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Journal Articles RNA Year : 2021

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

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Abstract

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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Origin : Publication funded by an institution

Dates and versions

pasteur-03591131 , version 1 (28-02-2022)

Licence

Attribution - NonCommercial - CC BY 4.0

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Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, et al.. sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs. RNA, 2021, 28 (3), pp.277-289. ⟨10.1261/rna.078969.121⟩. ⟨pasteur-03591131⟩
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