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Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data
Matthew D Parker1,2,3, Benjamin B Lindsey4,5, Shay Leary6
1Sheffield Bioinformatics Core, The University of Sheffield, Sheffield S10 2HQ, United Kingdom.
Genome Research
|March 16, 2021
Summary
We developed periscope, a tool to detect and quantify subgenomic RNAs (sgRNAs) in SARS-CoV-2 genomes. This method accurately identifies canonical and noncanonical sgRNAs, aiding COVID-19 research.
Area of Science:
- Virology
- Molecular Biology
- Bioinformatics
Background:
- Subgenomic RNAs (sgRNAs) are crucial intermediates for SARS-CoV-2 gene expression.
- Understanding sgRNA dynamics is essential for comprehending viral replication and pathogenesis.
- Current methods for sgRNA detection and quantification have limitations.
Purpose of the Study:
- To develop and validate 'periscope,' a novel tool for detecting and quantifying SARS-CoV-2 subgenomic RNAs (sgRNAs).
- To analyze sgRNA profiles in a large cohort of SARS-CoV-2 genomes.
- To assess the fidelity of variant transmission from genomic RNA to sgRNAs.
Main Methods:
- Development of the 'periscope' tool utilizing local alignment to detect leader sequences on SARS-CoV-2 reads.
- Application of periscope to 1155 SARS-CoV-2 genomes from Sheffield, UK.
- Validation using orthogonal datasets, in vitro cell systems (VeroE6 ACE2+/-), and technical replicates.
Main Results:
- Periscope successfully detected and quantified canonical sgRNAs, except for ORF10, at expected abundances.
- Recurrent noncanonical sgRNAs were identified.
- High fidelity of variant transmission from genomic RNA to sgRNAs was observed.
- Periscope demonstrated reproducibility and identified optimal read counts for analysis.
Conclusions:
- Periscope is a robust and reproducible tool for comprehensive SARS-CoV-2 sgRNA analysis.
- The tool can be applied globally to all sequenced COVID-19 samples.
- Findings contribute to a deeper understanding of SARS-CoV-2 gene expression and evolution.
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