Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes

Neal G. Ravindra; Mia Madel Alfajaro; Victor Gasque; Nicholas C. Huston; Han Wan; Klara Szigeti-Buck; Yuki Yasumoto; Allison M. Greaney; Victoria Habet; Ryan D. Chow; Jennifer S. Chen; Jin Wei; Renata B. Filler; Bao Wang; Guilin Wang; Laura E. Niklason; Ruth R. Montgomery; Stephanie C. Eisenbarth; Sidi Chen; Adam Williams; Akiko Iwasaki; Tamas L. Horvath; Ellen F. Foxman; Richard W. Pierce; Anna Marie Pyle; David van Dijk; Craig B. Wilen

doi:10.1371/JOURNAL.PBIO.3001143

Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes

Neal G. Ravindra, Mia Madel Alfajaro, Victor Gasque, Nicholas C. Huston, Han Wan, Klara Szigeti-Buck, Yuki Yasumoto, Allison M. Greaney, Victoria Habet, Ryan D. Chow, Jennifer S. Chen, Jin Wei, Renata B. Filler, Bao Wang, Guilin Wang, Laura E. Niklason, Ruth R. Montgomery, Stephanie C. Eisenbarth, Sidi Chen, Adam WilliamsAkiko Iwasaki, Tamas L. Horvath, Ellen F. Foxman, Richard W. Pierce, Anna Marie Pyle, David van Dijk^*, Craig B. Wilen^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

98 Scopus citations

Abstract

There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host–viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air–liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.

Original language	English (US)
Article number	e3001143
Journal	PLoS biology
Volume	19
Issue number	3
DOIs	https://doi.org/10.1371/JOURNAL.PBIO.3001143
State	Published - Mar 17 2021
Externally published	Yes

ASJC Scopus subject areas

Agricultural and Biological Sciences(all)
Biochemistry, Genetics and Molecular Biology(all)
Immunology and Microbiology(all)
Neuroscience(all)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1371/JOURNAL.PBIO.3001143

Cite this

Ravindra, N. G., Alfajaro, M. M., Gasque, V., Huston, N. C., Wan, H., Szigeti-Buck, K., Yasumoto, Y., Greaney, A. M., Habet, V., Chow, R. D., Chen, J. S., Wei, J., Filler, R. B., Wang, B., Wang, G., Niklason, L. E., Montgomery, R. R., Eisenbarth, S. C., Chen, S., ... Wilen, C. B. (2021). Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLoS biology, 19(3), Article e3001143. https://doi.org/10.1371/JOURNAL.PBIO.3001143

@article{9b45038a6f1849d29b0986df1821cc79,

title = "Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes",

abstract = "There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host–viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air–liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.",

author = "Ravindra, {Neal G.} and Alfajaro, {Mia Madel} and Victor Gasque and Huston, {Nicholas C.} and Han Wan and Klara Szigeti-Buck and Yuki Yasumoto and Greaney, {Allison M.} and Victoria Habet and Chow, {Ryan D.} and Chen, {Jennifer S.} and Jin Wei and Filler, {Renata B.} and Bao Wang and Guilin Wang and Niklason, {Laura E.} and Montgomery, {Ruth R.} and Eisenbarth, {Stephanie C.} and Sidi Chen and Adam Williams and Akiko Iwasaki and Horvath, {Tamas L.} and Foxman, {Ellen F.} and Pierce, {Richard W.} and Pyle, {Anna Marie} and {van Dijk}, David and Wilen, {Craig B.}",

note = "Publisher Copyright: {\textcopyright} 2021 Ravindra et al.",

year = "2021",

month = mar,

day = "17",

doi = "10.1371/JOURNAL.PBIO.3001143",

language = "English (US)",

volume = "19",

journal = "PLoS biology",

issn = "1544-9173",

publisher = "Public Library of Science",

number = "3",

}

Ravindra, NG, Alfajaro, MM, Gasque, V, Huston, NC, Wan, H, Szigeti-Buck, K, Yasumoto, Y, Greaney, AM, Habet, V, Chow, RD, Chen, JS, Wei, J, Filler, RB, Wang, B, Wang, G, Niklason, LE, Montgomery, RR, Eisenbarth, SC, Chen, S, Williams, A, Iwasaki, A, Horvath, TL, Foxman, EF, Pierce, RW, Pyle, AM, van Dijk, D & Wilen, CB 2021, 'Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes', PLoS biology, vol. 19, no. 3, e3001143. https://doi.org/10.1371/JOURNAL.PBIO.3001143

TY - JOUR

T1 - Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes

AU - Ravindra, Neal G.

AU - Alfajaro, Mia Madel

AU - Gasque, Victor

AU - Huston, Nicholas C.

AU - Wan, Han

AU - Szigeti-Buck, Klara

AU - Yasumoto, Yuki

AU - Greaney, Allison M.

AU - Habet, Victoria

AU - Chow, Ryan D.

AU - Chen, Jennifer S.

AU - Wei, Jin

AU - Filler, Renata B.

AU - Wang, Bao

AU - Wang, Guilin

AU - Niklason, Laura E.

AU - Montgomery, Ruth R.

AU - Eisenbarth, Stephanie C.

AU - Chen, Sidi

AU - Williams, Adam

AU - Iwasaki, Akiko

AU - Horvath, Tamas L.

AU - Foxman, Ellen F.

AU - Pierce, Richard W.

AU - Pyle, Anna Marie

AU - van Dijk, David

AU - Wilen, Craig B.

PY - 2021/3/17

Y1 - 2021/3/17

N2 - There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host–viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air–liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.

AB - There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host–viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air–liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.

UR - http://www.scopus.com/inward/record.url?scp=85103684001&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85103684001&partnerID=8YFLogxK

U2 - 10.1371/JOURNAL.PBIO.3001143

DO - 10.1371/JOURNAL.PBIO.3001143

M3 - Article

C2 - 33730024

AN - SCOPUS:85103684001

SN - 1544-9173

VL - 19

JO - PLoS biology

JF - PLoS biology

IS - 3

M1 - e3001143

ER -

Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes

Abstract

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this