Evidence map›Paper›PMID 38517939›Full record

SynthesisPLoS genetics2024

Canadian COVID-19 host genetics cohort replicates known severity associations.

Elika Garg, Paola Arguello-Pascualli, Olga Vishnyakova, Anat R Halevy, Samantha Yoo, Jennifer D Brooks, Shelley B Bull, France Gagnon, Celia M T Greenwood, Rayjean J Hung and 12 more

Erratum issuedOpen access · goldAbstract readMeta-Analysis
PubMed Full text at PMC Publisher
In one paragraph

Synthesis in PLoS genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
1.9field-weighted citation impact, top 15% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 5 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors at 9 institutions in 1 country.

Elika GargDepartment of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada.ORCID https://orcid.org/0000-0002-3093-7940
Paola Arguello-PascualliBC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
Olga VishnyakovaDepartment of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada.
Anat R HalevyGenetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.ORCID https://orcid.org/0000-0001-7474-5783
Samantha YooGenetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.ORCID https://orcid.org/0009-0009-8943-3761
Jennifer D BrooksDalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.ORCID https://orcid.org/0000-0001-7574-4256
Shelley B BullDalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.ORCID https://orcid.org/0000-0002-3280-7154
France GagnonDalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.
Celia M T GreenwoodGerald Bronfman Department of Oncology, Department of Epidemiology, Biostatistics and Occupational Health, Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
Rayjean J HungDalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.ORCID https://orcid.org/0000-0002-4486-7496
Jerald F LawlessDepartment of Statistics and Actuarial Science, University of Waterloo, Waterloo, Ontario, Canada.ORCID https://orcid.org/0000-0002-3192-0470
Jordan Lerner-EllisLunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada.ORCID https://orcid.org/0000-0003-3685-5679
Jessica K DennisBC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.ORCID https://orcid.org/0000-0002-8507-9699
Rohan J S AbrahamCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
Jean-Michel GarantCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.ORCID https://orcid.org/0000-0002-0559-5598
Bhooma ThiruvahindrapuramGenetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
Steven J M JonesCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.ORCID https://orcid.org/0000-0003-3394-2208
CGEn HostSeq Initiative
Lisa J StrugGenetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
Andrew D PatersonGenetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
Lei SunDalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.
Lloyd T ElliottDepartment of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada.ORCID https://orcid.org/0000-0003-2187-7314
University of Toronto · CABC Cancer Agency · CASimon Fraser University · CAHospital for Sick Children · CAUniversity of British Columbia · CAJewish General Hospital · CAMount Sinai Hospital · CAUniversity of Ottawa · CAUniversity of Waterloo · CA

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The HostSeq initiative recruited 10,059 Canadians infected with SARS-CoV-2 between March 2020 and March 2023, obtained clinical information on their disease experience and whole genome sequenced (WGS) their DNA. We analyzed the WGS data for genetic contributors to severe COVID-19 (considering 3,499 hospitalized cases and 4,975 non-hospitalized after quality control). We investigated the evidence for replication of loci reported by the International Host Genetics Initiative (HGI); analyzed the X chromosome; conducted rare variant gene-based analysis and polygenic risk score testing. Population stratification was adjusted for using meta-analysis across ancestry groups. We replicated two loci identified by the HGI for COVID-19 severity: the LZTFL1/SLC6A20 locus on chromosome 3 and the FOXP4 locus on chromosome 6 (the latter with a variant significant at P < 5E-8). We found novel significant associations with MRAS and WDR89 in gene-based analyses, and constructed a polygenic risk score that explained 1.01% of the variance in severe COVID-19. This study provides independent evidence confirming the robustness of previously identified COVID-19 severity loci by the HGI and identifies novel genes for further investigation.

Indexed as

COVID-19North American PeopleCanadaForkhead Transcription FactorsGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMembrane Transport ProteinsPolymorphism, Single NucleotideSARS-CoV-2Forkhead Transcription FactorsFOXP4 protein, humanMembrane Transport ProteinsSLC6A20 protein, human

Identifiers

PMID38517939
PMCPMC10990181
OpenAlexW4393097360

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.