TY  - JOUR
A1  - Parker, Matthew D.
A1  - Lindsey, Benjamin B.
A1  - Leary, Shay
A1  - Gaudieri, Silvana
A1  - Chopra, Abha
A1  - Wyles, Matthew
A1  - Angyal, Adrienn
A1  - Green, Luke R.
A1  - Parsons, Paul
A1  - Tucker, Rachel M.
A1  - Brown, Rebecca
A1  - Groves, Danielle
A1  - Johnson, Katie
A1  - Carrilero, Laura
A1  - Heffer, Joe
A1  - Partridge, David G.
A1  - Evans, Cariad
A1  - Raza, Mohammad
A1  - Keeley, Alexander J.
A1  - Smith, Nikki
A1  - Filipe, Ana Da Silva
A1  - Shepherd, James G.
A1  - Davis, Chris
A1  - Bennett, Sahan
A1  - Sreenu, Vattipally B.
A1  - Kohl, Alain
A1  - Aranday-Cortes, Elihu
A1  - Tong, Lily
A1  - Nichols, Jenna
A1  - Thomson, Emma C.
A1  - The COVID-19 Genomics UK (COG-UK) Consortium
A1  - Wang, Dennis
A1  - Mallal, Simon
A1  - de Silva, Thushan I.
T1  - Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data
Y1  - 2021/04/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 645 
EP  - 658 
DO  - 10.1101/gr.268110.120 
VL  - 31 
IS  - 4 
UR  - http://genome.cshlp.org/content/31/4/645.abstract 
N2  - We have developed periscope, a tool for the detection and quantification of subgenomic 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 “subgenomic 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 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical 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 data sets. 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. 
ER  -