RPXD034701

RPXD034701 is container for one or more analyses. The general container metadata is provided below and the table under Dataset History provides links to the various reanalyses have been provided (if any) in this container.

Title	PXD018241-2 Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site. [Reanalysis: PXD018241]
Description	Direct RNA sequencing using an Oxford Nanopore MinION characterised the transcriptome of SARS-CoV-2 grown in Vero E6 cells. This cell line is being widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. This revealed the pattern of viral transcripts, (i.e. subgenomic mRNAs), generally fitted the predicted replication and transcription model for coronaviruses. A 24 nt in-frame deletion was detected in subgenomic mRNAs encoding the spike (S) glycoprotein. This feature was identified in over half of the mapped transcripts and was predicted to remove a proposed furin cleavage site from the S glycoprotein. This motif directs cleavage of the S glycoprotein into functional subunits during virus entry or exit. Cleavage of the S glycoprotein can be a barrier to zoonotic coronavirus transmission and affect viral pathogenicity. Allied to this transcriptome analysis, tandem mass spectrometry was used to identify over 500 viral peptides and 44 phosphopeptides, covering almost all of the proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein reinforces the point that this and other regions of SARS-CoV-2 proteins may readily mutate. This is of clear significance given the interest in the S glycoprotein as a potential vaccine target and the observation that the furin cleavage site likely contributes strongly to the pathogenesis and zoonosis of this virus. The viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality. [Original project description]
HostingRepository	jPOST
AnnounceDate	2023-03-25
AnnouncementXML	Submission_2023-03-25_06:45:09.376.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/RPXD034701
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Reanalysis of PXD018241
RepositorySupport	Supported dataset by repository
PrimarySubmitter	jPOST reanalysis
SpeciesList	scientific name: cell culture; NCBI TaxID: BTO:0000214;
ModificationList	S-carboxamidomethyl-L-cysteine; unknown modification; unknown modification; L-methionine sulfoxide; O4'-phospho-L-tyrosine; O-phospho-L-threonine; O-phospho-L-serine
Instrument	Orbitrap Fusion Lumos

Reanalysis	Revision	Datetime	Status	Title / ChangeLog Entry
	0	2022-06-19 17:30:38	ID requested
0	1	2023-03-25 06:45:09	announced	PXD018241-2 Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleav

no publication

submitter keyword: reanalysis, Human, SARS-CoV-2, Coronavirus, Multiomics

Yasushi Ishihama
lab head
jPOST reanalysis
contact affiliation	jPOST
dataset submitter

jPOST dataset URI

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST001785/