sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M>ORF3a>N>ORF6>ORF7a>ORF8>S>E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes. ### Competing Interest Statement BDG is a consultant or received honoraria for Darwin Health, Merck, PMV Pharma, ROME Therapeutics (of which he is a co-founder), Bristol-Meyers Squibb, and Chugai Pharmaceuticals and has research funding from Bristol-Meyers Squibb and Merck. The other authors declare that they have no competing interests.