ArticleMolecular biology and evolution2023
Identification of RNA Virus-Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- RdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models.NAR genomics and bioinformatics · 2026Article
- Metatranscriptomic discovery of a novel viral class from the Yangshan deep-water port virosphere.Archives of virology · 2026Article
- Red clover RNA virus 1: functional analysis of ORF2 protein, associations with co-infecting viruses, and seed transmission.Archives of virology · 2026Article
- The analysis of the virome associated with Freesia refracta plants with necrotic disorder sheds new light on the phylogenetic relationships in the Konkoviridae and Yueviridae families.Virology journal · 2026Article
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- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Genomic characterization and phylogenetic placement of Matryoshka RNA virus 1 associated with Plasmodium vivax malaria in Africa.Access microbiology · 2026Article
- Summer drought impacts micropredator abundance and microbial food web structure in a rewetted fen peatland.ISME communications · 2026Article
- Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Fungal and Protist Viruses Subcommittee, 2025.The Journal of general virology · 2025Article
- Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans.Virus evolution · 2025Article
- Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases.Virus evolution · 2025Article
- Insights into diversity, host range, and evolution of iflaviruses in Lepidoptera through transcriptome mining.Virus evolution · 2025Article
- The virome of the panglobal, wide host-range plant pathogenVirus evolution · 2025Article
- Viroid-like colonists of human microbiomes.Cell · 2024Article
- Promotion of orderJournal of virology · 2024Article
- Predicting novel mosquito-associated viruses from metatranscriptomic dark matter.NAR genomics and bioinformatics · 2024Article
- Microbial Matryoshka: Addressing the Relationship between Pathogenic Flagellated Protozoans and Their RNA Viral Endosymbionts (FamilyVeterinary sciences · 2024Review
- ICTV Virus Taxonomy Profile:The Journal of general virology · 2024Article
- Article
- Virome profiling of fig wasps (Ceratosolen spp.) reveals virus diversity spanning four realms.Virology · 2024Article
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3 authors.
Funding
Abstract
RNA viruses are abundant and highly diverse and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost-effectively expand the diversity of known RNA virus sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA-dependent RNA polymerase (RdRp)-the only universal "hallmark" gene of RNA viruses. By using these to search the National Center for Biotechnology Information Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analyzed their diversity, taxonomic classification, phylogeny, and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp Profile Hidden Markov Models provide a useful resource for the virus discovery community.
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