Evidence map›Paper›PMID 36563487›Full record

ArticleEBioMedicine2023

Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes.

Justin T Reese, Hannah Blau, Elena Casiraghi, Timothy Bergquist, Johanna J Loomba, Tiffany J Callahan, Bryan Laraway, Corneliu Antonescu, Ben Coleman, Michael Gargano and 23 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in EBioMedicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
121citing papers in PubMed, 2 pooled it
21.3field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

121 citing papers in PubMed, 2 syntheses or guidelines pooled it, 174 citations in OpenAlex.

  1. Pooled it
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  7. Metformin and Severe Post-COVID-19 Outcomes Among Individuals with Diabetes Mellitus.medRxiv : the preprint server for health sciences · 2026
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61 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

33 authors at 19 institutions in 2 countries.

Justin T ReeseEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Hannah BlauThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA.
Elena CasiraghiEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; AnacletoLab, Dipartimento di Informatica, Università Degli Studi di Milano, Milan, Italy.
Timothy BergquistSage Bionetworks, Seattle, WA, USA.
Johanna J LoombaThe Integrated Translational Health Research Institute of Virginia (iTHRIV), University of Virginia, Charlottesville, VA, USA.
Tiffany J CallahanDepartment of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
Bryan LarawayDepartments of Biomedical Informatics and Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Corneliu AntonescuUniversity of Arizona - Banner Health, Phoenix, AZ, USA.
Ben ColemanThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA.
Michael GarganoThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA.
Kenneth J WilkinsBiostatistics Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
Luca CappellettiAnacletoLab, Dipartimento di Informatica, Università Degli Studi di Milano, Milan, Italy.
Tommaso FontanaAnacletoLab, Dipartimento di Informatica, Università Degli Studi di Milano, Milan, Italy.
Nariman AmmarHealth Science Center, University of Tennessee, Memphis, TN, USA.
Blessy AntonyDepartment of Computer Science, Virginia Tech, Blacksburg, VA, USA.
T M MuraliDepartment of Computer Science, Virginia Tech, Blacksburg, VA, USA.
J Harry CaufieldEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Guy KarlebachThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA.
Julie A McMurryDepartments of Biomedical Informatics and Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Andrew WilliamsTufts Medical Center Clinical and Translational Science Institute, Tufts Medical Center, Boston, MA, USA; Tufts University School of Medicine, Institute for Clinical Research and Health Policy Studies, Boston, MA, USA; Northeastern University, OHDSI Center at the Roux Institute, Boston, MA, USA.
Richard MoffittDepartment of Biomedical Informatics and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA.
Jineta BanerjeeSage Bionetworks, Seattle, WA, USA.
Anthony E SolomonidesHealthSystem Research Institute, NorthShore University, Evanston, IL, USA.
Hannah DavisPatient-Led Research Collaborative, NY, USA.
Kristin KostkaNortheastern University, OHDSI Center at the Roux Institute, Boston, MA, USA.
Giorgio ValentiniAnacletoLab, Dipartimento di Informatica, Università Degli Studi di Milano, Milan, Italy.
David SahnerAxle Informatics, Rockville, MD, USA.
Christopher G ChuteSchools of Medicine, Public Health and Nursing, Johns Hopkins University, Baltimore, MD, USA.
Charisse Madlock-BrownHealth Science Center, University of Tennessee, Memphis, TN, USA.
Melissa A HaendelDepartments of Biomedical Informatics and Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Peter N RobinsonThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA. Electronic address: Peter.Robinson@jax.org.
N3C Consortium
RECOVER Consortium
Jackson Laboratory · USLawrence Berkeley National Laboratory · USUniversity of Colorado Anschutz Medical Campus · USUniversity of Milan · ITSage Bionetworks · USUniversity of Arizona · USUniversity of Tennessee Health Science Center · USVirginia Tech · USAmerican Axle & Manufacturing (United States) · USColumbia University Irving Medical Center · USJohns Hopkins University · USNational Institutes of Health · USNortheastern University · USNorthShore University HealthSystem · USPatient-Led Research CollaborativeStony Brook University · USTufts University · USUniversity of Connecticut · USUniversity of Virginia · US

Funding

OTA-21-015A Post-Acute Sequelae of SARS-CoV-2 Infection Initiative: NYU Langone Health Clinical Science Core, Data Resource Core, and PASC Biorepository CoreOT2HL161847 · NHLBI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI GROSS, RACHEL SHARON, HORWITZ, LEORA · 2021 to 2025
$651.0M
Vanderbilt Institute for Clinical and Translational Research (VICTR) -Identifying correlates of functional immunity in SARS-CoV-2 convalescent plasmaUL1TR002243 · NCATS · VANDERBILT UNIVERSITY MEDICAL CENTER · PI Paul A. Harris, Wesley H Self · 2017 to 2026
$130.7M
UCLA Clinical Translational Science InstituteUL1TR001881 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ARLEEN F. BROWN, ARASH NAEIM · 2016 to 2026
$118.1M
Clinical and Translational Science InstituteUL1TR001872 · NCATS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI COLLARD, HAROLD R, JACOBY, VANESSA · 2016 to 2025
$112.1M
Project-005UL1TR001445 · NCATS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI BREDELLA, MIRIAM ANTOINETTE, HOCHMAN, JUDITH S · 2015 to 2025
$103.5M
Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9M
Phenotypic Diversity in COVID-19UL1TR001878 · NCATS · UNIVERSITY OF PENNSYLVANIA · PI FITZGERALD, GARRET A · 2016 to 2025
$102.4M
Transform Dissemination and Implementation Science in CTSA ProgramsUL1TR002319 · NCATS · UNIVERSITY OF WASHINGTON · PI John K. Amory · 2017 to 2026
$100.0M
Clinical and Translational Science AwardUL1TR001873 · NCATS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI REILLY, MUREDACH P · 2016 to 2025
$99.0M
WU INSTITUTE OF CLINICAL AND TRANSLATIONAL SCIENCESUL1TR002345 · NCATS · WASHINGTON UNIVERSITY · PI William G. Powderly · 2017 to 2026
$97.8M
The Harvard Clinical and Translational Science CenterUL1TR002541 · NCATS · HARVARD MEDICAL SCHOOL · PI NADLER, LEE MARSHALL · 2018 to 2022
$93.0M
Implementing a Maternal health and PRegnancy Outcomes Vision for Everyone (IMPROVE)UL1TR002378 · NCATS · EMORY UNIVERSITY · PI Andres J Garcia, Elizabeth O. Ofili · 2017 to 2026
$92.1M
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6 · The paper itself

Abstract

backgroundStratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies. However, long COVID is incompletely understood and characterised by a wide range of manifestations that are difficult to analyse computationally. Additionally, the generalisability of machine learning classification of COVID-19 clinical outcomes has rarely been tested.

methodsWe present a method for computationally modelling PASC phenotype data based on electronic healthcare records (EHRs) and for assessing pairwise phenotypic similarity between patients using semantic similarity. Our approach defines a nonlinear similarity function that maps from a feature space of phenotypic abnormalities to a matrix of pairwise patient similarity that can be clustered using unsupervised machine learning.

findingsWe found six clusters of PASC patients, each with distinct profiles of phenotypic abnormalities, including clusters with distinct pulmonary, neuropsychiatric, and cardiovascular abnormalities, and a cluster associated with broad, severe manifestations and increased mortality. There was significant association of cluster membership with a range of pre-existing conditions and measures of severity during acute COVID-19. We assigned new patients from other healthcare centres to clusters by maximum semantic similarity to the original patients, and showed that the clusters were generalisable across different hospital systems. The increased mortality rate originally identified in one cluster was consistently observed in patients assigned to that cluster in other hospital systems.

interpretationSemantic phenotypic clustering provides a foundation for assigning patients to stratified subgroups for natural history or therapy studies on PASC.

fundingNIH (TR002306/OT2HL161847-01/OD011883/HG010860), U.S.D.O.E. (DE-AC02-05CH11231), Donald A. Roux Family Fund at Jackson Laboratory, Marsico Family at CU Anschutz.

Indexed as

COVID-19Post-Acute COVID-19 SyndromeDisease ProgressionHumansSARS-CoV-2COVID-19Human Phenotype OntologyLong COVIDMachine learningPrecision medicineSemantic similarity

Identifiers

PMID36563487
PMCPMC9769411
OpenAlexW4312061512

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.