Boosting with variant-matched or historical mRNA vaccines protects against Omicron infection in mice

Abstract

The large number of spike substitutions in Omicron lineage variants (BA.1, BA.1.1., and BA.2) could jeopardize the efficacy of SARS-CoV-2 vaccines. We evaluated in mice the protective efficacy of the Moderna mRNA-1273 vaccine against BA.1 before or after boosting. Whereas two doses of mRNA-1273 vaccine induced high levels of neutralizing antibodies against historical WA1/2020 strains, lower levels against BA.1 were associated with breakthrough infection and inflammation in the lungs. A primary vaccination series with mRNA-1273.529, an Omicron-matched vaccine, potently neutralized BA.1 but inhibited historical or other SARS-CoV-2 variants less effectively. However, boosting with either mRNA-1273 or mRNA-1273.529 vaccines increased neutralizing titers and protection against BA.1 and BA.2 infection. Nonetheless, the neutralizing antibody titers were higher, and lung viral burden and cytokines were slightly lower in mice boosted with mRNA-1273.529 and challenged with BA.1. Thus, boosting with mRNA-1273 or mRNA-1273.529 enhances protection against Omicron infection with limited differences in efficacy measured.

Keywords: Omicron; SARS-CoV-2; antibody; booster; immunity; mRNA vaccine; mice; neutralization; pathogenesis.

Graphical abstract

Figure 1

Antibody responses of mRNA vaccines in K18-hACE2 mice 7-week-old female K18-hACE2 mice were immunized with 5 or 0.1 μg of mRNA vaccines. (A) Scheme of immunizations and blood draw. (B) Binding of Sarbecovirus cross-reactive mAbs to Wuhan-1 and BA.1 spike and RBD proteins. (C–F) Serum IgG responses at 3 weeks after the second 5 μg (C and D) or 0.1 μg (E and F) dose of mRNA vaccines (control or mRNA-1273) against indicated spike (C and E) or RBD (D and F) proteins (n = 12, two experiments, boxes illustrate geometric mean titers [GMT], dotted lines show limit of detection [LOD]). (G) Serum neutralizing antibody responses 3 weeks after second vaccine dose against WA1/2020 D614G (left) and BA.1 (right) in mice immunized with 5 or 0.1 μg of control (n = 4) or mRNA-1273 (n = 12) vaccines (two experiments, boxes illustrate GMT, dotted lines show the LOD). (H) Paired analysis of serum neutralizing titers against WA1/2020 D614G and BA.1 from individual mice (data from G) from samples obtained 3 weeks after the second 5 μg (left) or 0.1 μg (right) dose of mRNA-1273 (n = 12, two experiments, dotted lines show the LOD). GMT and fold-change values are indicated at the top of the graphs. (C–F) Mann-Whitney test. (G) One-way ANOVA with Dunn’s post-test. (H) Wilcoxon signed-rank test (^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001). See also Figure S1.

Figure S1

Serum neutralization of WA1/2020 D614G and BA.1 viruses, related to Figure 1 Seven-week-old female K18-hACE2 mice were immunized with 5 or 0.1 μg of mRNA vaccines. Serum neutralizing antibody responses against WA1/2020 D614G and BA.1 were assessed 3 weeks after the second vaccine dose (control mRNA, top; mRNA-1273, bottom) from mice immunized with 5 or 0.1 μg of control (n = 4) or mRNA-1273 (n = 12) vaccines. Neutralization curves corresponding to individual mice are shown for the indicated vaccines. Each point represents the mean of two technical replicates.

Figure 2

Protection against SARS-CoV-2 infection after mRNA vaccination in K18-hACE2 mice 7-week-old female K18-hACE2 mice were immunized with 5 or 0.1 μg of mRNA vaccines. 5 weeks after a primary vaccination series, mice were challenged with 10⁴ focus-forming units (FFU) of WA1/2020 D614G or BA.1. (A) Scheme of immunizations, blood draws, and virus challenge. (B and C) Body weight in animals immunized with 5 μg (B) or 0.1 μg (C) of control or mRNA-1273 vaccines between days 0 and 6 after challenge with WA1/2020 D614G or BA.1. Data show mean values (n = 7–8, two experiments). (D–I) Viral burden at 6 dpi in the nasal washes (D and G), nasal turbinates (E and H), and lungs (F and I) as assessed by qRT-PCR of the N gene after WA1/2020 D614G or BA.1 challenge of mice immunized with 5 μg (D–F) or 0.1 μg (G–I) of control or mRNA-1273 vaccines (n = 7–8, two experiments, boxes illustrate median values, dotted lines show LOD). (B and C) Unpaired t test. (D–I) Mann-Whitney test (ns, not significant; ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001). (J) Correlation analyses comparing serum neutralizing antibody concentrations 3 weeks after the second vaccine dose and lung viral titers (6 dpi) after challenge with WA1/2020 D614G (left) or BA.1 (right); Pearson’s correlation R² and p values are indicated as insets; closed symbols 5 μg vaccine dose; open symbols, 0.1 μg vaccine dose.

Figure 3

mRNA vaccine protection against disease in K18-hACE2 mice 7-week-old female K18-hACE2 mice were immunized with two 5 or 0.1 μg doses of mRNA vaccines and challenged with WA1/2020 D614G or BA.1, as described in Figures 1A and 2A. (A and B) Heat-maps of cytokine and chemokine levels in lung homogenates at 6 dpi in animals immunized with 5 μg (A) or 0.1 μg (B) doses of indicated mRNA vaccines. Fold-change was calculated relative to naive uninfected mice, and log₂ values are plotted (2 experiments, n = 7–8 per group except naive, n = 4). The full data set is shown in Tables S1 and S2. (C–E) Hematoxylin and eosin staining of lung sections harvested from control or mRNA-1273 vaccinated animals (5-μg dose, C; 0.1-μg dose, D) at 6 dpi with WA1/2020 D614G or BA.1. A section from an uninfected animal (E) is shown for comparison. Low (left; scale bars, 1 mm), moderate (middle, scale bars, 200 μm), and high (bottom; scale bars, 50 μm) power images are shown. Representative images of multiple lung sections from n = 3 per group. See also Tables S1 and S2.

Figure 4

A booster dose of mRNA-1273 enhances neutralizing antibody responses and confers protection in K18-hACE2 mice 7-week-old female K18-hACE2 mice were immunized with 5 or 0.25 μg of mRNA vaccines and boosted 16–19 weeks later with 1 μg of mRNA-1273. (A) Scheme of immunizations, blood draws, and virus challenge. (B and C) Serum neutralizing antibody responses immediately before (B, pre-boost) and 4 weeks after (C, post-boost) a control or mRNA-1273 booster dose against WA1/2020 D614G (left) and BA.1 (right) in mice immunized with 5 or 0.25 μg of control (n = 4) or mRNA-1273 (5 μg, n = 8; 0.25 μg, n =4) vaccines (one experiment, boxes illustrate GMT, dotted lines show the LOD). (D and E) Paired analysis of pre-boost (D) and post-boost (E) serum neutralizing titers against WA1/2020 D614G and BA.1 from individual mice (data from B and C) from samples obtained from animals that received a primary 5 μg (left) or 0.25 μg (right) dose series of mRNA-1273 vaccine (n = 4–8, one experiment, dotted lines show the LOD). GMT and fold-change values are indicated at the top of the graphs. (F and G) 4 weeks after boosting with control or mRNA-1273, mice were challenged with 10⁴ FFU of BA.1. Viral burden at 6 dpi in the nasal washes, nasal turbinates, and lungs as assessed by N gene levels in animals that had received a primary series immunization with 5 μg (F) or 0.25 μg (G) doses of control or mRNA-1273 vaccines (n = 7–8, two experiments, boxes illustrate median values, dotted lines show LOD). (B and C) One-way ANOVA with Kruskal-Wallis post-test. (D and E) Wilcoxon signed-rank test. (F and G) Mann-Whitney test (ns, not significant; ^∗∗p < 0.01; ^∗∗∗p < 0.001). See also Figure S2.

Figure S2

Serum neutralization of WA1/2020 D614G and BA.1 viruses, related to Figure 4 Seven-week-old female K18-hACE2 mice were immunized with 5 or 0.25 μg of mRNA vaccines and then boosted approximately 17–19 weeks later with 1 μg of mRNA-1273. Serum neutralizing antibody responses against WA1/2020 D614G and BA.1 immediately before (top, pre-boost) and 4 weeks after (bottom, post-boost) a control or mRNA-1273 booster dose from mice immunized with 5 or 0.25 μg of control (n = 4) or mRNA-1273 (5 μg, n = 8; 0.25 μg, n = 4) vaccines. Neutralization curves corresponding to individual mice are shown for the indicated immunizations. Each point represents the mean of two technical replicates.

Figure 5

Antibody responses in BALB/c mice after immunization with mRNA-1273 and mRNA-1273.529 vaccines (A) 6-to-8-week-old female BALB/c mice were immunized twice over a 3-week interval with 1 or 0.1 μg of mRNA-1273 or mRNA-1273.529 vaccine or a PBS control (not shown, all values at the LOD). Immediately before (day 21) or 2 weeks after (day 36) the second vaccine dose, serum was collected. (B and C) Serum antibody binding to Wuhan-1 or BA.1 spike proteins by ELISA at days 21 (B) and 36 (C) (n = 8, two experiments, boxes illustrate mean values, dotted lines show the LOD). (D) Serum antibody binding at day 36 to Wuhan-1, BA.1, B.1.351 (Beta), or B.1.617.2 (Delta) RBD proteins by ELISA (n = 8, two experiments, boxes illustrate mean values, dotted lines show the LOD). (E) Neutralizing activity of serum at day 36 against VSV pseudoviruses displaying the spike proteins of Wuhan-1 D614G, BA.1, BA.1.1, B.1.351, or B.1.617.2 (n = 8, two experiments, boxes illustrate GMT, dotted lines show the LOD). GMT values are indicated above the columns. (B–E) Mann-Whitney test (ns, not significant; ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001).

Figure 6

Booster doses of mRNA-1273 or mRNA-1273.529 enhance neutralizing antibody responses in 129S2 mice 7-week-old female 129S2 mice were immunized with 5 or 0.25 μg of mRNA vaccines and then boosted 10–11 weeks later with 1 μg of control mRNA, mRNA-1273, or mRNA-1273.529. (A) Scheme of immunizations and blood draws. (B and C) Serum neutralizing antibody responses immediately before (B, pre-boost) and 3–4 weeks after (C, post-boost) a control, mRNA-1273, or mRNA-1273.529 booster dose against WA1/2020 N501Y/D614G (left), BA.1 (middle), and BA.2 (right) in 129S2 mice that received primary series immunizations with 5 or 0.25 μg of control (n = 6) or mRNA-1273 (n = 30) vaccines (two experiments, boxes illustrate GMTs, dotted lines show the LOD). (D–F) Paired analysis of pre- and post-boost serum neutralizing titers against WA1/2020 D614G (D), BA.1 (E), and BA.2 (F) viruses from samples obtained from animals (data from B and C) that received the following primary and booster immunizations: mRNA-1273 (5 or 0.25 μg) + control booster, mRNA-1273 (5 or 0.25 μg) + mRNA-1273 booster, and mRNA-1273 (5 or 0.25 μg) + mRNA-1273.529 booster (n = 10, two experiments, dotted lines show the LOD). GMT values are indicated at the top of the graphs. (B and C) One-way ANOVA with Dunn’s post-test. (D–F) Wilcoxon signed-rank test (ns, not significant; ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001). See also Figures S3 and S4.

Figure S3

Pre- and post-boost serum neutralization of WA1/2020 N501Y/D614G, BA.1, and BA.2 viruses, related to Figure 6 Seven-week-old female 129S2 mice were immunized with 5 or 0.25 μg of mRNA vaccines and then boosted 10–11 weeks later with 1 μg of control mRNA, mRNA-1273, or mRNA-1273.529. Neutralizing antibody responses against WA1/2020 N501Y/D614G, BA.1, and BA.2 from serum immediately before (top, pre-boost) or 1 month after boosting (bottom, post-boost) with indicated vaccines from 129S2 mice that had received primary series immunizations with 5 or 0.25 μg of control or mRNA-1273 vaccines. Neutralization curves corresponding to individual mice are shown for the indicated immunizations. Sera are from two independent experiments, and each point represents the mean of two technical replicates.

Figure S4

Pre- and post-boost serum neutralization of B.1.351 virus, related to Figure 6 7-week-old female 129S2 mice were immunized with 5 or 0.25 μg of mRNA vaccines and boosted 10–11 weeks later with 1 μg of control mRNA, mRNA-1273, or mRNA-1273.529. (A and B) Serum neutralizing antibody responses immediately before (A, pre-boost) and 3–4 weeks after (B, post-boost) administering a control, mRNA-1273, or mRNA-1273.529 booster dose as judged by FRNT with B.1.351 (two experiments, boxes illustrate GMT, dotted lines show the LOD). (C) Paired analysis of pre- and post-boost serum neutralizing titers against B.1.351 from samples obtained from animals (data from A to B) that received the following primary and booster immunizations: mRNA-1273 (5 or 0.25 μg) + control booster, mRNA-1273 (5 or 0.25 μg) + mRNA-1273 booster, mRNA-1273 (5 or 0.25 μg) + mRNA-1273.529 booster (n = 10, two experiments, dotted lines show the LOD). GMT values are indicated at the top of the graphs. (D) Neutralizing antibody responses against B.1.351 from serum before (top, pre-boost) or 1 month after boosting (bottom, post-boost) with indicated vaccines from 129S2 mice that had received primary series immunizations with 5 or 0.25 μg of control or mRNA-1273 vaccines. Neutralization curves corresponding to individual mice are shown. Sera are from two independent experiments, and each point represents the mean of two technical replicates. (B and C) One-way ANOVA with Dunn’s post-test. (D–F) Wilcoxon signed-rank test (ns, not significant; ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001).

Figure 7

Booster doses of mRNA-1273 or mRNA-1273.529 enhance protection against BA.1 infection in 129S2 mice 7-week-old female 129S2 mice were immunized with 5 or 0.25 μg of mRNA vaccines, boosted with 1 μg of control mRNA, mRNA-1273, or mRNA-1273.529 and challenged with WA1/2020 N501Y/D614G or BA.1. (A) Scheme of immunizations, blood draws, and virus challenge. (B) Viral RNA levels at 3 dpi in the nasal washes, nasal turbinates, and lungs after WA1/2020 N501Y/D614G or BA.1 challenge of mice immunized with 5 μg (left) or 0.25 μg (right) of control or mRNA-1273 vaccines and boosted with control, mRNA-1273, or mRNA-1273.529 vaccines (n = 8–10 per group, two experiments, boxes illustrate mean values, dotted lines show LOD; one-way ANOVA with Tukey’s post-test: ns, not significant; ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001). (C and D) Heat-maps of cytokine and chemokine levels in lung homogenates at 3 dpi with WA1/2020 N501Y/D614G or BA.1 in animals immunized with 5 μg (C) or 0.25 μg (D) doses of control or mRNA-1273 vaccines and then boosted with control, mRNA-1273, or mRNA-1273.529 vaccines. Fold-change was calculated relative to naive mice, and log₂ values are plotted (2 experiments, n = 8 per group except naive, n = 4). See also Tables S3 and S4.