DOI: 10.7272/q6wd3xtb
title: Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2

description: Long COVID (LC) occurs after at least 10% of SARS-CoV-2 infections, yet
 its etiology remains poorly understood. We used “omic” assays and serology
 to deeply characterize the global and SARS-CoV-2-specific immunity in the
 blood of individuals with clear LC and non-LC clinical trajectories, 8
 months post-infection. We found that LC individuals exhibited systemic
 inflammation and immune dysregulation. This was evidenced by global
 differences in T cell subset distribution implying ongoing immune
 responses, as well as by sex-specific perturbations in cytolytic subsets.
 LC individuals displayed increased frequencies of CD4+ T cells poised to
 migrate to inflamed tissues and exhausted SARS-CoV-2-specific CD8+ T
 cells, higher levels of SARS-CoV-2 antibodies and a mis-coordination
 between their SARS-CoV-2-specific T and B cell responses. Our analysis
 suggested an improper crosstalk between the cellular and humoral adaptive
 immunity in LC, which can lead to the immune dysregulation, inflammation
 and clinical symptoms associated with this debilitating condition.
description: **READ ME FILE** ### General Information Title: Long COVID manifests with
 T cell dysregulation, inflammation, and an uncoordinated adaptive immune
 response to SARS-CoV-2 Contact: Nadia Roan, PhD Gladstone Institutes
 University of California, San Francisco
 Dates of
 collection: 12/23/21 -- 2/16/22 Information about geographic location of
 data collection: San Francisco Bay Area Key Words: COVID-19, SARS-CoV-2,
 Long Covid, LC, CyTOF, T cells ### Data and File Overview Included are 172
 FCS files total from 86 different CyTOF specimens total. Each file name
 begins with the de-identified patient ID (PID), followed by whether the
 individual was classified as LC or Recovered (R) individual. Next, the
 file name indicates CD4+ or CD8+ T cells were analyzed. Finally, the file
 name indicates "Atlas" for samples that were analyzed at
 baseline, and "resp" for responding cells that were identified
 after spike peptide stimulation. The table at the end of this ReadMe file
 includes additional information about each sample. All files were created
 in February - April 2022. Also included is a CSV file for the data
 generated using the Olink Proteomics platform. The data are in a format
 compatible with the commercial Olink analysis platform. PID corresponds to
 the patient ID matching the CyTOF data. OlinkID is an ID given by the
 commercial Olink platform. UniProt refers to the protein sequence
 identifier, and Assay refers to the common name of the protein identified.
 Also included are the Olink panel used, and QC metrics and limit of
 detection (LOD). The important data used for quantification are the NPX,
 which indicates relative expression levels. The entire output of the Olink
 platform, however, is provided in the CSV file so that it can be directly
 inputted into the Olink analysis software. #### Sharing and access
 information No licenses or restrictions are placed on the data. ####
 Methodological Information Methods used for generating and analyzing the
 CyTOF datasets are similar to those described:
 
 Methods for the commercial Olink platform are described on the manufacturer's website. ### Data-specific information Please see above information under "data and file overview" and "methodological information". Please see table at end for additional information about each sample, including whether they were from male or female participants, hospitalized or non-hospitalized participants, and the batch they were analyzed in. --- **PID^1^** **Category** **Sex** **Hospitalized** **Cells** **Sub-gate** **Batch^2^** --- PID111 LC^3^ Female Nho^5^ CD4 Atlas^7^ Batch2 PID111 LC Female Nho CD8 Atlas Batch2 PID234 R^4^ Female Nho CD4 Atlas Batch5 PID234 R Female Nho CD8 Atlas Batch5 PID338 R Female Nho CD4 Atlas Batch3 PID338 R Female Nho CD8 Atlas Batch3 PID942 R Female Nho CD4 Atlas Batch3 PID942 R Female Nho CD8 Atlas Batch3 PID913 R Female Nho CD4 Atlas Batch4 PID913 R Female Nho CD8 Atlas Batch4 PID608 R Female Nho CD4 Atlas Batch2 PID608 R Female Nho CD8 Atlas Batch2 PID914 R Male Nho CD4 Atlas Batch1 PID914 R Male Nho CD8 Atlas Batch1 PID912 R Male Nho CD4 Atlas Batch1 PID912 R Male Nho CD8 Atlas Batch1 PID283 LC Female Nho CD4 Atlas Batch2 PID283 LC Female Nho CD8 Atlas Batch2 PID526 R Female Nho CD4 Atlas Batch2 PID526 R Female Nho CD8 Atlas Batch2 PID313 R Male Nho CD4 Atlas Batch1 PID313 R Male Nho CD8 Atlas Batch1 PID204 LC Male Nho CD4 Atlas Batch1 PID204 LC Male Nho CD8 Atlas Batch1 PID564 R Male Nho CD4 Atlas Batch5 PID564 R Male Nho CD8 Atlas Batch5 PID900 LC Male Nho CD4 Atlas Batch1 PID900 LC Male Nho CD8 Atlas Batch1 PID233 LC Male Nho CD4 Atlas Batch1 PID233 LC Male Nho CD8 Atlas Batch1 PID709 LC Female Nho CD4 Atlas Batch3 PID709 LC Female Nho CD8 Atlas Batch3 PID652 LC Male Nho CD4 Atlas Batch3 PID652 LC Male Nho CD8 Atlas Batch3 PID871 LC Female Hos^6^ CD4 Atlas Batch6 PID871 LC Female Hos CD8 Atlas Batch6 PID560 LC Female Nho CD4 Atlas Batch2 PID560 LC Female Nho CD8 Atlas Batch2 PID230 R Male Hos CD4 Atlas Batch6 PID230 R Male Hos CD8 Atlas Batch6 PID546 LC Female Hos CD4 Atlas Batch6 PID546 LC Female Hos CD8 Atlas Batch6 PID799 LC Female Hos CD4 Atlas Batch6 PID799 LC Female Hos CD8 Atlas Batch6 PID670 LC Male Hos CD4 Atlas Batch6 PID670 LC Male Hos CD8 Atlas Batch6 PID753 LC Female Nho CD4 Atlas Batch2 PID753 LC Female Nho CD8 Atlas Batch2 PID741 R Male Hos CD4 Atlas Batch6 PID741 R Male Hos CD8 Atlas Batch6 PID439 R Male Nho CD4 Atlas Batch4 PID439 R Male Nho CD8 Atlas Batch4 PID831 LC Female Hos CD4 Atlas Batch6 PID831 LC Female Hos CD8 Atlas Batch6 PID247 LC Male Nho CD4 Atlas Batch3 PID247 LC Male Nho CD8 Atlas Batch3 PID245 LC Female Nho CD4 Atlas Batch4 PID245 LC Female Nho CD8 Atlas Batch4 PID476 LC Male Nho CD4 Atlas Batch4 PID476 LC Male Nho CD8 Atlas Batch4 PID161 LC Female Nho CD4 Atlas Batch4 PID161 LC Female Nho CD8 Atlas Batch4 PID213 LC Male Nho CD4 Atlas Batch4 PID213 LC Male Nho CD8 Atlas Batch4 PID804 LC Female Nho CD4 Atlas Batch4 PID804 LC Female Nho CD8 Atlas Batch4 PID717 LC Female Nho CD4 Atlas Batch5 PID717 LC Female Nho CD8 Atlas Batch5 PID414 LC Female Hos CD4 Atlas Batch6 PID414 LC Female Hos CD8 Atlas Batch6 PID621 LC Male Nho CD4 Atlas Batch5 PID621 LC Male Nho CD8 Atlas Batch5 PID102 R Female Nho CD4 Atlas Batch2 PID102 R Female Nho CD8 Atlas Batch2 PID693 R Male Nho CD4 Atlas Batch3 PID693 R Male Nho CD8 Atlas Batch3 PID896 R Male Nho CD4 Atlas Batch4 PID896 R Male Nho CD8 Atlas Batch4 PID923 LC Male Nho CD4 Atlas Batch5 PID923 LC Male Nho CD8 Atlas Batch5 PID927 LC Female Hos CD4 Atlas Batch6 PID927 LC Female Hos CD8 Atlas Batch6 PID447 LC Female Nho CD4 Atlas Batch5 PID447 LC Female Nho CD8 Atlas Batch5 PID147 LC Female Nho CD4 Atlas Batch5 PID147 LC Female Nho CD8 Atlas Batch5 PID111 LC Female Nho CD4 Resp^8^ Batch2 PID111 LC Female Nho CD8 Resp Batch2 PID234 R Female Nho CD4 Resp Batch5 PID234 R Female Nho CD8 Resp Batch5 PID338 R Female Nho CD4 Resp Batch3 PID338 R Female Nho CD8 Resp Batch3 PID942 R Female Nho CD4 Resp Batch3 PID942 R Female Nho CD8 Resp Batch3 PID913 R Female Nho CD4 Resp Batch4 PID913 R Female Nho CD8 Resp Batch4 PID608 R Female Nho CD4 Resp Batch2 PID608 R Female Nho CD8 Resp Batch2 PID914 R Male Nho CD4 Resp Batch1 PID914 R Male Nho CD8 Resp Batch1 PID912 R Male Nho CD4 Resp Batch1 PID912 R Male Nho CD8 Resp Batch1 PID283 LC Female Nho CD4 Resp Batch2 PID283 LC Female Nho CD8 Resp Batch2 PID526 R Female Nho CD4 Resp Batch2 PID526 R Female Nho CD8 Resp Batch2 PID313 R Male Nho CD4 Resp Batch1 PID313 R Male Nho CD8 Resp Batch1 PID204 LC Male Nho CD4 Resp Batch1 PID204 LC Male Nho CD8 Resp Batch1 PID564 R Male Nho CD4 Resp Batch5 PID564 R Male Nho CD8 Resp Batch5 PID900 LC Male Nho CD4 Resp Batch1 PID900 LC Male Nho CD8 Resp Batch1 PID233 LC Male Nho CD4 Resp Batch1 PID233 LC Male Nho CD8 Resp Batch1 PID709 LC Female Nho CD4 Resp Batch3 PID709 LC Female Nho CD8 Resp Batch3 PID652 LC Male Nho CD4 Resp Batch3 PID652 LC Male Nho CD8 Resp Batch3 PID871 LC Female Hos CD4 Resp Batch6 PID871 LC Female Hos CD8 Resp Batch6 PID560 LC Female Nho CD4 Resp Batch2 PID560 LC Female Nho CD8 Resp Batch2 PID230 R Male Hos CD4 Resp Batch6 PID230 R Male Hos CD8 Resp Batch6 PID546 LC Female Hos CD4 Resp Batch6 PID546 LC Female Hos CD8 Resp Batch6 PID799 LC Female Hos CD4 Resp Batch6 PID799 LC Female Hos CD8 Resp Batch6 PID670 LC Male Hos CD4 Resp Batch6 PID670 LC Male Hos CD8 Resp Batch6 PID753 LC Female Nho CD4 Resp Batch2 PID753 LC Female Nho CD8 Resp Batch2 PID741 R Male Hos CD4 Resp Batch6 PID741 R Male Hos CD8 Resp Batch6 PID439 R Male Nho CD4 Resp Batch4 PID439 R Male Nho CD8 Resp Batch4 PID831 LC Female Hos CD4 Resp Batch6 PID831 LC Female Hos CD8 Resp Batch6 PID247 LC Male Nho CD4 Resp Batch3 PID247 LC Male Nho CD8 Resp Batch3 PID245 LC Female Nho CD4 Resp Batch4 PID245 LC Female Nho CD8 Resp Batch4 PID476 LC Male Nho CD4 Resp Batch4 PID476 LC Male Nho CD8 Resp Batch4 PID161 LC Female Nho CD4 Resp Batch4 PID161 LC Female Nho CD8 Resp Batch4 PID213 LC Male Nho CD4 Resp Batch4 PID213 LC Male Nho CD8 Resp Batch4 PID804 LC Female Nho CD4 Resp Batch4 PID804 LC Female Nho CD8 Resp Batch4 PID717 LC Female Nho CD4 Resp Batch5 PID717 LC Female Nho CD8 Resp Batch5 PID414 LC Female Hos CD4 Resp Batch6 PID414 LC Female Hos CD8 Resp Batch6 PID621 LC Male Nho CD4 Resp Batch5 PID621 LC Male Nho CD8 Resp Batch5 PID102 R Female Nho CD4 Resp Batch2 PID102 R Female Nho CD8 Resp Batch2 PID693 R Male Nho CD4 Resp Batch3 PID693 R Male Nho CD8 Resp Batch3 PID896 R Male Nho CD4 Resp Batch4 PID896 R Male Nho CD8 Resp Batch4 PID923 LC Male Nho CD4 Resp Batch5 PID923 LC Male Nho CD8 Resp Batch5 PID927 LC Female Hos CD4 Resp Batch6 PID927 LC Female Hos CD8 Resp Batch6 PID447 LC Female Nho CD4 Resp Batch5 PID447 LC Female Nho CD8 Resp Batch5 PID147 LC Female Nho CD4 Resp Batch5 PID147 LC Female Nho CD8 Resp Batch5 * PID^1^: Participant ID enrolled in this study * Batch^2^: samples running on CyTOF at the same timepoint * LC^3^: participants with long covid * R^4^: participants without long covid * Nho^5^: participants were not hospitalized during acute infection * Hos^6^: participants were hospitalized during acute infection * Atlas^7^: baseline T cells * Resp^8^: SARS-CoV-2-specific T cells