Identification of patient demographic, clinical, and SARS-CoV-2 genomic factors associated with severe COVID-19 using supervised machine learning: a retrospective multicenter study.

Journal: BMC infectious diseases
PMID: 39875869

Abstract

BACKGROUND: Drivers of COVID-19 severity are multifactorial and include multidimensional and potentially interacting factors encompassing viral determinants and host-related factors (i.e., demographics, pre-existing conditions and/or genetics), thus complicating the prediction of clinical outcomes for different severe acute respiratory syndrome coronavirus (SARS-CoV-2) variants. Although millions of SARS-CoV-2 genomes have been publicly shared in global databases, linkages with detailed clinical data are scarce. Therefore, we aimed to establish a COVID-19 patient dataset with linked clinical and viral genomic data to then examine associations between SARS-CoV-2 genomic signatures and clinical disease phenotypes.

Authors

  • Kuganya Nirmalarajah
    Sunnybrook Research Institute, Toronto, ON, Canada.
  • Patryk Aftanas
    Shared Hospital Laboratory, Toronto, ON, Canada.
  • Shiva Barati
    Sinai Health System, Toronto, ON, Canada.
  • Emily Chien
    Sunnybrook Research Institute, Toronto, ON, Canada.
  • Gloria Crowl
    Sinai Health System, Toronto, ON, Canada.
  • Amna Faheem
    Sinai Health System, Toronto, ON, Canada.
  • Lubna Farooqi
    Sinai Health System, Toronto, ON, Canada.
  • Alainna J Jamal
    Sinai Health System, Toronto, ON, Canada.
  • Saman Khan
    Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.
  • Jonathon D Kotwa
    Sunnybrook Research Institute, Toronto, ON, Canada.
  • Angel X Li
    Sinai Health System, Toronto, ON, Canada.
  • Mohammad Mozafarihashjin
    Sinai Health System, Toronto, ON, Canada.
  • Jalees A Nasir
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Altynay Shigayeva
    Sinai Health System, Toronto, ON, Canada.
  • Winfield Yim
    Sunnybrook Research Institute, Toronto, ON, Canada.
  • Lily Yip
    Sunnybrook Research Institute, Toronto, ON, Canada.
  • Xi Zoe Zhong
    Sinai Health System, Toronto, ON, Canada.
  • Kevin Katz
    Shared Hospital Laboratory, Toronto, ON, Canada.
  • Robert Kozak
    Sunnybrook Research Institute, Toronto, ON, Canada.
  • Andrew G McArthur
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Nick Daneman
    Sunnybrook Research Institute, Toronto, ON, Canada.
  • Finlay Maguire
    Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.
  • Allison J McGeer
    Sinai Health System, Toronto, ON, Canada.
  • Venkata R Duvvuri
    Public Health Ontario, Toronto, ON, Canada.
  • Samira Mubareka
    Sunnybrook Research Institute, Toronto, ON, Canada. samira.mubareka@sunnybrook.ca.

Keywords

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