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

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

doi:10.3389/fimmu.2025.1488851

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

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

Authors

Sean Nolan¹, Marissa Vignali¹, Mark Klinger¹, Jennifer N Dines¹, Ian M Kaplan¹, Emily Svejnoha¹, Tracy Craft¹, Katie Boland¹, Mitchell W Pesesky¹, Rachel M Gittelman¹, Thomas M Snyder¹, Christopher J Gooley², Simona Semprini³, Claudio Cerchione⁴, Fabio Nicolini⁵, Massimiliano Mazza⁵, Ottavia M Delmonte⁶, Kerry Dobbs⁶, Gonzalo Carreño-Tarragona⁷, Santiago Barrio⁷, Vittorio Sambri³, Giovanni Martinelli⁴, Jason D Goldman^{8

9}, James R Heath¹⁰, Luigi D Notarangelo⁶, Joaquin Martinez-Lopez⁷, Bryan Howie¹, Jonathan M Carlson², Harlan S Robins¹

Affiliations

¹ Adaptive Biotechnologies, Seattle, WA, United States.
² Microsoft Research, Redmond, WA, United States.
³ Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Italy.
⁴ IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy.
⁵ Immunotherapy, Cell Therapy and Biobank (ITCB), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy.
⁶ Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.
⁷ Hematology Department, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain.
⁸ Swedish Medical Center, Seattle, WA, United States.
⁹ Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States.
¹⁰ Institute for Systems Biology, Seattle, WA, United States.

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.

Copyright © 2025 Nolan, Vignali, Klinger, Dines, Kaplan, Svejnoha, Craft, Boland, Pesesky, Gittelman, Snyder, Gooley, Semprini, Cerchione, Nicolini, Mazza, Delmonte, Dobbs, Carreño-Tarragona, Barrio, Sambri, Martinelli, Goldman, Heath, Notarangelo, Martinez-Lopez, Howie, Carlson and Robins.

MeSH terms

COVID-19* / immunology
Databases, Genetic
Humans
Receptors, Antigen, T-Cell, alpha-beta* / genetics
Receptors, Antigen, T-Cell, alpha-beta* / immunology
Receptors, Antigen, T-Cell, alpha-beta* / metabolism
SARS-CoV-2* / immunology

Substances

Receptors, Antigen, T-Cell, alpha-beta

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. The ISB INCOV study supported by Dept. of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, Biomedical Advanced Research and Development Authority, under Contract No. HHSO100201600031C. L. D. Notarangelo is supported by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health. Sample collection in Brescia and Pavia was supported by Regione Lombardia, Italy. Sample collections from i+12/CNIO were supported by CRIS foundation.