ArticleNature communications2021
Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
64 citing papers in PubMed, 94 citations in OpenAlex.
- DeCoRE: A computational method to resolve RNA structural heterogeneity from RNA structure probing data by direct RNA sequencing.Science advances · 2026Article
- Cross-genus analysis reveals architecturally programmed sgRNA synthesis patterns in coronaviruses.Molecular systems biology · 2026Article
- A potential RNA-RNA distal interaction competing with a functional pseudoknot in the 3'-untranslated region of SARS-like coronaviruses.Nucleic acids research · 2026Article
- RNA Folding Energy of Long-Range Genomic Interactions Regulates Discontinuous Transcription in SARS-CoV-2.Viruses · 2026Article
- Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell.Nature methods · 2026Article
- Characterization of the virus-host RNA-RNA interactome across important human pathogenic RNA viruses.PLoS pathogens · 2026Article
- Evolutionary Insight into Fatal Human Coronaviruses (hCoVs) with a Focus on Circulating SARS-CoV-2 Variants Under Monitoring (VUMs).Biomedicines · 2025Review
- A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation.Nature communications · 2025Article
- Delivery strategies for RNA-targeting therapeutic nucleic acids and RNA-based vaccines against respiratory RNA viruses: IAV, SARS-CoV-2, RSV.Molecular therapy. Nucleic acids · 2025Review
- Article
- Mapping HIV-1 RNA structure, homodimers, long-range interactions and persistent domains by HiCapR.eLife · 2025Article
- Strategies and efforts in circumventing the emergence of antiviral resistance against conventional antivirals.npj antimicrobials and resistance · 2025Review
- SARS-CoV-2 point mutations are over-represented in terminal loops of RNA stem-loop structures that can be resolved by Nsp13 helicase in a unique manner with respect to nucleotide dependence.Nucleic acids research · 2025Article
- RNA Through Time: From the Origin of Life to Therapeutic Frontiers in Transcriptomics and Epitranscriptional Medicine.International journal of molecular sciences · 2025Review
- Biomolecular condensates control and are defined by RNA-RNA interactions that arise in viral replication.Research square · 2025Article
- Transcriptomic profiles of monocyte-derived macrophages exposed to SARS-CoV-2 VOCs reveal immune-evasion escape driven by delta.Journal of translational medicine · 2025Article
- The detection, function, and therapeutic potential of RNA 2'-O-methylation.The innovation life · 2025Article
- CParty: hierarchically constrained partition function of RNA pseudoknots.Bioinformatics (Oxford, England) · 2024Article
- KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions.Nature biotechnology · 2024Article
- Phase separation and viral factories: unveiling the physical processes supporting RNA packaging in dsRNA viruses.Biochemical Society transactions · 2024Review
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2 is a major threat to global health. Here, we investigate the RNA structure and RNA-RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 in cells using Illumina and Nanopore platforms. We identify twelve potentially functional structural elements within the SARS-CoV-2 genome, observe that subgenomic RNAs can form different structures, and that WT and Δ382 virus genomes fold differently. Proximity ligation sequencing identify hundreds of RNA-RNA interactions within the virus genome and between the virus and host RNAs. SARS-CoV-2 genome binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2'-O-methylated. 2'-O-methylation sites are enriched in viral untranslated regions, associated with increased virus pair-wise interactions, and are decreased in host mRNAs upon virus infection, suggesting that the virus sequesters methylation machinery from host RNAs towards its genome. These studies deepen our understanding of the molecular and cellular basis of SARS-CoV-2 pathogenicity and provide a platform for targeted therapy.
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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.