Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine immunogenicity varies between individuals, and immune responses correlate with vaccine efficacy. Using data from 1,076 participants enrolled in ChAdOx1 nCov-19 vaccine efficacy trials in the United Kingdom, we found that inter-individual variation in normalized antibody responses against SARS-CoV-2 spike and its receptor-binding domain (RBD) at 28 days after first vaccination shows genome-wide significant association with major histocompatibility complex (MHC) class II alleles. The most statistically significant association with higher levels of anti-RBD antibody was HLA-DQB1*06 (P = 3.2 × 10−9), which we replicated in 1,677 additional vaccinees. Individuals carrying HLA-DQB1*06 alleles were less likely to experience PCR-confirmed breakthrough infection during the ancestral SARS-CoV-2 virus and subsequent Alpha variant waves compared to non-carriers (hazard ratio = 0.63, 0.42–0.93, P = 0.02). We identified a distinct spike-derived peptide that is predicted to bind differentially to HLA-DQB1*06 compared to other similar alleles, and we found evidence of increased spike-specific memory B cell responses in HLA-DQB1*06 carriers at 84 days after first vaccination. Our results demonstrate association of HLA type with Coronavirus Disease 2019 (COVID-19) vaccine antibody response and risk of breakthrough infection, with implications for future vaccine design and implementation.

Metadata

Item Type:	Article
Authors/Creators:	Mentzer, A.J. https://orcid.org/0000-0002-4502-2209 O’Connor, D. https://orcid.org/0000-0002-6902-9886 Bibi, S. Chelysheva, I. https://orcid.org/0000-0001-7802-7025 Clutterbuck, E.A. Demissie, T. Dinesh, T. Edwards, N.J. https://orcid.org/0000-0002-7030-7839 Felle, S. Feng, S. https://orcid.org/0000-0001-7855-0991 Flaxman, A.L. https://orcid.org/0000-0001-6460-1372 Karp-Tatham, E. Li, G. Liu, X. Marchevsky, N. https://orcid.org/0000-0003-1055-0033 Godfrey, L. Makinson, R. Bull, M.B. Fowler, J. Alamad, B. Malinauskas, T. Chong, A.Y. https://orcid.org/0000-0003-4919-2632 Sanders, K. Shaw, R.H. Voysey, M. https://orcid.org/0000-0001-6324-6559 Cavey, A. Minassian, A. Stuart, A. Khozoee, B. Hanumunthadu, B. Angus, B. Smith, C.C. Turnbull, I. Kwok, J. Emary, K.R.W. Cifuentes, L. Ramasamy, M.N. Cicconi, P. Finn, A. McGregor, A.C. Collins, A.M. Smith, A. Goodman, A.L. Green, C.A. Duncan, C.J.A. Williams, C.J.A. Ferreira, D.M. Turner, D.P.J. Thomson, E.C. Hill, H. Pollock, K. Toshner, M. Lillie, P.J. Heath, P. Lazarus, R. Sutherland, R.K. Payne, R.O. https://orcid.org/0000-0002-8490-671X Faust, S.N. Darton, T. https://orcid.org/0000-0003-2209-9956 Libri, V. Anslow, R. Provtsgaard-Morys, S. Hart, T. Beveridge, A. Adlou, S. Snape, M.D. Pollard, A.J. https://orcid.org/0000-0001-7361-719X Lambe, T. Knight, J.C. https://orcid.org/0000-0002-0377-5536
Copyright, Publisher and Additional Information:	© The Author(s) 2023. Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Keywords:	Humans; Alleles; Antibodies, Viral; Breakthrough Infections; ChAdOx1 nCoV-19; COVID-19; COVID-19 Vaccines; Histocompatibility Antigens Class II; Immunogenicity, Vaccine; SARS-CoV-2; Vaccination
Dates:	Published: January 2023 Published (online): 13 October 2022 Accepted: 7 October 2022
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield) > Department of Infection, Immunity and Cardiovascular Disease
Depositing User:	Symplectic Sheffield
Date Deposited:	10 Feb 2023 14:33
Last Modified:	10 Feb 2023 14:33
Status:	Published
Publisher:	Springer Science and Business Media LLC
Refereed:	Yes
Identification Number:	10.1038/s41591-022-02078-6
Related URLs:	PubMed URL
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:196264

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Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection

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