ArticleScience advances2020
Expansion of known ssRNA phage genomes: From tens to over a thousand.
Article in Science advances, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 citing papers in PubMed.
- Revisiting the life cycle of temperate phages.Nature reviews. Microbiology · 2026Review
- Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive RNA virome from molluscan transcriptomes reveals extensive diversity and modular genome evolution.Virologica Sinica · 2026Article
- ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families.Protein science : a publication of the Protein Society · 2026Article
- Article
- Limited effect of short- to mid-term storage conditions on an Australian farmland soil RNA virome.Journal of virology · 2026Article
- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Identification and characterization of a novel plaque-invisible lytic single-stranded RNA phage.Journal of virology · 2025Article
- The dynamics of single stranded, positive sense RNA bacteriophages in the rumen virome.Scientific reports · 2025Article
- Gut Virome and Aging: Phage-Driven Microbial Stability and Immune Modulation.Aging and disease · 2025Review
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- Engineering of extracellular vesicles for efficient intracellular delivery of multimodal therapeutics including genome editors.Nature communications · 2025Article
- Advancing RNA phage biology through meta-omics.Nucleic acids research · 2025Review
- VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.Nature communications · 2025Article
- An Assessment of the Efficacy of Commercial Air Ionizer Systems Against a SARS-CoV-2 Surrogate.Microorganisms · 2025Article
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- Pseudomonas aeruginosa as a model bacterium in antiphage defense research.FEMS microbiology reviews · 2025Review
- Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression.bioRxiv : the preprint server for biology · 2025Article
- Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases.Virus evolution · 2025Article
- Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA phage genome sequences are available from the NCBI Genome database (June 2019). The difficulty in detecting RNA phages in metagenomic datasets raises questions as to their abundance, taxonomic structure, and ecological importance. In this study, we iteratively applied profile hidden Markov models to detect conserved ssRNA phage proteins in 82 publicly available metatranscriptomic datasets generated from activated sludge and aquatic environments. We identified 15,611 nonredundant ssRNA phage sequences, including 1015 near-complete genomes. This expansion in the number of known sequences enabled us to complete a phylogenetic assessment of both sequences identified in this study and known ssRNA phage genomes. Our expansion of these viruses from two environments suggests that they have been overlooked within microbiome studies.
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Registered trials
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.