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

Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection
Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection
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.
1078-8956
147-157
Mentzer, Alexander J.
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Oxford COVID Vaccine Trial Genetics Study Team Group
Mentzer, Alexander J.
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O’connor, Daniel
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Bibi, Sagida
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Chelysheva, Irina
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Dinesh, Tanya
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Edwards, Nick J.
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Felle, Sally
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Faust, Saul N.
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Mentzer, Alexander J., O’connor, Daniel, Bibi, Sagida, Chelysheva, Irina, Clutterbuck, Elizabeth A. and Demissie, Tesfaye , Oxford COVID Vaccine Trial Genetics Study Team Group (2023) Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection. Nature Medicine, 29 (1), 147-157. (doi:10.1038/s41591-022-02078-6).

Record type: Article

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.

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s41591-022-02078-6 - Version of Record
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Accepted/In Press date: 7 October 2022
e-pub ahead of print date: 13 October 2022
Published date: 1 January 2023
Additional Information: Funding Information: This study is funded by the University of Oxford COVID-19 Research Response Fund and UK Research and Innovation. The ChAdOx1 nCoV-19 (AZD1222) vaccine efficacy trials were funded by the UK National Institute for Health Research (NIHR), UK Research and Innovation, the Bill & Melinda Gates Foundation, the Lemann Foundation, Rede D’OR, the Brava and Telles Foundation and the South African Medical Research Council. The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care. The authors are grateful to the volunteers who participated in this study. AstraZeneca reviewed the data from the study and the final manuscript before submission, but the authors retained editorial control. J.C.K. is supported by a Wellcome Trust Investigator Award (grant no. 204969/Z/16/Z) and the NIHR Oxford Biomedical Research Centre. A.J.M. is an NIHR Academic Clinical Lecturer. The research was supported by the Wellcome Trust Core Award (grant no. 203141/Z/16/Z), with additional support from the NIHR Oxford Biomedical Research Centre and an Academy of Medical Sciences Starter Grant awarded to A.J.M. (SGL024\1096). Publisher Copyright: © 2023, The Author(s).

Identifiers

Local EPrints ID: 476011
URI: http://eprints.soton.ac.uk/id/eprint/476011
ISSN: 1078-8956
PURE UUID: 06f126ff-7915-4ca3-9fa2-0188471498cc
ORCID for Saul N. Faust: ORCID iD orcid.org/0000-0003-3410-7642

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Date deposited: 04 Apr 2023 16:39
Last modified: 06 Jun 2024 01:44

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Contributors

Author: Alexander J. Mentzer
Author: Daniel O’connor
Author: Sagida Bibi
Author: Irina Chelysheva
Author: Elizabeth A. Clutterbuck
Author: Tesfaye Demissie
Author: Tanya Dinesh
Author: Nick J. Edwards
Author: Sally Felle
Author: Shuo Feng
Author: Amy L. Flaxman
Author: Eleanor Karp-tatham
Author: Grace Li
Author: Xinxue Liu
Author: Natalie Marchevsky
Author: Leila Godfrey
Author: Rebecca Makinson
Author: Maireid B. Bull
Author: Jamie Fowler
Author: Bana Alamad
Author: Tomas Malinauskas
Author: Amanda Y. Chong
Author: Katherine Sanders
Author: Robert H. Shaw
Author: Merryn Voysey
Author: Ana Cavey
Author: Angela Minassian
Author: Arabella Stuart
Author: Baktash Khozoee
Author: Brama Hanumunthadu
Author: Brian Angus
Author: Catherine C. Smith
Author: Iain Turnbull
Author: Jonathan Kwok
Author: Katherine R. W. Emary
Author: Liliana Cifuentes
Author: Maheshi N. Ramasamy
Author: Paola Cicconi
Author: Adam Finn
Author: Alastair C. Mcgregor
Author: Andrea M. Collins
Author: Andrew Smith
Author: Anna L. Goodman
Author: Christopher A. Green
Author: Christopher J. A. Duncan
Author: Christopher J. A. Williams
Author: Daniela M. Ferreira
Author: David P. J. Turner
Author: Emma C. Thomson
Author: Saul N. Faust ORCID iD
Corporate Author: Oxford COVID Vaccine Trial Genetics Study Team Group

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