Immunological imprinting shapes the cross-reactive antibody responses to the KP.2 and LP.8.1 vaccine doses

Variant-specific and cross-reactive antibody responses following COVID-19 booster vaccinations and SARS-CoV-2 breakthrough infections.

SARS-CoV-2 has evolved into several genetic variants, all bearing mutations that reduce antibody binding and affect vaccine and treatment effectiveness. Updated COVID-19 vaccines, including bivalent formulations (wild type [WT]/BA.1 or WT/BA.5) and more recent monovalent versions targeting emerging variants such as XBB.1.5, JN.1, KP.2 or LP.8.1, were developed to broaden protection. However, immune imprinting may limit the induction of neutralizing antibodies against strains that differ significantly, even after receiving several variant-specific boosters. A deeper understanding of how booster vaccination reshapes antibody specificity remains essential for rational vaccine design. We examined the antibody response to a bivalent WT/BA.5 booster, focusing on antibody levels and neutralization. Serum samples collected before and after a fourth dose of monovalent WT or bivalent (WT/BA.5) mRNA vaccines were compared with sera from individuals after primary WT infections and Omicron BA.1, BA.2, or BA.5 breakthrough infections. We found that both monovalent and bivalent boosters significantly increased IgG and neutralizing antibodies, but breakthrough infections induced broader cross-reactive responses. Depletion experiments revealed that booster-induced immunity was predominantly mediated by cross-reactive antibodies, with the highest levels after breakthrough infections and the lowest after a primary WT infection. These findings provide functional insights into the antibody specificities associated with imprinting effects following variant-adapted booster vaccination.

Cross-neutralization of SARS-CoV-2 BA.3.2.2 lineage by JN.1 mRNA vaccine-induced immunity.

The SARS-CoV-2 BA.3.2.2 sublineage has emerged globally as the dominant branch of BA.3.2 by late 2025, yet its antigenic relationship with JN.1 vaccine-induced immunity remains unclear. We evaluated neutralizing antibody responses in 25 JN.1 mRNA vaccinees against eight variants, stratified by anti-nucleocapsid antibody serostatus. Post-vaccination titers increased significantly against all variants in both N antibody-negative and -positive groups. Cross-neutralization against BA.3.2.2 was detected in both groups despite lower titers compared to JN.1. Antigenic cartography revealed that BA.3.2.2 was antigenically isolated from all JN.1-descendant variants. AZD3152/sipavibart retained potent neutralization against BA.3.2.2 but completely lost activity against all F456L-harboring JN.1-descendant variants, while VYD222/pemivibart and SA55 maintained broad activity. Retention of wild-type F456 in BA.3.2.2 preserves class 1/2 antibody epitopes, providing a mechanistic basis for cross-neutralization and suggesting a potential therapeutic window for sipavibart should BA.3.2.2 expand globally, pending clinical confirmation.

Intranasal SARS-CoV-2 vaccine boosting alters immune imprinting and B cell repertoire 2331448

Immune imprinting is a phenomenon in which prior antigen exposure limits variant-specific de novo immune responses to subsequent related antigens. The serum response to Omicron boosters in mice and human are strongly imprinted by prior vaccines encoding SARS-CoV-2 Wuhan-1 spike (e.g., mRNA-1273). Strategies including changes of dosage and interval have had limited success in enhancing variant-specific immunity. Intranasal (i.n.) vaccination is a promising approach that elicits mucosal and systemic immunity. Here we analysed the response of variant boosters delivered i.m. or i.n. after mRNA-1273 priming at the serum, cellular, and B cell repertoire levels to understand how boosting routes modulate the imprinting effect. C57BL/6 mice were primed i.m. with mRNA-1273 and heterologously boosted i.m. or i.n. with a chimpanzee adenoviral-vectored vaccine (ChAd-SARS-CoV-2-S) against XBB.1.5 spike. Serum and bronchoalveolar lavage fluid (BALF) were analysed for cross-reactive and strain-specific spike-binding IgG/IgA. Neutralizing activity was assessed using pseudovirus neutralization assays. Cross-reactive and strain-specific spike-binding memory B cells (MBCs) in draining lymph nodes (dLNs) were quantified. Ongoing studies are using single-cell BCR sequencing to analyse plasmablast clonotypes, with selected ones expressed as mAbs for functional and epitope analyses. Intranasal boosting with ChAd-SARS-CoV-2-S against XBB.1.5 spike induced higher fractions of XBB.1.5-specific serum IgG and BALF IgA with greater neutralizing activity. Intranasal vaccination increased XBB.1.5-specific MBCs in dLNs, indicating a route-dependent shift in B cell specificity. Intranasal boosting promotes greater variant-specific response at both the serum and cellular levels than i.m. boosting. Ongoing B cell repertoire and mAb analyses will provide mechanistic insight into how vaccination route reshapes clonal selection and maturation, informing rational vaccination design. Moderna and NIH R01AI157155 Vaccines and Immunotherapy (VAC)

JN.1-adapted vaccination is associated with readjustment of ancestral memory B cells toward neutralization within the JN.1 antigenic space

The antigenic drift of SARS-CoV-2 toward the JN.1 lineage has prompted the development of variant-adapted COVID-19 booster vaccines. However, these boosters are thought to primarily recall pre-existing memory B cells (MBC), raising concerns about their ability to realign the immune response in highly pre-exposed populations. Here we analyze antibody and B cell responses in pre-exposed individuals (n = 42; median 4.5 prior COVID-19 vaccinations; 90% with at least one prior SARS-CoV-2 infection) following vaccination with a JN.1-adapted mRNA vaccine. Vaccination is associated with increased IgG binding and enhanced neutralization of JN.1 and related descendant variants. Longitudinal profiling of antigen-specific MBC shows that Wu01-only and Wu01/JN.1 cross-reactive cells remain dominant, while JN.1-only cells modestly increase by day 21. Single-cell RNA-sequencing of antigen-specific MBC in a representative sub-cohort (n = 7), combined with functional monoclonal antibody analyses, demonstrates that somatic hypermutation (SHM) drives intra-clonotype specialization toward improved JN.1 binding and neutralization. These findings indicate maturation of pre-existing, class-switched MBC rather than substantial de novo recruitment of naïve B cells. In conclusion, JN.1-adapted booster vaccination is associated with refinement of pre-existing MBC repertoires toward the JN.1 antigenic space and with enhanced neutralization of contemporary and antigenically proximate variants. Because of the continuous evolution of SARS-CoV-2, pre-existing immune responses may not be as effective against new viral variants. Here the authors investigate whether B cell responses to ancestral SARS-CoV-2 are stimulated by JN.1-adapted booster vaccines and propose that there is somatic hypermutation of existing B cell clones rather than de novo generation from naive B cells.

Durability and Breadth of Neutralizing Antibodies Against SARS-CoV-2 Variants Following XBB.1.5 Vaccination in a Multiply Exposed Cohort.

Background Widespread immunity from vaccination and infection has reduced COVID-19 morbidity and mortality, but this immunity varies across the population. Understanding how repeated antigenic exposures influence antibody responses helps to inform future vaccination strategies. Methods We characterized neutralizing antibody (nAb) responses in serum samples collected 1- and 6-months after XBB.1.5 vaccination from 25 healthcare workers with varying, complex histories of vaccination and reported infections. Neutralizing activity was assessed against a range of variants, from pre-Omicron to recent Omicron JN.1 sublineage, and divergent BA.3.2 variants using lentiviral pseudoviruses. Participants were stratified into 5 exposure groups based on their documented vaccination and reported infection history. Results XBB.1.5 vaccination elicited broad neutralizing responses, with strong boosting against previously encountered antigens relative to vaccine-matched XBB.1.5 and newer variants. Geometric mean neutralization titers were generally comparable across exposure groups, though small subgroup sizes and considerable intragroup heterogeneity precluded definitive conclusions about the influence of prior exposure history. At 6 months, titers declined by 36-62% across all variants. Titers remained highest against pre-Omicron variants and were lowest against JN.1 sublineage variants, with some falling to very low levels. Conclusions In this cohort with extensive prior antigenic exposures, broad nAb profiles were observed following XBB.1.5 vaccination, though these responses waned substantially after 6 months. The observed waning of cross-neutralizing antibodies against emerging variants underscores the challenge of maintaining durable protection and supports the need for continued monitoring of antibody responses to guide evidence-based updates to COVID-19 vaccines.

A human monoclonal antibody from hybrid immunity exhibits exceptional neutralization breadth against antigenically divergent contemporary Omicron JN.1 lineage variants