PXD029954

PXD029954 is an original dataset announced via ProteomeXchange.

Title	Altered Subgenomic RNA Abundance in SARS-CoV-2 B.1.1.7 Infections
Description	SARS-CoV-2 lineage B.1.1.7 viruses are more transmissible, may lead to greater clinical severity, and result 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 Nanopore 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 circulating UK lineage, B.1.177(n=943), which is independent of genomic reads, E-gene 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 during in vitro culture. We hypothesise that this enhanced presence of ORF9b in B.1.1.7 viruses 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 in sequence data to evaluate emerging potential variants of concern.
HostingRepository	PRIDE
AnnounceDate	2021-11-26
AnnouncementXML	Submission_2021-11-26_03:57:35.841.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mark Collins
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	amidated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-26 03:32:33	ID requested
⏵ 1	2021-11-26 03:57:36	announced

Dataset with its publication pending

submitter keyword: SARS-CoV-2, coronavirus, B.1.1.7

Mark Collins
contact affiliation	School of Biosciences University of Sheffield United Kingdom
contact email	mark.collins@sheffield.ac.uk
lab head
Mark Collins
contact affiliation	University of Sheffield
contact email	mark.collins@sheffield.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD029954
     1. Label: PRIDE project
     2. Name: Altered Subgenomic RNA Abundance in SARS-CoV-2 B.1.1.7 Infections