PreprintCited by 216SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesImmune responses and vaccinations

Two doses of SARS-CoV-2 vaccination induce more robust immune responses to emerging SARS-CoV-2 variants of concern than does natural infection.

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Skelly, Donal T., Harding, Adam C., Gilbert-Jaramillo, Javier, Knight, Michael L., Longet, Stephanie, Anthony Brown, Adele, Sandra, Adland, Emily +27 more·2021·Nature Communications

Preprint — published as 10.1038/s41467-021-25167-5

Abstract

Both natural infection with SARS-CoV-2 and immunization with vaccines induce protective immunity. However, the extent to which such immune responses protect against emerging variants is of increasing importance. Such variants of concern (VOC) include isolates of lineage B.1.1.7, first identified in the UK, and B.1.351, first identified in South Africa. Our data confirm that VOC, particularly those with substitutions at residues 484 and 417, escape neutralization by antibodies directed to the ACE2-binding Class 1 and the adjacent Class 2 epitopes but are susceptible to neutralization by the generally less potent antibodies directed to Class 3 and 4 epitopes on the flanks of the receptor-binding domain. To address the potential threat posed by VOC, we sampled a SARS-CoV-2 uninfected UK cohort recently vaccinated with BNT162b2 (Pfizer-BioNTech, two doses delivered 18-28 days apart), alongside a cohort sampled in the early convalescent stages after natural infection in the first wave of the pandemic in Spring 2020. We tested antibody and T cell responses against a reference isolate of the original circulating lineage, B, and the impact of sequence variation in the B.1.1.7 and B.1.351 VOC. Neutralization of the VOC compared to B isolate was reduced, and this was most evident for the B.1.351 isolate. This reduction in antibody neutralization was less marked in post-boost vaccine-induced responses compared to naturally induced immune responses and could be largely explained by the potency of the homotypic antibody response. After a single vaccination, which induced only modestly neutralizing homotypic antibody titres, neutralization against the VOC was completely abrogated in the majority of vaccinees. Importantly, high magnitude T cell responses were generated after two vaccine doses, with the majority of the T cell response directed against epitopes that are conserved between the prototype isolate B and the VOC. These data indicate that VOC may evade protective neutralizing responses induced by prior infection, and to a lesser extent by immunization, particularly after a single vaccine dose, but the impact of the VOC on T cell responses appears less marked. The results emphasize the need to generate high potency immune responses through vaccination in order to provide protection against these and other emergent variants.

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Authors
Skelly, D. T., Harding, A. C., Gilbert-Jaramillo, J., Knight, M. L., Longet, S., Brown, A., Adele, S., Adland, E., Brown, H., Team, M. L., Tipton, T., Stafford, L., Johnson, S. A., Amini, A., Group, O. C., Kit Tan, T., Schimanski, L., Huang, K.-Y. A., Rijal, P., Group, P. S., Group, C.-C., Frater, J., Goulder, P., Conlon, C. P., Jeffery, K., Dold, C., Pollard, A. J., Sigal, A., de Oliveira, T., Townsend, A. R., Klenerman, P., Dunachie, S. J., Barnes, E., Carroll, M. W., & James, W. S.
Affiliations
  • University of Oxford (GB)
  • Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
  • Public Health England, Porton Down, UK
  • Centre for Human Genetics (GB)
  • MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
  • Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
  • Tao Yuan General Hospital (TW)
  • KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa, 4001
Corresponding author
James, William S.
Venue
Nature Communications
Published
2021-03-29
Volume
12
Issue
1
Pages
5061-5061
ISSN
2041-1723 (ISSN-L)
OpenAlex
W3193567675
Cited by
216
References
50
Citations by year
2026: 4 · 2025: 12 · 2024: 21 · 2023: 49 · 2022: 75 · 2021: 55
FWCI
15.84
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Greater South Information System
Funders
  • Meso Scale Diagnostics
  • Wellcome Trust (216417/Z/19/Z, 204721/Z/16/Z, WT 109965MA, 110,110z/15/Z, 211153/Z/18/Z, 109965/Z/15/Z)
  • UK Research and Innovation (NIHR200907, MR/V027859/1)
  • National Institute for Health Research Health Protection Research Unit (NIHR200907)
  • National Institute for Health and Care Research (NIHR-INF-0067, CL-2018-13-007, NIHR-INF-1867, 10980107, U19 I082360, ACF-2019-13-003, DHCS/04/G121/68, COVID-19, ACF-2018-13-005, NIHR300791, MR/V027859/1, WT109965MA, COV19-RECPLA, NF-SI-0515-10005, CL-2020-13-002, NIHR200907, CL-2013-13-003, NF-SI-0617-10139)
  • British Heart Foundation (RE/18/3/34214)
  • Department of Health and Social Care (COVID-19)
  • University of Oxford (RE/18/3/34214, NIHR200907)
  • University of New South Wales
  • Public Health England
  • Huo Family Foundation
  • Hamilton Health Sciences Foundation
  • UK Coronavirus Immunology Consortium
  • National Institutes of Health (WT109965MA, U19 I082360, COVID-19)
  • Medical Research Council (MR/V027859/1, 75F40120C00085, MR/L006588/1, COVID-19)
  • Biotechnology and Biological Sciences Research Council
  • NIHR Oxford Biomedical Research Centre
Topics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
  • Life Sciences › Immunology and Microbiology › Immunology › Immune responses and vaccinations
Keywords
SARS-CoV-2, COVID-19 vaccines, variants of concern, Beta variant, Alpha variant, neutralizing antibodies, T cell response, booster vaccination, natural infection, conserved epitopes, vaccine efficacy
MeSH terms
Angiotensin-Converting Enzyme 2, COVID-19, SARS-CoV-2, COVID-19 Vaccines, Animals, Antibodies, Monoclonal, Antibodies, Viral, Epitopes, Carrier Proteins, Humans, Immunity, T-Lymphocytes, Antibodies, Neutralizing

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