PT  - JOURNAL ARTICLE
AU  - Matthew D Parker
AU  - Benjamin B Lindsey
AU  - Shay Leary
AU  - Silvana Gaudieri
AU  - Abha Chopra
AU  - Matthew Wyles
AU  - Adrienn Angyal
AU  - Luke R Green
AU  - Paul Parsons
AU  - Rachel M Tucker
AU  - Rebecca Brown
AU  - Danielle Groves
AU  - Katie Johnson
AU  - Laura Carrilero
AU  - Joe Heffer
AU  - David G Partridge
AU  - Cariad Evans
AU  - Mohammad Raza
AU  - Alexander J Keeley
AU  - Nikki Smith
AU  - Ana Da Silva Filipe
AU  - James G Shepherd
AU  - Chris Davis
AU  - Sahan Bennett
AU  - Alain Kohl
AU  - Elihu Aranday-Cortes
AU  - Lily Tong
AU  - Jenna Nichols
AU  - Emma C Thomson
AU  - The COVID-19 Genomics UK (COG-UK) consortium
AU  - Dennis Wang
AU  - Simon Mallal
AU  - Thushan I de Silva
TI  - periscope: sub-genomic RNA identification in SARS-CoV-2 Genomic Sequencing Data
AID  - 10.1101/2020.07.01.181867
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.07.01.181867
4099  - http://biorxiv.org/content/early/2020/11/06/2020.07.01.181867.short
4100  - http://biorxiv.org/content/early/2020/11/06/2020.07.01.181867.full
AB  - 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.Competing Interest StatementThe authors have declared no competing interest.