(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 using ELISA (Figure 1—figure supplement 1) and isolated PBMCs in two biological replicates. Additionally, CD4+ and CD8+ cells were isolated from a separate portion of blood, and EM, CM, EMRA, and SCM memory subpopulations were FACS sorted on days 30, 45, and 85. For each sample, we sequenced TCRalpha and TCRbeta repertoires. For both donors, pre-infection PBMC repertoires were sampled in 2018 and 2019 for other projects. (b, c) PCA of clonal temporal trajectories identifies three groups of clones with distinctive behaviours. Left: First two principal components of the 1000 most abundant TCRbeta clonotype frequencies normalized by maximum value for each clonotype in PBMC at post-infection time points. Colour indicates hierarchical clustering results of principal components; symbol indicates if clonotype was called as significantly contracted from day 15 to day 85 (triangles) or expanded from day 15 to day 37 (circles) by both edgeR and NoisET (Figure 1—figure supplement 5 shows overlap between clonal trajectory clusters and edgeR/NoisET hits). Right: Each curve shows the average ±2.96 SE of normalized clonal frequencies from each cluster. Contracting (d) and expanding (e) clones include both CD4+ and CD8+ T cells and are less abundant in pre-infection repertoires. T-cell clones significantly contracted from day 15 to day 85 (d) and significantly expanded from day 15 to day 37 (e) were identified in both donors. The fraction of contracting (d) and expanding (e) TCRbeta clonotypes in the total repertoire (calculated as the sum of frequencies of these clonotypes in the second PBMC replicate at a given time point and corresponding to the fraction of responding cells of all T cells) is plotted in log-scale for all reactive clones (left) and reactive clones with the CD4 (middle) and CD8 (right) phenotypes. Similar dynamics were observed in TCRalpha repertoires (Figure 1—figure supplement 3) and for significantly expanded/contracted clones identified with the NoisET Bayesian differential expansion statistical model alone (Figure 1—figure supplement 4).