sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
- Andrea Di Gioacchino1,
- Rachel Legendre2,
- Yannis Rahou3,
- Valérie Najburg4,
- Pierre Charneau5,
- Benjamin D. Greenbaum6,7,
- Frédéric Tangy4,
- Sylvie van der Werf3,
- Simona Cocco1 and
- Anastassia V. Komarova3
- 1Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France
- 2Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, 75015, Paris, France
- 3Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
- 4Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France
- 5Institut Pasteur, Pasteur-TheraVectys joined unit, 75015, Paris, France
- 6Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York 10065, USA
- 7Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York 10065, USA
- Corresponding authors: anastasia.komarova{at}pasteur.fr, andrea.digioacchino{at}phys.ens.fr
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.
Keywords
- Received August 30, 2021.
- Accepted December 7, 2021.
This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
