Observational Study

. 2025 Sep;91(3):106598.

doi: 10.1016/j.jinf.2025.106598. Epub 2025 Aug 21.

Third exposure to COVID-19 infection or vaccination differentially impacts T cell responses

Gift Ahimbisibwe¹, David Greenwood¹, Katalin Andrea Wilkinson², Joshua Gahir³, Hermaleigh Townsley³, Murad Miah¹, Philip Bawumia¹, Charlotte Chaloner⁴, Dina Levi¹, Philip Hobson¹, Andy Riddell¹, Agnieszka Hobbs⁵, Giulia Dowgier⁵, Rebecca Penn¹, Theo Sanderson¹, Phoebe Stevenson-Leggett⁵, Odiesia Daley¹, James Bazire⁵, Ruth Harvey⁶, Ashley S Fowler¹, Callie Smith⁷, Mauro Miranda¹, Nicola O'Reilly¹, Scott Warchal¹, Karen Ambrose¹, Amy Strange¹, Gavin Kelly¹, Svend Kjar¹; Legacy Investigators; Bryan Williams⁸, Vincenzo Libri⁸, Steve Gamblin¹, Sonia Gandhi⁴, Charles Swanton⁴, David Lv Bauer⁹, Robert John Wilkinson¹⁰, Edward J Carr⁴, Emma C Wall¹¹

Affiliations

¹ The Francis Crick Institute, NW1 1AT London, UK.
² The Francis Crick Institute, NW1 1AT London, UK; Welcome Discovery Research Platforms in Infection, Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town 7925, Republic of South Africa.
³ The Francis Crick Institute, NW1 1AT London, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, UK.
⁴ The Francis Crick Institute, NW1 1AT London, UK; University College London, Gower Street, London, Uk.
⁵ COVID Surveillance Unit, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
⁶ Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
⁷ King's College London, St Thomas' Campus, Westminster Bridge Road, London, UK.
⁸ National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, UK; University College London, Gower Street, London, Uk.
⁹ The Francis Crick Institute, NW1 1AT London, UK; Genotype-to-Phenotype 2 Consortium (G2P2-UK), UK.
¹⁰ The Francis Crick Institute, NW1 1AT London, UK; Welcome Discovery Research Platforms in Infection, Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town 7925, Republic of South Africa; Department of Infectious Diseases, Imperial College London, W12 0NN London, UK.
¹¹ The Francis Crick Institute, NW1 1AT London, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, UK; Research Department of Infection, Division of Infection and Immunity, University College London, UK. Electronic address: emma.wall@crick.ac.uk.

PMID: 40848990
PMCID: PMC7618389
DOI: 10.1016/j.jinf.2025.106598

Observational Study

Third exposure to COVID-19 infection or vaccination differentially impacts T cell responses

Gift Ahimbisibwe et al. J Infect. 2025 Sep.

. 2025 Sep;91(3):106598.

doi: 10.1016/j.jinf.2025.106598. Epub 2025 Aug 21.

Authors

Affiliations

¹ The Francis Crick Institute, NW1 1AT London, UK.
² The Francis Crick Institute, NW1 1AT London, UK; Welcome Discovery Research Platforms in Infection, Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town 7925, Republic of South Africa.
³ The Francis Crick Institute, NW1 1AT London, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, UK.
⁴ The Francis Crick Institute, NW1 1AT London, UK; University College London, Gower Street, London, Uk.
⁵ COVID Surveillance Unit, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
⁶ Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
⁷ King's College London, St Thomas' Campus, Westminster Bridge Road, London, UK.
⁸ National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, UK; University College London, Gower Street, London, Uk.
⁹ The Francis Crick Institute, NW1 1AT London, UK; Genotype-to-Phenotype 2 Consortium (G2P2-UK), UK.
¹⁰ The Francis Crick Institute, NW1 1AT London, UK; Welcome Discovery Research Platforms in Infection, Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town 7925, Republic of South Africa; Department of Infectious Diseases, Imperial College London, W12 0NN London, UK.
¹¹ The Francis Crick Institute, NW1 1AT London, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, UK; Research Department of Infection, Division of Infection and Immunity, University College London, UK. Electronic address: emma.wall@crick.ac.uk.

PMID: 40848990
PMCID: PMC7618389
DOI: 10.1016/j.jinf.2025.106598

Abstract

Background: In 2021, the rapid rollout of two doses of SARS-CoV-2 vaccines reduced COVID-19 severity and mortality. However, further vaccine doses as a prime-boost schedule were limited, and lifting of public health restrictions by late 2021 frequently led to infection, rather than vaccine, as a third exposure.

Objective: To compare how the third exposure through mRNA booster or SARS-CoV-2 infection shapes humoral and cellular immunity following two vaccine doses.

Methods: We compared immune responses after the third exposure in healthy adults enrolled in the UCLH-Crick Legacy cohort study (NCT04750356) between those receiving ancestral spike-encoded mRNA booster (vaccine immunity, n = 38) or COVID-19 infection (hybrid immunity, n = 13) following two vaccine doses. Immune profiles were evaluated using live virus neutralization assays, IFN-γ ELISpot, Luminex assay, flow cytometry and mass cytometry.

Results: Both total anti-Spike IgG and variant-specific neutralising antibodies were comparable following infection or vaccine as a third exposure. Overall, T cell populations were similar but functionally different. CD8⁺ Effector Memory (TEM) cells in the vaccine group showed higher expression of CD69 and Granzyme B following stimulation with SARS-CoV-2 Spike peptides. In contrast, the hybrid group produced higher levels of innate immune associated cytokines IL-10 and IL-34, as well as the T cell homing chemokine CCL25, after stimulation.

Conclusions: While both exposures generated comparable breadth of protection against SARS-CoV-2 variants, our findings suggest that the route of third exposure influences different aspects of the immune response, warranting further investigation into long-term immunity at both systemic and mucosal sites.

Keywords: Immunity; Infection exposure; SARS-CoV-2; T cells; Vaccination.

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Conflict of interest statement

Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: CSw reports interests unrelated to this Correspondence: grants from BMS, Ono- Pharmaceuticals, Boehringer-Ingelheim, Roche-Ventana, Pfizer and Archer Dx, unrelated to this Correspondence; personal fees from Genentech, Sarah Canon Research Institute, Medicxi, Bicycle Therapeutics, GRAIL, Amgen, AstraZeneca, BMS, Illumina, GlaxoSmithKline, MSD, and Roche-Ventana, unrelated to this Correspondence; and stock options from Apogen Biotech, Epic Biosciences, GRAIL, and Achilles Therapeutics, unrelated to this Correspondence. DLVB reports discussions between the Crick and GSK for commercial antiviral testing, and grants to the Crick from AstraZeneca unrelated to this Correspondence. EW reports consulting for AstraZeneca and CSL-Seqirus unrelated to this article. All other authors declare no competing interests.

Figures

**Fig. 1. Neutralization titres after third exposure are comparable between vaccine and hybrid immunity.**
(A, B) Calendar dates of SARS-COV-2 exposure and sample collection following the third exposure for vaccine immunity group (A) and hybrid immunity group (B). (C) Neutralization titres against SARS-CO-2 variants, including the ancestral strain, Alpha, Beta, Delta and Omicron (BA.1, BA.2, BA.5), measured after the third exposure.

**Fig. 2. Circulating immune profiles are comparable after third exposures between vaccine-only and hybrid groups.**
(A) UMAP visualization of major immune cell lineages, including Monocytes & Dendritic cells, Neutrophils, NK cells, B cells, CD4 T cells, CD8 T cells, and γδ T cells, in individuals with vaccine and hybrid Immunity. (B) UMAP showing T cell subclusters stratified by vaccine and hybrid Immunity groups. (C) UMAP of T cell subclusters highlighting differences in CD69 expression within the CD8 TEM cluster between vaccine and hybrid Immunity groups. (D) Violin plot illustrating increased CD69 expression in the CD8 TEM cluster, as identified in (C).

**Fig. 3. Higher production of IL-10, IL-34 and CCL25 in the hybrid immunity group upon stimulation with SARS-CoV-2 S antigen Pool.**
(A) Spot-forming cells (SFC) per million PBMC, comparing responses between the vaccine immunity and hybrid immunity groups. (B) MA plot showing the log fold change of analytes (Luminex assay) from baseline (0 on the y-axis) upon stimulation with the SARS-CoV-2 S antigen pool. The x-axis represents mean analyte concentration (pg/mL). Analytes highlighted in pink were statistically significant different between Vaccine and Hybrid immunity groups upon stimulation as shown in violin plots (C).

**Fig. 4. Higher Granzyme B production in vaccine immunity group following stimulation with SARS-CoV-2 S antigen Pool.**
(A) Changes in the proportion of Granzyme B (GzB)-positive cells among CD69+CD8TEM cells upon stimulation with S antigen pool for vaccine and hybrid immunity groups. (B, C) Polyfunctionality of CD69+CD8TEM cells based on Granzyme A and B expression. (B) Pie charts depict the distribution of polyfunctional subsets in vaccine and hybrid immunity groups. (C) Bar plots illustrate statistical significance between groups.

See this image and copyright information in PMC

References

1. Tregoning JS, Flight KE, Higham SL, Wang Z, Pierce BF. Progress of the COVID-19 vaccine effort: viruses, vaccines and variants versus efficacy, effectiveness and escape. Nat Rev Immunol. 2021;21(10):626–36. doi: 10.1038/s41577-021-00592-1. - DOI - PMC - PubMed
1. Imai N, Rawson T, Knock ES, Sonabend R, Elmaci Y, Perez-Guzman PN, et al. Quantifying the effect of delaying the second COVID-19 vaccine dose in England: a mathematical modelling study. Lancet Public Health. 2023;8(3):e174–83. doi: 10.1016/S2468-2667(22)00337-1. - DOI - PMC - PubMed
1. De Salazar PM, Link NB, Lamarca K, Santillana M. High coverage COVID-19 mRNA vaccination rapidly controls SARS-CoV-2 transmission in long-term care facilities. Commun Med. 2021;1(1):16. doi: 10.1038/s43856-021-00015-1. - DOI - PMC - PubMed
1. Office NA. The rollout of the COVID-19 vaccination programme in England. National Audit Office; 2022.
1. Graham C, Lechmere T, Rehman A, Seow J, Kurshan A, Huettner I, et al. The effect of Omicron breakthrough infection and extended BNT162b2 booster dosing on neutralization breadth against SARS-CoV-2 variants of concern. PLoS Pathog. 2022;18(10):e1010882. doi: 10.1371/journal.ppat.1010882. - DOI - PMC - PubMed

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Third exposure to COVID-19 infection or vaccination differentially impacts T cell responses

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Third exposure to COVID-19 infection or vaccination differentially impacts T cell responses

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