UMMS Affiliation

Department of Medicine, Division of Infectious Diseases and Immunology; Department of Medicine, Division of Rheumatology; Graduate School of Biomedical Sciences

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Immunology and Infectious Disease | Infectious Disease | Microbiology | Respiratory Tract Diseases | Virus Diseases


BACKGROUND Influenza A virus (IAV) and SARS-CoV-2 are pandemic viruses causing millions of deaths, yet their clinical manifestations are distinctly different.

METHODS With the hypothesis that upper airway immune and epithelial cell responses are also distinct, we performed single-cell RNA sequencing (scRNA-Seq) on nasal wash cells freshly collected from adults with either acute COVID-19 or influenza or from healthy controls. We focused on major cell types and subtypes in a subset of donor samples.

Results Nasal wash cells were enriched for macrophages and neutrophils for both individuals with influenza and those with COVID-19 compared with healthy controls. Hillock-like epithelial cells, M2-like macrophages, and age-dependent B cells were enriched in COVID-19 samples. A global decrease in IFN-associated transcripts in neutrophils, macrophages, and epithelial cells was apparent in COVID-19 samples compared with influenza samples. The innate immune response to SARS-CoV-2 appears to be maintained in macrophages, despite evidence for limited epithelial cell immune sensing. Cell-to-cell interaction analyses revealed a decrease in epithelial cell interactions in COVID-19 and highlighted differences in macrophage-macrophage interactions for COVID-19 and influenza.

Conclusions Our study demonstrates that scRNA-Seq can define host and viral transcriptional activity at the site of infection and reveal distinct local epithelial and immune cell responses for COVID-19 and influenza that may contribute to their divergent disease courses.

Funding Massachusetts Consortium on Pathogen Readiness, the Mathers Foundation, and the Department of Defense (W81XWH2110029) "COVID-19 Expansion for AIRe Program."


COVID-19, Infectious disease, Influenza, Innate immunity

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Copyright © 2021 Gao et al. This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit

DOI of Published Version



Gao KM, Derr AG, Guo Z, Nündel K, Marshak-Rothstein A, Finberg RW, Wang JP. Human nasal wash RNA-Seq reveals distinct cell-specific innate immune responses in influenza versus SARS-CoV-2. JCI Insight. 2021 Nov 22;6(22):e152288. doi: 10.1172/jci.insight.152288. PMID: 34618691; PMCID: PMC8663782. Link to article on publisher's site

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JCI insight

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Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.