Deep immunological imprinting due to the ancestral spike in the current bivalent COVID-19 vaccine

Abstract

To combat the evolving SARS-CoV-2 Omicron variants, bivalent COVID-19 mRNA vaccines, encoding both ancestral and Omicron BA.5 spikes, have replaced monovalent vaccines in numerous countries. However, fourth doses of either vaccine result in similar neutralizing antibody titers against Omicron subvariants, raising the possibility of immunological imprinting. To address this, we investigate antibody responses in 72 participants given three doses of a monovalent mRNA vaccine, followed by a bivalent or monovalent booster, or those with breakthrough infections with BA.5 or BQ. Bivalent boosters do not show notably higher binding or virus-neutralizing titers against various SARS-CoV-2 variants compared to monovalent ones. However, breakthrough infections lead to significantly better neutralization of Omicron subvariants. Multiple analyses, including antigenic mapping, suggest that the ancestral spike in bivalent vaccines is causing deep immunological imprinting, preventing broadening of antibodies to the BA.5 component, thereby defeating its intended goal. Its removal from future vaccine compositions is therefore strongly recommended.

Keywords: COVID-19; Omicron BA.5 spike; SARS-CoV-2; ancestral spike; antigenic distance; bivalent mRNA vaccine; immunological imprinting; serum neutralization.

Graphical abstract

Figure 1

SARS-CoV-2 antibody responses to D614G and Omicron subvariants following monovalent booster, bivalent booster, or breakthrough infection (A) EC₅₀ titers of binding antibodies in the serum samples from participants who received four doses of a monovalent mRNA vaccine (4-dose monovalent), three doses of a monovalent mRNA vaccine followed by one dose of a bivalent vaccine (3-dose monovalent + bivalent), and experienced BA.5 (BA.5 breakthrough) or BQ (BQ breakthrough) breakthrough infections after two to four doses of vaccine. (B) ID₅₀ titers of neutralizing antibodies in the serum samples from “4-dose monovalent,” “3-dose monovalent + bivalent,” “BA.5 breakthrough,” and “BQ breakthrough” cohorts against D614G and Omicron subvariants. Breakthrough serum samples were separated into two sub-groups using two distinct symbols. Square symbols indicate samples from individuals who received three doses of monovalent vaccines followed by a breakthrough infection. Round symbols indicate samples from individuals who received four or five doses of monovalent vaccines and subsequently had a breakthrough infection. dpv, days post last vaccination; dpi, days post infection. The numbers in parentheses represent the mean days post last vaccination (dpv) or the mean days post infection (dpi). (C) Serum-neutralizing ID₅₀ titers against XBB.1.5, XBB.1.16, and XBB.1.5 carrying the individual spike mutations found in XBB.1.16. Values above symbols indicate the geometric mean EC₅₀ or IC₅₀ titers for each cohort. The neutralization assay limit of detection (LOD) is 50 (dotted line), and the number of samples below the LOD is denoted above the x axis. Comparisons were made against “3-dose monovalent + bivalent” cohort (A) or XBB.1.5 (B and C) by Mann-Whitney tests. ns, not significant; ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001. Sample sizes (n) are shown in (B). See also Tables S1 and S2.

Figure 2

Deep immunological imprinting caused by the ancestral spike in bivalent COVID-19 mRNA vaccines impaired serum-neutralizing antibody responses to Omicron subvariants (A) Antigenic map derived from the neutralization data in Figure 1B. SARS-CoV-2 variants and sera are shown as colored circles and squares, respectively. The x and y axes represent antigenic units (AU), with each grid corresponding to a 2-fold serum dilution of the neutralization titer, as defined by the RACMACS package (https://github.com/acorg/Racmacs/tree/master). (B) Neutralizing antibody responses induced by a fourth dose of a bivalent mRNA vaccine compared to a fourth dose of the original monovalent booster or breakthrough infections. The values above the symbols indicate the geometric mean ID₅₀ titer for each cohort. The assay limit of detection (LOD = 50) is represented by a dotted line. Comparisons were made against 3-dose monovalent + bivalent cohort by Mann-Whitney test, and the statistical significance is represented as ∗p < 0.05 or ∗∗p < 0.01. The numbers in parentheses represent the mean days post last vaccination (dpv) or the mean days post infection (dpi). (C) Antigenic maps for individual cohorts against D614G, BA.5, and BQ.1.1. Arrows indicate the antigenic distances from D614G to BA.5 (green) and BQ.1.1 (magenta). See also Figure S1.