About: 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

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About: 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 Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	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
Creator	Zambon, Maria Davidson, Andrew Hiscox, Julian Ellis, Joanna Heesom, Kate Matthews, David Carroll, Miles Lewis, Phillip Lewis, Sebastian Matthews, D Shoemark, Deborah Williamson, Maia
Source	BioRxiv
abstract	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.
has issue date	2020-03-24(xsd:dateTime)
bibo:doi	10.1101/2020.03.22.002204
has license	biorxiv
sha1sum (hex)	6ad39be296a7e5c6c7f03a5f41348fc3339fdaf1
schema:url	https://doi.org/10.1101/2020.03.22.002204
resource representing a document's title	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
schema:publication	bioRxiv
resource representing a document's body	covid:6ad39be296a7e5c6c7f03a5f41348fc3339fdaf1#body_text
is schema:about of	named entity 'glycoprotein' named entity 'RNA' named entity 'subgenomic' named entity 'viable' named entity 'mapped' named entity 'glycoprotein' named entity 'sequence' named entity 'passage' named entity 'VIRAL GENOME' named entity 'ALMOST ALL' named entity 'SITE' named entity 'VIRUS' named entity 'IN-FRAME DELETION' named entity 'TO IDENTIFY' named entity 'CENTRIC' named entity 'genome' named entity 'coronaviruses' named entity 'motif' named entity 'glycoprotein' named entity 'peptides' named entity 'viral' named entity 'deleted' named entity 'Cleavage' named entity 'generally' named entity 'transmission' named entity 'mRNAs' named entity 'samples' named entity 'deletion' named entity 'cleavage' named entity 'glycoprotein' named entity 'variations' named entity 'propagate' named entity 'proteins' named entity 'in-frame deletion' named entity 'coronavirus' named entity 'coronaviruses' named entity 'MinION' named entity 'tandem mass spectrometry' named entity 'SARS-CoV-2' named entity 'RNA sequencing' named entity 'mRNAs' named entity 'cleavage site' named entity 'furin' named entity 'cleavage site' named entity 'genome sequence' named entity 'transcriptome' named entity 'cleavage site' named entity 'morbidity' named entity 'transcription' named entity 'phosphorylation sites' named entity 'virus' named entity 'viral proteins' named entity 'class I fusion protein' named entity 'host cell' named entity 'polyA tail' named entity 'Coronaviridae' named entity 'transcription' named entity 'transcriptomic' named entity 'glycoprotein' named entity 'Tandem mass spectrometry' named entity 'peptides' named entity 'cleavage' named entity 'SARS-CoV-2' named entity 'herpes viruses' named entity 'respiratory syncytial virus' named entity 'peptides' named entity 'polyA' named entity 'protein' named entity 'number of reads' named entity 'mRNAs' named entity 'proteases' named entity 'SARS-CoV-2' named entity 'immune response'

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