mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant

Abstract

Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured the neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild-type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that received their primary series recently (<3 months), distantly (6-12 months), or an additional "booster" dose, while accounting for prior SARS-CoV-2 infection. Remarkably, neutralization of Omicron was undetectable in most vaccinees. However, individuals boosted with mRNA vaccines exhibited potent neutralization of Omicron, only 4-6-fold lower than wild type, suggesting enhanced cross-reactivity of neutralizing antibody responses. In addition, we find that Omicron pseudovirus infects more efficiently than other variants tested. Overall, this study highlights the importance of additional mRNA doses to broaden neutralizing antibody responses against highly divergent SARS-CoV-2 variants.

Keywords: COVID-19; Delta; Omicron; SARS-CoV-2; breadth; infectivity; neutralizing antibodies; spike; vaccination; variants.

Graphical abstract

Figure 1

Emergence of SARS-CoV-2 Omicron among global variants of concern (A) Phylogenetic tree of SARS-CoV-2 variants with sampling dates shows emergence of Omicron variant by December 2021 (adapted from nextstrain.org; updated as of December 14, 2021). (B) Schematic of SARS-CoV-2 spike protein structure and mutations of variants used in this study are illustrated. Omicron variant mutations used in this study were based on the most prevalent mutations (>85% frequency) found in GISAID and reflect the dominant Omicron variant. The regions within the spike protein are abbreviated as follows: SP, signal peptide; RBD, receptor binding domain; TM, transmembrane domain. (C) Crystal structure of pre-fusion stabilized SARS-Cov-2 spike trimer (PDB ID 7JJI) highlighting the mutational landscape of SARS-CoV-2 Delta and Omicron variants relative to SARS-CoV-2 wild type. Top views (left panels) and side views (right panels) of spike protein are shown with mutations in RBD (in red), S1 (in blue), and S2 (in yellow), highlighted with residue atoms as colored spheres.

Figure 2

Additional mRNA vaccine dose (“booster”) induces potent neutralizing responses against SARS-CoV-2 Omicron variant that are low-to-absent in primary series (“non-boosted”) vaccinees (A) Schematic representation of vaccinee cohorts of healthy adult community dwellers and healthcare workers. Participants who completed their primary series of vaccination with two-dose mRNA-1273 (Moderna), two-dose BNT162b (Pfizer), or 1-dose Ad26.COV2.S (Janssen) were included in this study. Vaccinees were stratified into four subgroups, as follows: infection-naive, non-boosted individuals that received primary vaccination series within last 3 months (“recent vax”); individuals that received primary vaccination series 6–12 months before and were either without (“distant vax”) or with a history or serologic evidence of SARS-CoV-2 infection (“distant vax + infection”); and infection-naive individuals that were boosted within the last 3 months (“booster vax”). History of SARS-CoV-2 infection was determined by either self-reported history of positive PCR test and/or positive anti-SARS-CoV-2 nucleocapsid antibody test. (B) Schematic of experimental workflow of high-throughput SARS-CoV-2 pseudovirus neutralization assay used to determine neutralization titer of vaccinee sera against variants. Select images were created with BioRender.com. (C) Neutralization titers (in WHO IU/mL) of wild-type (WT), Delta, and Omicron pseudoviruses were determined for people who received primary vaccination series with mRNA-1273 (top panel; in red), BNT162b2 (middle panel; in blue), or Ad26.COV2.S (bottom panel; in green) and classified into the aforementioned subgroups (in A). Dark horizontal lines for each group denote geometric mean titer. Pie charts show the proportion of vaccinees within each group that had detectable neutralization against the indicated SARS-CoV-2 pseudovirus. Fold-decrease in geometric mean neutralization titer of Omicron relative to wild type within a subgroup is shown as a number with “×” symbol within the gray region; this was done only for vaccinee subgroups where neutralization against wild-type pseudovirus was detected in 100% of individuals. All fold-decreases shown have unadjusted p < 0.05 with paired t test. Within “booster vax” subgroups (far right), boosters were homologous (same vaccine) except for 1 of 33 mRNA-1273 vaccinees that crossed-over to BNT162b (top panel; in blue), 6 of 30 BNT162b vaccinees that crossed-over to mRNA-1273 (middle panel; in red), and 7 of 8 Ad26.COV2.S vaccinees that crossed-over to mRNA-1273 (bottom panel; in red).

Figure 3

Cross-reactivity of neutralizing antibody response is increased by an additional dose (“booster”) of mRNA vaccine relative to primary vaccination series and can be predicted by anti-spike antibody levels (A) Neutralization titers (in WHO IU/mL) of wild-type (WT; left panel), Delta (middle panel), and Omicron (right panel) SARS-CoV-2 pseudoviruses were analyzed for infection-naive participants that were recently vaccinated with primary series or booster (<3 months). Recently vaccinated individuals received mRNA-1273 (×2), BNT162b (×2), or Ad26.COV2.S (×1), and boosted individuals received a homologous booster of mRNA-1273 (×3), or BNT162b (×3), or a cross-over booster of mRNA-1273 for Ad26.COV2.S vaccinees (×1 + 1). Fold-increase in geometric mean neutralization titer of boosted versus non-boosted individuals is shown as a number with “×” symbol. This analysis is based on experimental data depicted in Figure 2C but excludes participants with prior SARS-CoV-2 infection, distant vaccination (>6 months), and/or cross-over between mRNA-1273 and BNT162b to understand differences in neutralizing responses soon after primary vaccination series versus boosting. The single Ad26.COV2.S vaccinee that received a homologous boost with Ad26.COV2.S was also excluded from this analysis. Dark horizontal lines for each group denote geometric mean titer. (B) Aggregate data from study participants in (A) that recently received primary vaccination series (“primary series”; white circles) or were recently boosted (“boosted”; dark gray squares) were used for linear regression analysis of wild type versus Delta (left panel) or wild type versus Omicron (right panel) pseudovirus neutralization. Wild-type neutralization titers correlated with Delta neutralization in “primary series” individuals (R² = 0.35; slope = 0.44; p < 0.0001) and even more strongly in “boosted” individuals (R² = 0.68; slope = 1.00; p < 0.0001). Wild-type neutralization titers showed no significant relationship with Omicron neutralization in “primary series” individuals (R² = 0.03; slope = 0.05; p = 0.16); however, “boosted” individuals showed a significant correlation with Omicron neutralization titers (R² = 0.56; slope = 0.94; p < 0.0001). (C) Anti-SARS-CoV-2 spike antibodies levels (measured by an EUA-approved clinical diagnostic test) of all vaccinees were plotted against neutralization of wild-type (left panel; white circles), Delta (middle panel; orange circles), and Omicron (right panel; purple circles) SARS-CoV-2 pseudoviruses. Optimal spike antibody cut-offs for predicting positive neutralization were determined by ROC analyses in (D) and are indicated with a vertical dashed line. (D) Receiver operating characteristic (ROC) analyses assessing the ability of spike antibody levels to predict neutralization of wild-type (black line), Delta (orange line), and Omicron (purple line) pseudoviruses. Positive neutralization was defined as >33 IU/mL (previously defined with a cohort of 1,200 pre-pandemic samples (Garcia-Beltran et al., 2021b) and converted to WHO IU/mL). Area under curve (AUC) for wild type was 0.97, Delta was 0.91, and Omicron was 0.84, with p < 0.0001 for all three. Optimal cut-offs that maximized sensitivity (Se) and specificity (Sp) were determined using the “Se + Sp” method, and were as follows: for wild type, optimal cut-off of 711 U/mL achieved 88.4% Se and 96.7% Sp; for Delta, optimal cut-off of 1,591 U/mL achieved 88.4% Se and 83.8% Sp; and for Omicron variant, optimal cut-off of 10,300 achieved 67.2% Se and 90.6% Sp. These optimal cut-off values are plotted as a vertical dashed line in (C).

Figure 4

SARS-CoV-2 Omicron pseudovirus demonstrates a substantial increase in infectivity of ACE2⁺ cells relative to other SARS-CoV-2 variants in vitro (A) Flow cytometry histogram depicting ACE2 surface staining on parental 293T cell line (in black), and 293T-ACE2 cell line stably expressing human ACE2 (in lilac). Dashed line indicates unstained control. (B) Representative dot plots show percentage of 293T (left panel) and 293T-ACE2 (right panel) cells that were infected with wild-type, Delta, or Omicron SaRS-CoV-2 pseudoviruses (within ZsGreen⁺ gate) after 48 h of co-culture. Pseudoviruses were produced in parallel and under identical conditions. (C) Titering of SARS-CoV-2 pseudoviruses of wild-type, Gamma, Beta, Delta, and Omicron variants was performed on 293T-ACE2 cells and correlated to pseudovirus concentration in genome copies (GC)/mL as determined by qPCR. Two technical replicates (n = 2) and a linear regression were performed to fit data, given that a linear relationship of virus concentration versus infected cells can be assumed at infection rates <10%. (D) Pseudovirus infectivity relative to wild type was measured for each SARS-CoV-2 variant in (C) by calculating fold change in slope from (C) for each pseudovirus relative to wild type. Bars and error bars depict mean and standard error of the mean.