Evidence map›Paper›PMID 36042219›Full record

ArticleNature communications2022

Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.

Victoria N Parikh, Alexander G Ioannidis, David Jimenez-Morales, John E Gorzynski, Hannah N De Jong, Xiran Liu, Jonasel Roque, Victoria P Cepeda-Espinoza, Kazutoyo Osoegawa, Chris Hughes and 60 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
1.1field-weighted citation impact, top 23% 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, 7 citations in OpenAlex.

  1. The Landscape of Genomic and Socioeconomic Variables in Patients with Colorectal Cancer Based on Genetic Ancestry.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2026
    Article
  2. Biographical Feature: Benjamin A. Pinsky, MD, PhD.Journal of clinical microbiology · 2026
    Article
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

70 authors at 11 institutions in 2 countries.

Victoria N Parikh *Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-5138-5559
Alexander G Ioannidis *Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID 0000-0002-4735-7803
David Jimenez-MoralesDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-4356-6461
John E GorzynskiDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Hannah N De JongDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-8699-9702
Xiran LiuInstitute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.ORCID 0000-0002-3955-9026
Jonasel RoqueDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-7818-6958
Victoria P Cepeda-EspinozaDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Kazutoyo OsoegawaHistocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA.
Chris HughesDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-7881-1036
Shirley C SuttonDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-9044-3224
Nathan YoultonDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Ruchi JoshiDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
David AmarDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-9719-0837
Yosuke TanigawaDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID 0000-0001-9759-157X
Douglas RussoDepartment of Statistics, Stanford University, Stanford, CA, USA.
Justin WongDepartment of Statistics, Stanford University, Stanford, CA, USA.
Jessie T LauzonDepartment of Aeronautics and Astronautics, Stanford University, Stanford, CA, USA.ORCID 0000-0003-3925-780X
Jacob EdelsonDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Daniel Mas MontserratDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Yongchan KwonDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Simone RubinacciDepartment of Computational Biology and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.ORCID 0000-0002-7725-4813
Olivier DelaneauDepartment of Computational Biology and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.ORCID 0000-0002-3906-8446
Lorenzo CappelloDepartment of Statistics, Stanford University, Stanford, CA, USA.
Jaehee KimDepartment of Computational Biology, Cornell University, Ithaca, NY, USA.ORCID 0000-0002-5210-2004
Massa J ShouraDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Archana N RajaDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Nathaniel WatsonDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-4547-3285
Nathan HammondDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-9635-2294
Elizabeth SpiteriDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Kalyan C MallempatiHistocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA.
Gonzalo Montero-MartínHistocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA.ORCID 0000-0002-4523-1027
Jeffrey ChristleDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Jennifer KimDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Anna KirillovaMedical Scientist Training Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA, USA.
Kinya SeoDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Yong HuangDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Chunli ZhaoDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Sonia Moreno-GrauDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Steven G HershmanDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Karen P DaltonDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-2834-8001
Jimmy ZhenDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Jack KammChan Zuckerburg Biohub, San Francisco, CA, USA.ORCID 0000-0003-2412-756X
Karan D BhattChan Zuckerburg Biohub, San Francisco, CA, USA.
Alina IsakovaDepartment of Bioengineering, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1113-6889
Maurizio MorriChan Zuckerburg Biohub, San Francisco, CA, USA.
Thanmayi RanganathDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-9865-2119
Catherine A BlishDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-6946-7627
Angela J RogersDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-6969-6200
Kari NadeauDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Samuel YangDepartment of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-1123-9036
Andra BlomkalnsDepartment of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Ruth O'HaraDepartment of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA.
Norma F NeffChan Zuckerburg Biohub, San Francisco, CA, USA.ORCID 0000-0001-7141-5420
Christopher DeBoeverTakeda Development Center, Americas, Inc, San Diego, CA, USA.
Sándor SzalmaTakeda Development Center, Americas, Inc, San Diego, CA, USA.ORCID 0000-0001-7591-3902
Matthew T WheelerDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-8721-3022
Christian M GatesIllumina, Inc, San Diego, CA, USA.
Kyle FarhIllumina, Inc, San Diego, CA, USA.ORCID 0000-0001-6947-8537
Gary P SchrothIllumina, Inc, San Diego, CA, USA.ORCID 0000-0002-3055-056X
Phil FebboIllumina, Inc, San Diego, CA, USA.ORCID 0000-0002-6496-4664
Francis deSouzaIllumina, Inc, San Diego, CA, USA.
Omar E CornejoSchool of Biological Sciences, Washington State University, Pullman, WA, USA.ORCID 0000-0003-4076-4227
Marcelo Fernandez-VinaHistocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA.
Amy KistlerChan Zuckerburg Biohub, San Francisco, CA, USA.
Julia A PalaciosDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID 0000-0003-4501-7378
Benjamin A PinskyDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-8751-4810
Carlos D Bustamante *Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Manuel A Rivas *Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1457-9925
Euan A Ashley *Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. euan@stanford.edu.ORCID 0000-0001-9418-9577
Stanford University · USChan Zuckerberg Initiative (United States) · USIllumina (United States) · USStanford Health Care · USCornell University · USSIB Swiss Institute of Bioinformatics · CHTakeda (United States) · USStanford Medicine · USUniversity of Pittsburgh · USVaughn College of Aeronautics and Technology · USWashington State University · US

Funding

Stanford MoTrPAC Bioinformatics CenterU24OD026629 · OD · STANFORD UNIVERSITY · PI ASHLEY, EUAN A, WHEELER, MATTHEW THOMAS · 2018 to 2023
$13.9M
Optimizing imputation for diverse populations in a distributed frameworkU01HG009080 · NHGRI · STANFORD UNIVERSITY · PI KENNY, EIMEAR ELIZABETH · 2016 to 2020
$5.2M
Structure function relationships from deep mutational scanning in human cardiomyopathyR01HL144843 · NHLBI · STANFORD UNIVERSITY · PI ASHLEY, EUAN A · 2020 to 2023
$2.8M
Mechanistic analyses of a novel RNA polymerase I transcription checkpointR01GM121404 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI LAIHO, MARIKKI, SCHNEIDER, DAVID ALAN · 2017 to 2020
$2.0M
The Role of RBM20 Sequence and Expression in Dilated CardiomyopathiesK08HL143185 · NHLBI · STANFORD UNIVERSITY · PI PARIKH, VICTORIA · 2019 to 2023
$725k
NHGRI NIH HHS U01 HG009080NHLBI NIH HHS K08 HL143185NHLBI NIH HHS R01 HL144843NIGMS NIH HHS R01 GM121404NIH HHS U24 OD026629
6 · The paper itself

Abstract

The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.

Indexed as

COVID-19PandemicsGenome, ViralGenome-Wide Association StudyHumansSARS-CoV-2

Identifiers

PMID36042219
PMCPMC9426371
OpenAlexW4293582077

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.