RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data

Virus Evolution, Год журнала: 2022, Номер 8(2)

Опубликована: Июль 1, 2022

Despite a rapid expansion in the number of documented viruses following advent metagenomic sequencing, identification and annotation highly divergent RNA remain challenging, particularly from poorly characterized hosts environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal viral 'dusk matter': sequences with low, but detectable, levels identity known available protein structures. Here, we present new open computational resource-RdRp-scan-that contains standardized bioinformatic toolkit identify annotate data based on detection RNA-dependent polymerase (RdRp) sequences. By combining RdRp-specific hidden Markov models (HMMs) structural comparisons, show RdRp-scan can efficiently detect RdRp as low 10 per cent those not identifiable using standard sequence-to-sequence comparisons. In addition, facilitate placement newly detected virus-like into diversity viruses, provides custom curated databases core motifs, well pre-built multiple alignments. parallel, our analysis by revealed while most taxonomically unassigned RdRps fell pre-established clusters, some potentially orders related Wolframvirales Tolivirales. Finally, survey A, B, C motifs within database additional variations both position might insights structure, function, evolution polymerases.

Язык: Английский

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Host traits shape virome composition and virus transmission in wild small mammals

Cell, Год журнала: 2023, Номер 186(21), С. 4662 - 4675.e12

Опубликована: Сен. 20, 2023

Язык: Английский

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Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting

The ISME Journal, Год журнала: 2023, Номер 17(6), С. 916 - 930

Опубликована: Апрель 8, 2023

Abstract While decomposition of organic matter by bacteria plays a major role in nutrient cycling terrestrial ecosystems, the significance viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study mesophilic thermophilic their on during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics activity are tightly coupled, where specific track host densities, triggering microbial community succession via top-down control HTC. Moreover, encoded expressed several auxiliary metabolic genes (AMGs) linked carbon cycling, impacting turnover alongside bacteria. Nutrient correlated positively virus–host ratio, indicative positive relationship between ecosystem functioning, viral abundances, activity. These effects were predominantly driven DNA as most detected RNA associated eukaryotes not phase composting. findings suggest could drive HTC recycling bacterial biomass through cell lysis expressing key AMGs. Viruses hence potentially be used indicators functioning optimize productivity biotechnological agricultural systems.

Язык: Английский

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Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

Journal of General Virology, Год журнала: 2023, Номер 104(8)

Опубликована: Авг. 25, 2023

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote newly proposed taxa, phylum Negarnaviricota was amended and emended. The expanded by one new family, 14 genera, 140 species. Two genera 538 species were renamed. One moved, four abolished. This article presents updated taxonomy as now accepted ICTV.

Язык: Английский

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Using artificial intelligence to document the hidden RNA virosphere

Cell, Год журнала: 2024, Номер 187(24), С. 6929 - 6942.e16

Опубликована: Окт. 9, 2024

Highlights•AI-based metagenomic mining greatly expands the diversity of global RNA virosphere•Developed a deep learning model that integrates sequence and structural information•161,979 putative virus species 180 supergroups were identified•RNA viruses are ubiquitous even found in most extreme environmentsSummaryCurrent tools can fail to identify highly divergent viruses. We developed algorithm, termed LucaProt, discover RNA-dependent polymerase (RdRP) sequences 10,487 metatranscriptomes generated from diverse ecosystems. LucaProt both predicted information, enabling accurate detection RdRP sequences. Using this approach, we identified 161,979 potential supergroups, including many previously poorly studied groups, as well genomes exceptional length (up 47,250 nucleotides) genomic complexity. A subset these novel was confirmed by RT-PCR RNA/DNA sequencing. Newly discovered present environments, air, hot springs, hydrothermal vents, with abundance varying substantially among This study advances discovery, highlights scale virosphere, provides computational better document virome.Graphical abstract

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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Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(4)

Опубликована: Апрель 1, 2023

RNA viruses are abundant and highly diverse infect all or most eukaryotic organisms. However, only a tiny fraction of the number diversity virus species have been catalogued. To cost-effectively expand known sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for viral RNA-dependent polymerase (RdRp)-the universal "hallmark" gene viruses. By using these to search National Center Biotechnology Information Transcriptome Shotgun Assembly database, identified 5,867 contigs encoding RdRps fragments thereof analyzed their diversity, taxonomic classification, phylogeny, host associations. Our study expands viruses, curated RdRp Profile Models provide useful resource discovery community.

Язык: Английский

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Host phylogeny shapes viral transmission networks in an island ecosystem

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(11), С. 1834 - 1843

Опубликована: Сен. 7, 2023

Abstract Virus transmission between host species underpins disease emergence. Both phylogenetic relatedness and aspects of their ecology, such as interactions predator–prey relationships, may govern rates patterns cross-species virus hence zoonotic risk. To address the impact phylogeny ecology on diversity evolution, we characterized virome structure a relatively isolated island ecological community in Fiordland, New Zealand, that are linked through food web. We show barriers inhibited occurred at level phyla (between Chordata, Arthropoda Streptophyta) well lower taxonomic levels. By contrast, manifest diet, had smaller influence composition, especially higher The virus–host comprised ‘small world’ network, which hosts with high viruses were more likely to acquire new viruses, generalist infect multiple additional compared specialist viruses. Such highly connected increases likelihood transmission, particularly among closely related species, suggests present greatest risk

Язык: Английский

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Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Microbiome, Год журнала: 2023, Номер 11(1)

Опубликована: Окт. 27, 2023

Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral have been identified, with a global distribution seemingly driven by multiple biotic abiotic factors, especially soil temperature moisture. However, our current understanding of the stability across time response to strong seasonal changes in environmental parameters remains limited. Here, we investigated diversity activity DNA RNA viruses, focusing bacteriophages, dynamics' snow-dominated mountainous watershed examining paired metagenomes metatranscriptomes.

Язык: Английский

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Tackling Soil ARG‐Carrying Pathogens with Global‐Scale Metagenomics

Advanced Science, Год журнала: 2023, Номер 10(26)

Опубликована: Июль 9, 2023

Abstract Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in spread antibiotic resistance genes (ARGs) through horizontal gene transfer. Although occurrence, distribution, driving factors ARGs soils have been widely investigated, little is known about soilborne pathogens at global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG‐carrying (APs) with least one ARG; APs detected 1443 samples (sample detection rate 87.8%). The richness greater agricultural (with median 20) than non‐agricultural ecosystems. Agricultural possess high prevalence clinical affiliated Escherichia, Enterobacter, Streptococcus , Enterococcus . tend to coexist multidrug bacA A map soil AP generated, where anthropogenic climatic explained hot spots East Asia, South eastern United States. results herein advance understanding distribution determine regions prioritized control worldwide.

Язык: Английский

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