Petabase-scale sequence alignment catalyses viral discovery

Nature, Год журнала: 2022, Номер 602(7895), С. 142 - 147

Опубликована: Янв. 26, 2022

Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by lack efficient methods for searching this corpus, which (at the time writing) exceeds 20 petabases and is growing exponentially1. Here we developed cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at petabase scale. We searched 5.7 million biologically diverse samples (10.2 petabases) hallmark gene RNA-dependent RNA polymerase identified well over 105 novel viruses, thereby expanding number known species roughly an order magnitude. characterized viruses related coronaviruses, hepatitis delta virus huge phages, respectively, analysed environmental reservoirs. To catalyse ongoing revolution viral discovery, established free comprehensive database these data tools. Expanding diversity can reveal evolutionary origins emerging pathogens improve pathogen surveillance anticipation mitigation future pandemics.

Язык: Английский

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Optimising predictive models to prioritise viral discovery in zoonotic reservoirs

The Lancet Microbe, Год журнала: 2022, Номер 3(8), С. e625 - e637

Опубликована: Янв. 10, 2022

Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify monitor wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but predictions from any given model might be highly uncertain; moreover, systematic validation is rare, drivers performance are consequently under-documented. Here, we use bat hosts betacoronaviruses as a case study for data-driven process comparing validating predictive probable reservoir hosts. In early 2020, generated an ensemble eight statistical that predicted host–virus associations developed priority recommendations potential bridge SARS-CoV-2. During time frame more than year, tracked discovery 47 new betacoronaviruses, validated initial predictions, dynamically updated our analytical pipeline. We found ecological trait-based performed well at predicting these hosts, whereas network methods consistently approximately or worse expected random. These findings illustrate importance modelling buffer against mixed-model quality highlight value including host ecology models. Our revised showed improved compared with ensemble, 400 species globally could undetected betacoronavirus show, through validation, machine learning help optimise undiscovered viruses illustrates how such approaches best implemented dynamic prediction, data collection, updating.

Язык: Английский

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Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Cell, Год журнала: 2023, Номер 186(3), С. 646 - 661.e4

Опубликована: Янв. 24, 2023

Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins hijack cellular enzymes for replication. The extent diversity of agents poorly understood. We developed a computational pipeline to identify cccRNAs applied it 5,131 metatranscriptomes 1,344 plant transcriptomes. search yielded 11,378 spanning 4,409 species-level clusters, 5-fold increase compared the previously identified elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, ribozy-like viruses. Diverse ribozyme combinations unusual ribozymes within were identified. Self-cleaving in ambiviruses, some mito-like viruses capsid-encoding virus-like cccRNAs. broad presence transcriptomes ecosystems implies their host range is far broader than currently known, matches CRISPR spacers suggest replicate prokaryotes.

Язык: Английский

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Megataxonomy and global ecology of the virosphere

The ISME Journal, Год журнала: 2024, Номер 18(1)

Опубликована: Янв. 1, 2024

Nearly all organisms are hosts to multiple viruses that collectively appear be the most abundant biological entities in biosphere. With recent advances metagenomics and metatranscriptomics, known diversity of substantially expanded. Comparative analysis these using advanced computational methods culminated reconstruction evolution major groups enabled construction a virus megataxonomy, which has been formally adopted by International Committee on Taxonomy Viruses. This comprehensive taxonomy consists six realms, aspired monophyletic assembled based conservation hallmark proteins involved capsid structure formation or genome replication. The different taxa differ host range accordingly ecological niches. In this review article, we outline latest developments megataxonomy discoveries will likely lead reassessment some taxa, particular, split three current realms into two more independent realms. We then discuss correspondence between distribution among niches, as well abundance versus cells habitats. across environments appears primarily determined ranges, i.e. virome is shaped composition biome given habitat, itself affected abiotic factors.

Язык: Английский

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Viroid-like colonists of human microbiomes

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 21, 2024

Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA ~1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing entire genome, and (iii) open reading frames coding for novel protein superfamily, which call "Oblins". We find Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, are prevalent tested microbiome metatranscriptomes representatives detected ~7% analysed stool (29/440) ~50% oral (17/32). Obelisk compositions appear differ between anatomic sites capable persisting individuals, continued presence over >300 days observed one case. Large scale searches 29,959 (clustered at 90% nucleotide identity), examples from all seven continents diverse ecological niches. From this search, subset code Obelisk-specific variants hammerhead type-III self-cleaving ribozyme. Lastly, case bacterial species (Streptococcus sanguinis) defined laboratory strains harboured specific population. As such, comprise RNAs have colonised, gone unnoticed in, human, global microbiomes.

Язык: Английский

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Zoonotic disease and virome diversity in bats

Current Opinion in Virology, Год журнала: 2021, Номер 52, С. 192 - 202

Опубликована: Дек. 23, 2021

The emergence of zoonotic viral diseases in humans commonly reflects exposure to mammalian wildlife. Bats (order Chiroptera) are arguably the most important reservoir for viruses, with notable examples including Severe Acute Respiratory Syndrome coronaviruses 1 and 2, Middle East coronavirus, henipaviruses lyssaviruses. Herein, we outline our current knowledge on diversity bat viromes, particularly through lens metagenomic next-generation sequencing context disease emergence. A key conclusion is that although bats harbour abundant virus diversity, vast majority viruses have not emerged cause new hosts such better regarded as critical but endangered components global ecosystems.

Язык: Английский

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The Ecology of Viral Emergence

Annual Review of Virology, Год журнала: 2022, Номер 9(1), С. 173 - 192

Опубликована: Июнь 15, 2022

The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes underpin emergence of COVID-19 other zoonotic diseases. Herein, I review mechanisms determine why how viruses emerge in new hosts, as well barriers process. show traditional studies virus have an inherent anthropocentric bias, with humans considered inevitable outcome emergence, when reality are integral components global ecosystem characterized by continual host jumping also transmitting their animals. illustrate these points using coronaviruses, including severe acute respiratory syndrome 2, case study. outline potential steps can be followed help mitigate prevent future pandemics, combating climate change central component.

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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Viroid-like colonists of human microbiomes

Cell, Год журнала: 2024, Номер 187(23), С. 6521 - 6536.e18

Опубликована: Окт. 31, 2024

Язык: Английский

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Viruses Defined by the Position of the Virosphere within the Replicator Space

Microbiology and Molecular Biology Reviews, Год журнала: 2021, Номер 85(4)

Опубликована: Сен. 1, 2021

Originally, viruses were defined as miniscule infectious agents that passed through filters retain even the smallest cells. Subsequently, considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks.

Язык: Английский

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