Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19

Genome Med. 2022 Feb 17;14(1):16. doi: 10.1186/s13073-022-01021-1.


Background: Understanding the host genetic architecture and viral immunity contributes to the development of effective vaccines and therapeutics for controlling the COVID-19 pandemic. Alterations of immune responses in peripheral blood mononuclear cells play a crucial role in the detrimental progression of COVID-19. However, the effects of host genetic factors on immune responses for severe COVID-19 remain largely unknown.

Methods: We constructed a computational framework to characterize the host genetics that influence immune cell subpopulations for severe COVID-19 by integrating GWAS summary statistics (N = 969,689 samples) with four independent scRNA-seq datasets containing healthy controls and patients with mild, moderate, and severe symptom (N = 606,534 cells). We collected 10 predefined gene sets including inflammatory and cytokine genes to calculate cell state score for evaluating the immunological features of individual immune cells.

Results: We found that 34 risk genes were significantly associated with severe COVID-19, and the number of highly expressed genes increased with the severity of COVID-19. Three cell subtypes that are CD16+monocytes, megakaryocytes, and memory CD8+T cells were significantly enriched by COVID-19-related genetic association signals. Notably, three causal risk genes of CCR1, CXCR6, and ABO were highly expressed in these three cell types, respectively. CCR1+CD16+monocytes and ABO+ megakaryocytes with significantly up-regulated genes, including S100A12, S100A8, S100A9, and IFITM1, confer higher risk to the dysregulated immune response among severe patients. CXCR6+ memory CD8+ T cells exhibit a notable polyfunctionality including elevation of proliferation, migration, and chemotaxis. Moreover, we observed an increase in cell-cell interactions of both CCR1+ CD16+monocytes and CXCR6+ memory CD8+T cells in severe patients compared to normal controls among both PBMCs and lung tissues. The enhanced interactions of CXCR6+ memory CD8+T cells with epithelial cells facilitate the recruitment of this specific population of T cells to airways, promoting CD8+T cell-mediated immunity against COVID-19 infection.

Conclusions: We uncover a major genetics-modulated immunological shift between mild and severe infection, including an elevated expression of genetics-risk genes, increase in inflammatory cytokines, and of functional immune cell subsets aggravating disease severity, which provides novel insights into parsing the host genetic determinants that influence peripheral immune cells in severe COVID-19.

Keywords: COVID-19; GWAS; Immune cells; Inflammatory storm; Single-cell sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CD8-Positive T-Lymphocytes / virology*
  • COVID-19 / genetics*
  • COVID-19 / immunology
  • COVID-19 / pathology*
  • Computational Biology / methods
  • GPI-Linked Proteins / metabolism
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study
  • Humans
  • Megakaryocyte Progenitor Cells / immunology
  • Megakaryocyte Progenitor Cells / virology
  • Monocytes / metabolism
  • Monocytes / virology*
  • Quantitative Trait Loci
  • Receptors, CCR1 / immunology
  • Receptors, CCR1 / metabolism
  • Receptors, CXCR6 / immunology
  • Receptors, CXCR6 / metabolism
  • Receptors, IgG / metabolism
  • Sequence Analysis, RNA
  • Severity of Illness Index
  • Single-Cell Analysis / methods*


  • CCR1 protein, human
  • CXCR6 protein, human
  • FCGR3B protein, human
  • GPI-Linked Proteins
  • Receptors, CCR1
  • Receptors, CXCR6
  • Receptors, IgG