Single-Cell Sequencing of Peripheral Mononuclear Cells Reveals Distinct Immune Response Landscapes of COVID-19 and Influenza Patients

Immunity. 2020 Sep 15;53(3):685-696.e3. doi: 10.1016/j.immuni.2020.07.009. Epub 2020 Jul 19.


The coronavirus disease 2019 (COVID-19) pandemic poses a current world-wide public health threat. However, little is known about its hallmarks compared to other infectious diseases. Here, we report the single-cell transcriptional landscape of longitudinally collected peripheral blood mononuclear cells (PBMCs) in both COVID-19- and influenza A virus (IAV)-infected patients. We observed increase of plasma cells in both COVID-19 and IAV patients and XIAP associated factor 1 (XAF1)-, tumor necrosis factor (TNF)-, and FAS-induced T cell apoptosis in COVID-19 patients. Further analyses revealed distinct signaling pathways activated in COVID-19 (STAT1 and IRF3) versus IAV (STAT3 and NFκB) patients and substantial differences in the expression of key factors. These factors include relatively increase of interleukin (IL)6R and IL6ST expression in COVID-19 patients but similarly increased IL-6 concentrations compared to IAV patients, supporting the clinical observations of increased proinflammatory cytokines in COVID-19 patients. Thus, we provide the landscape of PBMCs and unveil distinct immune response pathways in COVID-19 and IAV patients.

Keywords: COVID-19; IL-6R; apoptosis; influenza; scRNA-seq.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Betacoronavirus / immunology
  • COVID-19
  • Coronavirus Infections / immunology*
  • Cytokines / immunology*
  • Humans
  • Influenza A Virus, H1N1 Subtype / immunology
  • Influenza, Human / immunology*
  • Leukocytes, Mononuclear / immunology*
  • Pandemics
  • Pneumonia, Viral / immunology*
  • SARS-CoV-2
  • Signal Transduction / immunology*


  • Cytokines