Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Federation
- Pirogov Russian National Research Medical University, Russian Federation
- National Research Center for Hematology, Russian Federation
- Laboratoire de physique de l'École Normale Supérieure, ENS, PSL, Sorbonne Universite, Universite de Paris, and CNRS, France
- Institute of Clinical Molecular Biology, Kiel University, Germany
- Masaryk University, Central European Institute of Technology, Czech Republic
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Russian Federation
- Moscow State University, Russian Federation
Figures
Figure 1 with 5 supplements
Longitudinal tracking of T-cell clones after mild COVID-19.
(a) Study design. Peripheral blood of two donors was sampled longitudinally on days 15, 30, 37, 45, and 85 after arrival in Russia. At each time point, we evaluated SARS-CoV-2-specific antibodies …
Figure 1—figure supplement 1
Both donors developed anti-SARS-CoV-2 IgG and IgM responses by day 15 post-infection.
(a) The relative level of SARS-CoV-2 S-RBD domain-specific IgG (y-axis) is plotted against time. Solid black line shows the threshold for positive testing. (b) Relative IgM levels in donors M and W …
Figure 1—figure supplement 2
Gating strategy for T cell subsets.
(a) Memory subpopulation gating strategy. Three populations of memory T cells: EM, CM, and EMRA are defined by CCR7 and CD45RA markers; SCM are distinguished from naive CCR7+ CD45RA+ T cells by CD95 …
Figure 1—figure supplement 3
Longitudinal tracking of T-cell clones after mild COVID-19 with TCRalpha repertoire sequencing.
(a, b) PCA of clonal temporal trajectories identifies three groups of clones with distinctive behaviours. Left: First two principal components of the 1000 most abundant TCRalpha clonotype …
Figure 1—figure supplement 4
Comparison of edgeR and NoisET clonal expansion detection procedures.
The fraction (plotted in the log-scale) of contracting (a) and expanding (d) TCRbeta clonotypes in the total repertoire was estimated using subsets of expanded and contracted clones called by edgeR …
Figure 1—figure supplement 5
The overlap between clusters of clonal trajectories identified by PCA and groups of expanding/contracting clones identified with edgeR/NoisET.
For each cluster of clonal trajectories identified on Figure 1b,c, Figure 1—figure supplement 3a,b, we show overlap with groups of significantly (called by edgeR and NoisET simultaneously) expanding …
Figure 2 with 2 supplements
Memory phenotypes of responding clonotypes contracting after day 15.
(a) A large fraction of contracting clonotypes is identified in T-cell memory subsets after infection. Bars show the fraction of contracting CD4+ and CD8+ TCRbeta clonotypes present in 2 year; 1 …
Figure 2—figure supplement 1
Memory phenotypes of responding clonotypes expanding from day 15 to day 37.
(a) A fraction of expanding clonotypes is identified in T-cell memory subsets after infection. Bars show the fraction of expanding CD4+ and CD8+ TCRbeta clonotypes present in 2 year; 1 year …
Figure 2—figure supplement 2
Dynamics of pre-existing SARS-CoV-2 responding clones.
The fraction of pre-existing (identified in −1 year and/or −2 year time point pre-infection) contracting (a) and expanding (b) TCRbeta clonotypes in the total repertoire (corresponding to the …
Figure 3 with 2 supplements
Distinctive TCR sequence motifs and epitope specificity of contracting CD8+ T cell clones.
(a) SARS-CoV-2-specific TCRs are independently identified by clonal contraction. On day 25, donor M participated in a study by Shomuradova et al., 2020, where TCR sequences responding to the …
Figure 3—figure supplement 1
HLA-A*02:01-YLQPRTFLL-specific TCRs are independently identified by clonal contraction.
Each dot corresponds to the frequency of HLA-A*02:01-YLQPRTFLL-tetramer-specific TCRalpha in bulk repertoire from donor M (donor p1434 from Shomuradova et al., 2020) at given time point (an estimate …
Figure 3—figure supplement 2
ALICE algorithm output for TCRalpha PBMC repertoire of donor M on day 15.
Similarity network shows ALICE hits (clones in repertoire with more neighbours than expected by chance), which differ by two mismatches or less in TCRalpha amino acid sequence. Darker colours …
Figure 4 with 2 supplements
Analysis of TCR amino acid sequences of CD4+contracting clones reveals distinctive motifs.
(a) Each vertex in the similarity network corresponds to a contracting clonotype. An edge indicates two or less amino acid mismatches in the CDR3 region (and identical V and J segments). Networks …
Figure 4—figure supplement 1
Expanding CD4+ (but not CD8+) clonotypes show unexpected TCRalpha and TCRbeta sequence convergence.
(a) For each set of CD4alpha, CD4beta, CD8alpha, and CD8beta expanded clonotypes, we constructed separate similarity networks. Each vertex in the similarity network corresponds to an expanding …
Figure 4—figure supplement 2
Identification of COVID-19 patients by frequency of TCR motifs from contracting CD4+ clones from donors M (a) and W (b).
Receiver operating characteristic (ROC) curves for classifying TCRbeta repertoires from COVID cohort vs control by cumulative frequency of clones from CD4beta motifs. Blue curve shows ROC curve …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | Anti-CD3-FITC (mouse monoclonal) | eBioscience | CAT# 11-0038-42 | FACS (5 µl per test) |
| Antibody | Anti-CD45RA-eFluor450 (mouse monoclonal) | eBioscience | CAT# 48-0458-42 | FACS (5 µl per test) |
| Antibody | Anti-CCR7-APC (rat monoclonal) | eBioscience | CAT# 17-1979-42 | FACS (5 µl per test) |
| Antibody | Anti-CD95-PE (mouse monoclonal) | eBioscience | CAT# 12-0959-42 | FACS (5 µl per test) |
| Commercial assay or kit | Dynabeads CD4 Positive Isolation Kit | Invitrogen | CAT# 11331D | |
| Commercial assay or kit | Dynabeads CD8 Positive Isolation Kit | Invitrogen | CAT# 11333D |
Additional files
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Supplementary file 1
List of all TCRbeta and TCRalpha libraries produced in this study.
- https://cdn.elifesciences.org/articles/63502/elife-63502-supp1-v2.tsv
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Supplementary file 2
HLA-typing results for donors M and W.
- https://cdn.elifesciences.org/articles/63502/elife-63502-supp2-v2.tsv
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Supplementary file 3
List of TCRbeta clonotypes contracting from day 15 to day 85.
- https://cdn.elifesciences.org/articles/63502/elife-63502-supp3-v2.tsv
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Supplementary file 4
List of TCRalpha clonotypes contracting from day 15 to day 85.
- https://cdn.elifesciences.org/articles/63502/elife-63502-supp4-v2.tsv
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Supplementary file 5
List of TCRbeta clonotypes expanding from day 15 to day 37.
- https://cdn.elifesciences.org/articles/63502/elife-63502-supp5-v2.tsv
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Supplementary file 6
List of TCRalpha clonotypes expanding from day 15 to day 37.
- https://cdn.elifesciences.org/articles/63502/elife-63502-supp6-v2.tsv
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Transparent reporting form
- https://cdn.elifesciences.org/articles/63502/elife-63502-transrepform-v2.docx
