SARS-CoV-2 and COVID-19 pathway (Homo sapiens)

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1414surfaceglycoprotein S22116208, 31151121163229915323, 721168321816832151524264, 26, 30VirionProtein ExpressionHuman cellnsp140SpolymerasecomplexActivation of NLRP3InflammasomeHijack ofUbiquitinationheparan sulfatePathogenesistrimerType I InterferonInduction andSignalingHDLFURINTMPRSS4Integrative stressresponseCTSLSCARB1NSP3-NSP4-NSP6complexsphingosineTLR7viral RNA synthesisSLC6A19complex27241321S2 subunitSARS-CoV-2proteinsorf1a22TMPRSS226, 28orf1abACE2dimerORF3aORF6ORF7aORF8nucleocapsidprotein17membraneglycoprotein17envelopeprotein17surfaceglycoprotein10, 17SARS-CoV-2RNAorf1ORF3aORF6ORF7aORF8ORF10nucleocapsidphosphoproteinmembraneglycoproteinenvelopeproteinsurfaceglycoproteinsurfaceglycoprotein Ssurfaceglycoprotein S10, 17membraneglycoprotein M17orf1abnsp2PL2-PRO3CL-PRO25nsp4nsp7nsp8nsp923nsp10nsp1212, 19, 25nsp13ExoN19nsp15nsp16nsp6nsp5SARS-CoV-2RNAnucleocapsidprotein N17envelopeprotein E17ORF10nsp9nsp9orf1ORF7bORF7bnsp16nsp10surfaceglycoprotein Ssurfaceglycoprotein Ssurfaceglycoprotein SACE2recognition complexVirionPL2-PROnsp4nsp6ACE2VirionORF3ansp9nsp10nsp1-40Scomplexnsp1ORF141S2 subunitnsp8NRP1Endocytosis9Virionorf1nsp7nsp8nsp12orf1ab12, 19, 25orf1abcomplexType I InterferonInduction andSignaling5surfaceglycoprotein Ssurfaceglycoprotein Ssurfaceglycoprotein Srecognition complexACE2surfaceglycoprotein Ssurfaceglycoprotein Ssurfaceglycoprotein SVirionsurfaceglycoprotein Ssurfaceglycoprotein Ssurfaceglycoprotein SVirionHDLACE2Virionsurfaceglycoprotein Ssurfaceglycoprotein Ssurfaceglycoprotein Srecognition complexSCARB1HDL


Description

Collaborative project for curation biological processes involved in the COVID-19 disease after SARS-Cov-2 infection. It focuses on experimental evidence and plays with improved annotation of complexes and with the Evidence and Conclusion Ontology. The complexes link to EBI's Complex Portal, resulting from a collaboration with that database at the recent online ELIXIR biohackathon.

Editing this pathway is (at this moment) coordinated via the wikipathways.slack.com #sarscov2 channel. Additionally, please feel free to add suggestions to the discussion page (see the tab at the top of this page).

The large viral Spike protein (S or surface glycoprotein) forms trimers. It interacts with the host's ACE2 receptor to establish binding (Hoffmann et al 2020). There are suggestions for more than one cell entry mechanism, with the evidence for ACE2/TMPRSS2 entry being most clear now. Lack of expression of TMPRSS2 may explain age differences in COVID19 severity. In this mechanism, to enter the virus needs to be primed by the host protease TMPRSS2 that splits the Spike protein into 2 peptides S1 and S2. S1 contains the ACE2 receptor binding site, S2 binds to the host cell membrane which leads to membrane fusion, the start of the uptake process. The ACE2 receptor interaction was also suggested as the start of specific lung-damaging effects.

Other human genes that may be involved in alternative cell uptake mechanisms include CTSL and SLC6A19.

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Bibliography

View all...
  1. ''From SARS and MERS CoVs to SARS-CoV-2: moving toward more biased codon usage in viral structural and non-structural genes.''; J Med Virol, 2020 PubMed Europe PMC Scholia
  2. ''A potential role for integrins in host cell entry by SARS-CoV-2.''; Antiviral Res, 2020 PubMed Europe PMC Scholia
  3. ''Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system''; https://doi.org/10.1101/2020.06.07.137802, 2020
  4. ''Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-membrane vesicles.''; mBio, 2013 PubMed Europe PMC Scholia
  5. ''Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?''; Elife, 2020 PubMed Europe PMC Scholia
  6. ''Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites.''; Antiviral Res, 2020 PubMed Europe PMC Scholia
  7. ''The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2.''; J Virol, 2020 PubMed Europe PMC Scholia
  8. ''Simultaneous Treatment of COVID-19 With Serine Protease Inhibitor Camostat and/or Cathepsin L Inhibitor?''; J Clin Med Res, 2020 PubMed Europe PMC Scholia
  9. ''Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2.''; Science, 2020 PubMed Europe PMC Scholia
  10. ''Sphingosine prevents binding of SARS-CoV-2 spike to its cellular receptor ACE2.''; J Biol Chem, 2020 PubMed Europe PMC Scholia
  11. ''Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load.''; PeerJ, 2020 PubMed Europe PMC Scholia
  12. ''Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9.''; iScience, 2020 PubMed Europe PMC Scholia
  13. ''HDL-scavenger receptor B type 1 facilitates SARS-CoV-2 entry.''; Nat Metab, 2020 PubMed Europe PMC Scholia
  14. ''The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine.''; bioRxiv, 2020 PubMed Europe PMC Scholia
  15. ''Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species.''; Infect Genet Evol, 2020 PubMed Europe PMC Scholia
  16. ''Identification of novel mutations in themethyltransferase complex (Nsp10-Nsp16) of SARS-CoV-2.''; Biochem Biophys Rep, 2020 PubMed Europe PMC Scholia
  17. ''Characterization of heparin and severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) spike glycoprotein binding interactions.''; Antiviral Res, 2020 PubMed Europe PMC Scholia
  18. ''Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target.''; Intensive Care Med, 2020 PubMed Europe PMC Scholia
  19. ''Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity.''; Science, 2020 PubMed Europe PMC Scholia
  20. ''Presence of Genetic Variants Among Young Men With Severe COVID-19.''; JAMA, 2020 PubMed Europe PMC Scholia
  21. ''TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes.''; Sci Immunol, 2020 PubMed Europe PMC Scholia
  22. ''Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant.''; J Transl Med, 2020 PubMed Europe PMC Scholia
  23. ''Cell entry mechanisms of SARS-CoV-2.''; Proc Natl Acad Sci U S A, 2020 PubMed Europe PMC Scholia
  24. ''SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2.''; Cell, 2020 PubMed Europe PMC Scholia
  25. ''Structure of replicating SARS-CoV-2 polymerase.''; Nature, 2020 PubMed Europe PMC Scholia
  26. ''''; https://www.youtube.com/watch?v=e2Qi-hAXdJo,
  27. ''Presence of Genetic Variants Among Young Men With Severe COVID-19.''; JAMA, 2020 PubMed Europe PMC Scholia
  28. ''Cholesterol 25-Hydroxylase inhibits SARS-CoV-2 and other coronaviruses by depleting membrane cholesterol.''; EMBO J, 2020 PubMed Europe PMC Scholia
  29. ''Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.''; Science, 2020 PubMed Europe PMC Scholia
  30. ''Preprint: TMPRSS2 and furin are both essential for proteolytic activation and spread of SARS-1 CoV-2 in human airway epithelial cells and provide promising drug targets''; 10.1101/2020.04.15.042085v1, 2020
  31. ''The crystal structure of Nsp9 replicase protein of COVID-19''; https://www.ebi.ac.uk/pdbe/entry/pdb/6w4b, 2020
  32. ''Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.''; Cell, 2020 PubMed Europe PMC Scholia
  33. ''SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.''; Cell, 2020 PubMed Europe PMC Scholia
  34. ''Chemistry and Biology of SARS-CoV-2.''; Chem, 2020 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
124663view13:52, 18 November 2022NhungPupdate viral proteins shapes, colors and labels
124656view13:28, 18 November 2022Mkutmonupdate virus protein style
124588view05:55, 13 November 2022EgonwAdded missing datasources
124587view05:54, 13 November 2022EgonwAdded missing identifiers
122702view14:57, 3 May 2022NhungPImprove layout
122701view14:54, 3 May 2022NhungPIncrease font and adjust layout to improve readability
120585view19:04, 17 December 2021EweitzFix case
120249view15:50, 20 November 2021EgonwAdded a missing identifier
118977view06:25, 6 June 2021EgonwTyped an interaction
118845view09:23, 2 June 2021EweitzOntology Term : 'COVID-19' added !
118844view09:23, 2 June 2021EweitzOntology Term : 'DOID:2945' removed !
118843view09:22, 2 June 2021EweitzModified title
115843view15:10, 18 March 2021Fehrhartadded S2 identifiers
115453view20:45, 19 February 2021EgonwFixed some references
115447view11:56, 19 February 2021EgonwAnnotated a number of interactions has translocations
115428view09:49, 19 February 2021EgonwAdded more references on interactions
115282view16:49, 9 February 2021FehrhartAdded peer reviewed paper to preprint version of reference
114429view19:16, 10 January 2021EgonwCholesterol depletion results in inhibition of membrane fusion.
114428view18:14, 10 January 2021EgonwAdded an alternative uptake mechanism.
114246view13:22, 29 December 2020EgonwTwo more articles
114234view06:23, 28 December 2020EgonwAdded a reported role of nsp14
113854view20:14, 1 December 2020EgonwAdded a role suggested for sphingosine.
113819view10:11, 28 November 2020EgonwAdded citation for nsp9 crystal structure and added heparan sulfate binding
113702view08:59, 17 November 2020Fehrhartsmall graphical updates
111980view19:27, 13 September 2020EgonwMore literature references linked to interactions.
111364view05:28, 3 August 2020EgonwConverted two interacting Label's to DataNode's.
111358view11:24, 2 August 2020EgonwAnother preprint is published now.
111357view11:18, 2 August 2020EgonwReplaced a DOI by the PubMed ID.
111348view04:56, 30 July 2020EgonwCompleted the TLR7 route, now with PubMed ID.
111317view09:38, 28 July 2020EgonwAdded new recent insight
111242view09:19, 27 July 2020EgonwAdded another reference.
111228view16:08, 26 July 2020EgonwRemoved another bit of info backed by the removed preprint.
111227view16:02, 26 July 2020EgonwRemoved a preprint marked for image duplication: https://pubpeer.com/publications/E7FD45D01851101DF958911F6F0F45
111226view15:59, 26 July 2020EgonwAdded another complex, and a nice YouTube video.
110895view09:40, 18 June 2020EgonwAdded another article about the role of FURIN
110894view06:59, 18 June 2020EgonwRestructured the map.
110893view06:49, 18 June 2020EgonwAdded NRP1
110890view20:54, 17 June 2020EgonwAdded the polymerase cmoplex.
110889view20:06, 17 June 2020EgonwA bit more literature
110886view17:44, 17 June 2020EgonwAdded another reference
110832view13:05, 11 June 2020Egonw
110811view22:26, 9 June 2020Mkutmonfix unconnected line
110668view18:35, 27 May 2020EgonwMade a few pathway nodes have a shape
110650view05:27, 25 May 2020EgonwAdded the missing protein identifier
110619view16:04, 21 May 2020EgonwOkay, it's getting complex :/
110618view15:42, 21 May 2020EgonwAdded two more recent papers (HT Chem2W)
110617view15:05, 21 May 2020EgonwAdded a new protein reported by UniProt.
110616view10:32, 21 May 2020EgonwAdded the Wikidata identifier for nsp1
110615view10:13, 21 May 2020EgonwLinked the preprint also to the inhibition interaction.
110614view10:12, 21 May 2020EgonwAdded the ECO code

External references

DataNodes

View all...
NameTypeDatabase referenceComment
3CL-PROProteinQ87917582 (Wikidata)
40SComplexCPX-5223 (Complex Portal)
ACE2ProteinQ9BYF1 (Uniprot-TrEMBL)
Activation of

NLRP3

Inflammasome		PathwayWP4876 (WikiPathways)
CTSLProteinP07711 (Uniprot-TrEMBL)
EndocytosisPathway
ExoNProteinQ94648393 (Wikidata) nsp14
FURINProteinP09958 (Uniprot-TrEMBL)
HDLMetaboliteCHEBI:39025 (ChEBI)
Hijack of UbiquitinationPathwayWP4860 (WikiPathways)
Integrative stress responsePathwayWP4861 (WikiPathways)
NRP1ProteinO14786 (Uniprot-TrEMBL)
NSP3-NSP4-NSP6 complexComplexCPX-5691 (Complex Portal)
ORF10GeneProduct43740576 (Entrez Gene)
ORF10ProteinQ89227548 (Wikidata)
ORF14ProteinP0DTD3 (Uniprot-TrEMBL)
ORF3aGeneProduct43740569 (Entrez Gene)
ORF3aProteinP0DTC3 (Uniprot-TrEMBL)
ORF6GeneProduct43740572 (Entrez Gene)
ORF6ProteinQ89226299 (Wikidata)
ORF7aGeneProduct43740573 (Entrez Gene)
ORF7aProteinQ88658500 (Wikidata)
ORF7bGeneProduct43740574 (Entrez Gene)
ORF7bProteinQ88089438 (Wikidata)
ORF8GeneProduct43740577 (Entrez Gene)
ORF8ProteinQ89225654 (Wikidata)
PL2-PROProteinQ87917581 (Wikidata) nsp3
PathogenesisPathwayWP4884 (WikiPathways)
Protein ExpressionPathway
S2 subunitProtein
SARS-CoV-2 RNARnaQ82069695 (Wikidata)
SARS-CoV-2 proteinsProteinQ82069695 (Wikidata)
SCARB1GeneProductENSG00000073060 (Ensembl)
SLC6A19GeneProductENSG00000174358 (Ensembl)
TLR7ProteinQ9NYK1 (Uniprot-TrEMBL)
TMPRSS2ProteinO15393 (Uniprot-TrEMBL)
TMPRSS4ProteinQ9NRS4 (Uniprot-TrEMBL)
Type I Interferon

Induction and

Signaling		PathwayWP4868 (WikiPathways)
complexComplexCPX-5685 (Complex Portal)
complexComplexCPX-5688 (Complex Portal)
dimerComplexCPX-5687 (Complex Portal)
envelope protein EProteinP0DTC4 (Uniprot-TrEMBL)
envelope proteinGeneProduct43740570 (Entrez Gene)
envelope proteinProteinP0DTC4 (Uniprot-TrEMBL)
heparan sulfateMetaboliteCHEBI:28815 (ChEBI)
membrane glycoprotein MProteinP0DTC5 (Uniprot-TrEMBL)
membrane glycoproteinGeneProduct43740571 (Entrez Gene)
membrane glycoproteinProteinP0DTC5 (Uniprot-TrEMBL)
nsp1-40S

complex

Complex
nsp10ProteinQ87917572 (Wikidata) nsp10
nsp12ProteinQ94647436 (Wikidata) RdRp
nsp13ProteinQ94648377 (Wikidata) Helicase
nsp15ProteinQ87917579 (Wikidata) NendoU
nsp16ProteinQ87917579 (Wikidata) 2'-O-methyltransferase
nsp1ProteinQ90038952 (Wikidata) Host translation inhibitor nsp1
nsp2ProteinQ89006922 (Wikidata)
nsp4ProteinQ90038956 (Wikidata)
nsp5ProteinQ87917582 (Wikidata)
nsp6ProteinQ88656943 (Wikidata)
nsp7ProteinQ90038963 (Wikidata)
nsp8ProteinQ88659350 (Wikidata)
nsp9ProteinQ89686805 (Wikidata)
nucleocapsid phosphoproteinGeneProduct43740575 (Entrez Gene)
nucleocapsid protein NProteinP0DTC9 (Uniprot-TrEMBL)
nucleocapsid proteinProteinP0DTC9 (Uniprot-TrEMBL)
orf1GeneProduct43740578 (Entrez Gene)
orf1aProteinP0DTC1 (Uniprot-TrEMBL)
orf1abProteinP0DTD1 (Uniprot-TrEMBL)
polymerase complexComplexCPX-5742 (Complex Portal)
recognition complexComplexCPX-5683 (Complex Portal)
recognition complexComplexCPX-5684 (Complex Portal)
sphingosineMetaboliteCHEBI:16393 (ChEBI)
surface glycoprotein SProteinP0DTC2 (Uniprot-TrEMBL)
surface glycoproteinGeneProduct43740568 (Entrez Gene)
surface glycoproteinProteinP0DTC2 (Uniprot-TrEMBL)
trimerComplexCPX-5682 (Complex Portal)
viral RNA synthesisPathway

Annotated Interactions

No annotated interactions

Retrieved from "https://classic.wikipathways.org/index.php/Pathway:WP4846"
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