Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data

The COVID-19 Genomics UK (COG-UK) consortium, Matthew D. Parker, Benjamin B. Lindsey, Shay Leary, Silvana Gaudieri, Abha Chopra, Matthew Wyles, Adrienn Angyal, Luke R. Green, Paul Parsons, Rachel M. Tucker, Rebecca Brown, Danielle Groves, Katie Johnson, Laura Carrilero, Joe Heffer, David G. Partridge, Cariad Evans, Mohammad Raza, Alexander J. KeeleyNikki Smith, Ana Da Silva Filipe, James G. Shepherd, Chris Davis, Sahan Bennett, Vattipally B. Sreenu, Alain Kohl, Elihu Aranday-Cortes, Lily Tong, Jenna Nichols, Emma C. Thomson, Dennis Wang, Simon Mallal, Thushan I. de Silva*, Matthew Bashton, Greg Young, John Allan, Joshua Loh, Andrew Nelson, Darren Smith, Wen Yew

*Corresponding author for this work

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Abstract

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.
Original languageEnglish
Pages (from-to)645-658
Number of pages14
JournalGenome Research
Volume31
Issue number4
Early online date15 Mar 2021
DOIs
Publication statusPublished - 1 Apr 2021

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