ArticleMolecular cell2021
The SARS-CoV-2 subgenome landscape and its novel regulatory features.
Article in Molecular cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed.
- An ATP-Driven N Protein-DDX21 Molecular Switch Dynamically Controls SARS-CoV-2 RNA G-Quadruplex Heterogeneity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- A potential RNA-RNA distal interaction competing with a functional pseudoknot in the 3'-untranslated region of SARS-like coronaviruses.Nucleic acids research · 2026Article
- Mechanism and key RNA determinants of SARS-CoV-2 Nsp1-induced endonucleolytic cleavage of mRNA.bioRxiv : the preprint server for biology · 2026Article
- Evidence for Powassan virus deletions and defective RNA in field-collected ticks.Journal of virology · 2026Article
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- Development of the coronavirus reverse genetic system: Core technology for pathogenesis mechanisms research and vaccine/drug development.Virulence · 2025Review
- Discontinuous template switching generates coronavirus subgenomic RNAs from the 3' viral genome end by 5' to 3' transcription.Journal of virology · 2025Article
- Antisense oligonucleotides targeting the SARS-CoV-2 nucleocapsid gene decrease viral titers in hamsters.Molecular therapy. Nucleic acids · 2025Article
- Enhanced identification of novel pathogenic variants in hereditary hearing loss through physical phasing with integrated short and long-read sequencing data.Molecular genetics and genomics : MGG · 2025Article
- The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure.Nucleic acids research · 2025Article
- Review
- Analysis of RNA translation with a deep learning architecture provides new insight into translation control.Nucleic acids research · 2025Article
- Integrative single-cell and metagenomic analysis dissects SARS-CoV-2 shedding modes in human respiratory tract.Biosafety and health · 2025Article
- The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure.bioRxiv : the preprint server for biology · 2025Article
- A fusion ORF3a-E subgenomic RNA involved in SARS-CoV-2 infection efficacy by influencing cellular protein synthesis.Frontiers in immunology · 2025Article
- Inhibition of SARS-CoV-2 growth in the lungs of mice by a peptide-conjugated morpholino oligomer targeting viral RNA.Molecular therapy. Nucleic acids · 2024Article
- SARS-CoV-2 N protein coordinates viral particle assembly through multiple domains.Journal of virology · 2024Article
- RNA architecture of porcine deltacoronavirus genome inside virions detected by vRIC-seq.Scientific data · 2024Article
- Epitranscriptomic mScience advances · 2024Article
21 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
22 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently a global pandemic. CoVs are known to generate negative subgenomes (subgenomic RNAs [sgRNAs]) through transcription-regulating sequence (TRS)-dependent template switching, but the global dynamic landscapes of coronaviral subgenomes and regulatory rules remain unclear. Here, using next-generation sequencing (NGS) short-read and Nanopore long-read poly(A) RNA sequencing in two cell types at multiple time points after infection with SARS-CoV-2, we identified hundreds of template switches and constructed the dynamic landscapes of SARS-CoV-2 subgenomes. Interestingly, template switching could occur in a bidirectional manner, with diverse SARS-CoV-2 subgenomes generated from successive template-switching events. The majority of template switches result from RNA-RNA interactions, including seed and compensatory modes, with terminal pairing status as a key determinant. Two TRS-independent template switch modes are also responsible for subgenome biogenesis. Our findings reveal the subgenome landscape of SARS-CoV-2 and its regulatory features, providing a molecular basis for understanding subgenome biogenesis and developing novel anti-viral strategies.
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