
Medicine and Health
Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination
R. K. Suryawanshi, I. P. Chen, et al.
This study by authors including Rahul K. Suryawanshi and Irene P. Chen explores the intriguing landscape of cross-variant immunity following Omicron infection. It reveals that while Omicron infection shows limited immune response and milder symptoms compared to Delta, it raises questions about the potential for broader protection among unvaccinated individuals. Dive into this compelling research to uncover the nuances of variant immunity!
~3 min • Beginner • English
Introduction
The study addresses whether infection with the SARS-CoV-2 Omicron variant can induce cross-variant immunity comparable to or broader than that induced by other variants, and whether widespread Omicron infection could contribute to broader population immunity. Contextually, since the beginning of the COVID-19 pandemic, successive waves driven by variants of concern (VOCs) such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and most recently Omicron (BA.1) have occurred. Omicron is characterized by an unusually large number of mutations, particularly in the spike glycoprotein, contributing to antigenic differences. These mutations are associated with increased transmission and decreased neutralizing antibody efficacy from prior infection, vaccination, and therapeutic monoclonal antibodies, leading to higher risks of breakthrough and reinfection. Despite this, Omicron infections tend to result in lower disease severity than Delta. The purpose of the current study is to experimentally compare pathogenicity, innate and adaptive immune responses, and cross-variant neutralization after infection with ancestral WA1, Delta, and Omicron in mouse models and to assess neutralization breadth in human sera from vaccinated and unvaccinated individuals with Delta or Omicron infections.
Literature Review
Prior reports indicate that Omicron spike mutations reduce spike cleavage and cell–cell fusion and limit the effectiveness of neutralizing antibodies elicited by prior infection, vaccination, and monoclonal antibody therapies, thereby increasing the risk of breakthrough infections and reinfections. Clinical observations suggest lower disease severity with Omicron compared to Delta. These findings frame the hypothesis that Omicron may not elicit broad cross-variant immunity without prior vaccination.
Methodology
Animal model and infections: Transgenic K18-hACE2 mice, which overexpress human ACE2, were used to permit efficient replication of WA1 and Delta variants. Fifteen mice per group were intranasally infected with 1×10^6 p.f.u. of SARS-CoV-2 WA1 (ancestral), Delta, or Omicron. Body temperature and weight were monitored daily to indicate disease progression. At specified days post-infection (2, 4, and 7 d.p.i.; n=5 per time point), tissues from the upper respiratory tract (nasal turbinates and bronchi) and lungs were harvested for analyses. Survival was monitored in separate cohorts (n=10 per group). Viral replication and pathology: Infectious virus titers in respiratory tissues were quantified by plaque assays at multiple time points. Viral RNA levels were assessed in the respiratory tract and lungs (methods imply qRT–PCR). Lung histology included nucleocapsid immunostaining to visualize infected foci. Brain tissue, a replication site in K18-hACE2 mice, was examined for viral replication at 2 and 4 d.p.i. In vitro infection: Human airway organoids and A549 lung alveolar epithelial cells overexpressing ACE2 were infected with WA1, Delta, or Omicron, and production of infectious particles was quantified. Cytokine and interferon responses: Expression of pro-inflammatory cytokines (for example, CXCL10 and CCL2) and IL-10, as well as type I interferon (IFNα) and downstream interferon-stimulated genes (ISG15, OAS1), were measured in lung tissues at early and later time points (methods imply transcript quantification). T cell phenotyping and function: Single-cell suspensions from lungs of mock-infected and variant-infected mice were analyzed by mass cytometry (CyTOF). Activation/exhaustion markers PD1 and CTLA4 on CD4+ and CD8+ T cells were quantified. For functional assays, pulmonary T cells were stimulated ex vivo for 6 hours with overlapping SARS-CoV-2 spike peptide pools and assessed for intracellular cytokine production (IFN-γ and TNF) to identify SARS-CoV-2-specific T cells. Neutralization assays in mice: Sera were collected 7 d.p.i. from mice infected with WA1, Delta, or Omicron and tested for live-virus neutralization against WA1, Alpha, Beta, Delta, and Omicron isolates. 50% neutralization titers (NT50) were calculated across serial serum dilutions. A repeat experiment assessed sera at 9 d.p.i. Neutralization assays in humans: Human sera were grouped as follows: unvaccinated individuals with likely Omicron infection (based on collection date; n=10), unvaccinated individuals with likely Delta infection (n=11), vaccinated individuals with confirmed Omicron infection (n=8), and vaccinated individuals with confirmed Delta infection (n=7). NT50 values against multiple variants were determined. Statistical analysis: Data were analyzed using two-way ANOVA with multiple-comparison adjustments (Bonferroni where noted) and two-tailed unpaired Student’s t-tests. Data are presented as mean ± s.e.m.
Key Findings
- Disease severity in mice: WA1- and Delta-infected K18-hACE2 mice developed progressive hypothermia and severe weight loss; many reached humane endpoints within 7 days. Omicron-infected mice showed only mild symptoms, slight temperature increases, and no visible illness; survival was markedly better than WA1 and Delta groups. - Viral replication and pathology: WA1 and Delta produced high infectious titers in upper airways and lungs across time points, whereas Omicron replication was significantly lower in these organs and in brain tissue at 2 and 4 d.p.i. Lung histology showed small localized foci of infection with Omicron, more foci with WA1, and large patches of infected cells with Delta, consistent with enhanced cell-to-cell spread. In human airway organoids and A549-ACE2 cells, Omicron produced fewer infectious particles than WA1 and Delta. - Innate and T cell responses: WA1 and Delta robustly induced pro-inflammatory cytokines associated with severe COVID-19 (e.g., CXCL10, CCL2), whereas Omicron elicited significantly reduced induction early after infection. IL-10 induction showed no significant differences but trended lower with Omicron at 2 d.p.i. IFNα and ISG responses (ISG15, OAS1) showed no significant differences across variants, though later time points had small animal numbers. T cells from infected mice exhibited increased activation/exhaustion markers (PD1 and CTLA4), with significantly lower levels in Omicron-infected mice compared to WA1/Delta. Despite signs of exhaustion, functional SARS-CoV-2-specific CD4+ and CD8+ T cells producing IFN-γ and/or TNF were detected after peptide stimulation in lungs of mice infected with all three variants. - Cross-variant neutralization in mice: • Sera from WA1-infected mice effectively neutralized WA1 and Alpha, with reduced efficacy against Beta and Delta, and no efficacy against Omicron (Omicron NT50 ≈ 6). • Sera from Delta-infected mice effectively neutralized Delta (NT50 ≈ 422), WA1 (NT50 ≈ 275), and Alpha (NT50 ≈ 356), with lower neutralization of Omicron (NT50 ≈ 115) and Beta (NT50 ≈ 62). • Sera from Omicron-infected mice neutralized Omicron (NT50 ≈ 113) but showed no neutralization of other variants (NT50 ≈ 3–7). In a repeat at 9 d.p.i., Omicron sera had NT50 ≈ 92 against Omicron and negligible against other VOCs (NT50 reported 76–17, described as non-neutralizing/poor). - Human serum neutralization: Unvaccinated individuals with likely Omicron infection showed limited neutralization breadth (mainly against Omicron). Unvaccinated individuals with likely Delta infection exhibited broader neutralization than Omicron-infected unvaccinated individuals. Vaccinated individuals with Omicron breakthrough infections had the highest and broadest neutralization titers across all VOCs. Vaccinated and infected animals also showed enhanced neutralization of Omicron compared to Delta.
Discussion
The findings demonstrate that Omicron infection in the absence of prior vaccination induces a narrow humoral response largely limited to the infecting variant, with minimal cross-neutralization of other VOCs. In contrast, Delta infection elicited broader neutralization, including against WA1 and Alpha and partial activity against Omicron and Beta. Reduced pro-inflammatory cytokine induction and lower activation/exhaustion marker expression on lung-resident T cells during Omicron infection correlate with the milder disease phenotype and may contribute to weaker humoral responses. Despite T cell activation/exhaustion, functional SARS-CoV-2-specific T cells were detectable across variants, suggesting that cellular immunity is generated but may not compensate for limited antibody breadth after Omicron infection alone. Importantly, Omicron breakthrough infections in vaccinated individuals markedly boosted neutralization breadth and titers across VOCs, indicating that Omicron can act as a potent booster of vaccine-primed immunity. These results suggest that relying on natural Omicron infection in unvaccinated populations is unlikely to confer broad protection against other variants, whereas vaccination followed by exposure provides enhanced cross-variant immunity.
Conclusion
Omicron infection produces milder disease and lower replication in K18-hACE2 mice compared to WA1 and Delta, and induces reduced pro-inflammatory responses and T cell activation/exhaustion. Critically, Omicron infection without prior vaccination elicits limited humoral immunity with poor cross-variant neutralization, whereas Delta infection induces broader neutralization. Vaccination combined with Omicron breakthrough infection yields robust, broad neutralizing responses against multiple VOCs. The study underscores the importance of vaccination to achieve cross-variant protection and suggests that Omicron circulation alone will not end the pandemic via broad natural immunity. Future work should assess the durability of Omicron-elicited immunity, the breadth and longevity of T cell responses, the impact of additional Omicron-lineage subvariants, and the performance of variant-adapted or multivalent vaccines in eliciting broad, durable protection.
Limitations
- Animal model limitations: K18-hACE2 mice overexpress human ACE2 and may not fully recapitulate human disease or immune responses. - Sample size and timing: Small numbers of animals at later time points limited statistical power for interferon/ISG analyses. - Human cohort classification: Some human infections were designated as Delta or Omicron based on collection date rather than sequencing, introducing potential misclassification. - Limited time points: Neutralization assays were performed early (7–9 d.p.i.) and may not capture maturation of antibody responses. - Variants tested: Neutralization breadth was evaluated against a defined panel (WA1, Alpha, Beta, Delta, Omicron BA.1); results may differ for other sublineages or later VOCs.
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