A Table of all published Omics studies with Covid-19

posted in: Resources

A number of Covid-19 studies with metabolomics and proteomics phenotypes are currently in the making. Here I maintain a table of these studies to keep track of what has been published so far (last updated 23 March 2021.

Should you know about any study that is missing here, please let me know.

A list of all proteins linked to Covid-19 can be found at UniProt.

ReferenceTitleStudy populationOmics platform# participants# analyzed samples# omics traitsGeneral comments
Shen et al., Cell, 27 May 2020Proteomic and Metabolomic Characterization of COVID-19 Patient SeraRetrospective cohort study in Taizhou Public Health Medical Center, ChinaIsotope labeled proteomics & UPLC-MS/MS untargeted metabolomics99: 46 COVID-19 and 53 controlsSingle time point894 proteins, 941 metabolites
Messner et al., Cell Systems 1 June 2020 and medRxiv 3 May 2020Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infectionprocessing paper
Lucas etal., Nature, 27 July 2020Longitudinal analyses reveal immunological misfiring in severe COVID-19Patients admitted to the Yale New Haven Hospital, USAImmune profiling, flow cytometry219: 33 severe, 80 moderate, and 106 healthyFive time points72 cytokines
D'Alessandro et al., J. Proteome Res., 29 July 2020 and medRxiv 29 May 2020Serum proteomics in COVID-19 patients: Altered coagulation and complement status as a function of IL-6 levelprocessing paper
Appelberg et al., Emerging Microbes & Infections, 31 Jul 2020Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cellsStudy in COVID-19 infected cellsNANANANAMay be removed from this table, not a study on patient samples
Arunachalam et al., Science, 4 Sep 2020Systems biological assessment of immunity to mild versus severe COVID-19 infection in humansHong Kong and Atlanta, USASingle cell transcriptomics, cytokines, mass cytometry of blood leucocytes, OLINK inflammation panel, ...145: 76 COVID-19 patients and 69 healthy individualsSingle time point92 proteins (71 detected), many other (see platform)
Overmyer et al., Cell Systems 7 Oct 2020 and medRxiv 19 Jul 2020Large-Scale Multi-omic Analysis of COVID-19 Severityprocessing paper
Su et al., Cell, 28 Oct 2020 Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19North American (different ethnicities)5 Olink panels, Metabolon non-targeted metabolomics, single-cell multiplex secretome assay, single cell RNAseq, ...397: 139 COVID-19 patients + 258 healthy controlsTwo time points464 proteins, 1050 metabolitesData freely shared in Supplement
Mudd et al., Science Advances, 9 Dec 2020Distinct inflammatory profiles distinguish COVID-19 from influenza with limited contributions from cytokine stormCOVID-19 and influenza patientscytokines using Luminex, single cell RNAseq, flow cytometry168: 79 COVID-19, 26 seasonal influenza, ...Single time point35 cytokines, 12 antigens
Delafiori et al., Analytical Chemistry, 20 Jan 2021 and
medRxiv 27 July 2020
Covid-19 automated diagnosis and risk assessment through Metabolomics and Machine-LearningBrasilmass-spectrometry 815: 442 COVID-19, 350 controls, 23 COVID-19 suspiciousSingle time point19 molecules related to the disease’s pathophysiology and several discriminating features to patient’s health-related outcomes
Gisby et al., eLife, 11 Mar 2021 and medRxiv, 6 Nov 2020Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal diseaseEnd-stage kidney disease patients5 OLINK panels: ‘inflammation’, ‘immune response’, ‘cardiometabolic' 1-3152: 55 pos, 51 neg; +replication 46 pos Single time point436 plasma proteins (replication in serum)Data freely shared in Supplement
Tang et al., medRxiv 19 June 2020Proteomics Uncovers Immunosuppression in COVID-19 Patients with Long Disease Courseprocessing paper
Chen et al., medRxiv 22 Jun 2020COVID-19 severity is associated with immunopathology and multi-organ damageprocessing paper
Patel et al., medRxiv 23 Jun 2020Proteomic blood profiling in mild, severe and critical COVID-19 patientsSweden4 Olink panels: inflammation, autoimmune, cardiovascular, neurology 87: 59 COVID-19 mild (n=26), severe (n=9) or critical (n=24) cases and 28 controlsSingle time point344 unique proteins after QCplot data using a Shiny App
Chen et al., medRxiv 24 June 2020Breath-borne VOC Biomarkers for COVID-19processing paper
Soares, medRxiv 3 July 2020A novel specific artificial intelligence-based method to identify COVID-19 cases using simple blood examsprocessing paperuses public data
Maras et al., medRxiv 7 Jul 2020Multi-Omics integration analysis of respiratory specimen characterizes baseline molecular determinants associated with COVID-19 diagnosis.processing paper
Wu et al., medRxiv 22 July 2020The Trans-omics Landscape of COVID-19processing paper
Nie et al., medRxiv 19 August 2020Multi-organ Proteomic Landscape of COVID-19 Autopsiesprocessing paper
Cai et al., medRxiv 8 Sep 2020Kynurenic acid underlies sex-specific immune responses to COVID-19processing paper
Reyes et al., medRxiv 18 September 2020Proteomics identifies a type I IFN, prothrombotic hyperinflammatory circulating COVID-19 neutrophil signature distinct from non-COVID-19 ARDSprocessing paper
Bernardes et al., medRxiv 18 Sep 2020Longitudinal multi-omics analysis identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectoriesprocessing paper
Cardoso et al., medRxiv 4 Oct 2020Prognostic accuracy of MALDI mass spectrometric analysis of plasma in COVID-19processing paper
Huang, medRxiv, 5 Oct 2020Comparing biomarkers for COVID-19 disease with commonly associated preexisting conditions and complicationsSee table entry below (Filbin et al.)See belowSee belowSee belowSee belowThis paper appears to describe the same study as Filbin et al., bioRxiv 2020
Garcia et al., medRxiv 14 Oct 2020Innate lymphoid cell composition associates with COVID-19 disease severityprocessing paper
Petrović et al., medRxiv 20 Oct 2020Composition of the immunoglobulin G glycome associates with the severity of COVID-19processing paperglycomics
Filbin et al., bioRxiv 3 Nov 2020 (v1)Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patientsPatients presenting with Cov19 symptoms at Massachusetts General HospitalOLINK Explore 1536384: 306 positive, 78 negativeThree time points: 383 (day0), 218 (day3), 136 (day7), 44 (event driven)1472 unique plasma proteinsStudy has also collected SOMAscan data; OLINK data freely shared on web-site
Livanos et al., medRxiv 11 Nov 2020Gastrointestinal involvement attenuates COVID-19 severity and mortalityprocessing paper
Dierckx et al. medRxiv 12 Nov 2020The metabolic fingerprint of COVID-19 severityprocessing paper
Demichev et al., medRxiv 12 Nov 2020A time-resolved proteomic and diagnostic map characterizes COVID-19 disease progression and predicts outcomeprocessing paper
Meoni etal., medRxiv 13 Nov 2020Metabolomic/lipidomic profiling of COVID-19 and individual response to tocilizumabprocessing paper
Giron et al., medRxiv 16 Nov 2020Severe COVID-19 Is Fueled by Disrupted Gut Barrier Integrityprocessing paper
Crunfli et al., medRxiv 18 Nov 2020SARS-CoV-2 infects brain astrocytes of COVID-19 patients and impairs neuronal viabilityprocessing paper
Chioh et al., medRxiv 18 Nov 2020Convalescent COVID-19 patients are susceptible to endothelial dysfunction due to persistent immune activationprocessing paper
Spick et al., medRxiv 28 Nov 2020Changes to the sebum lipidome upon COVID-19 infection observed via non-invasive and rapid sampling from the skinprocessing paperskin lipidomics
Sindelar et al., medRxiv 8 Feb 2021Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of COVID-19 Disease SeverityBarnes Jewish Hospital, Christian Hospital, and
Washington University
untargeted metabolomics341: 67 negative, 274 positive, thereof 253 admitted to the hospital, 129 ended up in ICU, 48 Covid deaths>700 samples, up to six longitudinal time points25 metabolites measured at admission predict disease severityraw LC/MS data and processed metabolic profiles with corresponding
deidentified metadata will be made publicly available on the
Metabolomics Workbench repository
Geyer et al., medRxiv 23 Feb 2021High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversionGerman University hospitalunbiased MS-based proteomics, five different SARS-CoV-2 antibody immunoassays293: 263 controls + 31 patients720 proteomes of 262 controls and 458 longitudinal samples (average of 31 days) of 31 patients502 quantified proteinssee also Buchholtz et al., medXriv 23 Feb 2021 for companion paper on seroconversion in the same cohort
Völlmy et al., medRxiv 13 Mar 2021Is there a serum proteome signature to predict mortality in severe COVID-19 patients?University Hospital of Ferrara, Italyserum proteome profiles (DIA-MS)33 COVID-19 patients admitted to respiratory and intensive care, 17 survivors, 16 deceasedup to three time points 452 proteins quantified on average