Persistent immune imprinting occurs after vaccination with the COVID-19 XBB.1.5 mRNA booster in humans

Abstract

Immune imprinting describes how the first exposure to a virus shapes immunological outcomes of subsequent exposures to antigenically related strains. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron breakthrough infections and bivalent COVID-19 vaccination primarily recall cross-reactive memory B cells induced by prior Wuhan-Hu-1 spike mRNA vaccination rather than priming Omicron-specific naive B cells. These findings indicate that immune imprinting occurs after repeated Wuhan-Hu-1 spike exposures, but whether it can be overcome remains unclear. To understand the persistence of immune imprinting, we investigated memory and plasma antibody responses after administration of the updated XBB.1.5 COVID-19 mRNA vaccine booster. We showed that the XBB.1.5 booster elicited neutralizing antibody responses against current variants that were dominated by recall of pre-existing memory B cells previously induced by the Wuhan-Hu-1 spike. Therefore, immune imprinting persists after multiple exposures to Omicron spikes through vaccination and infection, including post XBB.1.5 booster vaccination, which will need to be considered to guide future vaccination.

Keywords: COVID-19 mRNA vaccines; SARS-CoV-2; SARS-CoV-2 variants; coronaviruses; depletion assays; immune imprinting; memory B cells; neutralizing antibodies; spike glycoprotein.

Figure 1.. Plasma neutralizing antibody responses elicited by XBB.1.5 S and Wuhan-Hu-1/BA.5 bivalent S mRNA booster vaccination in humans.

A,C, Timeline of vaccination and blood draws for the XBB.1.5 S (A) and the Wuhan-Hu-1/BA.5 bivalent S (C) mRNA booster vaccine cohorts. B,D, Plasma neutralizing antibody titers evaluated using a vesicular stomatitis virus (VSV) pseudotyped with the Wuhan-Hu-1 S harboring the D614G mutation (red), the XBB.1.5 mutations (green), the HK.3 mutation (purple), the BA.2.86 mutations (yellow) or the JN.1 mutation (blue) using plasma obtained 7 to 13 days (mean: 10 days, C left) or 30-63 days (mean: 51 days, C right) after vaccination with the XBB.1.5 S mRNA booster or 22 to 51 days (mean: 36 days) after vaccination with the Wuhan-Hu-1/BA.5 bivalent booster (D). Each data point represents the half-maximal inhibitory dilution (ID₅₀) for an individual obtained from averaging two biological replicates with each one comprising two to four technical replicates (excepted for individual 491C for which the ID₅₀ values were obtained from four technical replicates for HK.3 and JN.1). For BA.2.86 S VSV neutralization using the plasma samples from the Wuhan-Hu-1/BA.5 bivalent S mRNA booster vaccinated cohort, the ID₅₀ values were obtained from one batch of pseudovirus using technical duplicates. Geometric mean titers (GMTs) for each cohort against each pseudotype are indicated above the corresponding bar graph. The dotted dashed lines indicate the limit of detection which is 1/20 for all assays except for neutralizations of Wuhan-Hu-1 G614 S, XBB.1.5 S and BA 2.86 S VSV with XBB.1.5 S booster-elicited vaccinee plasma at day 10 and Wuhan-Hu-1/BA.5 bivalent S booster-elicited vaccinee plasma for which it is 1/40. See also Figures S1 and S2.

Figure 2.. Depletion of Wuhan-Hu-1 S-reactive plasma antibodies abrogates XBB.1.5 S binding and neutralizing antibody titers.

A-D, Antibody binding titers (expressed as half-maximal effective dilution, ED₅₀) against Wuhan-Hu-1 S (A,C) and XBB.1.5 S (B,D) in XBB.1.5 S booster-elicited vaccinee plasma that were either mock-depleted (left) or depleted (right) of antibodies recognizing Wuhan-Hu-1 S as determined by ELISA. E-H, Neutralizing antibody titers against Wuhan-Hu-1 S VSV (E,G) and XBB.1.5 S VSV (F, H) in XBB.1.5 S booster-elicited vaccinee plasma that were mock-depleted (left) or depleted (right) from antibodies recognizing Wuhan-Hu-1 S. Samples were collected 7-13 days (mean: 10 days, A-B and E-F) or 30-63 days (mean: 51 days, C-D and G-H) after receiving the XBB.1.5 S mRNA booster. The dotted lines indicate the limit of detection of 1/50 for the ELISA and 1/40 or 1/10 for the neutralization assays. In panels A-D, each data point represents the half-maximal effective dilution (ED₅₀) for an individual obtained from averaging technical duplicates from one representative out of 2 biological replicates. In panels E-H, each data point represents the half-maximal inhibitory dilution (ID₅₀) for an individual obtained from the average of two biological experiments each done with technical duplicates which were averaged. Geometric mean titers (GMTs) for each cohort against each pseudovirus are shown as bar graphs. See also Figures S3 and S4.

Figure 3.. Wuhan-Hu-1 S-reactive memory B cells dominate humoral immune responses elicited by XBB.1.5 S mRNA booster vaccination in humans.

A, Gating strategy to evaluate the cross-reactivity with the Wuhan-Hu-1 RBD of XBB.1.5 RBD+ memory B cells. Dump includes markers for CD3, CD8, CD14, and CD16. B-C, XBB.1.5 RBD double positive memory B cells (left) were analyzed for cross-reactivity with the Wuhan-Hu-1 (Wu) RBD (right). Memory B cells were obtained from peripheral blood collected from individuals 7-13 days (mean: 10 days, B) or 30-63 days (mean: 51 days, C) after receiving the XBB.1.5 S mRNA booster using flow cytometry. See also Figure S5.