sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs.
RNA, 2021/12/22;
Di Gioacchino A[1], Legendre R[2], Rahou Y[2], Najburg V[2], Charneau P[2], Greenbaum BD[3], Tangy F[2], van der Werf S[2], Cocco S[4], Komarova AV[2]
Affiliations
PMID: 34937774DOI: 10.1261/rna.078969.121
Impact factor: 5.636
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
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