Record W4406239214 · doi:10.1038/s41467-025-55823-z

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

2025· article· en· W4406239214 on OpenAlexaff

Harry Pickering, Joanna Schaenman, Hoang Van Phan, Cole Maguire, Alexandra Tsitsiklis, Nadine Rouphael, Nelson Iván Agudelo Higuita, Mark A. Atkinson, Scott C. Brakenridge, Monica Fung, William B. Messer, Adreanne M. Rivera, Subha Sen, David Elashoff, Dawn C. Ward, Jenny Brook, Estefania Ramires‐Sanchez, Megan Llamas, Claudia Perdomo, Clara E. Magyar, Jennifer A. Fulcher, David J. Erle, Carolyn S. Calfee, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Nguyễn Hoàng Việt, Deanna Lee, Suzanna Chak, Rajani Ghale, Ana Gonzalez, Alejandra Jáuregui, Carolyn Leroux, Luz Torres Altamirano, Ahmad Sadeed Rashid, Andrew Willmore, Prescott G. Woodruff, Matthew F. Krummel, Sidney Carrillo, Alyssa Ward, Ravi K. Patel, Michael R. Wilson, Ravi Dandekar, Bonny D. Alvarenga, Jayant V. Rajan, Andrew Schroeder, Gabriela K. Fragiadakis, Eran Mick, Yanedth Sanchez Guerrero, Christina Love, Lenka Maliskova, Michael Adkisson, Aleksandra Leligdowicz, Alexander J. Beagle, Arjun A. Rao, Austin Sigman, Bushra Samad, Cindy Curiel, Cole Shaw, Gayelan Tietje-Ulrich, Jeff Milush, Jonathan P. Singer, Joshua Vasquez, Kevin Tang, Legna Betancourt, Lekshmi Santhosh, Logan Pierce, Maria Paz, Michael M. Matthay, Neeta Thakur, Nicklaus Rodriguez, Nicole Sutter, Norman L. Jones, Pratik Sinha, Priya Prasad, Raphael Lota, Sadeed Rashid, Saurabh Asthana, Sharvari Bhide, Tasha Lea, Yumiko Abe‐Jones, Lauren I. R. Ehrlich, Esther Melamed, Dennis Wylie, Justin F. Rousseau, Kerin Hurley, Janelle N. Geltman, Nadia Siles, Jacob E. Rogers, Pablo Guaman Tipan, Arun K. Boddapati, Greg K. Tharp, Kathryn L. Pellegrini, Brandi Johnson, Bernadine Panganiban, Christopher Huerta, Evan J. Anderson, Hady Samaha, Jonathan Sevransky, Laurel Bristow, Elizabeth Beagle, David Cowan, Sydney Hamilton, Thomas Hodder, Amer Bechnak, Andrew Cheng, Aneesh K. Mehta, Caroline Ciric, Christine Spainhour, Erin Carter, Erin M. Scherer, Jacob Usher, Kieffer Hellmeister, Laila Hussaini, Lauren T. Hewitt, Nina McNair, Susan Pereira Ribeiro, S. Wimalasena, Jordan P. Metcalf, Lauren A. Sinko, J. Leland Booth, Douglas A. Drevets, Brent R. Brown, Ricardo Ungaro, Brittany Roth Manning, Lyle L. Moldawer, Catherine L. Hough, Sarah Siegel, Peter E. Sullivan, Zhengchun Lu, Amanda E. Brunton, Matthew Strand, Zoë L. Lyski, Felicity J. Coulter, Courtney Micheletti, Naresh Doni Jayavelu, Scott Presnell, Bernard Kohr, Tomasz Jancsyk, Azlann Arnett, Alison D. Augustine, Steven M. Holland, Lindsey B. Rosen, Serena Lee, Tatyana Vaysman, Al Ozonoff, Jing Chen, Alvin T. Kho, Carly E. Milliren, Ana C. Chang, Kerry McEnaney, Caitlin Syphurs, Brenda Barton, Claudia Lentucci, Maimouna D. Murphy, Mehmet Saluvan, Tanzia Shaheen, Shanshan Liu, Albert Marisa, Arash Nemati Hayati, Robert W. Bryant, James Abraham, Mitchell Cooney, Meagan Karoly, Hanno Steen, Patrick van Zalm, Benoit Fatou, Kinga K. Smolen, Arthur Viodé, Simon D. van Haren, Meenakshi Jha, David K. Stevenson, Sanya Thomas, Boryana Petrova, Naama Kanarek, Ana Fernández-Sesma, Viviana Simon, Harm van Bakel, Ana S. Gonzalez‐Reiche, Jingjing Qi, Brian Lee, Juan Manuel Carreño, Gagandeep Singh, Ariel Raskin, Johnstone Tcheou, Zain Khalil, Adriana van de Guchte, Keith Farrugia, Zenab Khan, Geoffrey Kelly, Komal Srivastava, Lily Eaker, Maria C. Bermúdez‐González, Lubbertus C. F. Mulder, Katherine F. Beach, Miti Saksena, Deena R. Altman, Erna Milunka Kojic, Levy A. Sominsky, Arman R. Azad, Dominika Bielak, Hisaaki Kawabata, Temima Yellin, M. Fried, Leeba Sullivan, Sara Morris, Giulio Kleiner, Daniel Stadlbauer, Jayeeta Dutta, Hui Xie, Manishkumar Patel, Kai Nie, Brian Monahan, David A. Hafler, Ruth R. Montgomery, Albert C. Shaw, Jeremy P. Gygi, Dylan Duchen, Shrikant Pawar, Anna Konstorum, Ernie Chen, Chris Cotsapas, Xiaomei Wang, Charles S. Dela Cruz, Akiko Iwasaki, Subhasis Mohanty, Allison Nelson, Yujiao Zhao, Shelli Farhadian, Hiromitsu Asashima, Omkar Chaudhary, Andreas Coppi, John Fournier, M. Catherine Muenker, Khadir Raddassi, Michael Rainone, William Ruff, Syim Salahuddin, Wade L. Shulz, Pavithra Vijayakumar, Haowei Wang, Elsio A. Wunder, H. P. Young, Albert I. Ko, Gisela Gabernet, Denise Esserman, Leying Guan, Anderson F. Brito, Jessica E. Rothman, Nathan D. Grubaugh, Kexin Wang, Leqi Xu, Holden T. Maecker, Bali Pulendran, Kari C. Nadeau, Yael Rosenberg‐Hasson, Michael D. Leipold, Natalia Sigal, Angela J. Rogers, Andrea Fernandes, Monali Manohar, Evan Do, Iris Chang, Alexandra S. Lee, Catherine A. Blish, Henna Naz Din, Jonasel Roque, Linda N. Geng, Maja Artandi, Mark M. Davis, Neera Ahuja, Samuel Yang, R. Sharon Chinthrajah, Thomas Hagan, Tyson H. Holmes, Koji Abe, Lindsey R. Baden, Kevin Mendez, Jessica Lasky‐Su, Alexandra Tong, Rebecca Rooks, Michaël Desjardins, Amy C Sherman, Stephen R. Walsh, Xhoi Mitre, Jessica Cauley, Xiaofang Li, Bethany Evans, Christina Montesano, Jose Humberto Licona, Jonathan Krauß, Nicolas C. Issa, Jun Bai Park Chang, Natalie Izaguirre, David B. Corry, Farrah Kheradmand, Li-Zhen Song, Ebony Nelson, Monica Kraft, Chris Bime, Jarrod Mosier, Heidi L. Erickson, Ron Schunk, Hiroki Kimura, Michelle Conway, David Francisco, Allyson Molzahn, Connie Cathleen Wilson, Trina Hughes, Bianca Sierra, Jordan Oberhaus, Faheem W. Guirgis, Brittney Borresen, Matthew L. Anderson, Bjoern Peters, James A. Overton, Randi Vita, Kerstin Westendorf, Scott J. Tebbutt, Casey P. Shannon, Rafick‐Pierre Sékaly, Slim Fourati, Grace A. McComsey, Paul Harris, Scott F. Sieg, George A. Yendewa, Mary Consolo, Heather Tribout, Charles B. Cairns, Elias K. Haddad, Michele A. Kutzler, Mariana Bernui, Gina Cusimano, Jennifer Connors, Kyra Woloszczuk, David Joyner, Carolyn Pope Edwards, Edward Lee, Edward H. Lin, Nataliya Melnyk, Debra Powell, James N. Kim, I. Michael Goonewardene, Brent Simmons, Cecilia M. Smith, Mark G. Martens, Brett Croen, Nicholas C. Semenza, Matthew R. Bell, Sara Furukawa, Renee McLin, George P. Tegos, Brandon Rogowski, Nathan Mege, Kristen Ulring, Pam Schearer, Judie Sheidy, Crystal Nagle, Scott R. Hutton, Gregory A. Michelotti, Kari E. Wong, Adeeb Rahman, Vicki Seyfert‐Margolis, Ramin Salehi‐Rad, Matthew C. Altman, Patrice M. Becker, Steven E. Bosinger, Walter L. Eckalbar, Annmarie Hoch, Seunghee Kim‐Schulze, Meagan M. Jenkins, Steven H. Kleinstein, Florian Krammer, Joann Diray‐Arce, Lindsey R. Baden, Ofer Levy, Charles Langelier

Bibliographic record

VenueNature Communications · 2025

Typearticle

Languageen

FieldMedicine

TopicCOVID-19 Clinical Research Studies

Canadian institutionsPrevention of Organ FailureUniversity of British Columbia

FundersNational Center for Advancing Translational SciencesNational Institute of Allergy and Infectious DiseasesNational Heart, Lung, and Blood InstituteU.S. Department of Health and Human ServicesYale UniversityUniversity of California, Los AngelesNational Institutes of HealthU.S. Department of Veterans Affairs

KeywordsImmunologyChemokineImmune systemOrgan transplantationBiologyImmune dysregulationInnate immune systemTransplantationProinflammatory cytokineMedicineInflammationInternal medicine

DOI10.1038/s41467-025-55823-z

Abstract

fetched live from OpenAlex

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.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.000

metaresearch head score (Gemma)0.000

Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated

Candidate categoriesnone

Consensus categoriesnone

DomainCandidate signal: none · Consensus signal: none

Study designCandidate signal: Observational · Consensus signal: Observational

GenreCandidate signal: Empirical · Consensus signal: Empirical

Teacher disagreement score0.001

Threshold uncertainty score0.004

Distilled classifier scores by category (both heads)

Category	Codex	Gemma
Metaresearch	0.000	0.000
Meta-epidemiology (narrow)	0.000	0.000
Meta-epidemiology (broad)	0.000	0.000
Bibliometrics	0.000	0.000
Science and technology studies	0.000	0.000
Scholarly communication	0.000	0.000
Open science	0.000	0.000
Research integrity	0.000	0.000
Insufficient payload (model declined to judge)	0.001	0.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.044

GPT teacher head0.453

Teacher spread0.409 · how far apart the two teachers sit on this one work

Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.

Study designObservational

Domainnot available

GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

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Citations6

Published2025

Admission routes1

Has abstractyes

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