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

Autor:	Di Gioacchino A; Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France., Legendre R; Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, 75015, Paris, France., Rahou Y; Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France., Najburg V; Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France., Charneau P; Institut Pasteur, Pasteur-TheraVectys joined unit, 75015, Paris, France., Greenbaum BD; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York 10065, USA.; Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York 10065, USA., Tangy F; Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France., van der Werf S; Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France., Cocco S; Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France., Komarova AV; Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France.
Jazyk:	angličtina
Zdroj:	RNA (New York, N.Y.) [RNA] 2022 Mar; Vol. 28 (3), pp. 277-289. Date of Electronic Publication: 2021 Dec 22.
DOI:	10.1261/rna.078969.121
Abstrakt:	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. (© 2022 Di Gioacchino et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)
Databáze:	MEDLINE
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