SARS-CoV-2-Queries

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Viruses

Coronaviruses are not new and some of them are pretty harmless. For example, the human coronaviruses HCoV-229E and HCoV-OC43 normally result in a common cold [1]. However, for the severe acute respiratory syndrome-related coronaviruses (SARSr viruses) this is different. SARS-CoV-2, of course, is the main topic of this book [2].

All SARSr viruses

The SARS-CoV-2 virus is not the first coronavirus (CoV). In fact, quite a few SARS-related CoVs are known, as clear from this NCBI Taxonomy list [3,4].

We first list all the SARSr-CoV viruses in Wikidata:

SPARQL sparql/allSARSCoVViruses.rq (run, edit)

SELECT ?virus ?virusLabel ?ncbi WHERE {
  ?virus wdt:P171+ wd:Q278567 .
  OPTIONAL { ?virus wdt:P685 ?ncbi }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}

This gives us:

virus ncbi
Bat SARS-like coronavirus WIV1 (edit) 1415852
SARS-CoV-2 (edit) 2697049
SARS-CoV-1 (edit)
SHC014-CoV (edit) 1415851
Bat SARS coronavirus Rp1 (edit) 349342
SARS coronavirus B024 (edit) 305407
RaTG13 (edit) 2709072
Bat SARS CoV Rf1 (edit) 347537
Bat SARS CoV Rm1 (edit) 347536
Bat SARS CoV Rp3 (edit) 349344
501.V2 Variant (edit)
Civet SARS-CoV (edit)
RacCS203 (edit)
Rc-o319 (edit)
BtKY72/Rhinolophus sp./Kenya/2007 (edit)
BtCoV/BM48-31/Rhi bla/Bulgaria/2008 (edit)

If we compare this list with that in Section 2.2 we note that these two lists do not fully overlap.

The seven coronaviruses that infect human

However, for the current pandemic, the seven human corona viruses may be of particular interest [5]. We can use this query to just list these:

SPARQL sparql/humanCoronaviruses.rq (run, edit)

SELECT ?virus ?virusLabel ?ncbi 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
  }
  OPTIONAL { ?virus wdt:P685 ?ncbi }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}

This gives us a good starting point to study the virus in more detail:

virus ncbi
SARSr-CoV (edit) 694009
SARSr-CoV (edit) 227859
Middle East respiratory syndrome coronavirus (edit) 1335626
Human Coronavirus NL63 (edit) 277944
Human coronavirus 229E (edit) 11137
Human coronavirus HKU1 (edit) 290028
Human coronavirus OC43 (edit) 31631
SARS-CoV-2 (edit) 2697049

All betacoronaviruses

But the SARS-related coronavirusses is just a subgroup. Another subgroup of coronaviruses is that of the betacoronaviruses:

SPARQL sparql/allBetacoronaViruses.rq (run, edit)

SELECT ?virus ?virusLabel ?ncbi WHERE {
  ?virus wdt:P171+ wd:Q16532287 .
  OPTIONAL { ?virus wdt:P685 ?ncbi }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} ORDER BY ?virusLabel

Because there are quite a few of them in Wikidata, we rather make a graph dependency plot:

SPARQL sparql/allBetacoronaVirusesGraph.rq (run, edit)

#defaultView:Graph
SELECT ?parent ?parentLabel ?virus ?virusLabel ?ncbi WHERE {
  ?virus wdt:P171+ wd:Q16532287 .
  ?virus wdt:P171 ?parent .
  OPTIONAL { ?virus wdt:P685 ?ncbi }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}

This gives this output:

All coronaviruses

The full list of coronaviruses looks like this:

SPARQL sparql/allCoronaViruses.rq (run, edit)

SELECT ?virus ?virusLabel ?ncbi WHERE {
  ?virus wdt:P171+ wd:Q57751738 .
  OPTIONAL { ?virus wdt:P685 ?ncbi }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} ORDER BY ASC(?virus)

Again, we rather make a graph dependency plot:

SPARQL sparql/allCoronaVirusesGraph.rq (run, edit)

#defaultView:Graph
SELECT ?parent ?parentLabel ?virus ?virusLabel ?ncbi WHERE {
  ?virus wdt:P171+ wd:Q57751738 .
  ?virus wdt:P171 ?parent .
  OPTIONAL { ?virus wdt:P685 ?ncbi }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} ORDER BY ASC(?parent) ASC(?virus)

This gives this output:

Comparing viruses

We can also query for articles that compare a human coronavirus with another coronavirus:

SPARQL sparql/compareViruses.rq (run, edit)

SELECT DISTINCT ?virus ?virusLabel ?work ?workLabel WITH {
  SELECT DISTINCT ?virus ?virus2 ?work 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
    }
    ?virus2 wdt:P171+ wd:Q57751738 .
    ?work wdt:P921 ?virus, ?virus2 .
    FILTER ( ?virus != ?virus2 )
  }
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}
ORDER BY ?virusLabel ?virus ?workLabel ?work

NCBI Taxonomy IDs

For the coronaviruses we can list the NCBI Taxonomy [3,4] identifiers with:

SPARQL sparql/allSARSCoVVirusesTaxonomy.rq (run, edit)

SELECT ?virus ?virusLabel ?ncbi WHERE {
  ?virus wdt:P171+ wd:Q278567 .
  OPTIONAL { ?virus wdt:P685 ?ncbi }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}

This gives us:

virus ncbi
Bat SARS-like coronavirus WIV1 (edit) 1415852
SARS-CoV-2 (edit) 2697049
SARS-CoV-1 (edit)
SHC014-CoV (edit) 1415851
Bat SARS coronavirus Rp1 (edit) 349342
SARS coronavirus B024 (edit) 305407
RaTG13 (edit) 2709072
Bat SARS CoV Rf1 (edit) 347537
Bat SARS CoV Rm1 (edit) 347536
Bat SARS CoV Rp3 (edit) 349344
501.V2 Variant (edit)
Civet SARS-CoV (edit)
RacCS203 (edit)
Rc-o319 (edit)
BtKY72/Rhinolophus sp./Kenya/2007 (edit)
BtCoV/BM48-31/Rhi bla/Bulgaria/2008 (edit)

References

  1. Pyrc K, Berkhout B, van der Hoek L. The novel human coronaviruses NL63 and HKU1. J Virol. 2006 Nov 1;81(7):3051–7. doi:10.1128/JVI.01466-06 (Scholia)
  2. Gorbalenya AE, of the International Committee on Taxonomy of Viruses CSG, Baker SC, Drosten C, Haagmans BL, Neuman BW, et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology. 2020 Mar 2;5(4):536–44. doi:10.1038/S41564-020-0695-Z (Scholia)
  3. Federhen S. The NCBI Taxonomy database. NAR. 2012 Jan;40(Database issue):D136-43. doi:10.1093/NAR/GKR1178 (Scholia)
  4. Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database. 2020 Jul 13;2020. doi:10.1093/DATABASE/BAAA062 (Scholia)
  5. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. NEJM [Internet]. 2020 Feb 20;382(8):727–33. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092803/ doi:10.1056/NEJMOA2001017 (Scholia)