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Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients

Author

Listed:
  • Harry Pickering

    (University of California Los Angeles)

  • Joanna Schaenman

    (University of California Los Angeles)

  • Hoang Van Phan

    (University of California San Francisco)

  • Cole Maguire

    (The University of Texas at Austin)

  • Alexandra Tsitsiklis

    (University of California San Francisco)

  • Nadine Rouphael

    (Emory School of Medicine)

  • Nelson Iván Agudelo Higuita

    (Oklahoma University Health Sciences Center)

  • Mark A. Atkinson

    (University of Florida)

  • Scott Brakenridge

    (University of Florida)

  • Monica Fung

    (University of California San Francisco)

  • William Messer

    (Oregon Health Sciences University)

  • Ramin Salehi-rad

    (University of California Los Angeles)

  • Matthew C. Altman

    (University of Washington)

  • Patrice M. Becker

    (National Institute of Allergy and Infectious Diseases/National Institutes of Health)

  • Steven E. Bosinger

    (Emory School of Medicine)

  • Walter Eckalbar

    (University of California San Francisco)

  • Annmarie Hoch

    (Boston Children’s Hospital)

  • Naresh Doni Jayavelu

    (University of Washington)

  • Seunghee Kim-Schulze

    (Icahn School of Medicine at Mount Sinai)

  • Meagan Jenkins

    (University of California Los Angeles)

  • Steven H. Kleinstein

    (Yale School of Medicine)

  • Florian Krammer

    (Icahn School of Medicine at Mount Sinai)

  • Holden T. Maecker

    (Stanford University School of Medicine)

  • Al Ozonoff

    (Boston Children’s Hospital
    Broad Institute of MIT & Harvard
    Harvard Medical School)

  • Joann Diray-Arce

    (Boston Children’s Hospital
    Harvard Medical School)

  • Albert Shaw

    (Yale School of Medicine)

  • Lindsey Baden

    (Harvard Medical School
    Brigham & Women’s Hospital)

  • Ofer Levy

    (Boston Children’s Hospital
    Broad Institute of MIT & Harvard
    Harvard Medical School)

  • Elaine F. Reed

    (University of California Los Angeles)

  • Charles R. Langelier

    (University of California San Francisco
    Chan Zuckerberg Biohub San Francisco)

Abstract

Coronavirus disease 2019 (COVID-19) poses significant risks for solid organ transplant recipients, who have atypical but poorly characterized immune responses to infection. We aim to understand the host immunologic and microbial features of COVID-19 in transplant recipients by leveraging a prospective multicenter cohort of 86 transplant recipients age- and sex-matched with 172 non-transplant controls. We find that transplant recipients have higher nasal SARS-CoV-2 viral abundance and impaired viral clearance, and lower anti-spike IgG levels. In addition, transplant recipients exhibit decreased plasmablasts and transitional B cells, and increased senescent T cells. Blood and nasal transcriptional profiling demonstrate unexpected upregulation of innate immune signaling pathways and increased levels of several proinflammatory serum chemokines. Severe disease in transplant recipients, however, is characterized by a less robust induction of pro-inflammatory genes and chemokines. Together, our study reveals distinct immune features and altered viral dynamics in solid organ transplant recipients.

Suggested Citation

  • Harry Pickering & Joanna Schaenman & Hoang Van Phan & Cole Maguire & Alexandra Tsitsiklis & Nadine Rouphael & Nelson Iván Agudelo Higuita & Mark A. Atkinson & Scott Brakenridge & Monica Fung & William, 2025. "Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-55823-z
    DOI: 10.1038/s41467-025-55823-z
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    References listed on IDEAS

    as
    1. Huang Lin & Shyamal Das Peddada, 2020. "Analysis of compositions of microbiomes with bias correction," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
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