Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients

Emerg Microbes Infect. 2020 Dec;9(1):761-770. doi: 10.1080/22221751.2020.1747363.


Circulating in China and 158 other countries and areas, the ongoing COVID-19 outbreak has caused devastating mortality and posed a great threat to public health. However, efforts to identify effectively supportive therapeutic drugs and treatments has been hampered by our limited understanding of host immune response for this fatal disease. To characterize the transcriptional signatures of host inflammatory response to SARS-CoV-2 (HCoV-19) infection, we carried out transcriptome sequencing of the RNAs isolated from the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) specimens of COVID-19 patients. Our results reveal distinct host inflammatory cytokine profiles to SARS-CoV-2 infection in patients, and highlight the association between COVID-19 pathogenesis and excessive cytokine release such as CCL2/MCP-1, CXCL10/IP-10, CCL3/MIP-1A, and CCL4/MIP1B. Furthermore, SARS-CoV-2 induced activation of apoptosis and P53 signalling pathway in lymphocytes may be the cause of patients' lymphopenia. The transcriptome dataset of COVID-19 patients would be a valuable resource for clinical guidance on anti-inflammatory medication and understanding the molecular mechansims of host response.

Keywords: COVID-19; cytokine; inflammation; lymphopenia; transcriptome profiling.

MeSH terms

  • Apoptosis
  • Betacoronavirus
  • Bronchoalveolar Lavage Fluid*
  • COVID-19
  • Chemokines / analysis*
  • Coronavirus Infections / blood
  • Coronavirus Infections / genetics*
  • Coronavirus Infections / immunology
  • Cytokines / analysis*
  • Humans
  • Leukocytes, Mononuclear*
  • Lymphopenia
  • Pandemics
  • Pneumonia, Viral / blood
  • Pneumonia, Viral / genetics*
  • Pneumonia, Viral / immunology
  • RNA-Seq
  • SARS-CoV-2
  • Signal Transduction
  • Transcriptome*
  • Tumor Suppressor Protein p53


  • Chemokines
  • Cytokines
  • TP53 protein, human
  • Tumor Suppressor Protein p53

Grants and funding

This study was supported by Special Fund for COVID-19 Research of Wuhan University, National Science and Technology Major Project (#2018ZX10733403), China NSFC grants (#81672008, 31871316), Hubei Natural Science Foundation (#2018CFA035), Basic Scientific Research Foundation of Central Universities (#2042019gf0026), Ministry of Science and Technology of China, the National Mega Project on Major Infectious Disease Prevention (#2017ZX10103005) and National Key Research and Development Program of China (#2018YFE0204500).