An mRNA vaccine encoding the SARS-CoV-2 Omicron XBB.1.5 receptor-binding domain protects mice from the JN.1 variant

Abstract

Background: The SARS-CoV-2 Omicron BA.2.86 variant and its descendant lineages, including JN.1, are rapidly spreading globally. We developed mRNA encoding the SARS-CoV-2 RBD derived from XBB.1.5 (XBB.1.5-type LNP-mRNA-RBD), in line with WHO recommendations. Many individuals have acquired immunity specific to the ancestral SARS-CoV-2 strain or early Omicron variants, such as BA.1, BA.2, or BA.5, through natural infection and/or vaccination. However, the efficacy of XBB.1.5-type LNP-mRNA-RBD boost vaccination against a clinical isolate of JN.1 remains uncertain.

Methods: In this study, we used a small amount of LNP-mRNA-RBD as a prime dose compared with a booster shot to mimic the waning immunity against the ancestral and BA.4/5 strains. We immunised female mice with XBB.1.5-type LNP-mRNA-RBD as a booster vaccine and examined the cellular and humoural responses as well as the protective efficacy against a JN.1 variant.

Findings: We found that immunisation of mice with the XBB.1.5-type LNP-mRNA-RBD as a booster shot induced XBB.1.5-specific neutralising activity and T cell responses. Moreover, immunisation with a bivalent vaccine consisting of the ancestral-type and BA.4/5-type LNP-mRNA-RBD as the primary dose followed by XBB.1.5-type LNP-mRNA-RBD boosting induced enhanced levels of cross-reactive antibodies against the JN.1 strain, compared to using the ancestral-type vaccine as the primary dose. In addition, we found that a booster shot of LNP-mRNA-RBD based on the XBB.1.5 strain reduced the viral burden in the respiratory organs after JN.1 challenge.

Interpretation: Our findings suggest that XBB.1.5-type LNP-mRNA-RBD is effective against antigenically distinct JN.1 infection.

Funding: This work was supported by grants from the Japan Program for Infectious Diseases Research and Infrastructure (JP25wm0125002), the Japan Initiative for World-leading Vaccine Research and Development Centers (JP253fa627001), and the Vaccine Development project (JP21nf0101625) from the Japan Agency for Medical Research and Development, and the National Institutes of Allergy and Infectious DiseasesCenter for Research on Influenza Pathogenesis and Transmission (CRIPT) (75N93021C00014).

Keywords: LNP-mRNA-RBD; Mouse model; Omicron JN.1 variant; SARS-CoV-2.

Fig. 1

RBD-specific cellular responses in spleen induced in LNP-mRNA-RBD-immunised mice. (a) Schematic diagram showing the experimental workflow. K18-hACE2 mice were immunised with LNP-mRNA-RBD by intramuscular inoculation, followed by a booster dose 21 days later. At 2–3 weeks after the second immunisation, splenocytes were harvested from the immunised mice. Splenocytes from the immunised mice were re-stimulated with peptide pools designed from ancestral, XBB.1.5 or BA.2.86 S protein. (b) IFNγ– and TNFα–secreting cells from spleens were analysed by flow cytometry after 6 h of stimulation with 1 μg/mL peptide pool. Representative FACS plots to identify IFNγ⁺TNFα⁺CD8⁺ or CD4⁺ T cells are shown. The frequencies of IFNγ⁺TNFα⁺CD8⁺ or CD4⁺ T cells are represented as the mean ± standard deviation (SD) (n = 5 for the group). Points indicate data from individual mice. Data were analysed using a Kruskal–Wallis test with Dunn's multiple comparisons. (c) the AIM⁺(4-1BB⁺CD69⁺)CD8⁺ T cells and AIM⁺(4-1BB⁺OX40⁺)CD4⁺ T cells from spleens were analysed by flow cytometry after 18 h of stimulation with 1 μg/mL peptide pool. Representative FACS plots to identify AIM⁺(4-1BB⁺CD69⁺)CD8⁺ or AIM⁺(4-1BB⁺OX40⁺)CD4⁺ T cells are shown. The frequencies of AIM⁺(4-1BB⁺CD69⁺)CD8⁺ or AIM⁺(4-1BB⁺OX40⁺)CD4⁺ T cells are represented as the mean ± standard deviation (SD) (n = 5 for the group). Points indicate data from individual mice. Data were analysed using a Kruskal–Wallis test with Dunn's multiple comparisons. Additional statistical test results (P values) that were not shown in the figures are described in the Supplementary Table.

Fig. 2

RBD-specific antibody responses induced in LNP-mRNA-RBD-immunised mice. (a) Schematic diagram showing the experimental workflow. K18-hACE2 mice were immunised with LNP-mRNA-RBD by intramuscular inoculation, followed by a booster dose 21 days later. At 2 weeks after the second immunisation, serum was harvested from the immunised mice. (b) The neutralising titres (FRNT₅₀ values) of the serum samples were determined in Vero E6-TMPRSS2-T2A-ACE2 cells. Each dot represents data from one mouse (n = 48 for group 1, n = 49 for the other groups). The lower limit of detection (value = 10) is indicated by the horizontal dashed line. Samples under the detection limit (<10) were assigned an FRNT₅₀ of 10. Geometric mean titres are shown. Neutralising titres were compared by using the Friedman test with Dunn's multiple comparisons test, analysing in two directions: the immunisation groups and the tested viruses. The statistical results for the immunisation groups are indicated in red, whereas the results for the tested viruses are shown in black.

Fig. 3

Infection with antigenically matched and distinct variants in LNP-mRNA-RBD-immunised mice. (a) Schematic diagram showing the experimental workflow. K18-hACE2 mice immunised with LNP-mRNA-RBD were challenged with 10⁵ PFU of the ancestral strain (NC002) (b–d), 10⁵ PFU of XBB.1.5 (HP40900) (e–g), or 10^4.6 PFU of JN.1 (Stanford165) (h–j). The details of the groups are described in the table. (b, c, e, f, h, i) Body weights (b, e, h) and survival (c, f, i) of virus-infected (n = 5) mice were monitored daily for 10 days after viral challenge. Data are the mean percentage ± SD of the starting weight. Body weight changes were analysed using linear mixed-effects modelling (lmer, lme4) with post-hoc comparisons (lsmeans, cld, emmeans) in R. Statistical test results (P values) of body weight changes are described in the Supplementary Table. All groups were compared to each other at different time points. Survival data were analysed with the log-rank (Mantel–Cox) test. (d, g, j) Five mice per group were euthanised at 2 or 5 days post-infection for virus titration. Virus titres in the nasal turbinates and lungs were determined using plaque assays. Data are the mean ± SD; points represent data from individual mice. The lower limit of detection is indicated by the horizontal dashed line. Data were analysed by using the Kruskal–Wallis test with Dunn's multiple comparisons.