SARS-CoV-2-Queries

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The Human

Interacting genes and proteins

Understanding the biological processes by which the CoV virion works, requires knowing which human genes and proteins are involved. This is towards the next section of course, but we may first want to know what literature has to say here (annotation is still limited):

SPARQL sparql/humanInteractionCounts.rq (run, edit)

SELECT ?virus ?virusLabel ?gene ?geneLabel ?count WITH {
  SELECT ?virus ?gene (COUNT(DISTINCT ?work) AS ?count) WHERE {
    ?virus wdt:P171+ wd:Q57751738 .
    ?work wdt:P921 ?virus, ?gene .
    ?gene wdt:P703 wd:Q15978631 .
    { ?gene wdt:P31 wd:Q7187 } UNION { ?gene wdt:P31 wd:Q8054 }
  } GROUP BY ?virus ?gene
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}
ORDER BY DESC(?count) ?virus ?gene

This gives us these numbers of papers:

virus gene count
SARS-CoV-2 (edit) Angiotensin I converting enzyme 2 (edit) 19
SARS-CoV-2 (edit) Transmembrane serine protease 2 (edit) 7
SARS-CoV-1 (edit) Angiotensin I converting enzyme 2 (edit) 5
SARS-CoV-1 (edit) Transmembrane serine protease 2 (edit) 3
Betacoronavirus (edit) Angiotensin I converting enzyme 2 (edit) 2
SARSr-CoV (edit) Angiotensin I converting enzyme 2 (edit) 2
Middle East respiratory syndrome coronavirus (edit) Dipeptidyl peptidase 4 (edit) 2
SARS-CoV-2 (edit) ACE2 (edit) 2
SARS-CoV-2 (edit) TMPRSS2 (edit) 2
SARS-CoV-2 (edit) Furin, paired basic amino acid cleaving enzyme (edit) 2
Human coronavirus 229E (edit) TMPRSS2 (edit) 1
Human coronavirus 229E (edit) Transmembrane serine protease 2 (edit) 1
Human coronavirus 229E (edit) Peptidylprolyl isomerase A (edit) 1
Human coronavirus 229E (edit) Alanyl aminopeptidase, membrane (edit) 1
Human coronavirus 229E (edit) Angiotensin I converting enzyme 2 (edit) 1
SARSr-CoV (edit) MASP2 (edit) 1
SARSr-CoV (edit) TNF (edit) 1
SARSr-CoV (edit) Interferon induced transmembrane protein 3 (edit) 1
SARSr-CoV (edit) Interferon induced transmembrane protein 2 (edit) 1
SARSr-CoV (edit) Interferon induced transmembrane protein 1 (edit) 1
Middle East respiratory syndrome coronavirus (edit) Transmembrane serine protease 2 (edit) 1
SARS-CoV-2 (edit) IL6 (edit) 1
SARS-CoV-2 (edit) FURIN (edit) 1
SARS-CoV-2 (edit) MX1 (edit) 1
SARS-CoV-2 (edit) PIKFYVE (edit) 1
SARS-CoV-2 (edit) Transmembrane serine protease 4 (edit) 1
SARS-CoV-2 (edit) Translocase of outer mitochondrial membrane 70 (edit) 1
SARS-CoV-2 (edit) Von Willebrand factor (edit) 1
SARS-CoV-2 (edit) ADAM metallopeptidase with thrombospondin type 1 motif 13 (edit) 1
SARS-CoV-2 (edit) Heme oxygenase 1 (edit) 1
Human Coronavirus NL63 (edit) Angiotensin I converting enzyme 2 (edit) 1
SARS-CoV-1 (edit) MASP2 (edit) 1
SARS-CoV-1 (edit) TNF (edit) 1
SARS-CoV-1 (edit) C-type lectin domain family 4 member G (edit) 1
SARS-CoV-1 (edit) C-type lectin domain family 4 member M (edit) 1
SARS-CoV-1 (edit) Interferon induced transmembrane protein 3 (edit) 1
SARS-CoV-1 (edit) Interferon induced transmembrane protein 2 (edit) 1
SARS-CoV-1 (edit) Interferon induced transmembrane protein 1 (edit) 1
SARS-CoV-1 (edit) BCL2 like 1 (edit) 1
SARS-CoV-1 (edit) BCL2 associated X, apoptosis regulator (edit) 1

If you want to see the specific papers (a growing list), use this query:

SPARQL sparql/humanInteractions.rq (run, edit)

SELECT ?date ?virus ?virusLabel ?gene ?geneLabel ?work ?workLabel ?doi WITH {
  SELECT (MAX(?dates) as ?date) ?virus ?gene ?work WHERE {
    ?virus wdt:P171+ wd:Q57751738 .
    ?work wdt:P921 ?virus, ?gene .  
    OPTIONAL { ?work wdt:P577 ?dates . }
    ?gene wdt:P703 wd:Q15978631 .   
    { ?gene wdt:P31 wd:Q7187 } UNION { ?gene wdt:P31 wd:Q8054 }
  } GROUP BY ?virus ?gene ?work
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  OPTIONAL { ?work wdt:P356 ?doi . }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}
ORDER BY DESC(?date) ?doi ?virus ?gene

Biological processes

WikiPathways [1] is one of the projects involved in the international #covidpathways COVID-19 curation effort and the WikiPathways contributions can be found on this portal.

Reactome [2] and WikiPathways pathways are indexed in Wikidata, and we can query for pathways that have HCoV genes and proteins in their pathways:

SPARQL sparql/pathways.rq (run, edit)

SELECT ?virus ?virusLabel ?thing ?thingLabel ?pathway ?pathwayLabel WHERE {
  VALUES ?virus {
    wd:Q82069695 # SARS-CoV-2
    wd:Q16983360 # HKU1
    wd:Q16991954 # OC43
    wd:Q8351095  # NL63 
    wd:Q16983356 # 229E
    wd:Q4902157  # MERS-CoV
    wd:Q278567   # SARS-CoV
  }
  ?thing wdt:P703 ?virus .
  ?pathway wdt:P31 wd:Q4915012 ; wdt:P527 ?thing .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} ORDER BY ASC(?virus) ASC(?thing) ASC(?pathway)

This currently lists the following pathways, but with the active curation, it is expected to grow quickly too:

virus thing pathway
SARSr-CoV (edit) Protein 3a [SARS-Cov] (edit) Host-pathogen interaction of human corona viruses - apoptosis (edit)
SARSr-CoV (edit) Protein 3a [SARS-Cov] (edit) Host-pathogen interaction of human corona viruses - MAPK signaling (edit)
SARSr-CoV (edit) Protein 3a [SARS-Cov] (edit) Host-pathogen interaction of human corona viruses - Interferon induction (edit)
SARS-CoV-2 (edit) ORF9c protein [SARS CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) S1 Subunit of Spike Protein (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) S1 Subunit of Spike Protein (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) S1 Subunit of Spike Protein (edit) SARS-CoV-2 altering angiogenesis via NRP1 (edit)
SARS-CoV-2 (edit) S2 Subunit of Spike Protein (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) S2 Subunit of Spike Protein (edit) SARS-CoV-2 altering angiogenesis via NRP1 (edit)
SARS-CoV-2 (edit) S2 Subunit of Spike Protein (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 10 [SARS CoV-2] (edit) A draft map of SARS-COV-2 signaling pathway map (edit)
SARS-CoV-2 (edit) Non-structural protein 10 [SARS CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 10 [SARS CoV-2] (edit) Pathogenesis of SARS-CoV-2 Mediated by nsp9-nsp10 Complex (edit)
SARS-CoV-2 (edit) non-structural protein 15 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) non-structural protein 15 [SARS-CoV-2] (edit) Endoplasmic reticulum stress response in Coronavirus infection (edit)
SARS-CoV-2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) Type I Interferon Induction and Signaling During SARS-CoV-2 Infection (edit)
SARS-CoV-2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) Host-pathogen interaction of human corona viruses - Interferon induction (edit)
SARS-CoV-2 (edit) non-structural protein 5 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) SARS-CoV-2 altering angiogenesis via NRP1 (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) Downregulation of ACE2 expression by SARS-CoV infection and SARS-CoV Spike protein (edit)
SARS-CoV-2 (edit) orf1ab polyprotein [SARS-Cov 2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) orf1ab polyprotein [SARS-Cov 2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Viroporin 3a [SARS-CoV-2] (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) Viroporin 3a [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) envelope protein [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) envelope protein [SARS-CoV-2] (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) envelope protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) non-structural protein 6 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF1a polyprotein (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Protein 7a [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF8 protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 2 [SARS CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF6 protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF10 protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF10 protein [SARS-CoV-2] (edit) Hijack of Ubiquitination by SARS-CoV-2 (edit)
SARS-CoV-2 (edit) Protein ORF9b [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) Protein ORF9b [SARS-CoV-2] (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) Pathogenesis of SARS-CoV-2 Mediated by nsp9-nsp10 Complex (edit)
SARS-CoV-2 (edit) SARS-CoV-2 NSP9 complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 Spike - human ACE2 receptor complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 Spike - human ACE2-SLC6A19 complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 Spike protein complex (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) SARS-CoV-2 Spike protein complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 main protease complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 NSP10-NSP16 2'-O-methyltransferase complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 NSP3-NSP4-NSP6 complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) nsp1 from SARS-CoV-2 inhibits translation initiation in the host cell (edit)
SARS-CoV-2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 4 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 7 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Uncharacterized protein 14 (edit) SARS-CoV-2 and COVID-19 Pathway (edit)

References

  1. Slenter DN, Kutmon M, Hanspers K, Hanspers K, Riutta A, Windsor J, et al. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. NAR. 2018 Jan 4;46(D1):D661–7. doi:10.1093/NAR/GKX1064 (Scholia)
  2. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, et al. The Reactome pathway knowledgebase. NAR. 2014 Jan;42(Database issue):D472-7. doi:10.1093/NAR/GKT1102 (Scholia)