periscope: sub-genomic RNA identification in SARS-CoV-2 genomic sequencing data
About Matthew Parker
Dr. Matthew Parker is a Clinical Bioinformatician (HCPC registered) based at the Sheffield Bioinformatics Core in the Sheffield Biomedical research centre. His main interests are in the application of cutting edge genomics to healthcare problems, from cancer to rare disease, and most recently infectious diseases.
We have developed periscope, a tool for the detection and quantification of sub-genomic RNA (sgRNA) in ARTIC network protocol generated nanopore 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 sgRNAs. We applied periscope to 1155 nanopore SARS-CoV-2 and validated our findings using orthogonal datasets and in vitro cell systems. Using a simple local alignment to detect reads which contain the leader sequence, we were able to identify and quantify reads arising from canonical and non-canonical sgRNA. We show that the results are reproducible, and in VeroE6 ACE2+/- cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing datasets. This tool can be applied to many sequences worldwide to provide the most comprehensive analysis of SARS-CoV-2 sgRNA to date.