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. 2025 Feb 17:16:1488851.
doi: 10.3389/fimmu.2025.1488851. eCollection 2025.

A large-scale database of T-cell receptor beta sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Sean Nolan  1 , Marissa Vignali  1 , Mark Klinger  1 , Jennifer N Dines  1 , Ian M Kaplan  1 , Emily Svejnoha  1 , Tracy Craft  1 , Katie Boland  1 , Mitchell W Pesesky  1 , Rachel M Gittelman  1 , Thomas M Snyder  1 , Christopher J Gooley  2 , Simona Semprini  3 , Claudio Cerchione  4 , Fabio Nicolini  5 , Massimiliano Mazza  5 , Ottavia M Delmonte  6 , Kerry Dobbs  6 , Gonzalo Carreño-Tarragona  7 , Santiago Barrio  7 , Vittorio Sambri  3 , Giovanni Martinelli  4 , Jason D Goldman  8   9 , James R Heath  10 , Luigi D Notarangelo  6 , Joaquin Martinez-Lopez  7 , Bryan Howie  1 , Jonathan M Carlson  2 , Harlan S Robins  1
Affiliations

A large-scale database of T-cell receptor beta sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Sean Nolan et al. Front Immunol. .

Abstract

We describe the establishment and current content of the ImmuneCODE™ database, which includes hundreds of millions of T-cell Receptor (TCR) sequences from over 1,400 subjects exposed to or infected with the SARS-CoV-2 virus, as well as over 160,000 high-confidence SARS-CoV-2-associated TCRs. This database is made freely available, and the data contained in it can be used to assist with global efforts to understand the immune response to the SARS-CoV-2 virus and develop new interventions.

Keywords: COVID-19; SARS-CoV-2; T cell; TCR repertoire; cellular immunity; immune response.

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Conflict of interest statement

SN, MV, MK, JD, IK, ES, TC, KB, MP, RG, TS, BH, and HR have a financial interest in Adaptive Biotechnologies. CG. and JC. have a financial interest in Microsoft. JM-L is a consultant for Adaptive Biotechnologies in projects outside of COVID-19. Funding for the ISB INCOV project from BARDA was managed by Merck; Merck had no role in planning the research or writing the paper. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision

Figures

Figure 1
Figure 1
Results from a typical MIRA experiment. Hundreds of “addresses” (subsets of pools) are queried in parallel, and each point on the x-axis corresponds to one address. The height of each bar shows the number of TCR sequences confidently assigned to that address by our statistical model. The addresses on the left side of the figure correspond to SARS-CoV-2 epitopes, while the addresses on the right side were not assigned to any particular antigen.
See this image and copyright information in PMC

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References

    1. Grifoni A, Weiskopf D, Ramirez SI, Mateus J, Dan JM, Moderbacher CR, et al. . Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell. (2020) 181:1489–1501.e15. doi: 10.1016/j.cell.2020.05.015 - DOI - PMC - PubMed
    1. Weiskopf D, Schmitz KS, Raadsen MP, Grifoni A, Okba NMA, Endeman H, et al. . Phenotype and kinetics of SARS-CoV-2–specific T cells in COVID-19 patients with acute respiratory distress syndrome. Sci Immunol. (2020) 5. doi: 10.1126/sciimmunol.abd2071 - DOI - PMC - PubMed
    1. Sekine T, Perez-Potti A, Rivera-Ballesteros O, Strålin K, Gorin JB, Olsson A, et al. . Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19. Cell. (2020) 183:158–168.e14. doi: 10.1016/j.cell.2020.08.017 - DOI - PMC - PubMed
    1. Azkur AK, Akdis M, Azkur D, Sokolowska M, Van De Veen W, Brüggen M, et al. . Immune response to SARS-CoV-2 and mechanisms of immunopathological changes in COVID-19. Allergy. (2020) 75:1564–81. doi: 10.1111/all.14364 - DOI - PMC - PubMed
    1. Robins HS, Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, et al. . Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells. Blood. (2009) 114:4099–107. doi: 10.1182/blood-2009-04-217604 - DOI - PMC - PubMed

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