-β induced by DNA virus, RNA virus, and various Toll-like receptor ligands in multiple cell types. Because PINLYP deficiency in mice engendered an early embryonic lethality in mice, we generated a conditional mouse in which PINLYP was depleted in dendritic cells. Mice lacking PINLYP in dendritic cells were defective in type I IFN induction and more susceptible to lethal virus infection. Thus, PINLYP is a positive regulator of type I IFN innate immunity and important for effective host defense against viral infection.
Topics: Animals; Cell Line; DNA Virus Infections; DNA Viruses; Dendritic Cells; Enzyme Inhibitors; Humans; Immunity, Innate; Interferon-beta; Mice; Mice, Knockout; RNA Virus Infections; RNA Viruses
PubMed: 34969857
DOI: 10.1073/pnas.2111115119 -
Diseases of Aquatic Organisms Jun 2018The order Herpesvirales includes viruses that infect aquatic and terrestrial vertebrates and several aquatic invertebrates (i.e. mollusks), and share the commonality of...
The order Herpesvirales includes viruses that infect aquatic and terrestrial vertebrates and several aquatic invertebrates (i.e. mollusks), and share the commonality of possessing a double-stranded DNA core surrounded by an icosahedral capsid. Herpesviruses of the family Alloherpesviridae that infect fish and amphibians, including channel catfish virus and koi herpesvirus, negatively impact aquaculture. Here, we describe a novel herpesvirus infection of wild European perch from lakes in Finland. Infected fish exhibited white nodules on the skin and fins, typically in the spring when prevalence reached nearly 40% in one of the sampled lakes. Transmission electron microscopic examination of affected tissues revealed abundant nuclear and cytoplasmic virus particles displaying herpesvirus morphology. Degenerate PCR targeting a conserved region of the DNA polymerase gene of large DNA viruses amplified a 520 bp product in 5 of 5 affected perch skin samples tested. Phylogenetic analysis of concatenated partial DNA polymerase and terminase (exon 2) gene sequences produced a well-supported tree grouping the European perch herpesvirus with alloherpesviruses infecting acipenserid, esocid, ictalurid, and salmonid fishes. The phenetic analysis of the European perch herpesvirus partial DNA polymerase and terminase nucleotide gene sequences ranged from 34.6 to 63.9% and 39.6 to 59.6% to other alloherpesviruses, respectively. These data support the European perch herpesvirus as a new alloherpesvirus, and we propose the formal species designation of Percid herpesvirus 2 (PeHV2) to be considered for approval by the International Committee on Taxonomy of Viruses.
Topics: Animals; DNA Virus Infections; DNA Viruses; Finland; Fish Diseases; Perches
PubMed: 29862976
DOI: 10.3354/dao03228 -
Phytopathology Sep 2011A severe vein-clearing and vine decline syndrome has emerged on grapevines (Vitis vinifera) and hybrid grape cultivars in the Midwest region of the United States. The...
A severe vein-clearing and vine decline syndrome has emerged on grapevines (Vitis vinifera) and hybrid grape cultivars in the Midwest region of the United States. The typical symptoms are translucent vein-clearing on young leaves, short internodes and decline of vine vigor. Known viral pathogens of grapevines were not closely associated with the syndrome. To obtain a comprehensive profile of viruses in a diseased grapevine, small RNAs were enriched and two cDNA libraries were constructed from a symptomatic grapevine and a symptomless grapevine, respectively. Deep sequencing of the two cDNA libraries showed that the most abundant viral small RNAs align with the genomes of viruses in the genus Badnavirus, the family Caulimoviridae. Amplification of the viral DNA by polymerase chain reaction allowed the assembly of the whole genome sequence of a grapevine DNA virus, which shared the highest homology with the Badnavirus sequences. This is the first report of a DNA virus in grapevines. The new DNA virus is closely associated with the vein-clearing symptom, and thus has been given a provisional name Grapevine vein clearing virus (GVCV). GVCV was detected in six grapevine cultivars showing vein-clearing and vine decline syndrome in Missouri, Illinois, and Indiana, suggesting its wide distribution in the Midwest region of the United States. Discovery of DNA viruses in grapevines merits further studies on their epidemics and economic impact on grape production worldwide.
Topics: Badnavirus; DNA Viruses; DNA, Circular; DNA, Viral; Gene Library; Genome, Viral; High-Throughput Nucleotide Sequencing; Midwestern United States; Open Reading Frames; Phylogeny; Plant Diseases; Plant Leaves; Plant Shoots; Plant Viruses; RNA, Small Interfering; RNA, Viral; Sequence Analysis, DNA; Vitis
PubMed: 21554183
DOI: 10.1094/PHYTO-02-11-0034 -
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 -
The Journal of General Virology Sep 2020is a family of icosahedral, internal membrane-containing bacterial viruses with circular, single-stranded DNA genomes. The family includes the genus, , with the...
is a family of icosahedral, internal membrane-containing bacterial viruses with circular, single-stranded DNA genomes. The family includes the genus, , with the species, . Flavobacterium phage FLiP was isolated with its Gram-negative host bacterium from a boreal freshwater habitat in Central Finland in 2010. It is the first described single-stranded DNA virus with an internal membrane and shares minimal sequence similarity with other known viruses. The virion organization (pseudo =21 ) and major capsid protein fold (double-β-barrel) resemble those of Pseudoalteromonas phage PM2 (family ), which has a double-stranded DNA genome. A similar major capsid protein fold is also found in other double-stranded DNA viruses in the kingdom . This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family , which is available at ictv.global/report/finnlakeviridae.
Topics: Bacteriolysis; Bacteriophages; DNA Viruses; DNA, Single-Stranded; DNA, Viral; Flavobacterium; Genome, Viral; Virion; Virus Replication
PubMed: 32840474
DOI: 10.1099/jgv.0.001488 -
Uirusu Dec 2008
Review
Topics: Acanthamoeba; Animals; DNA Viruses; DNA, Viral; Genome, Viral; Open Reading Frames; Viral Proteins; Virus Replication
PubMed: 19374201
DOI: No ID Found -
The ISME Journal Dec 2017Phaeoviruses are latent double-stranded DNA viruses that insert their genomes into those of their brown algal (Phaeophyceae) hosts. So far these viruses are known only...
Phaeoviruses are latent double-stranded DNA viruses that insert their genomes into those of their brown algal (Phaeophyceae) hosts. So far these viruses are known only from members of the Ectocarpales, which are small and short-lived macroalgae. Here we report molecular and morphological evidence for a new Phaeovirus cluster, referred to as sub-group C, infecting kelps (Laminariales) of the genera Laminaria and Saccharina, which are ecologically and commercially important seaweeds. Epifluorescence and TEM observations indicate that the Laminaria digitata Virus (LdigV), the type species of sub-group C, targets the host nucleus for its genome replication, followed by gradual degradation of the chloroplast and assembly of virions in the cytoplasm of both vegetative and reproductive cells. This study is the first to describe phaeoviruses in kelp. In the field, these viruses infected two thirds of their host populations; however, their biological impact remains unknown.
Topics: DNA Viruses; Kelp; Phylogeny; Seaweed
PubMed: 28742072
DOI: 10.1038/ismej.2017.130 -
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