ArticleVirus evolution2022
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data.
Article in Virus evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 2 of them syntheses that pooled it.
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Who cites it
67 citing papers in PubMed, 2 syntheses or guidelines pooled it, 104 citations in OpenAlex.
- Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.Viruses · 2025Pooled it
- Systematic Review of Phylogenetic Analysis Techniques for RNA Viruses Using Bioinformatics.International journal of molecular sciences · 2025Pooled it
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- Identification of Partitivirus-like RdRPs in theViruses · 2026Article
- Occurrence and Genomic Characterization of Japanese Iris Necrotic Ring Virus Isolated from Narcissus spp. in Korea.The plant pathology journal · 2026Article
- Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.Applied and environmental microbiology · 2026Article
- Diversity of RNA Viruses in Declining Mediterranean Forests.Microorganisms · 2026Article
- Virome diversity, evolution, transmission networks, and zoonotic potential of wildlife on the Qinghai-Tibet plateau.NPJ biofilms and microbiomes · 2026Article
- Geographic genetic divergence and ecological viral communities shape the virome of Chilo suppressalis.Microbiome · 2026Article
- Uncovering viral protein acquisition events and human-specific folds with pairwise comparisons of predicted protein structures.Molecular biology and evolution · 2026Article
- Longitudinal sampling of New Zealand cockles (Austrovenus stutchburyi) reveals high viral diversity and taxa-specific responses to environmental factors.FEMS microbiology ecology · 2026Article
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- Primary transcript enrichment reveals a density-dependentFrontiers in microbiology · 2026Article
- Viral diversity, ecological interconnectedness, and the identification of mammalian chuviruses in Australian microbats.Virus evolution · 2026Article
- Genomic characterization and phylogenetic placement of Matryoshka RNA virus 1 associated with Plasmodium vivax malaria in Africa.Access microbiology · 2026Article
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
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- HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements.Bioinformatics (Oxford, England) · 2025Article
- Leveraging Classical Virology and High Throughput Sequencing for Viral Discovery Using a Historical Viral Collection.Viruses · 2025Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite a rapid expansion in the number of documented viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remain challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral 'dusk matter': viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational resource-RdRp-scan-that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA-dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific hidden Markov models (HMMs) and structural comparisons, we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10 per cent to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motifs, as well as pre-built RdRp multiple sequence alignments. In parallel, our analysis of the sequence diversity detected by the RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some fell into potentially new orders of RNA viruses related to the
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.