A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium
Abstract
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated comparison with influenza and sepsis patients versus healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity involved cells, their inflammatory mediators and networks, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism, and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Systems-based integrative analyses including tensor and matrix decomposition of all modalities revealed feature groupings linked with severity and specificity compared to influenza and sepsis. Our approach and blood atlas will support future drug development, clinical trial design, and personalized medicine approaches for COVID-19.
Datasets
1. COMBAT project: single cell gene expression data from COVID-19, sepsis and flu patient PBMCs
Metadata
Source
GEX_region
minor_subset
major_subset
cell_type_source
assay_ontology_term_id
self_reported_ethnicity_ontology_term_id
disease_ontology_term_id
tissue_ontology_term_id
cell_type_ontology_term_id
cell_type_original
development_stage_ontology_term_id
sex_ontology_term_id
organism_ontology_term_id
suspension_type
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
COVID_HCW_MILD88898 cells A: CD4/naive/reg. T cells301696 cells C: Monocytes/cDC261120 cells B: TEM/prolif. T/NK cells180392 cells D: B/Plasma cells57438 cells F: pDC/HSC/platelets etc.9515 cells NK.CD56hi.CD16int.XCL1/26514 cells CD8.TEFF.prolif4899 cells CD4.TEFF.prolif4773 cells T_COVID_HCW_MILD52264 cells MNP_COVID_MILD28749 cells MNP_COVID_CRIT26145 cells MNP_COVID_HCW_MILD19667 cells NK_COVID_HCW_MILD7853 cells nan_COVID_HCW_MILD4350 cells B_COVID_HCW_MILD4308 cells PB_COVID_HCW_MILD338 cells ERYTH_COVID_CRIT100 cells HSC_COVID_HCW_MILD93 cells PLT_COVID_HCW_MILD22 cells ERYTH_COVID_HCW_MILD3 cells MONDO:0100096724710 cells UBERON:0000178836148 cells HsapDv:0000099253263 cells HsapDv:0000101210081 cells HsapDv:0000098119244 cells HsapDv:000009778783 cells HsapDv:000010066906 cells HsapDv:000010250418 cells HsapDv:000024643551 cells HsapDv:000010313902 cells NCBITaxon:9606836148 cells CD4-positive, alpha-beta T cell269661 cells classical monocyte213697 cells CD8-positive, alpha-beta T cell106025 cells natural killer cell70299 cells non-classical monocyte33172 cells gamma-delta T cell9580 cells double-positive, alpha-beta thymocyte6561 cells double negative T regulatory cell4557 cells mucosal invariant T cell4541 cells hematopoietic stem cell1868 cells megakaryocyte-erythroid progenitor cell1563 cells enucleated reticulocyte304 cells 5-year-old human stage253263 cells 7-year-old human stage210081 cells 4-year-old human stage119244 cells 3-year-old human stage78783 cells 6-year-old human stage66906 cells 8-year-old human stage50418 cells 1-year-old human stage43551 cells 9-year-old human stage13902 cells Analyze this study
Source data
https://cellxgene.cziscience.com/collections/8f126edf-5405-4731-8374-b5ce11f53e82
Alias names
EGAS00001005493, PMID35216673, PMC8776501
Cite this study
Ahern, D.J., Ai, Z., Ainsworth, M., Allan, C., Allcock, A., Angus, B., Ansari, M.A., Arancibia-Cárcamo, C.V., Aschenbrenner, D., Attar, M. and Baillie, J.K., 2022. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell, 185(5), pp.916-938. https://doi.org/10.1016/j.cell.2022.01.012
