Nature Communications (Aug 2022)
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,
- Shirley C. Sutton,
- Nathan Youlton,
- Ruchi Joshi,
- David Amar,
- Yosuke Tanigawa,
- Douglas Russo,
- Justin Wong,
- Jessie T. Lauzon,
- Jacob Edelson,
- Daniel Mas Montserrat,
- Yongchan Kwon,
- Simone Rubinacci,
- Olivier Delaneau,
- Lorenzo Cappello,
- Jaehee Kim,
- Massa J. Shoura,
- Archana N. Raja,
- Nathaniel Watson,
- Nathan Hammond,
- Elizabeth Spiteri,
- Kalyan C. Mallempati,
- Gonzalo Montero-Martín,
- Jeffrey Christle,
- Jennifer Kim,
- Anna Kirillova,
- Kinya Seo,
- Yong Huang,
- Chunli Zhao,
- Sonia Moreno-Grau,
- Steven G. Hershman,
- Karen P. Dalton,
- Jimmy Zhen,
- Jack Kamm,
- Karan D. Bhatt,
- Alina Isakova,
- Maurizio Morri,
- Thanmayi Ranganath,
- Catherine A. Blish,
- Angela J. Rogers,
- Kari Nadeau,
- Samuel Yang,
- Andra Blomkalns,
- Ruth O’Hara,
- Norma F. Neff,
- Christopher DeBoever,
- Sándor Szalma,
- Matthew T. Wheeler,
- Christian M. Gates,
- Kyle Farh,
- Gary P. Schroth,
- Phil Febbo,
- Francis deSouza,
- Omar E. Cornejo,
- Marcelo Fernandez-Vina,
- Amy Kistler,
- Julia A. Palacios,
- Benjamin A. Pinsky,
- Carlos D. Bustamante,
- Manuel A. Rivas,
- Euan A. Ashley
Affiliations
- Victoria N. Parikh
- Department of Medicine, Stanford University School of Medicine
- Alexander G. Ioannidis
- Department of Biomedical Data Science, Stanford University
- David Jimenez-Morales
- Department of Medicine, Stanford University School of Medicine
- John E. Gorzynski
- Department of Medicine, Stanford University School of Medicine
- Hannah N. De Jong
- Department of Medicine, Stanford University School of Medicine
- Xiran Liu
- Institute for Computational and Mathematical Engineering, Stanford University
- Jonasel Roque
- Department of Medicine, Stanford University School of Medicine
- Victoria P. Cepeda-Espinoza
- Department of Biomedical Data Science, Stanford University
- Kazutoyo Osoegawa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care
- Chris Hughes
- Department of Medicine, Stanford University School of Medicine
- Shirley C. Sutton
- Department of Medicine, Stanford University School of Medicine
- Nathan Youlton
- Department of Medicine, Stanford University School of Medicine
- Ruchi Joshi
- Department of Medicine, Stanford University School of Medicine
- David Amar
- Department of Medicine, Stanford University School of Medicine
- Yosuke Tanigawa
- Department of Biomedical Data Science, Stanford University
- Douglas Russo
- Department of Statistics, Stanford University
- Justin Wong
- Department of Statistics, Stanford University
- Jessie T. Lauzon
- Department of Aeronautics and Astronautics, Stanford University
- Jacob Edelson
- Department of Biomedical Data Science, Stanford University
- Daniel Mas Montserrat
- Department of Biomedical Data Science, Stanford University
- Yongchan Kwon
- Department of Biomedical Data Science, Stanford University
- Simone Rubinacci
- Department of Computational Biology and Swiss Institute of Bioinformatics, University of Lausanne
- Olivier Delaneau
- Department of Computational Biology and Swiss Institute of Bioinformatics, University of Lausanne
- Lorenzo Cappello
- Department of Statistics, Stanford University
- Jaehee Kim
- Department of Computational Biology, Cornell University
- Massa J. Shoura
- Department of Genetics, Stanford University School of Medicine
- Archana N. Raja
- Department of Medicine, Stanford University School of Medicine
- Nathaniel Watson
- Department of Pathology, Stanford University School of Medicine
- Nathan Hammond
- Department of Pathology, Stanford University School of Medicine
- Elizabeth Spiteri
- Department of Pathology, Stanford University School of Medicine
- Kalyan C. Mallempati
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care
- Gonzalo Montero-Martín
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care
- Jeffrey Christle
- Department of Medicine, Stanford University School of Medicine
- Jennifer Kim
- Department of Medicine, Stanford University School of Medicine
- Anna Kirillova
- Medical Scientist Training Program, University of Pittsburgh and Carnegie Mellon University
- Kinya Seo
- Department of Medicine, Stanford University School of Medicine
- Yong Huang
- Department of Medicine, Stanford University School of Medicine
- Chunli Zhao
- Department of Medicine, Stanford University School of Medicine
- Sonia Moreno-Grau
- Department of Biomedical Data Science, Stanford University
- Steven G. Hershman
- Department of Medicine, Stanford University School of Medicine
- Karen P. Dalton
- Department of Medicine, Stanford University School of Medicine
- Jimmy Zhen
- Department of Medicine, Stanford University School of Medicine
- Jack Kamm
- Chan Zuckerburg Biohub
- Karan D. Bhatt
- Chan Zuckerburg Biohub
- Alina Isakova
- Department of Bioengineering, Stanford University
- Maurizio Morri
- Chan Zuckerburg Biohub
- Thanmayi Ranganath
- Department of Medicine, Stanford University School of Medicine
- Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine
- Angela J. Rogers
- Department of Medicine, Stanford University School of Medicine
- Kari Nadeau
- Department of Medicine, Stanford University School of Medicine
- Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine
- Andra Blomkalns
- Department of Emergency Medicine, Stanford University School of Medicine
- Ruth O’Hara
- Department of Psychiatry and Behavioral Sciences, 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
- Department of Medicine, 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
- School of Biological Sciences, Washington State University
- Marcelo Fernandez-Vina
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care
- Amy Kistler
- Chan Zuckerburg Biohub
- Julia A. Palacios
- Department of Biomedical Data Science, Stanford University
- Benjamin A. Pinsky
- Department of Medicine, Stanford University School of Medicine
- Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University
- Manuel A. Rivas
- Department of Biomedical Data Science, Stanford University
- Euan A. Ashley
- Department of Medicine, Stanford University School of Medicine
- DOI
- https://doi.org/10.1038/s41467-022-32397-8
- Journal volume & issue
-
Vol. 13,
no. 1
pp. 1 – 10
Abstract
There is a genetic component to the risk of severe COVID-19, but the genetic effects are difficult to separate from social constructs that covary with genetic ancestry. To address this, the authors identify determinants of COVID-19 severity using admixture mapping, viral phylodynamics, and host immune and metagenomic sequencing.
