periscope: sub-genomic RNA identification in SARS-CoV-2 Genomic Sequencing Data
periscope: sub-genomic RNA identification in SARS-CoV-2 Genomic Sequencing Data
Abstract We have developed periscope, a tool for the detection and quantification of sub-genomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed “sub-genomic RNAs”. sgRNAs are produced through discontinuous transcription which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L which is located in the 5’ UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5’ end of all sgRNA. We applied periscope to 1,155 SARS-CoV-2 genomes from Sheffield, UK and validated our findings using orthogonal datasets and in vitro cell systems. Using a simple local alignment to detect reads which contain the leader sequence we were able to identify and quantify reads arising from canonical and non-canonical sgRNA. We were able to detect all canonical sgRNAs at expected abundances, with the exception of ORF10. A number of recurrent non-canonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/? cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing datasets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA.
Wang Dennis、Aranday-Cortes Elihu、Davis Chris、Nichols Jenna、Parker Matthew D、Gaudieri Silvana、Wyles Matthew、Green Luke R、Heffer Joe、Lindsey Benjamin B、Kohl Alain、The COVID-19 Genomics UK (COG-UK) consortium、Mallal Simon、Shepherd James G、Brown Rebecca、Johnson Katie、Carrilero Laura、Angyal Adrienn、Partridge David G、Thomson Emma C、Tong Lily、Smith Nikki、Leary Shay、Bennett Sahan、de Silva Thushan I、Raza Mohammad、Keeley Alexander J、Filipe Ana Da Silva、Groves Danielle、Chopra Abha、Tucker Rachel M、Parsons Paul、Evans Cariad
Sheffield Bioinformatics Core, The University of Sheffield||Sheffield Biomedical Research Centre, The University of Sheffield||Sheffield Institute for Translational Neuroscience, The University of Sheffield||Department of Computer Science, The University of SheffieldCentre for Virus Research, The University of GlasgowCentre for Virus Research, The University of GlasgowCentre for Virus Research, The University of GlasgowSheffield Bioinformatics Core, The University of Sheffield||Sheffield Biomedical Research Centre, The University of Sheffield||Sheffield Institute for Translational Neuroscience, The University of SheffieldInstitute for Immunology and Infectious Diseases, Murdoch University||Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center||School of Human Sciences, University of Western Australia, CrawleySheffield Institute for Translational Neuroscience, The University of SheffieldThe Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldIT Services, The University of SheffieldSheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology||The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldCentre for Virus Research, The University of Glasgowhttps://www.cogconsortium.ukInstitute for Immunology and Infectious Diseases, Murdoch University||Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical CenterCentre for Virus Research, The University of GlasgowThe Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldSheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/MicrobiologySchool of Human Sciences, University of Western Australia, CrawleyThe Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldSheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology||The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldCentre for Virus Research, The University of GlasgowCentre for Virus Research, The University of GlasgowThe Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldInstitute for Immunology and Infectious Diseases, Murdoch UniversityCentre for Virus Research, The University of GlasgowSheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology||The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldSheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/MicrobiologySheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology||The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldCentre for Virus Research, The University of GlasgowThe Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity, Cardiovascular Disease, The University of SheffieldInstitute for Immunology and Infectious Diseases, Murdoch UniversitySchool of Human Sciences, University of Western Australia, CrawleySchool of Human Sciences, University of Western Australia, CrawleySheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology
基础医学分子生物学生物科学研究方法、生物科学研究技术
SARS-CoV-2sub-genomic RNAExpressionsgRNA
Wang Dennis,Aranday-Cortes Elihu,Davis Chris,Nichols Jenna,Parker Matthew D,Gaudieri Silvana,Wyles Matthew,Green Luke R,Heffer Joe,Lindsey Benjamin B,Kohl Alain,The COVID-19 Genomics UK (COG-UK) consortium,Mallal Simon,Shepherd James G,Brown Rebecca,Johnson Katie,Carrilero Laura,Angyal Adrienn,Partridge David G,Thomson Emma C,Tong Lily,Smith Nikki,Leary Shay,Bennett Sahan,de Silva Thushan I,Raza Mohammad,Keeley Alexander J,Filipe Ana Da Silva,Groves Danielle,Chopra Abha,Tucker Rachel M,Parsons Paul,Evans Cariad.periscope: sub-genomic RNA identification in SARS-CoV-2 Genomic Sequencing Data[EB/OL].(2025-03-28)[2025-04-26].https://www.biorxiv.org/content/10.1101/2020.07.01.181867.点此复制
评论