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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

RNA (Cambridge), 2022-03, Vol.28 (3), p.277-289 [Periódico revisado por pares]

United States: Cold Spring Harbor Laboratory Press

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Título:
sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
Autor: 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
Assuntos: Bioinformatics ; Computational Biology ; Computational Biology - methods ; Computer Science ; Coronaviruses ; Genome, Viral ; Genomes ; High-Throughput Nucleotide Sequencing ; Life Sciences ; Microbiology and Parasitology ; Next-generation sequencing ; Open Reading Frames ; Regulatory sequences ; Ribonucleic acid ; RNA ; RNA, Viral ; RNA, Viral - genetics ; Santé publique et épidémiologie ; SARS-CoV-2 ; SARS-CoV-2 - genetics ; Severe acute respiratory syndrome coronavirus 2 ; Transcription ; Virology
É parte de: RNA (Cambridge), 2022-03, Vol.28 (3), p.277-289
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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Descrição: 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.
Editor: United States: Cold Spring Harbor Laboratory Press
Idioma: Inglês

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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

United States: Cold Spring Harbor Laboratory Press

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