1
Mechanism of a COVID-19 nanoparticle vaccine candidate that elicits a broadly 1
neutralizing antibody response to SARS-CoV-2 variants 2
3
Yi-Nan Zhang
1
, Jennifer Paynter
1
, Cindy Sou
1
, Tatiana Fourfouris
1
, Ying Wang
3,4
, Ciril 4
Abraham
3
, Timothy Ngo
1
, Yi Zhang
3,4
, Linling He
1
, and Jiang Zhu
1, 2,
* 5
6
1
Department of Integrative Structural and Computational Biology,
2
Department of Immunology 7
and Microbiology, The Scripps Research Institute, La Jolla, California 92037, USA
8
3
Fels Institute for Cancer Research and Molecular Biology, and
4
Department of Microbiology 9
and Immunology, Temple University, Philadelphia, Pennsylvania 19140, USA. 10
11
*Corresponding author 12
JZ: Phone +1 (858) 784-8157; Email: jiang@scripps.edu
13
14
KEYWORDS 15
Ancestral strain; broadly neutralizing antibody (bNAb); coronavirus disease 2019 (COVID-19); 16
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); self-assembling protein 17
nanoparticle (SApNP); vaccine; variant of concern (VOC). 18
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2
ABSTRACT (150 words) 19
Vaccines that induce potent neutralizing antibody (NAb) responses against emerging variants of 20
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential for combating the 21
coronavirus disease 2019 (COVID-19) pandemic. We demonstrated that mouse plasma induced 22
by self-assembling protein nanoparticles (SApNPs) that present 20 rationally designed 23
S2GΔHR2 spikes of the ancestral Wuhan-Hu-1 strain can neutralize the B.1.1.7, B.1.351, P.1, 24
and B.1.617 variants with the same potency. The adjuvant effect on vaccine-induced immunity 25
was investigated by testing 16 formulations for the multilayered I3-01v9 SApNP. Using single-26
cell sorting, monoclonal antibodies (mAbs) with diverse neutralization breadth and potency were 27
isolated from mice immunized with the receptor binding domain (RBD), S2GΔHR2 spike, and 28
SApNP vaccines. The mechanism of vaccine-induced immunity was examined in mice. 29
Compared with the soluble spike, the I3-01v9 SApNP showed 6-fold longer retention, 4-fold 30
greater presentation on follicular dendritic cell dendrites, and 5-fold stronger germinal center 31
reactions in lymph node follicles. 32
33
34
ONE-SENTENCE SUMMARY (125 characters) 35
With a well-defined mechanism, spike nanoparticle vaccines can effectively counter SARS-36
CoV-2 variants. 37
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INTRODUCTION 38
The COVID-19 pandemic has led to more than 188 million infection cases and 4 million deaths 39
globally. Antibody responses to SARS-CoV-2 spike antigens can be sustained for several months 40
in most COVID-19 patients after infection (1-4). However, recently identified variants of 41
concern (VOCs) exhibit higher transmissibility and resistance to prior immunity as SARS-CoV-2 42
continues to adapt to the human host (5, 6). One such variant, B.1.1.7 (WHO classification: 43
Alpha), emerged from southeast England in October 2020 and accounted for two-thirds of new 44
infections in London in December 2020, with a higher transmission rate (43-90%) and risk of 45
mortality (32-104%) than previously circulating strains (7, 8). Other variants, such as B.1.351 46
(Beta) and P.1 (Gamma), also became prevalent in three provinces in South Africa and Manaus, 47
Brazil, respectively (6, 9, 10). The B.1.617.2 (Delta) variant, which was initially identified in 48
India, is becoming a dominant strain in many countries (11, 12) and responsible for the majority 49
of new COVID-19 cases. This variant was found to be ~60% more transmissible than the highly 50
infectious B.1.1.7 variant (12). The rise of SARS-CoV-2 VOCs and their rapid spread worldwide 51
result in more infection cases, hospitalizations, and potentially more deaths, further straining 52
healthcare resources (10). 53
To date, eight COVID-19 vaccines have been approved for emergency use in humans, 54
with more than 90 candidates assessed in various phases of clinical trials (13). With the 55
exception of inactivated whole-virion vaccines, diverse platforms have been used to deliver the 56
recombinant SARS-CoV-2 spike, such as mRNA-encapsulating liposomes (e.g., BNT162b2 and 57
mRNA-1273), adenovirus vectors (e.g., ChAdOx1 nCoV-19 [AZD1222], CTII-nCoV, Sputnik 58
V, and Ad26.COV2.S), and micelle-attached spikes (e.g., NVX-CoV2373). These vaccines 59
demonstrated 65-96% efficacy in Phase 3 trials, with lower morbidity and mortality associated 60
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with COVID-19 disease (14-19). However, a notable loss of vaccine efficacy against new SARS-61
CoV-2 variants was reported, likely caused by spike mutations in the receptor-binding domain 62
(RBD; e.g., K417N, E484K, and N501Y), N-terminal domain (NTD; e.g., L18F, D80A, D215G, 63
and
Δ
242-244), and other regions that are critical to spike stability and function (e.g., D614G and 64
P681R) (6, 11, 20-25). Among circulating VOCs, the B.1.351 lineage appeared to be most 65
resistant to neutralization by convalescent plasma (9.4-fold) and vaccine sera (10.3- to 12.4-fold) 66
(26), whereas a lesser degree of reduction was observed for an early variant, B.1.1.7 (27-29). 67
Based on these findings, it was suggested that vaccines would need to be updated periodically to 68
maintain protection against rapidly evolving SARS-CoV-2 (30-32). However, in a recent study, 69
convalescent sera from B.1.351 or P.1-infected individuals showed a more visible reduction of 70
B.1.617.2 neutralization than convalescent sera from individuals infected with early pandemic 71
strains (33). Together, these issues raise the concern that herd immunity may be difficult to 72
achieve, highlighting the necessity of developing vaccines that can elicit a broadly neutralizing 73
antibody (bNAb) response to current and emerging variants (25, 31). As previously reported (34-74
38), the production of a bNAb response relies on long-lived germinal center (GC) reactions to 75
activate precursor B cells, stimulate affinity maturation, and form long-term immune memory. In 76
particular, antigen retention and presentation within lymph node follicles are key to the induction 77
of long-lived GC reactions (34, 36, 39) and should be considered in the development of bNAb-78
producing vaccines (40). 79
We previously investigated the cause of SARS-CoV-2 spike metastability and rationally 80
designed the S2GΔHR2 spike, which was displayed on three self-assembling protein 81
nanoparticle (SApNP) platforms, including ferritin (FR) 24-mer and multilayered E2p and I3-82
01v9 60-mers, as COVID-19 vaccine candidates (41). In the present study, we investigated the 83
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vaccine-induced NAb response to SARS-CoV-2 VOCs and mechanism by which SApNP 84
vaccines (e.g., I3-01v9) generate such a response. We first examined the neutralizing activity of 85
mouse plasma from our previous study (41) against four representative SARS-CoV-2 variants, 86
B.1.1.7, B.1.351, P.1, and B.1.617
Rec
, which was derived from an early analysis of the B.1.617 87
lineage (11) and shares key spike mutations with VOC B.1.617.2. Mouse plasma induced by the 88
S2GΔHR2 spike-presenting I3-01v9 SApNP potently neutralized all four variants with 89
comparable titers to the wildtype strain, Wuhan-Hu-1. When a different injection route was 90
tested in mouse immunization, E2p and I3-01v9 SApNPs sustained neutralizing titers against the 91
four variants, even at a low dosage of 3.3 μg, whereas a significant reduction of plasma 92
neutralization was observed for the soluble spike. Next, we examined the adjuvant effect on 93
vaccine-induced humoral and T-cell responses for the I3-01v9 SApNP. While detectable plasma 94
neutralization was observed for the non-adjuvanted I3-01v9 group, conventional adjuvants, such 95
as aluminum hydroxide (AH) and phosphate (AP), boosted the titers by 8.6- to 11.3-fold (or 9.6 96
to 12.3 times). Adjuvants that target the stimulator of interferon genes (STING) and Toll-like 97
receptor 9 (TLR9) pathways enhanced neutralization by 21- to 35-fold, alone or combined with 98
AP, in addition to a Th1-biased cellular response. We then performed antigen-specific single-cell 99
sorting and isolated 20 monoclonal antibodies (mAbs) from RBD, spike, and I3-01v9 SApNP-100
immunized mice. These mAbs were derived from diverse B cell lineages, of which some 101
neutralized the wildtype Wuhan-Hu-1 strain and four variants with equivalent potency. Lastly, 102
we investigated how SApNPs behave in lymph nodes and induce GCs by characterizing vaccine 103
delivery and immunological responses at the intraorgan, intracellular, and intercellular levels in 104
mice. The I3-01v9 SApNP showed 6-fold longer retention, 4-fold greater presentation on 105
follicular dendritic cell (DC) dendrites, and 5-fold higher GC reactions than the soluble spike. 106
.CC-BY-NC 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted September 9, 2021. ; https://doi.org/10.1101/2021.03.26.437274doi: bioRxiv preprint