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sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs.
Di Gioacchino, Andrea; Legendre, Rachel; Rahou, Yannis; Najburg, Valérie; Charneau, Pierre; Greenbaum, Benjamin D; Tangy, Frédéric; van der Werf, Sylvie; Cocco, Simona; Komarova, Anastassia V.
  • 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.
  • Tangy F; Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York 10065, USA.
  • van der Werf S; Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France.
  • Cocco S; Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France.
  • Komarova AV; Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France.
RNA ; 28(3): 277-289, 2022 03.
Article in English | MEDLINE | ID: covidwho-1592848
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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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Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA, Viral / Genome, Viral / Computational Biology / SARS-CoV-2 Language: English Journal: RNA Journal subject: Molecular Biology Year: 2022 Document Type: Article Affiliation country: Rna.078969.121

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Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA, Viral / Genome, Viral / Computational Biology / SARS-CoV-2 Language: English Journal: RNA Journal subject: Molecular Biology Year: 2022 Document Type: Article Affiliation country: Rna.078969.121