ArticleGenome medicine2020
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2.
Article in Genome medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 69 citations in OpenAlex.
- Direct RNA sequencing reveals m6A modifications and isoform changes in SARS-CoV-2-infected HEK cells.Access microbiology · 2025Article
- Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses.BMC genomics · 2024Article
- Improved sub-genomic RNA prediction with the ARTIC protocol.Nucleic acids research · 2024Article
- Cellular dynamics shape recombination frequency in coronaviruses.PLoS pathogens · 2024Article
- Adaptive truncation of the S gene in IBV during chicken embryo passaging plays a crucial role in its attenuation.PLoS pathogens · 2024Article
- Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung.The Journal of experimental medicine · 2024Article
- Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2.Nucleic acids research · 2024Article
- Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer.Microbiology spectrum · 2024Article
- An RNA-Seq analysis of coronavirus in the skin of the Pangolin.Scientific reports · 2024Article
- Expression dynamics of the aplysia abyssovirus.Virology · 2024Article
- Identification of the protein coding capability of coronavirus defective viral genomes by mass spectrometry.Virology journal · 2023Article
- Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs.Life science alliance · 2023Article
- Unveiling the biology of defective viral genomes in vitro and in vivo: implications for gene expression and pathogenesis of coronavirus.Virology journal · 2023Article
- Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses.Virology journal · 2023Article
- sgRNAs: A SARS-CoV-2 emerging issue.Aspects of molecular medicine · 2023Review
- Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs.Virologica Sinica · 2022Article
- Biology of the SARS-CoV-2 Coronavirus.Biochemistry. Biokhimiia · 2022Review
- Subgenomic RNAs and Their Encoded Proteins Contribute to the Rapid Duplication of SARS-CoV-2 and COVID-19 Progression.Biomolecules · 2022Review
- The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness.Scientific reports · 2022Article
- On the Origins of Omicron's Unique Spike Gene Insertion.Vaccines · 2022Article
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3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundSARS-CoV-2, a positive-sense RNA virus in the family Coronaviridae, has caused a worldwide pandemic of coronavirus disease 2019 or COVID-19. Coronaviruses generate a tiered series of subgenomic RNAs (sgRNAs) through a process involving homology between transcriptional regulatory sequences (TRS) located after the leader sequence in the 5' UTR (the TRS-L) and TRS located near the start of ORFs encoding structural and accessory proteins (TRS-B) near the 3' end of the genome. In addition to the canonical sgRNAs generated by SARS-CoV-2, non-canonical sgRNAs (nc-sgRNAs) have been reported. However, the consistency of these nc-sgRNAs across viral isolates and infection conditions is unknown. The comprehensive definition of SARS-CoV-2 RNA products is a key step in understanding SARS-CoV-2 pathogenesis.
methodsHere, we report an integrative analysis of eight independent SARS-CoV-2 transcriptomes generated using three sequencing strategies, five host systems, and seven viral isolates. Read-mapping to the SARS-CoV-2 genome was used to determine the 5' and 3' coordinates of all junctions in viral RNAs identified in these samples.
resultsUsing junctional abundances, we show nc-sgRNAs make up as much as 33% of total sgRNAs in cell culture models of infection, are largely consistent in abundance across independent transcriptomes, and increase in abundance over time during infection. By assessing the homology between sequences flanking the 5' and 3' junction points, we show that nc-sgRNAs are not associated with TRS-like homology. By incorporating read coverage information, we find strong evidence for subgenomic RNAs that contain only 5' regions of ORF1a. Finally, we show that non-canonical junctions change the landscape of viral open reading frames.
conclusionsWe identify canonical and non-canonical junctions in SARS-CoV-2 sgRNAs and show that these RNA products are consistently generated by many independent viral isolates and sequencing approaches. These analyses highlight the diverse transcriptional activity of SARS-CoV-2 and offer important insights into SARS-CoV-2 biology.
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