IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-32397-8.html
   My bibliography  Save this article

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

Author

Listed:
  • Victoria N. Parikh

    (Stanford University School of Medicine)

  • Alexander G. Ioannidis

    (Stanford University
    Stanford University)

  • David Jimenez-Morales

    (Stanford University School of Medicine)

  • John E. Gorzynski

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Hannah N. Jong

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Xiran Liu

    (Stanford University)

  • Jonasel Roque

    (Stanford University School of Medicine)

  • Victoria P. Cepeda-Espinoza

    (Stanford University)

  • Kazutoyo Osoegawa

    (Stanford Blood Center, Stanford Health Care)

  • Chris Hughes

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Shirley C. Sutton

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Nathan Youlton

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Ruchi Joshi

    (Stanford University School of Medicine)

  • David Amar

    (Stanford University School of Medicine)

  • Yosuke Tanigawa

    (Stanford University)

  • Douglas Russo

    (Stanford University)

  • Justin Wong

    (Stanford University)

  • Jessie T. Lauzon

    (Stanford University)

  • Jacob Edelson

    (Stanford University)

  • Daniel Mas Montserrat

    (Stanford University)

  • Yongchan Kwon

    (Stanford University)

  • Simone Rubinacci

    (University of Lausanne)

  • Olivier Delaneau

    (University of Lausanne)

  • Lorenzo Cappello

    (Stanford University)

  • Jaehee Kim

    (Cornell University)

  • Massa J. Shoura

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Archana N. Raja

    (Stanford University School of Medicine)

  • Nathaniel Watson

    (Stanford University School of Medicine)

  • Nathan Hammond

    (Stanford University School of Medicine)

  • Elizabeth Spiteri

    (Stanford University School of Medicine)

  • Kalyan C. Mallempati

    (Stanford Blood Center, Stanford Health Care)

  • Gonzalo Montero-Martín

    (Stanford Blood Center, Stanford Health Care)

  • Jeffrey Christle

    (Stanford University School of Medicine)

  • Jennifer Kim

    (Stanford University School of Medicine)

  • Anna Kirillova

    (University of Pittsburgh and Carnegie Mellon University)

  • Kinya Seo

    (Stanford University School of Medicine)

  • Yong Huang

    (Stanford University School of Medicine)

  • Chunli Zhao

    (Stanford University School of Medicine)

  • Sonia Moreno-Grau

    (Stanford University)

  • Steven G. Hershman

    (Stanford University School of Medicine)

  • Karen P. Dalton

    (Stanford University School of Medicine)

  • Jimmy Zhen

    (Stanford University School of Medicine)

  • Jack Kamm

    (Chan Zuckerburg Biohub)

  • Karan D. Bhatt

    (Chan Zuckerburg Biohub)

  • Alina Isakova

    (Stanford University)

  • Maurizio Morri

    (Chan Zuckerburg Biohub)

  • Thanmayi Ranganath

    (Stanford University School of Medicine)

  • Catherine A. Blish

    (Stanford University School of Medicine)

  • Angela J. Rogers

    (Stanford University School of Medicine)

  • Kari Nadeau

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Samuel Yang

    (Stanford University School of Medicine)

  • Andra Blomkalns

    (Stanford University School of Medicine)

  • Ruth O’Hara

    (Stanford University School of Medicine)

  • Norma F. Neff

    (Chan Zuckerburg Biohub)

  • Christopher DeBoever

    (Takeda Development Center, Americas, Inc)

  • Sándor Szalma

    (Takeda Development Center, Americas, Inc)

  • Matthew T. Wheeler

    (Stanford University School of Medicine)

  • Christian M. Gates

    (Illumina, Inc)

  • Kyle Farh

    (Illumina, Inc)

  • Gary P. Schroth

    (Illumina, Inc)

  • Phil Febbo

    (Illumina, Inc)

  • Francis deSouza

    (Illumina, Inc)

  • Omar E. Cornejo

    (Washington State University)

  • Marcelo Fernandez-Vina

    (Stanford Blood Center, Stanford Health Care
    Stanford University School of Medicine)

  • Amy Kistler

    (Chan Zuckerburg Biohub)

  • Julia A. Palacios

    (Stanford University
    Stanford University)

  • Benjamin A. Pinsky

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Carlos D. Bustamante

    (Stanford University)

  • Manuel A. Rivas

    (Stanford University)

  • Euan A. Ashley

    (Stanford University School of Medicine
    Stanford University School of Medicine)

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.

Suggested Citation

  • Victoria N. Parikh & Alexander G. Ioannidis & David Jimenez-Morales & John E. Gorzynski & Hannah N. Jong & Xiran Liu & Jonasel Roque & Victoria P. Cepeda-Espinoza & Kazutoyo Osoegawa & Chris Hughes & , 2022. "Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32397-8
    DOI: 10.1038/s41467-022-32397-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-32397-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-32397-8?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Hugo Zeberg & Svante Pääbo, 2020. "The major genetic risk factor for severe COVID-19 is inherited from Neanderthals," Nature, Nature, vol. 587(7835), pages 610-612, November.
    2. Erola Pairo-Castineira & Sara Clohisey & Lucija Klaric & Andrew D. Bretherick & Konrad Rawlik & Dorota Pasko & Susan Walker & Nick Parkinson & Max Head Fourman & Clark D. Russell & James Furniss & Ann, 2021. "Genetic mechanisms of critical illness in COVID-19," Nature, Nature, vol. 591(7848), pages 92-98, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Shelly J. Robertson & Olivia Bedard & Kristin L. McNally & Carl Shaia & Chad S. Clancy & Matthew Lewis & Rebecca M. Broeckel & Abhilash I. Chiramel & Jeffrey G. Shannon & Gail L. Sturdevant & Rebecca , 2023. "Genetically diverse mouse models of SARS-CoV-2 infection reproduce clinical variation in type I interferon and cytokine responses in COVID-19," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Thomas Liechti & Yaser Iftikhar & Massimo Mangino & Margaret Beddall & Charles W. Goss & Jane A. O’Halloran & Philip A. Mudd & Mario Roederer, 2022. "Immune phenotypes that are associated with subsequent COVID-19 severity inferred from post-recovery samples," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    3. Maik Pietzner & Robert Lorenz Chua & Eleanor Wheeler & Katharina Jechow & Julian D. S. Willett & Helena Radbruch & Saskia Trump & Bettina Heidecker & Hugo Zeberg & Frank L. Heppner & Roland Eils & Mar, 2022. "ELF5 is a potential respiratory epithelial cell-specific risk gene for severe COVID-19," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Syed Abul Basher & Salim Rashid & Mohammad Riad Uddin, 2023. "Losing a Gold Mine?," Papers 2306.04946, arXiv.org.
    5. Katarzyna Orlewska & Justyna Klusek & Dorota Zarębska-Michaluk & Kamila Kocańda & Ruslan Oblap & Anna Cedro & Bartosz Witczak & Jolanta Klusek & Andrzej Śliwczyński & Ewa Orlewska, 2023. "Association between Glutathione S-Transferases Gene Variants and COVID-19 Severity in Previously Vaccinated and Unvaccinated Polish Patients with Confirmed SARS-CoV-2 Infection," IJERPH, MDPI, vol. 20(4), pages 1-11, February.
    6. Elsa Brunet-Ratnasingham & Sacha Morin & Haley E. Randolph & Marjorie Labrecque & Justin Bélair & Raphaël Lima-Barbosa & Amélie Pagliuzza & Lorie Marchitto & Michael Hultström & Julia Niessl & Rose Cl, 2024. "Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    7. Tomoko Nakanishi & Julian Willett & Yossi Farjoun & Richard J. Allen & Beatriz Guillen-Guio & Darin Adra & Sirui Zhou & J. Brent Richards, 2023. "Alternative splicing in lung influences COVID-19 severity and respiratory diseases," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    8. Benjamin J. Schmiedel & Job Rocha & Cristian Gonzalez-Colin & Sourya Bhattacharyya & Ariel Madrigal & Christian H. Ottensmeier & Ferhat Ay & Vivek Chandra & Pandurangan Vijayanand, 2021. "COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    9. Bellanca, Nicolo', 2021. "Strategie di governo e strutture egemoniche in tempo di pandemia [Governance strategies and hegemonic structures in times of pandemic]," MPRA Paper 111234, University Library of Munich, Germany.
    10. Yvonne M. Mueller & Thijs J. Schrama & Rik Ruijten & Marco W. J. Schreurs & Dwin G. B. Grashof & Harmen J. G. van de Werken & Giovanna Jona Lasinio & Daniel Álvarez-Sierra & Caoimhe H. Kiernan & Melis, 2022. "Stratification of hospitalized COVID-19 patients into clinical severity progression groups by immuno-phenotyping and machine learning," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    11. Guillermo Barturen & Elena Carnero-Montoro & Manuel Martínez-Bueno & Silvia Rojo-Rello & Beatriz Sobrino & Óscar Porras-Perales & Clara Alcántara-Domínguez & David Bernardo & Marta E. Alarcón-Riquelme, 2022. "Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    12. Takahiro Miyao, 2024. "Geographical Disparities in COVID Mortality: Regression Findings," International Journal of Economics & Business Administration (IJEBA), International Journal of Economics & Business Administration (IJEBA), vol. 0(1), pages 87-98.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32397-8. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.