Evidence for an aquatic origin of influenza virus and the orderArticulavirales DOI Creative Commons
Mary E. Petrone, Rhys Parry, Jonathon C.O. Mifsud

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Фев. 16, 2023

ABSTRACT The emergence of novel disease-causing viruses in mammals is part the long evolutionary history viruses. Tracing these histories contextualises virus spill over events and may help to elucidate how why they occur. We used a combination total RNA sequencing transcriptome data mining extend diversity order Articulavirales , which includes influenza From this, we identified first instance Cnidaria (including corals), constituting divergent family that tentatively named Cnidenomoviridae . This be basal group within also extended known lineage by identifying highly divergent, sturgeon-associated virus. suggests fish were among hosts Finally, substantially expanded quaranjaviruses proposed this genus reclassified as (the Quaranjaviridae ). find evidence vertebrate infecting have initially evolved crustaceans before spilling into terrestrial Chelicerata (i.e., ticks). Together, our findings indicate has at least 600 million years, emerging aquatic animals. Importantly, evolution was not shaped strict virus-host codivergence, but rather multiple aquatic-terrestrial transitions substantial host jumps, some are still observable today.

Язык: Английский

Host Specificity and Geographic Dispersion Shape Virome Diversity in Rhinolophus Bats DOI Open Access
Daxi Wang,

Linmiao Li,

Z. Y. Ren

и другие.

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 17, 2025

ABSTRACT Rhinolophus bats have been identified as natural reservoirs for viruses with global health implications, including severe acute respiratory syndrome–related coronaviruses (SARSr‐CoV) and swine diarrhoea syndrome‐related coronavirus (SADSr‐CoV). In this study, we characterised the individual viromes of 603 to systematically investigate diversity, abundance geographic distribution viral communities within R. affinis , sinicus 11 other bat species. The massive metatranscriptomic data revealed substantial genome resources 133 vertebrate‐infecting clusters, which contain occasional cross‐species transmission across mammalian orders especially families. Notably, those included nine clusters closely related human and/or livestock pathogens, such SARS‐CoVs SADS‐CoVs. investigation also highlighted distinct features diversity between colonies, appear be influenced by host population genetics comparison SARSr‐CoVs further showed varied impact specificity along genome‐wide diversification modular evolution among Overall, findings point a complex interaction genetic way spread structure populations, calling continued surveillance efforts understand factors driving emergence in populations. These results present underestimated spillover risk viruses, highlighting importance enhancing preparedness emerging zoonotic viruses.

Язык: Английский

Процитировано

3
Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets DOI Creative Commons
Ingrida Olendraitė, Katherine A. Brown, Andrew E. Firth

и другие.

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

Процитировано

34
A ~40-kb flavi-like virus does not encode a known error-correcting mechanism DOI Creative Commons
Mary E. Petrone, Joe Grove, Julien Mélade

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(30)

Опубликована: Июль 17, 2024

It is commonly held that there a fundamental relationship between genome size and error rate, manifest as notional “error threshold” sets an upper limit on sizes. The sizes of RNA viruses, which have intrinsically high mutation rates due to lack mechanisms for correction, must therefore be small avoid accumulating excessive number deleterious mutations will ultimately lead population extinction. proposed exceptions this evolutionary rule are viruses from the order Nidovirales (such coronaviruses) encode error-correcting exonucleases, enabling them reach lengths greater than 40 kb. recent discovery large-genome flavi-like ( Flaviviridae ), comprise genomes up 27 kb in length yet seemingly do not exonuclease domains, has led proposal proofreading mechanism required facilitate expansion nonsegmented virus above 30 Herein, we describe ~40 identified Haliclona sponge metatranscriptome does known exonuclease. Structural analysis revealed may instead captured cellular domains associated with nucleic acid metabolism been previously found viruses. Phylogenetic inference placed divergent pesti-like lineage, such provisionally termed it “Maximus virus.” This represents instance achieving comparable demonstrates evolved multiple solutions overcome threshold.

Язык: Английский

Процитировано

12
Virology—The next fifty years DOI Creative Commons
Edward C. Holmes,

Florian Krammer,

Felicia Goodrum

и другие.

Cell, Год журнала: 2024, Номер 187(19), С. 5128 - 5145

Опубликована: Сен. 1, 2024

Язык: Английский

Процитировано

10
A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics DOI

Xiaomin Yan,

Yang Liu, Tingsong Hu

и другие.

Nature Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 20, 2025

Язык: Английский

Процитировано

1
Beneath the surface: Unsolved questions in soil virus ecology DOI Creative Commons
Christina Hazard, Karthik Anantharaman, Luke S. Hillary

и другие.

Soil Biology and Biochemistry, Год журнала: 2025, Номер unknown, С. 109780 - 109780

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

1
Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation DOI Creative Commons
Daxi Wang, Xing‐Lou Yang, Z. Y. Ren

и другие.

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Апрель 10, 2024

Zoonotic viruses cause substantial public health and socioeconomic problems worldwide. Understanding how evolve spread within among wildlife species is a critical step when aiming for proactive identification of viral threats to prevent future pandemics. Despite the many proposed factors influencing diversity, genomic diversity structure communities in East Africa are largely unknown.

Язык: Английский

Процитировано

6
Evidence for an ancient aquatic origin of the RNA viral order Articulavirales DOI Creative Commons
Mary E. Petrone, Rhys Parry, Jonathon C.O. Mifsud

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(45)

Опубликована: Окт. 31, 2023

The emergence of previously unknown disease-causing viruses in mammals is part the result a long-term evolutionary process. Reconstructing deep phylogenetic histories helps identify major transitions and contextualizes new hosts. We used combination total RNA sequencing transcriptome data mining to extend diversity history virus order Articulavirales, which includes influenza viruses. identified instances Articulavirales invertebrate phylum Cnidaria (including corals), constituting novel divergent family that we provisionally named "Cnidenomoviridae." further extended lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting hypothesis fish were among first hosts In addition, substantially expanded quaranjaviruses proposed this genus be reclassified as family-the "Quaranjaviridae." Within putative family, arachnid-infecting genus, "Cheliceravirus." Notably, observed close relationship between Crustacea- Chelicerata-infecting "Quaranjaviridae" inconsistent with virus-host codivergence. Together, these suggest has evolved over at least 600 million years, emerging aquatic animals. Importantly, evolution was likely shaped multiple aquatic-terrestrial substantial host jumps, some are still observable today.

Язык: Английский

Процитировано

14
Characterisation of putative novel tick viruses and zoonotic risk prediction DOI Creative Commons
Yuting Lin, David J. Pascall

Ecology and Evolution, Год журнала: 2024, Номер 14(1)

Опубликована: Янв. 1, 2024

Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity tick has potential health consequences. Despite their importance, large amounts sequences in public data sets from meta-genomic and -transcriptomic projects unannotated, sequence that could contain undocumented viruses. Through mining bioinformatic analysis more than 37,800 sets, we found 83 unannotated contigs exhibiting high identity with known These putative viral were classified into three RNA families (Alphatetraviridae, Orthomyxoviridae Chuviridae) one DNA family (Asfarviridae). After manual checking quality dissimilarity towards other set, these reduced to five Alphatetraviridae four viruses, two Chuviridae which clustered tick-associated forming separate clade within families. We further attempted assess previously likely represent risks thus deserve investigation. ranked human infection 133 using genome composition-based machine learning model. high-risk (Langat virus, Lonestar chuvirus 1, Grotenhout Taggert virus Johnston Atoll virus) have not been infect (Nairoviridae Phenuiviridae) proportion This adds highlights importance surveillance newly emerging diseases.

Язык: Английский

Процитировано

5
Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities DOI Creative Commons
Justine Charon, Ingrida Olendraitė, Marco Forgia

и другие.

Frontiers in Virology, Год журнала: 2024, Номер 4

Опубликована: Апрель 4, 2024

Improved RNA virus understanding is critical to studying animal and plant health, environmental processes. However, the continuous rapid evolution makes their identification characterization challenging. While recent sequence-based advances have led extensive discovery, there growing variation in how viruses are identified, analyzed, characterized, reported. To this end, an RdRp Summit was organized a hybrid meeting took place Valencia, Spain May 2023 convene leading experts with emphasis on early career researchers (ECRs) across diverse scientific communities. Here we synthesize key insights recommendations offer these as first effort establish consensus framework for advancing discovery. First, need interoperability through standardized methodologies, data-sharing protocols, metadata provision interdisciplinary collaborations specific examples starting points. Second, emergent field, recognize incorporate cutting-edge technologies knowledge often improve omic-based viral detection annotation novel capabilities reveal new biology. Third, underscore significance of ECRs fostering international partnerships promote inclusivity equity discovery efforts. The proposed serves roadmap community collectively contribute tremendous challenge unveiling virosphere.

Язык: Английский

Процитировано

5