sgDI-tector: Defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs Journal Article
| Authors: | Di Gioacchino, A.; Legendre, R.; Rahou, Y.; Najburg, V.; Charneau, P.; Greenbaum, B. D.; Tangy, F.; van der Werf, S.; Cocco, S.; Komarova, A. V. |
| Article Title: | sgDI-tector: Defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs |
| 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. © 2022 Di Gioacchino et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. |
| Keywords: | sars-cov-2; defective viral genomes; subgenomic rna; user-friendly bioinformatics |
| Journal Title: | RNA |
| Volume: | 28 |
| Issue: | 3 |
| ISSN: | 1355-8382 |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Date Published: | 2022-03-01 |
| Start Page: | 277 |
| End Page: | 289 |
| Language: | English |
| DOI: | 10.1261/rna.078969.121 |
| PUBMED: | 34937774 |
| PROVIDER: | scopus |
| PMCID: | PMC8848934 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 March 2022 -- Source: Scopus |
