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