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

COVID-19 / epidemiology Genome, Viral Genome-Wide Association Study Humans Pandemics SARS-CoV-2 / genetics

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
30 08 2022
Historique:
received: 18 08 2021
accepted: 28 07 2022
entrez: 30 8 2022
pubmed: 31 8 2022
medline: 3 9 2022
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-022-32397-8 PMID: 36042219 PMC: PMC9426371
pubmed: 36042219
doi: 10.1038/s41467-022-32397-8
pii: 10.1038/s41467-022-32397-8
pmc: PMC9426371
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

5107

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM121404
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009080
Pays : United States
Organisme : NHLBI NIH HHS
ID : K08 HL143185
Pays : United States
Organisme : NIH HHS
ID : U24 OD026629
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL144843
Pays : United States

Informations de copyright

© 2022. The Author(s).

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Auteurs

Victoria N Parikh (VN)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0002-5138-5559

Alexander G Ioannidis (AG)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
ORCID: 0000-0002-4735-7803

David Jimenez-Morales (D)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0003-4356-6461

John E Gorzynski (JE)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

Hannah N De Jong (HN)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0002-8699-9702

Xiran Liu (X)

Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
ORCID: 0000-0002-3955-9026

Jonasel Roque (J)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-7818-6958

Victoria P Cepeda-Espinoza (VP)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

Kazutoyo Osoegawa (K)

Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA.

Chris Hughes (C)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0002-7881-1036

Shirley C Sutton (SC)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-9044-3224

Nathan Youlton (N)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

Ruchi Joshi (R)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

David Amar (D)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0002-9719-0837

Yosuke Tanigawa (Y)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
ORCID: 0000-0001-9759-157X

Douglas Russo (D)

Department of Statistics, Stanford University, Stanford, CA, USA.

Justin Wong (J)

Department of Statistics, Stanford University, Stanford, CA, USA.

Jessie T Lauzon (JT)

Department of Aeronautics and Astronautics, Stanford University, Stanford, CA, USA.
ORCID: 0000-0003-3925-780X

Jacob Edelson (J)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

Daniel Mas Montserrat (D)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

Yongchan Kwon (Y)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

Simone Rubinacci (S)

Department of Computational Biology and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
ORCID: 0000-0002-7725-4813

Olivier Delaneau (O)

Department of Computational Biology and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
ORCID: 0000-0002-3906-8446

Lorenzo Cappello (L)

Department of Statistics, Stanford University, Stanford, CA, USA.

Jaehee Kim (J)

Department of Computational Biology, Cornell University, Ithaca, NY, USA.
ORCID: 0000-0002-5210-2004

Massa J Shoura (MJ)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

Archana N Raja (AN)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Nathaniel Watson (N)

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0003-4547-3285

Nathan Hammond (N)

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-9635-2294

Elizabeth Spiteri (E)

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

Kalyan C Mallempati (KC)

Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA.

Gonzalo Montero-Martín (G)

Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA.
ORCID: 0000-0002-4523-1027

Jeffrey Christle (J)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Jennifer Kim (J)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Anna Kirillova (A)

Medical Scientist Training Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA, USA.

Kinya Seo (K)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Yong Huang (Y)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Chunli Zhao (C)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Sonia Moreno-Grau (S)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

Steven G Hershman (SG)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Karen P Dalton (KP)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0003-2834-8001

Jimmy Zhen (J)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Jack Kamm (J)

Chan Zuckerburg Biohub, San Francisco, CA, USA.
ORCID: 0000-0003-2412-756X

Karan D Bhatt (KD)

Chan Zuckerburg Biohub, San Francisco, CA, USA.

Alina Isakova (A)

Department of Bioengineering, Stanford University, Stanford, CA, USA.
ORCID: 0000-0003-1113-6889

Maurizio Morri (M)

Chan Zuckerburg Biohub, San Francisco, CA, USA.

Thanmayi Ranganath (T)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-9865-2119

Catherine A Blish (CA)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-6946-7627

Angela J Rogers (AJ)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-6969-6200

Kari Nadeau (K)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA.

Samuel Yang (S)

Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0003-1123-9036

Andra Blomkalns (A)

Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Ruth O'Hara (R)

Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA.

Norma F Neff (NF)

Chan Zuckerburg Biohub, San Francisco, CA, USA.
ORCID: 0000-0001-7141-5420

Christopher DeBoever (C)

Takeda Development Center, Americas, Inc, San Diego, CA, USA.

Sándor Szalma (S)

Takeda Development Center, Americas, Inc, San Diego, CA, USA.
ORCID: 0000-0001-7591-3902

Matthew T Wheeler (MT)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-8721-3022

Christian M Gates (CM)

Illumina, Inc, San Diego, CA, USA.

Kyle Farh (K)

Illumina, Inc, San Diego, CA, USA.
ORCID: 0000-0001-6947-8537

Gary P Schroth (GP)

Illumina, Inc, San Diego, CA, USA.
ORCID: 0000-0002-3055-056X

Phil Febbo (P)

Illumina, Inc, San Diego, CA, USA.
ORCID: 0000-0002-6496-4664

Francis deSouza (F)

Illumina, Inc, San Diego, CA, USA.

Omar E Cornejo (OE)

School of Biological Sciences, Washington State University, Pullman, WA, USA.
ORCID: 0000-0003-4076-4227

Marcelo Fernandez-Vina (M)

Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA.
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

Amy Kistler (A)

Chan Zuckerburg Biohub, San Francisco, CA, USA.

Julia A Palacios (JA)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Department of Statistics, Stanford University, Stanford, CA, USA.
ORCID: 0000-0003-4501-7378

Benjamin A Pinsky (BA)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-8751-4810

Carlos D Bustamante (CD)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

Manuel A Rivas (MA)

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
ORCID: 0000-0003-1457-9925

Euan A Ashley (EA)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. euan@stanford.edu.
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. euan@stanford.edu.
ORCID: 0000-0001-9418-9577

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Classifications MeSH

Recherchemedicale.com › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Deconvoluting complex correlates of COVID-19...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome viral › Deconvoluting complex correlates of COVID-19...
Recherchemedicale.com › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › Deconvoluting complex correlates of COVID-19...
Recherchemedicale.com › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Deconvoluting complex correlates of COVID-19...
Recherchemedicale.com › Environnement et santé publique › Santé publique › Épidémies de maladies › Épidémies › Pandémies › Deconvoluting complex correlates of COVID-19...
Recherchemedicale.com › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Deconvoluting complex correlates of COVID-19...