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. 2021 Oct 14;218(12):e20211327. doi: 10.1084/jem.20211327

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© 2021 Lu et al.

This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

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Figure S3. — Identification of the epitopes of public clonotypes. (A) A scheme of the rapid epitope determination platform used for identification of the epitopes for T cell clonotypes. 15-mer peptides with 11-amino acid overlap that cover the full length of the S protein of SARS-CoV-2 were synthesized and pooled as described in Materials and methods. Each peptide is present in a unique combination of two different pools; thus, the epitope can be revealed by the common peptides in the pools that activate the clonotype. Peptide pools of S, M, and N proteins of SARS-CoV-2 or HCoV S proteins were also added to the matrix as controls. S864 indicates S_864-882 peptide. (B) Identification of DRB1*15:01 as a restricting HLA of S_753–759 for clonotype 2. Reporter cells expressing clonotype 2 were activated by S_749–763 in the presence of HEK293T cells transfected with DRA*01:01-DRB1*15:01. Data are shown as mean ± SD of triplicates. (C) Exclusion of DPA1*02:02-DPB1*05:01 as a restricting HLA of S_353–367 for clonotype 3. Reporter cells expressing clonotype 3 were not activated by S353-including peptide pools, such as A5, E8, and E9 (S pool #1) in A, in the presence of HEK293T cells transfected with DPA1*02:02-DPB1*05:01. (D) DRB4*01:03 is a restricting HLA of S_353–367 for clonotype 3. Reporter cells expressing clonotype 3 were activated by S353 in the presence of B cells from Ts-009. (E) DQA1*01:01-DQB1*05:01 is a restricting HLA of S_833–843 for clonotypes 4 and 9. Reporter cells expressing clonotype 4 or 9 were activated by S_828–846 in the presence of B cells from donors Ts-025 (autologous), Ts-013, and Ts-003 but not activated in the presence of B cells from donors Ts-001 and HIWA. (F) DPA1*02:02-DPB1*05:01 is a restricting HLA of S_557–567 for clonotype 7. Reporter cells expressing clonotype 7 were activated by S553- or S557-including peptide pools, such as B7, B8, F4, and E9 (S pool #1) in A, in the presence of HEK293T cells transfected with DPA1*02:02-DPB1*05:01. (G) DPA1*02:02-DPB1*05:01 is a restricting HLA of S_957–967 for clonotype 10. Reporter cells expressing clonotype 10 were activated by S953- or S957-including peptide pools, such as C11, C12, G4, and E10 (S pool #2) in A, in the presence of HEK293T cells transfected with DPA1*02:02-DPB1*05:01. Data are representative of two independent experiments (B–G).