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| Main Authors: | , , , , , , |
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| Format: | Preprint |
| Published: |
2026
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2601.20343 |
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| _version_ | 1866911404202655744 |
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| author | Pan, Yunbei Hofmann, Christian Banbury, Barbara Patel, Harsh Bien, Stephanie A. Chou, Tom Yang, Otto O. |
| author_facet | Pan, Yunbei Hofmann, Christian Banbury, Barbara Patel, Harsh Bien, Stephanie A. Chou, Tom Yang, Otto O. |
| contents | Each T cell typically carries a specific T-cell receptor (TCR) that determines its specificity against an epitope presented by the HLA complex on a target cell. Antigenic challenge triggers the expansion of reactive cells within a diverse pool of T cells with randomly generated receptors, a process that results in epitope-driven shifts of TCR frequencies over time. Here, we analyze the effects of SARS-CoV-2 vaccination on the TCR populations in peripheral blood drawn from seven COVID-naive individuals, before vaccines were widely available. To identify SARS-CoV-2 vaccine-associated TCR sequences among the $\sim 10^{5}-10^{6}$ TCR sequences sampled before and after vaccination, we develop statistical criteria to detect significant increases in abundance of positive TCR clones. Application of our statistical methods shows a robust identification of TCR sequences that respond to SARS-CoV-2 vaccination in vivo, illustrating the feasibility of quantifying the clone-specific dynamics of T-cell abundance changes following immunological perturbations. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2601_20343 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | CEI: A Clonal Expansion Identifier for T-cell receptor clones following SARS-CoV-2 vaccination Pan, Yunbei Hofmann, Christian Banbury, Barbara Patel, Harsh Bien, Stephanie A. Chou, Tom Yang, Otto O. Quantitative Methods Each T cell typically carries a specific T-cell receptor (TCR) that determines its specificity against an epitope presented by the HLA complex on a target cell. Antigenic challenge triggers the expansion of reactive cells within a diverse pool of T cells with randomly generated receptors, a process that results in epitope-driven shifts of TCR frequencies over time. Here, we analyze the effects of SARS-CoV-2 vaccination on the TCR populations in peripheral blood drawn from seven COVID-naive individuals, before vaccines were widely available. To identify SARS-CoV-2 vaccine-associated TCR sequences among the $\sim 10^{5}-10^{6}$ TCR sequences sampled before and after vaccination, we develop statistical criteria to detect significant increases in abundance of positive TCR clones. Application of our statistical methods shows a robust identification of TCR sequences that respond to SARS-CoV-2 vaccination in vivo, illustrating the feasibility of quantifying the clone-specific dynamics of T-cell abundance changes following immunological perturbations. |
| title | CEI: A Clonal Expansion Identifier for T-cell receptor clones following SARS-CoV-2 vaccination |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2601.20343 |