Comprehensive Immune Profiling of COVID-19

Sample collection was designed to meet minimal risk guidelines for blood collection for hospitalized adults, and sample-sparing assays are used when feasible. Blood samples (10 ml per time point) and nasal swabs (mid-turbinate) are collected at each specified time point, and blood is processed within 6 hours of collection according to the IMPACC standardized operating procedure. Whole blood and peripheral blood mononuclear cells (PBMCs) are collected to identify distinct immune cell populations and quantify changes in cell populations, gene expression, and activation markers [e.g., cytometry by time-of-flight (CyTOF) and bulk RNA transcriptomics] over the course of COVID-19 and convalescence. DNA is collected from whole blood at a single time point for genetic analyses (e.g., whole-exome sequencing). Serum is used to characterize SARS-CoV-2–specific antibodies, including virus neutralization, both serum and plasma are used for proteomics and metabolomics, and plasma is used to measure soluble inflammatory mediators (e.g., cytokines and chemokines) using oligonucleotide-linked antibody detection (Olink). RNA from the nasal swab is used to assess SARS-CoV-2 viral load and genomic sequence and to evaluate changes in immune-related upper airway epithelial gene expression (i.e., bulk transcriptomics). In addition, EAs are collected from intubated patients and processed within 2 hours of collection according to the IMPACC standardized operating procedures. EA cells are assessed by CyTOF and bulk transcriptomics to identify and quantify changes in gene expression and activation state of distinct immune cell populations in the lower respiratory tract. Processed samples are barcoded and centrally tracked on a laboratory information management system (LDMS; Frontier Science). All supplies necessary for sample collection and sample processing are centrally procured and supplied to the participating sites. Sample collection, processing, and storage procedures (Fig. 3) are standardized across sites, and samples are transported to centralized core laboratories (Core Labs) in batches for testing and analysis. The complete sample processing manual of procedures is included as Supplementary Methods.

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Rouphael N., Maecker H., Montgomery R.R., Diray-Arce J., Kleinstein S.H., Altman M.C., Bosinger S.E., Eckalbar W., Guan L., Hough C.L., Krammer F., Langelier C., Levy O., McEnaney K., Peters B., Rahman A., Rajan J.V., Sigelman S., Steen H., van Bakel H., Ward A., Wilson M.R., Woodruff P., Zamecnik C.R., Augustine A.D., Ozonoff A., Reed E.F., Becker P.M., Higuita N.A., Altman M.C., Atkinson M.A., Baden L.R., Becker P.M., Bime C., Brakenridge S.C., Calfee C.S., Cairns C.B., Corry D., Davis M.M., Augustine A.D., Ehrlich L.I., Haddad E.K., Erle D.J., Fernandez-Sesma A., Hafler D.A., Hough C.L., Kheradmand F., Kleinstein S.H., Kraft M., Levy O., McComsey G.A., Melamed E., Messer W., Metcalf J., Montgomery R.R., Nadeau K.C., Ozonoff A., Peters B., Pulendran B., Reed E.F., Rouphael N., Sarwal M., Schaenman J., Sekaly R., Shaw A.C, & Simon V. (2021). Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study. Science Immunology, 6(62), eabf3733.

Publication 2021

Adults Antibodies Antibody Assays Blood Bulk Cell immune state Cells Chemokines Covid 19 Cytokines Gene expression Genomic Inflammatory mediators Nasal Oligonucleotide Patients Peripheral blood mononuclear cells Plasma Point Populations Respiratory tract Sample collection Sars cov 2 viral Serum Transcriptomics Turbinate Virus

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Immune cell populations
Gene expression
Activation markers
SARS-CoV-2 viral load
SARS-CoV-2 genomic sequence
Immune-related upper airway epithelial gene expression
Gene expression and activation state of distinct immune cell populations in the lower respiratory tract

control variables

Sample collection procedure (10 ml blood, mid-turbinate nasal swabs)
Sample processing (within 6 hours for blood, within 2 hours for endotracheal aspirates)
Standardized sample collection, processing, and storage procedures across sites
Centralized core laboratories for testing and analysis

positive controls

None explicitly mentioned

negative controls

None explicitly mentioned

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