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Authors
Pita-Juarez, Yered
Karagkouni, Dimitra
Kalavros, Nikolaos
Melms, Johannes C.
Niezen, Sebastian
Delorey, Toni M.
Essene, Adam L.
Brook, Olga R.
Pant, Deepti
Skelton-Badlani, Disha
Naderi, Pourya
Huang, Pinzhu
Pan, Liuliu
Hether, Tyler
Andrews, Tallulah S.
Ziegler, Carly G. K.
Reeves, Jason
Myloserdnyy, Andriy
Chen, Rachel
Nam, Andy
Phelan, Stefan
Liang, Yan
Gregory, Mark
He, Shanshan
Patrick, Michael
Rane, Tushar
Wardhani, Aster
Amin, Amit Dipak
Biermann, Jana
Hibshoosh, Hanina
Veregge, Molly
Kramer, Zachary
Jacobs, Christopher
Yalcin, Yusuf
Phillips, Devan
Slyper, Michal
Subramanian, Ayshwarya
Ashenberg, Orr
Bloom-Ackermann, Zohar
Tran, Victoria M.
Gomez, James
Sturm, Alexander
Zhang, Shuting
Fleming, Stephen J.
Warren, Sarah
Beechem, Joseph
Hung, Deborah
Babadi, Mehrtash
Padera, Robert F. Jr.
MacParland, Sonya A.
Bader, Gary D.
Imad, Nasser
Solomon, Isaac H.
Miller, Eric
Riedel, Stefan
Porter, Caroline B. M.
Villani, Alexandra-Chloé
Tsai, Linus T.-Y.
Hide, Winston
Szabo, Gyongyi
Hecht, Jonathan
Rozenblatt-Rosen, Orit
Shalek, Alex K.
Izar, Benjamin
Regev, Aviv
Popov, Yury V.
Jiang, Z. Gordon
Vlachos, Ioannis S. https://orcid.org/0000-0002-8849-808X
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Funding
Funding for this research was provided by:
U.S. Food and Drug Administration (HHSF223201810172C)
Bill and Melinda Gates Foundation (INV-027498)
National Cancer Institute (R01 CA258776)
National Cancer Institute (R01 HL129506-07)
National Blood Clot Alliance (PR200524P1)
Office of Research Infrastructure Programs, National Institutes of Health (Massachusetts Life Sciences Center)
National Cancer Institute (K08CA222663)
National Cancer Institute (R37CA258829)
National Cancer Institute (R21CA263381)
National Cancer Institute (U54CA225088)
NIH Support Grant (S10RR027050)
National Cancer Institute (P30CA013696)
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Article History
Received: 4 July 2023
Accepted: 7 February 2025
First Online: 14 March 2025
Declarations
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: All sample collection procedures were reviewed by the IRB of the relevant hospital. The related protocols were as follows: Beth Israel Deaconess Medical Center (IRB 2020P000406, 2020P000418), Brigham and Women’s Hospital and Massachusetts General Hospital (2020P000804, 2020P000849, 2015P002215), New York Presbyterian Hospital/Columbia University Medical Center (IRB-AAAT0785, IRB-AAAB2667, IRB-AAAS7370). All patients had confirmed COVID-19 by PCR testing. Consent for autopsy and research was obtained from the healthcare proxy or the next of kin. Massachusetts Institute of Technology (MIT) IRB protocols 1603505962 and 1612793224, and/or the not-involving-human-subjects research protocol ORSP-3635, cover all secondary analyses performed at the Broad Institute of MIT and Harvard. No subject recruitment or ascertainment was performed as part of the Broad protocol. Donor identities and accompanying information were encoded at the relevant hospital site prior to shipping to or sharing with the Broad Institute for sample processing or data analysis.
: Not applicable.
: A.K.S. reports compensation for consulting and/or SAB membership from Merck, Honeycomb Biotechnologies, Cellarity, Repertoire Immune Medicines, Ochre Bio, Third Rock Ventures, Hovione, Relation Therapeutics, FL82, Senda Biosciences, Empress Therapeutics, IntrECate Biotherapeutics, and Dahlia Biosciences unrelated to this work. A.R. is a founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics and until August 31, 2020 was an SAB member of Syros Pharmaceuticals, Neogene Therapeutics, Asimov and Thermo Fisher Scientific. From August 1, 2020, A.R. is an employee of Genentech, a member of the Roche Group, with equity in Roche. I.S.V. consults for Guidepoint Global, Mosaic, and Chronicle Medical Software. G.S. consults in Alnylam Pharmaceuticals, Merck, Generon, Glympse Bio, Inc., Mayday Foundation, Novartis Pharmaceuticals, Quest Diagnostics, Surrozen, Terra Firma, Zomagen Bioscience, Pandion Therapeutics, Inc., Durect Corporation; royalty from UpToDate Inc. and Editor service for Hepatology Communications. Y.V.P. receives grant support from Enanta Pharmaceuticals, CymaBay Therapeutics, Morphic Therapeutic; consulting and/or SAB in Ambys Medicines, Morphic Therapeutics, Enveda Therapeutics, BridgeBio Pharma, as well as being an Editor of American Journal of Physiology-Gastrointestinal and Liver Physiology. Z.G.J. receives grant support from Gilead Science, Pfizer and compensation for consulting from Olix Pharmaceuticals. L.P, T.H., S.W, J.B, E.M, and J.R. are employees and/or stockholders of NanoString Technologies. B.I. has received honoraria from consulting with Merck, Janssen Pharmaceuticals, AstraZeneca, and Volastra Therapeutics. A.R. and O.R.R. are inventors on multiple patents from the Broad Institute related to single-cell and spatial genomics.
