RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2021 
FD April 01 
VO 31 
IS 4 
SP 645 
OP 658 
DO 10.1101/gr.268110.120 
UL http://genome.cshlp.org/content/31/4/645.abstract 
AB 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.