tetano
Editor, Senior Moderator
RNA
. 2021 Dec 22;rna.078969.121.
doi: 10.1261/rna.078969.121. Online ahead of print.
sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
Andrea Di Gioacchino[SUP] 1 [/SUP], Rachel Legendre[SUP] 2 [/SUP], Yannis Rahou[SUP] 2 [/SUP], Valérie Najburg[SUP] 2 [/SUP], Pierre Charneau[SUP] 2 [/SUP], Benjamin D Greenbaum[SUP] 3 [/SUP], Frédéric Tangy[SUP] 2 [/SUP], Sylvie van der Werf[SUP] 2 [/SUP], Simona Cocco[SUP] 4 [/SUP], Anastassia V Komarova[SUP] 2 [/SUP]
Affiliations
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: Defective Viral Genomes; SARS-CoV-2; subgenomic RNA; user-friendly bioinformatics.
. 2021 Dec 22;rna.078969.121.
doi: 10.1261/rna.078969.121. Online ahead of print.
sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
Andrea Di Gioacchino[SUP] 1 [/SUP], Rachel Legendre[SUP] 2 [/SUP], Yannis Rahou[SUP] 2 [/SUP], Valérie Najburg[SUP] 2 [/SUP], Pierre Charneau[SUP] 2 [/SUP], Benjamin D Greenbaum[SUP] 3 [/SUP], Frédéric Tangy[SUP] 2 [/SUP], Sylvie van der Werf[SUP] 2 [/SUP], Simona Cocco[SUP] 4 [/SUP], Anastassia V Komarova[SUP] 2 [/SUP]
Affiliations
- PMID: 34937774
- DOI: 10.1261/rna.078969.121
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: Defective Viral Genomes; SARS-CoV-2; subgenomic RNA; user-friendly bioinformatics.