Trial reportCell2020
Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19.
2 registry-linked trialsOpen access · hybridAbstract readClinical TrialMulticenter Study
In one paragraph
Trial report in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to 2 registered trials, which are not on this map. Cited by 407 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
407citing papers in PubMed, 2 pooled it
87.6field-weighted citation impact, top 1% of its field
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.
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.
Emergency PanorOmic Wide Association Study in Respiratory Infectious Disease (ePWAS-RID)
Clinical Study on the Immune Response Characteristics of Novel Coronavirus and Influenza Virus Infection
Who cites it
407 citing papers in PubMed, 2 syntheses or guidelines pooled it, 631 citations in OpenAlex.
- Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis.Nature communications · 2025Pooled it
- Metabolomic characteristics and related pathways in patients with different severity of COVID-19: a systematic review and meta-analysis.Journal of global health · 2025Pooled it
- Machine learning and data-driven inverse modeling of metabolomics unveil key processes of active aging.NPJ systems biology and applications · 2025Trial
- Duvelisib plus romidepsin in relapsed/refractory T cell lymphomas: a phase 1b/2a trial.Nature medicine · 2024Trial
- Nasal administration of anti-CD3 mAb (Foralumab) downregulatesProceedings of the National Academy of Sciences of the United States of America · 2023Trial
- Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade.eLife · 2026Article
- A distinct effector B cell population drives autoantibody production in SARS-CoV-2 infection.Immunity · 2026Article
- Autoimmune disease patients with comorbid cancer exhibit prominent immunometabolic crosstalk.Science China. Life sciences · 2026Article
- DIVAS: an R package for identifying shared and individual variations of multiomics data.Bioinformatics (Oxford, England) · 2026Article
- Human primary antibody response to vaccination follows a partially sequential class-switching program with a checkpoint at IGHG2.Cell reports. Medicine · 2026Article
- Computational identification of antigen-specific T cell groups through generative epitope modeling.iScience · 2026Article
- DAMP Laden Extracellular Vesicles From the Airways of Patients With Severe SARS-CoV-2 Respiratory Infection Compromise Inflammation and Cellular Metabolism.Journal of extracellular vesicles · 2026Article
- Supervised deep learning with gene functional annotation for cell classification.PLoS computational biology · 2026Article
- Whole-protein screening and multi-modal profiling of antigen-specific CD4Nature communications · 2026Article
- Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity.Bioinformatics (Oxford, England) · 2026Article
- T-cell repertoire response in individuals with post-acute sequelae of COVID-19.bioRxiv : the preprint server for biology · 2026Article
- Plasma multi-omics profiling unravels molecular alterations and biomarker panels during recovery from severe coronavirus disease 2019: a pilot study.BMC infectious diseases · 2026Article
- A quantitative metabolic signature of host response during SARS-CoV-2 infection and recovery.iScience · 2026Article
- scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery.iScience · 2026Article
- phylobar: an R package for multiresolution compositional barplots in omics studies.Bioinformatics (Oxford, England) · 2026Article
347 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
56 authors at 10 institutions in 2 countries.
Yapeng SuInstitute for Systems Biology, Seattle, WA 98109, USA.
Daniel ChenInstitute for Systems Biology, Seattle, WA 98109, USA.
Dan YuanInstitute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
Christopher LaustedInstitute for Systems Biology, Seattle, WA 98109, USA.
Jongchan ChoiInstitute for Systems Biology, Seattle, WA 98109, USA.
Chengzhen L DaiInstitute for Systems Biology, Seattle, WA 98109, USA.
Valentin VoilletCape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, NPC (HCRISA), Cape Town 8001, South Africa; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Venkata R DuvvuriInstitute for Systems Biology, Seattle, WA 98109, USA.
Kelsey ScherlerInstitute for Systems Biology, Seattle, WA 98109, USA.
Pamela TroischInstitute for Systems Biology, Seattle, WA 98109, USA.
Priyanka BaloniInstitute for Systems Biology, Seattle, WA 98109, USA.
Guangrong QinInstitute for Systems Biology, Seattle, WA 98109, USA.
Brett SmithInstitute for Systems Biology, Seattle, WA 98109, USA.
Sergey A KornilovInstitute for Systems Biology, Seattle, WA 98109, USA.
Clifford RostomilyInstitute for Systems Biology, Seattle, WA 98109, USA.
Alex XuInstitute for Systems Biology, Seattle, WA 98109, USA.
Jing LiInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
Shen DongDiabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.
Alissa RothchildCenter for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA.
Jing ZhouIsoplexis Corporation, Branford, CT 06405, USA.
Kim MurrayInstitute for Systems Biology, Seattle, WA 98109, USA.
Rick EdmarkInstitute for Systems Biology, Seattle, WA 98109, USA.
Sunga HongInstitute for Systems Biology, Seattle, WA 98109, USA.
John E HeathInstitute for Systems Biology, Seattle, WA 98109, USA.
John EarlsInstitute for Systems Biology, Seattle, WA 98109, USA.
Rongyu ZhangInstitute for Systems Biology, Seattle, WA 98109, USA.
Jingyi XieInstitute for Systems Biology, Seattle, WA 98109, USA.
Sarah LiInstitute for Systems Biology, Seattle, WA 98109, USA.
Ryan RoperInstitute for Systems Biology, Seattle, WA 98109, USA.
Lesley JonesInstitute for Systems Biology, Seattle, WA 98109, USA.
Yong ZhouInstitute for Systems Biology, Seattle, WA 98109, USA.
Lee RowenInstitute for Systems Biology, Seattle, WA 98109, USA.
Rachel LiuInstitute for Systems Biology, Seattle, WA 98109, USA.
Sean MackayIsoplexis Corporation, Branford, CT 06405, USA.
D Shane O'MahonySwedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA.
Christopher R DaleSwedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA.
Julie A WallickSwedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA.
Heather A AlgrenSwedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA.
Michael A ZagerCenter for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
ISB-Swedish COVID19 Biobanking Unit
Wei WeiInstitute for Systems Biology, Seattle, WA 98109, USA.
Nathan D PriceInstitute for Systems Biology, Seattle, WA 98109, USA.
Sui HuangInstitute for Systems Biology, Seattle, WA 98109, USA.
Naeha SubramanianInstitute for Systems Biology, Seattle, WA 98109, USA; Department of Global Heath, and Department of Immunology, University of Washington, Seattle, WA 98109, USA.
Kai WangInstitute for Systems Biology, Seattle, WA 98109, USA.
Andrew T MagisInstitute for Systems Biology, Seattle, WA 98109, USA.
Jenn J HadlockInstitute for Systems Biology, Seattle, WA 98109, USA.
Leroy HoodInstitute for Systems Biology, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA.
Alan AderemCenter for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA.
Jeffrey A BluestoneDiabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.
Lewis L LanierDepartment of Microbiology and Immunology, University of California, San Francisco, and Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA.
Philip D GreenbergDivision of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Departments of Immunology and Medicine, University of Washington, Seattle, WA 98109, USA.
Raphael GottardoVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA.
Mark M DavisInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Jason D GoldmanSwedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA; Division of Allergy & Infectious Diseases, University of Washington, Seattle, WA 98109, USA. Electronic address: jason.goldman@swedish.org.
James R HeathInstitute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA. Electronic address: jim.heath@isbscience.org.
Institute for Systems Biology · USProvidence College · USUniversity of Washington · USUniversity of California, San Francisco · USInfectious Disease Research Institute · USIsoPlexis (United States) · USCape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa · ZAFred Hutch Cancer Center · USHoward Hughes Medical Institute · USStanford University · US
Funding
Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5MSystems Biology CoreU19AI128914 · NIAID · SEATTLE CHILDREN'S HOSPITAL · PI Margaret Juliana McElrath, KENNETH D STUART · 2017 to 2026
$29.5MNK MemoryR01AI068129 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LANIER, LEWIS LEE · 2006 to 2020
$6.0MDOCKET: accelerating knowledge extraction from biomedical data setsOT2TR003443 · NCATS · INSTITUTE FOR SYSTEMS BIOLOGY · PI GLUSMAN, GWÊNLYN, HADLOCK, JENNIFER · 2020 to 2024
$3.1MAccelerated emphysema in HIV-infected smokers: the role of extracellular vesiclesR01DA040395 · NIDA · OHIO STATE UNIVERSITY · PI DIAZ, PHILIP T, NANASINKAM, SERGE PATRICK · 2015 to 2019
$2.5MMicrofluidics Array Based Sorting, Isolation, and RNA Analysis in Single Extracellular V csiclesUG3TR002884 · NCATS · OHIO STATE UNIVERSITY · PI KIM, BETTY, REATEGUI, EDUARDO · 2019 to 2020
$822kCan a modest change in regulation of NOD1 expression have a major impact on inflammation and gastric cancer?R21AI138258 · NIAID · INSTITUTE FOR SYSTEMS BIOLOGY · PI SUBRAMANIAN, NAEHA · 2018 to 2019
$523kNCATS NIH HHS OT2 TR003443NCATS NIH HHS UG3 TR002884NIAID NIH HHS R01 AI068129NIAID NIH HHS R21 AI138258NIAID NIH HHS U19 AI128914NIDA NIH HHS R01 DA040395
Abstract
We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.
Indexed as
COVID-19GenomicsRNA-SeqSARS-CoV-2Single-Cell AnalysisAdolescentAdultAgedAged, 80 and overFemaleHumansMaleMiddle AgedSeverity of Illness IndexCITE-seqCOVID-19immune responseinfectionmetabolomicsmulti-omicsproteomicssingle-cell RNA-seqsingle-cell secretomesingle-cell TCR-seq
Identifiers
What Socratic holds
Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390
Registered trials
NCT05336851ClinicalTrials.gov
NCT06667063ClinicalTrials.gov
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 Socratic graph.