Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice

Abstract

As existing vaccines fail to completely prevent COVID-19 infections or community transmission, there is an unmet need for vaccines that can better combat SARS-CoV-2 variants of concern (VOC). We previously developed highly thermo-tolerant monomeric and trimeric receptor-binding domain derivatives that can withstand 100 °C for 90 min and 37 °C for four weeks and help eliminate cold-chain requirements. We show that mice immunised with these vaccine formulations elicit high titres of antibodies that neutralise SARS-CoV-2 variants VIC31 (with Spike: D614G mutation), Delta and Omicron (BA.1.1) VOC. Compared to VIC31, there was an average 14.4-fold reduction in neutralisation against BA.1.1 for the three monomeric antigen-adjuvant combinations and a 16.5-fold reduction for the three trimeric antigen-adjuvant combinations; the corresponding values against Delta were 2.5 and 3.0. Our findings suggest that monomeric formulations are suitable for upcoming Phase I human clinical trials and that there is potential for increasing the efficacy with vaccine matching to improve the responses against emerging variants. These findings are consistent with in silico modelling and AlphaFold predictions, which show that, while oligomeric presentation can be generally beneficial, it can make important epitopes inaccessible and also carries the risk of eliciting unwanted antibodies against the oligomerisation domain.

Keywords: AlphaFold; COVID-19; Omicron; SARS-CoV-2; biomolecular modelling; receptor-binding domain (RBD); thermotolerant vaccine; vaccine equity; vaccine matching; variants of concern (VOC).

Figure 1

COVID-19 vaccine storage temperature and cold-chain transport affects equitable access. The total doses (including boosters) administered per 100 people is shown in (A), while (B) shows the top 10 vaccines (grouped into three categories) inequitably distributed across the four World Bank country income brackets. (C) Storage temperatures for these top 10 vaccines (grouped under three headings) is compared to Mynvax formulation. (D) The average storage temperatures show a high level of correlation with vaccine inequity experienced by LICs and LMICs. In (B), the red line denotes the total number of countries used in our analysis (n = 202) based on availability of information from Our World in Data. The data in (A) was accurate as of 22 February 2022 and in (B) was accurate as of 6 February 2022.

Figure 2

Schematic diagram of vaccine formulations 1–6 evaluated by this study (c.f. Table 1). Supplementary Text A contains further amino acid information.

Figure 3

ANOVA analysis of neutralising antibody titres against SARS-CoV-2 VIC31-D614G, Delta and Omicron BA.1.1 variants following mouse immunisation with different vaccine formulations (A–I) and comparing monomeric to trimeric formulations (J–L). * p < 0.05; ** p < 0.01; *** p < 0.001.

Figure 4

Visualisation of variant mutations in the RBD of the SARS-CoV-2 spike protein (residues 330 to 530). Omicron BA.1.1 is notable for the numbers of new mutations in this region (15 compared to 3 in Beta/Gamma and 1 in Alpha). Our isolate also included the mutation R346K. Beta and Gamma variants present similar RBDs; differing at position 417, by Asn (N).

Figure 5

Visualisations of the AlphaFold predictions of the trimeric construct. (A,B) show the top and side views of one probable structure; (C,D) of another. RBD domains are shown in blues, while the trimerisation domain is shown in pink. (E) shows (C) in greater detail, highlighting in yellow the buried G339, S371, S373, S375 and N440 residues, which are mutation sites in Omicron.