1. Initial antigen encounter determines robust T-cell immunity against SARS-CoV-2 BA.2.86 variant three years later.
- Author
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Rubio R, Yavlinsky A, Escalera Zamudio M, Molinos-Albert LM, Martín Pérez C, Pradenas E, Canyelles M, Torres C, Tan C, Swadling L, Ramírez-Morros A, Trinité B, Vidal-Alaball J, Aguilar R, Ruiz-Comellas A, Blanco J, van Dorp L, Balloux F, Dobaño C, and Moncunill G
- Subjects
- Humans, Male, Female, Middle Aged, Adult, Interferon-gamma immunology, Interleukin-2 immunology, Interleukin-2 genetics, Aged, Mutation, Adaptive Immunity, Antigens, Viral immunology, Antigens, Viral genetics, SARS-CoV-2 immunology, SARS-CoV-2 genetics, COVID-19 immunology, Antibodies, Neutralizing immunology, Antibodies, Neutralizing blood, Epitopes, T-Lymphocyte immunology, Epitopes, T-Lymphocyte genetics, T-Lymphocytes immunology, Cross Reactions immunology, Antibodies, Viral blood, Antibodies, Viral immunology
- Abstract
Objectives: We aimed to evaluate the adaptive immune responses cross-recognition of the hypermutated SARS-CoV-2 BA.2.86 variant and identify the determinants influencing this recognition., Methods: We measured BA.2.86 neutralizing antibodies and T-cell responses cross-reactivity in previously exposed participants. We investigated clinical-demographic factors and used a novel in silico analysis to assess viral genetic determinants affecting T-cell responses., Results: Despite notable escape from neutralizing antibodies, T-cell responses remained generally preserved, albeit with a significant but small loss in T-cell cross-recognition (7.5%, 14.2%, and 10.8% average loss for IFN-γ, IL-2, and IFN-γ + IL-2, respectively, p<0.05). This is consistent with the prediction of 6 out of 10 immunodominant T-cell epitopes (TCEs) altered by BA.2.86 mutations to have reduced peptide presentation. This effect is expected to be mitigated by total TCEs across the genome. Remarkably, T-cell responses and cross-recognition were 3.5 (IFN-γ), 2 (IL-2) and 2.4 (IFN-γ + IL-2) times higher when first induced by infection rather than by vaccination three years earlier, by increasing number of infections, and by ancestral/Delta than Omicron infections., Conclusions: Our findings underscore the critical role and factors influencing T-cell immunity against evolving SARS-CoV-2 variants, such as first antigen encounter (vaccination or infection), as it is essential for developing effective control strategies., Competing Interests: Declaration of Competing Interest Unrelated to the present work JB received Institutional grants/agreements from/with MSD, HIPRA, GRIFOLS and NESAPOR; personal payments from HIPRA and NESAPOR; and was former CEO and founder of AlbaJuna Therapeutics, S.L. All other authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2025
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