Taxonomic update for mammalian anelloviruses (family Anelloviridae)

Archives of Virology, Год журнала: 2021, Номер 166(10), С. 2943 - 2953

Опубликована: Авг. 12, 2021

Язык: Английский

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Molecular‐based detection, genetic characterization and phylogenetic analysis of porcine circovirus 4 from Korean domestic swine farms

Transboundary and Emerging Diseases, Год журнала: 2021, Номер 69(2), С. 538 - 548

Опубликована: Фев. 5, 2021

Porcine circovirus 4 (PCV4), a novel and unclassified member of the genus Circovirus, was first reported in China 2019. Aiming to provide more evidence about active circulation PCV4, this study screened 335 pooled internal organs detected virus (i) at rate 3.28%, (ii) from both clinically healthy sick pigs various age groups, (iii) six out nine provinces Korea. The complete genomic sequence Korean PCV4 strain (E115) 1,770 nucleotides length had 98.5%-98.9% identity three strains currently available GenBank. Utilizing set bioinformatic programs, it revealed that contained several features palindrome stem-loop structure with conserved nonanucleotide, packed overlapping ORFs oriented different directions two intergenic regions between genes encoding putative replication-associated protein (Rep) capsid (Cap) proteins. This also predicted presence essential elements for replication circoviruses all strains, example origin DNA replication, endonuclease helicase domains Rep, nuclear localization signal on Cap protein. Finally, based phylogeny inferred sequences Rep protein, further clarified genetic relationships other CRESS viruses general particular.

Язык: Английский

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Family Genomoviridae: 2021 taxonomy update

Archives of Virology, Год журнала: 2021, Номер 166(10), С. 2911 - 2926

Опубликована: Июль 31, 2021

Язык: Английский

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Integrating Viral Metagenomics into an Ecological Framework

Annual Review of Virology, Год журнала: 2021, Номер 8(1), С. 133 - 158

Опубликована: Май 25, 2021

Viral metagenomics has expanded our knowledge of the ecology uncultured viruses, within both environmental (e.g., terrestrial and aquatic) host-associated plants animals, including humans) contexts. Here, we emphasize implementation an ecological framework in viral metagenomic studies to address questions virology rarely considered ecological, which can change perception viruses how they interact with their surroundings. An explicitly considers diverse variants populations that make up communities interacting ecosystem-level effects. It provides a structure for study diversity, distributions, dynamics, interactions one another, hosts, ecosystem, abiotic factors. stands poised broadly expand basic applied virology. We highlight specific fundamental research needs capitalize on its potential advance field.

Язык: Английский

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Integrated Immunologic Monitoring in Solid Organ Transplantation: The Road Toward Torque Teno Virus-guided Immunosuppression

Transplantation, Год журнала: 2022, Номер 106(10), С. 1940 - 1951

Опубликована: Май 5, 2022

Potent immunosuppressive drugs have been introduced into clinical care for solid organ transplant recipients. It is now time to guide these on an individual level optimize their efficacy. An ideal tool simultaneously detects overimmunosuppression and underimmunosuppression, highly standardized, straightforward implement routine. Randomized controlled interventional trials are crucial demonstrate value. To date, proposed assays mainly focused the prediction of rejection were based assessment few immune compartments. Recently, novel tools a more integrated approach characterize function cover broader spectrum system. In this respect, quantification plasma load prevalent apathogenic virus that might reflect its host has proposed: torque teno (TTV). Although TTV control driven by T cells, other major compartments contribute hosts’ response. A standardized in-house polymerase chain reaction conformité européenne-certified commercially available quantification. associated with infection in recipients, cutoff values risk stratification such events lung kidney transplantation. Test performance does not allow diagnosis but able define at-risk patients. Hitherto used settings, two randomized currently testing safety efficacy TTV-guided immunosuppression.

Язык: Английский

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Opportunities and Challenges of Data-Driven Virus Discovery

Biomolecules, Год журнала: 2022, Номер 12(8), С. 1073 - 1073

Опубликована: Авг. 4, 2022

Virus discovery has been fueled by new technologies ever since the first viruses were discovered at end of 19th century. Starting with mechanical devices that provided evidence for virus presence in sick hosts, gradually transitioned into a sequence-based scientific discipline, which, nowadays, can characterize identity and explore viral diversity an unprecedented resolution depth. Sequencing are now being used routinely ever-increasing scales, producing avalanche novel sequences found multitude organisms environments. In this perspective article, we argue started to undergo another transformation prompted emergence approaches sequence data-centered primarily computational, setting them apart from previous technology-driven innovations. The data-driven approach is largely uncoupled collection processing biological samples, exploits availability massive amounts publicly freely accessible data sequencing archives. We discuss open challenges be solved order unlock full potential discovery, highlight benefits it bring classical (mostly molecular) virology molecular biology general.

Язык: Английский

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Unraveling the viral dark matter through viral metagenomics

Frontiers in Immunology, Год журнала: 2022, Номер 13

Опубликована: Сен. 16, 2022

Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, disease progression. influence a wide variety systems processes, continued discovery novel viruses is anticipated to reveal new mechanisms influencing biology diverse environments. While identity continue be discovered understood through viral metagenomics, most sequences virome datasets cannot attributed known or may only distantly related species already described public sequence databases, at best. Such as dark matter. Ongoing discoveries from matter provided insights into environments, well their potential immunological virus disease, therapeutics, surveillance. Increased understanding will with combination cultivation, microscopy, sequencing, bioinformatic efforts, which discussed present review.

Язык: Английский

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The human gut virome: composition, colonization, interactions, and impacts on human health

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Май 24, 2023

The gut virome is an incredibly complex part of the ecosystem. Gut viruses play a role in many disease states, but it unknown to what extent impacts everyday human health. New experimental and bioinformatic approaches are required address this knowledge gap. colonization begins at birth considered unique stable adulthood. highly specific each individual modulated by varying factors such as age, diet, state, use antibiotics. primarily comprises bacteriophages, predominantly order Crassvirales, also referred crAss-like phages, industrialized populations other Caudoviricetes (formerly Caudovirales ). stability virome’s regular constituents disrupted disease. Transferring fecal microbiome, including its viruses, from healthy can restore functionality gut. It alleviate symptoms chronic illnesses colitis caused Clostridiodes difficile . Investigation relatively novel field, with new genetic sequences being published increasing rate. A large percentage sequences, termed ‘viral dark matter’, one significant challenges facing virologists bioinformaticians. To challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, utilizing cutting-edge tools quantify classify species. Here, we review literature surrounding virome, establishment, impact on health, methods used investigate it, matter veiling our understanding virome.

Язык: Английский

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CheckV: assessing the quality of metagenome-assembled viral genomes

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2020, Номер unknown

Опубликована: Май 8, 2020

Abstract Over the last several years, metagenomics has enabled assembly of millions new viral sequences that have vastly expanded our knowledge Earth’s diversity. However, these range from small fragments to complete genomes and no tools currently exist for estimating their quality. To address this problem, we developed CheckV, which is an automated pipeline completeness as well identification removal non-viral regions found on integrated proviruses. After validating approach mock datasets, CheckV was applied large diverse genome collections, including IMG/VR Global Ocean Virome, revealing majority were fragments, with just 3.6% classified high-quality (i.e. > 90% completeness) or genomes. Additionally, host contamination significantly improved auxiliary metabolic genes interpretation viral-encoded functions. We expect will be broadly useful all researchers studying reporting assembled metagenomes. freely available at: http://bitbucket.org/berkeleylab/CheckV .

Язык: Английский

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Partitiviruses Infecting Drosophila melanogaster and Aedes aegypti Exhibit Efficient Biparental Vertical Transmission

Journal of Virology, Год журнала: 2020, Номер 94(20)

Опубликована: Июль 31, 2020

Partitiviruses are segmented, multipartite double-stranded RNA (dsRNA) viruses that until recently were only known to infect fungi, plants, and protozoans. Metagenomic surveys have revealed partitivirus-like sequences also commonly associated with arthropods. One arthropod-associated partitivirus, galbut virus, is common in wild populations of

Язык: Английский

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