ArticleGenome research2021
Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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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
36 citing papers in PubMed, 58 citations in OpenAlex.
- How benchmarking of bioinformatics tools is essential for informed workflow selection: a case study on SARS-CoV-2 subgenomic RNA detection.Frontiers in bioinformatics · 2026Article
- PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance.Bioinformatics (Oxford, England) · 2025Article
- Direct RNA sequencing reveals m6A modifications and isoform changes in SARS-CoV-2-infected HEK cells.Access microbiology · 2025Article
- A fusion ORF3a-E subgenomic RNA involved in SARS-CoV-2 infection efficacy by influencing cellular protein synthesis.Frontiers in immunology · 2025Article
- Improved sub-genomic RNA prediction with the ARTIC protocol.Nucleic acids research · 2024Article
- Age-specific nasal epithelial responses to SARS-CoV-2 infection.Nature microbiology · 2024Article
- Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer.Microbiology spectrum · 2024Article
- Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs.Life science alliance · 2023Article
- Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single-cell RNA sequencing.Microbiology spectrum · 2023Article
- Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.Cell host & microbe · 2023Article
- Article
- Review
- SARS-CoV-2 Disease Severity in the Golden Syrian Hamster Model of Infection Is Related to the Volume of Intranasal Inoculum.Viruses · 2023Article
- Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single cell RNA sequencing.bioRxiv : the preprint server for biology · 2023Article
- Potential therapeutic applications of extracellular vesicles in the immunopathogenesis of COVID-19.Pathology, research and practice · 2023Review
- sgRNAs: A SARS-CoV-2 emerging issue.Aspects of molecular medicine · 2023Review
- Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs.Virologica Sinica · 2022Article
- Virological and Serological Assessment of US Army Trainees Isolated for Coronavirus Disease 2019.The Journal of infectious diseases · 2022Article
- Hydrophobic Alpha-Helical Short Peptides in Overlapping Reading Frames of the Coronavirus Genome.Pathogens (Basel, Switzerland) · 2022Article
- Human coronaviruses disassemble processing bodies.PLoS pathogens · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
34 authors at 4 institutions in 3 countries.
Funding
Abstract
We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5' end of all sgRNA. We applied periscope to 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6
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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.