Persistent cytolytic CD8+ T cells recognize SARS-CoV-2 and herpesvirus epitopes in Long COVID
Data files
Jun 19, 2026 version files 759.12 MB
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Acute_108.fcs
2.38 MB
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Acute_114.fcs
2.41 MB
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Acute_148.fcs
2.41 MB
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Acute_160.fcs
2.41 MB
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Acute_166.fcs
269.87 KB
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Acute_190.fcs
2.41 MB
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Acute_192.fcs
2.41 MB
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Acute_197.fcs
2.41 MB
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Acute_198.fcs
2.41 MB
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Acute_199.fcs
706.18 KB
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Acute_201.fcs
2.41 MB
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Acute_30.fcs
537.95 KB
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LC_161.fcs
24.01 MB
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LC_204.fcs
24.01 MB
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LC_245.fcs
24.01 MB
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LC_333_125_days.fcs
22.78 MB
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LC_333_220_days.fcs
15.99 MB
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LC_333_59_days.fcs
34.59 MB
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LC_333_66_days.fcs
58.89 MB
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LC_333_82_days.fcs
71.79 MB
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LC_414.fcs
24.01 MB
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LC_476.fcs
24.01 MB
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LC_560.fcs
24.01 MB
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LC_621.fcs
12.39 MB
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LC_652.fcs
24.01 MB
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LC_709.fcs
24.01 MB
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LC_753.fcs
24.01 MB
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R_102.fcs
24.01 MB
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R_313.fcs
24.01 MB
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R_439.fcs
24.01 MB
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R_526.fcs
24.01 MB
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R_564.fcs
24.01 MB
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R_608.fcs
24.01 MB
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R_666_169_days.fcs
5.80 MB
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R_666_2_days.fcs
20.67 MB
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R_666_22_days.fcs
15.01 MB
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R_666_73_days.fcs
6.60 MB
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R_666_9_days.fcs
15.24 MB
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R_741.fcs
24.01 MB
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R_912.fcs
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R_913.fcs
24.01 MB
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R_942.fcs
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README.md
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Tetramer_specificities_and_combinatorial_tetramer_code.csv
2.27 KB
Abstract
Viral-specific CD8+ T cells play roles in protective immunity and immunopathology including during COVID-19. Leveraging combinatorial tetramers, we profiled CD8+ T cells specific for SARS-CoV-2, as well as CMV and EBV – herpesviruses implicated in COVID-19 pathogenesis. During severe COVID-19, EBV-specific CD8+ T cells exhibit a stem-like state whereas CMV-specific ones are terminally differentiated and cytolytic. Comparing post-acute samples from Long COVID (LC) individuals to those recovered revealed that LC-associated CMV-specific CD8+ T cells are Tcm- instead of Temra-biased. In LC individuals, CD8+ T cells specific for SARS-CoV-2, CMV, and EBV are preferentially terminally differentiated, exhausted, and cytolytic. Cytolytic granzyme B-expressing CD8+ T cells are particularly prominent among LC women. As granzyme B is upregulated on viral-specific CD8+ T cells during acute viremia, an inability to shut down COVID-19-induced cytolytic effector expression may drive preferential persistence of cytolytic CD8+ T cells in people with LC which may contribute to LC pathogenesis.
Dataset DOI: 10.5061/dryad.g1jwstr51
Description of the data and file structure
This dataset includes a total of 42 FCS files of CD8+ T cells from 34 participants. The participants included those sampled at the time of severe acute COVID-19, or during the post-acute phase of COVID-19. Specifically, 12 of the datasets were obtained from 12 de-identified individuals hospitalized in the ICU for severe COVID-19 during the first wave of the COVID-19 pandemic in 2020, and termed “Acute”. Post-acute specimens included ten individuals that had recovered from COVID-19 without lingering symptoms (termed “R”), and ten matched individuals that had Long COVID after SARS-CoV-2 infection (termed “LC”); these twenty individuals were all analyzed 4 months post-COVID-19. In addition, one “R” individual that had fully recovered (666) and one “LC” individual that had Long COVID (333) were analyzed longitudinally, as indicated by the number of days post-COVID-19 at the end of the file name. Each file name begins with the treatment group, followed by the participant ID (PID), followed by the timepoint where appropriate.
Tetramers were encoded using an 8-channel combinatorial metal scheme to enable simultaneous detection of up to 56 peptide specificities within a single sample. The eight metal channels (designated Tetramer1–Tetramer8) correspond to the following isotopes: 1 = 150Nd, 2 = 153Eu, 3 = 155Gd, 4 = 157Gd, 5 = 158Gd, 6 = 163Dy, 7 = 168Er, and 8 = 173Yb. Each peptide specificity was assigned a unique three-of-eight code (a combination of three distinct channels), represented as a three-digit code using digits 1–8. For example, the code “1, 3, 7” would reflect cells that are positive for all three channels 150Nd, 155Gd, and 168Er. The complete list of the 56 peptides and their corresponding three-digit channel codes is provided as a CSV file (Tetramer_specificities_and_combinatorial_tetramer_code.csv).
Files and variables
Acute_108.fcs
Acute_114.fcs
Acute_148.fcs
Acute_160.fcs
Acute_166.fcs
Acute_190.fcs
Acute_192.fcs
Acute_197.fcs
Acute_198.fcs
Acute_199.fcs
Acute_201.fcs
Acute_30.fcs
LC_333_125_days.fcs
LC_333_220_days.fcs
LC_333_59_days.fcs
LC_333_66_days.fcs
LC_333_82_days.fcs
LC_204.fcs
LC_709.fcs
LC_652.fcs
LC_560.fcs
LC_753.fcs
LC_245.fcs
LC_476.fcs
LC_161.fcs
LC_414.fcs
LC_621.fcs
R_666_169_days.fcs
R_666_2_days.fcs
R_666_22_days.fcs
R_666_73_days.fcs
R_666_9_days.fcs
R_942.fcs
R_913.fcs
R_608.fcs
R_912.fcs
R_526.fcs
R_313.fcs
R_564.fcs
R_741.fcs
R_439.fcs
R_102.fcs
Tetramer_specificities_and_combinatorial_tetramer_code.csv
Code/software
NA
Access information
NA
Human subjects data
De-identified specimens from the severe hospitalized COVID-19 individuals were obtained under IRB approval #20-30387, and those from the LIINC cohort was approved under IRB approval # 20-30479 where all patients provided informed consent. There are no meta-data in the accompanying files that contain patient identifying information.