Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2
Cite this dataset
Roan, Nadia (2023). Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2 [Dataset]. Dryad. https://doi.org/10.7272/Q6WD3XTB
Abstract
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.
README
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:
https://elifesciences.org/articles/72619
https://doi.org/10.1016/j.celrep.2021.109414
https://doi.org/10.1016/j.xcrm.2020.100081
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
Funding
Gladstone Institutes