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

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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https://hal-pasteur.archives-ouvertes.fr/pasteur-03591131
Contributor : Rachel Legendre Connect in order to contact the contributor
Submitted on : Monday, February 28, 2022 - 1:51:24 PM
Last modification on : Thursday, September 1, 2022 - 4:01:36 AM
Long-term archiving on: : Sunday, May 29, 2022 - 7:27:23 PM

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Distributed under a Creative Commons Attribution - NonCommercial 4.0 International License

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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, Cold Spring Harbor Laboratory Press, 2021, 28 (3), pp.277-289. ⟨10.1261/rna.078969.121⟩. ⟨pasteur-03591131⟩

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