Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein.
Journal
Genome medicine
ISSN: 1756-994X
Titre abrégé: Genome Med
Pays: England
ID NLM: 101475844
Informations de publication
Date de publication:
28 07 2020
28 07 2020
Historique:
received:
31
03
2020
accepted:
10
07
2020
entrez:
30
7
2020
pubmed:
30
7
2020
medline:
8
8
2020
Statut:
epublish
Résumé
SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus's genomic and proteomic potential. We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells. Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all 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, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that 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.
Sections du résumé
BACKGROUND
SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus's genomic and proteomic potential.
METHODS
We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells.
RESULTS
Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein.
CONCLUSIONS
Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that 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.
Identifiants
pubmed: 32723359
doi: 10.1186/s13073-020-00763-0
pii: 10.1186/s13073-020-00763-0
pmc: PMC7386171
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
68Subventions
Organisme : Medical Research Council
ID : MR/P017509/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R020566/1
Pays : United Kingdom
Organisme : U.S. Food and Drug Administration
ID : HHSF223201510104C
Pays : International
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M02542X/1
Pays : United Kingdom
Références
Nat Methods. 2019 Dec;16(12):1297-1305
pubmed: 31740818
Genome Biol. 2014;15(11):532
pubmed: 25398248
Cell. 2020 May 14;181(4):914-921.e10
pubmed: 32330414
J Virol. 2009 Aug;83(15):7411-21
pubmed: 19439480
J Gen Virol. 2020 Jun 22;:
pubmed: 32568027
Nat Microbiol. 2020 Apr;5(4):562-569
pubmed: 32094589
Adv Virus Res. 2019;105:93-116
pubmed: 31522710
J Biol Chem. 2010 Jul 23;285(30):22758-63
pubmed: 20507992
Genome Res. 2019 Sep;29(9):1545-1554
pubmed: 31439691
Nature. 2020 Mar;579(7798):265-269
pubmed: 32015508
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
Science. 2020 Mar 13;367(6483):1260-1263
pubmed: 32075877
Nat Methods. 2018 Mar;15(3):201-206
pubmed: 29334379
J Biol Chem. 2009 Feb 20;284(8):5229-39
pubmed: 19106108
Euro Surveill. 2020 Jan;25(3):
pubmed: 31992387
J Mol Biol. 2003 Aug 29;331(5):991-1004
pubmed: 12927536
Viruses. 2014 Aug 07;6(8):2991-3018
pubmed: 25105276
Nat Med. 2020 Apr;26(4):450-452
pubmed: 32284615
Acta Pharm Sin B. 2020 Apr 20;:
pubmed: 32363136
Nat Methods. 2012 Dec;9(12):1207-11
pubmed: 23142869
Cell. 2020 Apr 16;181(2):281-292.e6
pubmed: 32155444
Annu Rev Virol. 2016 Sep 29;3(1):237-261
pubmed: 27578435
Cell Host Microbe. 2014 Oct 8;16(4):462-72
pubmed: 25299332
BMC Genomics. 2017 Jan 19;18(1):101
pubmed: 28103802
J Infect Dis. 2018 May 5;217(11):1728-1739
pubmed: 29741740
Nat Commun. 2019 Feb 14;10(1):754
pubmed: 30765700
Virus Res. 2015 Apr 16;202:120-34
pubmed: 25445340
J Virol. 2005 Jan;79(2):1164-79
pubmed: 15613344
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5871-6
pubmed: 19321428
Nature. 2016 Mar 3;531(7592):118-21
pubmed: 26935699
Virology. 2008 Jan 20;370(2):373-81
pubmed: 17931676
Virology. 1995 Nov 10;213(2):569-80
pubmed: 7491781
PLoS One. 2013 Jul 29;8(7):e70548
pubmed: 23923003
Emerg Microbes Infect. 2020 Dec;9(1):837-842
pubmed: 32301390
PLoS Pathog. 2016 Feb 26;12(2):e1005473
pubmed: 26919232
Lancet Infect Dis. 2020 May;20(5):533-534
pubmed: 32087114
Nat Rev Microbiol. 2009 Jun;7(6):439-50
pubmed: 19430490
Antiviral Res. 2020 Apr;176:104742
pubmed: 32057769
J Virol. 2007 Jan;81(1):20-9
pubmed: 16928755
FEBS J. 2008 Aug;275(16):4152-63
pubmed: 18631359
Viruses. 2019 Oct 10;11(10):
pubmed: 31658630
J Virol. 1995 Oct;69(10):6219-27
pubmed: 7666523
Cell. 2020 Apr 16;181(2):271-280.e8
pubmed: 32142651
Methods Mol Biol. 2015;1282:1-23
pubmed: 25720466
J Virol. 2011 Dec;85(24):13363-72
pubmed: 21994442
J Virol. 2006 Jul;80(14):6794-800
pubmed: 16809285
J Virol. 2003 Aug;77(16):8801-11
pubmed: 12885899
J Virol. 2008 Sep;82(17):8887-90
pubmed: 18562523
Commun Biol. 2020 Mar 13;3(1):124
pubmed: 32170151