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Multiantigen pan-sarbecovirus DNA vaccines generate protective T cell immune responses
Jeroen van Bergen, … , Gerben C. Zondag, Ferry Ossendorp
Jeroen van Bergen, … , Gerben C. Zondag, Ferry Ossendorp
Published September 14, 2023
Citation Information: JCI Insight. 2023;8(21):e172488. https://doi.org/10.1172/jci.insight.172488.
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Research Article COVID-19 Vaccines

Multiantigen pan-sarbecovirus DNA vaccines generate protective T cell immune responses

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Abstract

SARS-CoV-2 is the third zoonotic coronavirus to cause a major outbreak in humans in recent years, and many more SARS-like coronaviruses with pandemic potential are circulating in several animal species. Vaccines inducing T cell immunity against broadly conserved viral antigens may protect against hospitalization and death caused by outbreaks of such viruses. We report the design and preclinical testing of 2 T cell–based pan-sarbecovirus vaccines, based on conserved regions within viral proteins of sarbecovirus isolates of human and other carrier animals, like bats and pangolins. One vaccine (CoVAX_ORF1ab) encoded antigens derived from nonstructural proteins, and the other (CoVAX_MNS) encoded antigens from structural proteins. Both multiantigen DNA vaccines contained a large set of antigens shared across sarbecoviruses and were rich in predicted and experimentally validated human T cell epitopes. In mice, the multiantigen vaccines generated both CD8+ and CD4+ T cell responses to shared epitopes. Upon encounter of full-length spike antigen, CoVAX_MNS-induced CD4+ T cells were responsible for accelerated CD8+ T cell and IgG Ab responses specific to the incoming spike, irrespective of its sarbecovirus origin. Finally, both vaccines elicited partial protection against a lethal SARS-CoV-2 challenge in human angiotensin-converting enzyme 2–transgenic mice. These results support clinical testing of these universal sarbecovirus vaccines for pandemic preparedness.

Authors

Jeroen van Bergen, Marcel G.M. Camps, Iris N. Pardieck, Dominique Veerkamp, Wing Yan Leung, Anouk A. Leijs, Sebenzile K. Myeni, Marjolein Kikkert, Ramon Arens, Gerben C. Zondag, Ferry Ossendorp

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Figure 1

Antigen selection for T cell–based pan-sarbecovirus vaccine CoVAX_MNS.

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Antigen selection for T cell–based pan-sarbecovirus vaccine CoVAX_MNS.
(...
(A) Using the SARS-CoV-2 Wuhan-Hu-1 isolate (NC_045512.2) as the reference sequence, M, N, and S aa sequences from 41 sarbecoviruses (Supplemental Table 2) were aligned using Clustal Omega. For every Wuhan aa position in these proteins, the fraction of sarbecovirus sequences with a different aa at that position is plotted (difference to Wuhan). Full alignment results are presented in Supplemental Figures 1–3. (B) The selected conserved antigenic regions were incorporated into a multiantigen DNA vaccine in which these regions were separated by AAA spacers and reordered to minimize artificial junctional epitopes containing spacer-derived alanines. (C and D) Subsequently, the number of predicted HLA class I binders and experimentally validated CD8+ T cell epitopes present in the resulting vaccines were calculated using online tools. (C) First, peptides predicted to bind any of the most prominent HLA-A (A*01:01, A*02:01, A*03:01, A*11:01, A*23:01, A*24:02) or HLA-B (B*07:02, B*08:01, B*35:01, B*40:01, B*44:02, B*44:03) alleles (83) with affinities below 50 nM (black) or 500 nM (gray) were identified using MHCflurry (54). At every aa position, the number of predicted HLA-binding peptides to which this aa residue contributes is indicated (HLA binders). (D) Next, known human SARS-CoV-2 CD8+ T cell epitopes presented via the abovementioned HLA alleles were obtained from the IEDB database (55). For every aa position, the number of confirmed CD8+ T cell epitopes this aa residue contributes to is plotted (T cell epitopes).

Copyright © 2023 American Society for Clinical Investigation
ISSN 2379-3708

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