Journal
RNA
Volume 28, Issue 3, Pages 277-289Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.078969.121
Keywords
subgenomic RNA; SARS-CoV-2; defective viral genomes; user-friendly bioinformatics
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Funding
- Institut Pasteur, Paris, France
- ANR (Agence Nationale de la Recherche) [ANR-LBX-62 IBEID CoV-2SENSING/COVID 19]
- FRM (Fondation de la Recherche Medicale)
- France Genomique [ANR-10-INBS-09-09]
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Researchers have developed a user-friendly bioinformatic tool sgDI-tector to detect and quantify sgRNA production in SARS-CoV-2 NGS data, providing an effective method for studying subgenomic RNAs of coronaviruses.
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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