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

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Di Gioacchino, Andrea | Legendre, Rachel | Rahou, Yannis | Najburg, Valérie | Charneau, Pierre | Greenbaum, Benjamin | Tangy, Frédéric | van Der Werf, Sylvie | Cocco, Simona | Komarova, Anastassia

Edité par CCSD ; Cold Spring Harbor Laboratory Press -

International audience. 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.

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