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Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories

50 Pages Posted: 17 Aug 2020 Publication Status: Published

See all articles by Yapeng Su

Yapeng Su

Institute for Systems Biology

Daniel Chen

Institute for Systems Biology

Christopher Lausted

Institute for Systems Biology

Dan Yuan

Institute for Systems Biology

Jongchan Choi

Institute for Systems Biology

Cheng Dai

Institute for Systems Biology

Valentin Voillet

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Kelsey Scherler

Institute for Systems Biology

Pamela Troisch

Institute for Systems Biology

Venkata Duvvuri

Institute for Systems Biology

Priyanka Baloni

Institute for Systems Biology

Guangrong Qin

Institute for Systems Biology

Brett Smith

Institute for Systems Biology

Sergey Kornilov

Institute for Systems Biology

Clifford Rostomily

Institute for Systems Biology

Alex Xu

Institute for Systems Biology

Jing Li

Stanford University - Institute for Immunity, Transplantation and Infection

Shen Dong

University of California, San Francisco (UCSF) - Diabetes Center

Alissa Rothchild

Seattle Children’s Research Institute - Center for Global Infectious Disease Research

Jing Zhou

Isoplexis Corporation

Kim Murray

Institute for Systems Biology

Rick Edmark

Institute for Systems Biology

Sunga Hong

Institute for Systems Biology

Lesley Jones

Institute for Systems Biology

Yong Zhou

Institute for Systems Biology

Ryan Roper

Institute for Systems Biology

Sean Mackay

Isoplexis Corporation

Shane O'Mahony

Swedish Medical Center - Swedish Center for Research and Innovation

Christopher R. Dale

Swedish Medical Center - Swedish Center for Research and Innovation

Julie A. Wallick

Swedish Medical Center - Swedish Center for Research and Innovation

Heather A. Algren

Swedish Medical Center - Swedish Center for Research and Innovation

Zager A. Michael

Fred Hutchinson Cancer Research Center - Center for Data Visualization

Andrew Magis

Institute for Systems Biology

Wei Wei

Institute for Systems Biology

Nathan Price

Institute for Systems Biology

Sui Huang

Institute for Systems Biology

Naeha Subramanian

Institute for Systems Biology

Kai Wang

Institute for Systems Biology

Jennifer Hadlock

Institute for Systems Biology

Leroy Hood

Institute for Systems Biology

Alan Aderem

Seattle Children’s Research Institute - Center for Global Infectious Disease Research

Jeffrey A. Bluestone

University of California, San Francisco (UCSF) - Diabetes Center

Lewis L. Lanier

University of California, San Francisco (UCSF) - Department of Microbiology and Immunology

Phil Greenberg

Fred Hutchinson Cancer Research Center - Division of Clinical Research

Raphael Gottardo

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Mark M. Davis

Stanford University - Institute for Immunity, Transplantation and Infection

Jason D Goldman

Swedish Medical Group, Providence St Joseph Health

James Heath

Institute for Systems Biology

ISB-Swedish COVID19 Biobanking Unit

Independent

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Abstract

Host immune responses play central roles in controlling SARS-CoV2 infection, yet remain incompletely characterized and understood. Here, we present a comprehensive immune response map spanning 454 proteins and 847 metabolites in plasma integrated with single-cell multi-omic assays of 221,748 PBMCs in which whole transcriptome, 192 surface proteins, and T and B cell receptor sequence were analyzed within the context of clinical measures from 50 COVID19 patient samples. Our study reveals novel cellular subpopulations, such as proliferative exhausted CD8+ and CD4+ T cells, and cytotoxic CD4+ T cells, that may be features of severe COVID-19 infection. We condensed over 1 million immune features into a single immune response axis that independently aligns with many clinical features and is also strongly associated with disease severity. Our study represents an important resource towards understanding the heterogeneous immune responses of COVID-19 patients and may provide key information for informing therapeutic development.

Suggested Citation

Su, Yapeng and Chen, Daniel and Lausted, Christopher and Yuan, Dan and Choi, Jongchan and Dai, Cheng and Voillet, Valentin and Scherler, Kelsey and Troisch, Pamela and Duvvuri, Venkata R and Baloni, Priyanka and Qin, Guangrong and Smith, Brett and Kornilov, Sergey and Rostomily, Clifford and Xu, Alex and Li, Jing and Dong, Shen and Rothchild, Alissa and Zhou, Jing and Murray, Kim and Edmark, Rick and Hong, Sunga and Jones, Lesley and Zhou, Yong and Roper, Ryan and Mackay, Sean and O'Mahony, Shane and Dale, Christopher R. and Wallick, Julie A. and Algren, Heather A. and Michael, Zager A. and Magis, Andrew and Wei, Wei and Price, Nathan and Huang, Sui and Subramanian, Naeha and Wang, Kai and Hadlock, Jennifer and Hood, Leroy and Aderem, Alan and Bluestone, Jeffrey A. and Lanier, Lewis L. and Greenberg, Phil and Gottardo, Raphael and Davis, Mark M. and Goldman, Jason D and Heath, James and Unit, ISB-Swedish COVID19 Biobanking, Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories. Available at SSRN: https://ssrn.com/abstract=3659389 or http://dx.doi.org/10.2139/ssrn.3659389
This version of the paper has not been formally peer reviewed.

Yapeng Su

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Daniel Chen

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Christopher Lausted

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Dan Yuan

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Jongchan Choi

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Cheng Dai

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Valentin Voillet

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Kelsey Scherler

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Pamela Troisch

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Venkata R Duvvuri

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Priyanka Baloni

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Guangrong Qin

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Brett Smith

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Sergey Kornilov

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Clifford Rostomily

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Alex Xu

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Jing Li

Stanford University - Institute for Immunity, Transplantation and Infection

Stanford, CA 94305
United States

Shen Dong

University of California, San Francisco (UCSF) - Diabetes Center

Third Avenue and Parnassus
San Francisco, CA 94143
United States

Alissa Rothchild

Seattle Children’s Research Institute - Center for Global Infectious Disease Research ( email )

United States

Jing Zhou

Isoplexis Corporation

Kim Murray

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Rick Edmark

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Sunga Hong

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Lesley Jones

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Yong Zhou

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Ryan Roper

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Sean Mackay

Isoplexis Corporation ( email )

Shane O'Mahony

Swedish Medical Center - Swedish Center for Research and Innovation

Christopher R. Dale

Swedish Medical Center - Swedish Center for Research and Innovation

Julie A. Wallick

Swedish Medical Center - Swedish Center for Research and Innovation ( email )

Heather A. Algren

Swedish Medical Center - Swedish Center for Research and Innovation ( email )

Zager A. Michael

Fred Hutchinson Cancer Research Center - Center for Data Visualization ( email )

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Andrew Magis

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Wei Wei

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Nathan Price

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Sui Huang

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Naeha Subramanian

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Kai Wang

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Jennifer Hadlock

Institute for Systems Biology ( email )

401 Terry Ave N.
Seattle, WA 98109
United States

Leroy Hood

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

Alan Aderem

Seattle Children’s Research Institute - Center for Global Infectious Disease Research ( email )

United States

Jeffrey A. Bluestone

University of California, San Francisco (UCSF) - Diabetes Center ( email )

Third Avenue and Parnassus
San Francisco, CA 94143
United States

Lewis L. Lanier

University of California, San Francisco (UCSF) - Department of Microbiology and Immunology ( email )

San Francisco, CA 94143
United States

Phil Greenberg

Fred Hutchinson Cancer Research Center - Division of Clinical Research ( email )

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Raphael Gottardo

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division ( email )

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Mark M. Davis

Stanford University - Institute for Immunity, Transplantation and Infection

Stanford, CA 94305
United States

Jason D Goldman (Contact Author)

Swedish Medical Group, Providence St Joseph Health

1124 Columbia St. STE 600
Seattle, WA 98104
United States

James Heath

Institute for Systems Biology

401 Terry Ave N.
Seattle, WA 98109
United States

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