Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

Abstract

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3’ of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.

Metadata

Item Type:	Article
Authors/Creators:	Parker, M.D. Stewart, H. Shehata, O.M. Lindsey, B.B. https://orcid.org/0000-0003-4227-2592 Shah, D.R. Hsu, S. Keeley, A.J. https://orcid.org/0000-0001-9386-1157 Partridge, D.G. https://orcid.org/0000-0002-0417-2016 Leary, S. Cope, A. State, A. Johnson, K. Ali, N. Raghei, R. Heffer, J. https://orcid.org/0000-0001-8733-1117 Smith, N. Zhang, P. Gallis, M. Louka, S.F. https://orcid.org/0000-0003-3000-3504 Hornsby, H.R. https://orcid.org/0000-0002-6657-9743 Alamri, H. Whiteley, M. Foulkes, B.H. Christou, S. Wolverson, P. Pohare, M. https://orcid.org/0000-0003-2272-9946 Hansford, S.E. Green, L.R. https://orcid.org/0000-0002-2836-2041 Evans, C. Raza, M. Wang, D. https://orcid.org/0000-0003-0068-1005 Firth, A.E. Edgar, J.R. Gaudieri, S. Mallal, S. COVID-19 Genomics UK (COG-UK) consortium Collins, M.O. https://orcid.org/0000-0002-7656-4975 Peden, A.A. https://orcid.org/0000-0003-0144-7712 de Silva, T.I. https://orcid.org/0000-0002-6498-9212
Copyright, Publisher and Additional Information:	© The Author(s) 2022. Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Dates:	Published: 5 July 2022 Published (online): 5 July 2022 Accepted: 7 June 2022
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Professional Services (Sheffield) The University of Sheffield > Sheffield Teaching Hospitals
Depositing User:	Symplectic Sheffield
Date Deposited:	07 Jul 2022 09:58
Last Modified:	07 Jul 2022 09:58
Status:	Published
Publisher:	Nature Research (part of Springer Nature)
Refereed:	Yes
Identification Number:	10.1038/s42003-022-03565-9
Related URLs:	PubMed URL Dataset Dataset
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:188818