Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting

Abstract

The continuous emergence of highly immune evasive SARS-CoV-2 variants, like XBB.1.5 and XBB.1.16, highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by wildtype (WT)-based vaccination would compromise the antibody response to Omicron-based boosters. Vaccination strategies that can counter immune imprinting are critically needed. In this study, we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. Our results show that in mice, the efficacy of single Omicron-boosting is heavily limited by immune imprinting, especially when using variants antigenically distinct from WT, like XBB, while the concerning situation could be largely mitigated by a second Omicron booster. Similarly, in humans, we found that repeated Omicron infections could also alleviate WT-vaccination-induced immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. By isolating 781 RBD-targeting mAbs from repeated Omicron infection cohorts, we revealed that double Omicron exposure alleviates immune imprinting by generating a large proportion of highly matured and potent Omicron-specific antibodies. Importantly, epitope characterization using deep mutational scanning (DMS) showed that these Omicron-specific antibodies target distinct RBD epitopes compared to WT-induced antibodies, and the bias towards non-neutralizing epitopes observed in single Omicron exposures due to imprinting was largely restored after repeated Omicron stimulation, together leading to a substantial neutralizing epitope shift. Based on the DMS profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated the combinations of these mutations could further boost XBB.1.5's immune-evasion capability while maintaining high ACE2 binding affinity. Our findings suggest the WT component should be abandoned when updating COVID-19 vaccine antigen compositions to XBB lineages, and those who haven't been exposed to Omicron yet should receive two updated vaccine boosters.

Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding

“…These two sites are also located on a critical epitope that targeted by the public IGHV3-53/3-66 Class 1 NAbs [15][16][17]. Mutations on these sites are likely to escape this type of NAbs that are abundant in vaccinated and convalescent individuals, leading to substantial reduction of protection efficiency [18,19]. It is crucial to investigate the impacts on immune evasion and infection efficiency, especially for recent convalescents who recovered from XBB breakthrough infections, and the underlying mechanism of such synergistic effects that enables the unexpected advantage of L455F mutation on the basis of XBB*+F456L lineages, to explain the exceptional growth advantage of such lineages.…”

“…Consistent with previous studies, single BA.5/BF.7 or XBB BTI cannot elicit NAbs that efficiently neutralize all XBB subvariants due to immune imprinting, with 50% neutralization titers (NT50) lower than 100 [9, 22] (Figure 2A and S1). In contrast, convalescent plasma samples from the reinfection cohort exhibit higher titers against BA.5 than D614G and neutralize XBB subvariants well, which indicates that second exposure to Omicron helps alleviate imprinting [9, 18, 22, 23]. Notably, compared to F456L which is known to escape many NAbs elicited by Omicron reinfection, the additional L455F substitution further causes substantial evasion of plasma from the reinfection cohort [18, 24, 25].…”

“…In contrast, convalescent plasma samples from the reinfection cohort exhibit higher titers against BA.5 than D614G and neutralize XBB subvariants well, which indicates that second exposure to Omicron helps alleviate imprinting [9, 18, 22, 23]. Notably, compared to F456L which is known to escape many NAbs elicited by Omicron reinfection, the additional L455F substitution further causes substantial evasion of plasma from the reinfection cohort [18, 24, 25]. Specifically, an additional L455F mutation based on XBB.1.5+F456L or EG.5 reduces plasma NT50 by 1.2-fold and 1.3-fold in the XBB BTI and reinfection cohorts, respectively (Figure 2B).…”

“…As residues 455 and 456 on RBD are mainly recognized by Class 1 antibodies, which is also referred to as “Group A1/A2” in our previous study, we tested the pseudovirus-neutralizing activities of a panel of XBB.1.5-effective RBD-targeting monoclonal NAbs against these newly-emerged XBB subvariants, which were isolated in previous studies [9, 18] (Figure S2). The selected mAbs are expected to target L455/F456 as determined by deep mutational scanning (DMS) (Figure 3A).…”

“…Mutations on L455 and F456 exhibit correlated but distinct capability of escaping these NAbs (Figure 3B and S3). Group A1 NAbs generally utilize IGHV3-53/3-66 and can cross-neutralize the early D614G (B.1) strain, while Group A2 NAbs are usually specific to Omicron lineages (Figure S4A) [18]. Consequently, L455F and F456L single substitution escape 11 and 8 out of 34 Group A1/A2 NAbs, respectively.…”