Neutralization of omicron subvariants and antigenic cartography following multiple COVID 19 vaccinations and repeated omicron non JN.1 or JN.1 infections

Abstract

The ongoing emergence of SARS-CoV-2 variants, combined with antigen exposures from different waves and vaccinations, poses challenges in updating COVID-19 vaccine antigens. We collected 206 sera from individuals with vaccination-only, hybrid immunity, and single or repeated omicron post-vaccination infections (PVIs), including non-JN.1 and JN.1, and evaluated neutralization against omicron BA.5, BA.2.75, BQ.1.1, XBB.1.16, XBB.1.5, and JN.1. Neutralizing antibodies exhibited a narrow breadth against BA.5 and BA.2.75 and failed to neutralize BQ.1.1 and XBB lineages after three to five doses of the ancestral monovalent vaccine. Hybrid immunity elicited higher neutralizing titers than vaccination alone, but titers remained relatively low. A single omicron PVI elicited lower neutralization titers to all variants compared to wild-type (WT), indicating immunological imprinting. Repeated omicron PVIs, particularly JN.1, slightly mitigated these effects by increasing broad neutralization responses to all variants, though not significantly. Antigenic mapping demonstrated that XBB lineages and JN.1 are antigenically distant from WT and also evaded antibodies induced by earlier omicron variants (BA.1-5) PVIs. However, repeated JN.1 PVIs shortened this antigenic distance, indicating broader neutralization across omicron variants. These findings highlight SARS-CoV-2 immunity following various antigen boosts and the impact of repeated omicron JN.1 exposure on broad immunity, informing future COVID-19 vaccination strategies.

Keywords: Antigenic cartography; COVID-19; JN.1; Omicron; SARS-CoV-2; Vaccine.

Fig. 1

Study design and distribution of SARS-CoV-2 omicron variants in Thailand. (a) Sera samples were obtained from 206 individuals in three distinct cohorts: (1) vaccinated individuals were grouped according to the seropositivity of anti-N Ig and/or their reported history of infection into those with or without prior infection (blood sampling conducted between August 2021–October 2022); (2) individuals with post-vaccination infections (PVIs) with non-JN.1 (blood sampling conducted from April to May 2023) and (3) those with a recent JN.1 PVIs (blood sampling collected in May 2024) (Created in BioRender.com). (b) The relative frequency of SAR-CoV-2 subvariants distributed in Thailand was determined using the deposited SARS-CoV-2 sequences between Jan 1, 2022, and June 30, 2024. Data were retrieved from the Global Initiative on Sharing All Influenza Data (GISAID) (https://gisaid.org). (c) Heat map of spike protein mutations frequency of BA.2.5, BA.2.75, BQ.1.1, XBB.1.16, XBB.1.5, and JN.1 relative to ancestral Wuhan-H1 strain and their frequency of point mutations were retrieved from https://outbreak.info. CV CoronaVac, ChAd ChAdOx-1 nCov-19, mRNA BNT162b2 or mRNA-1273 vaccines, INF infection, PVI post-vaccination infection.

Fig. 2

Neutralization of WT and Omicron subvariants by sera from vaccinated individuals, with or without prior infection. (a) Total anti-RBD Ig levels in sera samples from vaccinated-only individuals who received three (3xV), four (4xV), or five doses (5xV) of the ancestral vaccines, and individuals with hybrid immunity who had three (2xV + INF), four (3xV + INF), or five (4xV + INF) antigen exposures. (b) Estimated fold reduction in neutralizing titers (FRNT50) against Omicron subvariants, including BA.5, BA.2.75, BQ.1.1, XBB.1.16, and XBB.1.5, relative to WT. Neutralizing antibody titers were compared among (c) vaccinated-only individuals who received different doses of the vaccine and (d) individuals with hybrid immunity who had distinct numbers of antigen exposures. Round and square symbols indicate samples from vaccinated-only individuals and those with hybrid immunity, respectively. The numbers above the symbols indicate geometric mean titers (GMT). The bars represent GMT with a 95% confidence interval. The dotted lines in panels c and d represent the threshold for detectable neutralizing antibody titers, set at 10. The number of samples with detectable neutralizing antibodies is indicated above the x-axis. Differences between groups in panel a were assessed using the Kruskal–Wallis test. Fold changes in neutralizing titers between groups in panles (c,d) are presented above the lines; a two-tailed Mann–Whitney test was used for statistical analysis. ns, not significant; *p < 0.05; **p < 0.01; ***p < 0.001. WT, wild-type Wuhan-H1 strain; V, vaccination; INF, prior infection.

Fig. 3

Neutralizing antibody titers against live SARS-CoV-2 Omicron subvariants from sera of individuals with post-vaccination infection (PVI) caused by non-JN.1 and JN.1 variants. (a) Anti-RBD Ig response in individuals exposed to Omicron either non-JN.1 or JN.1 after vaccination. Neutralization titers in individuals with (b) primary BA.1–5 infection and (c) repeated BA.1–5 + BA.1–5 PVIs were collected four to five months after the last antigen exposure. Neutralization titers were determined using sera from (d) individuals primarily infected with JN.1, (e) those who experienced BA.1–5 exposure followed by JN.1 PVI, and (f) those with BA.1–5 infection followed by XBB and JN.1 PVIs, collected one to two months after the last antigen exposure. (g) Difference in neutralizing titers was compared between a single BA.1–5 PVI and repeated BA.1–5 + BA.1–5 PVIs using Mann–Whitney U test. (h) Difference in neutralizing titers was compared between a single JN.1 PVI, repeated BA.1–5/XBB + JN.1 PVIs and BA.1–5 + XBB + JN.1 PVIs using Kruskal–Wallis test. The bars indicate GMT with a 95% confidence interval, and GMT values are shown for each variant. Significance values for each antigen are presented relative to WT. The dashed line indicates FRNT50 titers below 1:20, the lowest serum dilution, and set as 10 for statistical analysis. Differences between groups in panel a were assessed using the Kruskal–Wallis test. Fold-change comparisons in panels b and e were evaluated using the Wilcoxon signed-rank test, while panels c, d, and f were analyzed using the paired-sample t-test. ns, not significant; *p < 0.05; **p < 0.01; ***p < 0.001. PVI, post-vaccination infection.

Fig. 4

Antigenic cartography analysis with the serum virus neutralizing data against omicron subvariants. Antigenic maps generated from the sera neutralizing data against WT, BA.2.75, BA.5, BQ.1.1, XBB.1.16, XBB.1.5, JN.1 for (a) all cohorts, (b) vaccinated-only individuals (3xV, 4xV and 5xV), (c) individuals with hybrid immunity without presumed variants causing infection (2xV + INF, 3xV + INF and 4xV + INF), (d) a single omicron PVI (BA.1–5 PVI and JN.1 PVI), (e) repeated omicron PVIs (BA.1–5 + BA.1.5 PVIs, BA.1–5/XBB + JN.1 PVIs and BA.1–5 + XBB + JN.1 PVIs), (f) PVIs with non-JN.1 (BA.1–5 PVI and BA.1–5 + BA.1–5 PVIs) and (g) PVIs with JN.1 (JN.1 PVI, BA.1–5/XBB + JN.1 PVIs and BA.1–5 + XBB + JN.1 PVIs). Viruses are shown as colored circles. Sera from vaccinated-only individuals and PVIs are shown as colored squares. The distances between virus antigen and sera positioned in the map are inversely related to the neutralizing antibody titers, with minimized error. A spacing line of each square in the antigenic map refers to the antigenic unit which corresponds to two-fold dilution change in neutralizing FRNT50 titers. Number in parenthesis shows an approximately antigenic distance from WT to each virus antigen.