The Omicron variant rapidly became the globally dominant SARS-CoV-2 variant in early 2022, replacing the Delta variant despite widespread vaccination. This study aimed to understand the role of host immune responses in this shift. Retrospective studies showed reduced vaccine efficacy against Omicron compared to earlier variants, likely due to Omicron's numerous mutations in the receptor-binding domain (RBD) and high transmissibility. While natural infection induces broader and more potent antibody responses than vaccination, the interplay between different vaccination strategies (mRNA vs. inactivated), prior infection, and the subsequent infection with either Delta or Omicron variants remained unclear. Inactivated vaccines, widely used globally, demonstrated lower neutralizing antibody levels against Omicron after two doses, raising concerns about breakthrough infections. However, three doses improved protection. This study aimed to compare immune responses following Delta and Omicron breakthrough infections after inactivated vaccination and to analyze the immune response under various vaccination and infection patterns. The objective was to elucidate the factors that may have contributed to Delta's replacement by Omicron from the perspective of host immune response.

Existing research showed an increased breakthrough infection rate for SARS-CoV-2, with declining vaccine efficacy over time, particularly against the Omicron variant. Studies highlighted the superior ability of natural infection to induce broader and more potent antibody responses compared to vaccination. Memory B cells evolved after infection were more effective at producing antibodies against immune-evading variants. Inactivated vaccines, while effective against Alpha, Beta, and Delta variants, demonstrated lower neutralizing antibody (NAb) levels against Omicron after two doses. However, a three-dose regimen significantly improved efficacy, even approaching that of mRNA vaccines in elderly individuals. This variation in vaccine efficacy and the contrasting antibody response elicited by infection versus vaccination underscored the need to understand the interplay between prior vaccination, variant infection, and the resulting immune landscape.

The study compared immune responses in individuals with Delta breakthrough infection after two-dose inactivated vaccination (I-I-d), Omicron breakthrough infection after two-dose mRNA vaccination (M-M-o), Omicron breakthrough infection after two-dose inactivated vaccination (I-I-o), and after three-dose inactivated vaccination (I-I-I). Plasma samples were assessed for neutralizing antibody (NAb) levels against the wild-type (WT) strain, Delta, and Omicron variants using pseudovirus neutralization assays. The researchers also examined T-cell responses using ex vivo and in vitro assays, looking at the frequencies and functionalities of virus-specific CD4⁺ and CD8⁺ T cells. Specific monoclonal antibodies (13C2 and 08B3) targeting different B-cell epitopes on the S protein RBD were used to analyze the breadth of NAb responses. Statistical analyses were employed to compare differences in NAb levels and T-cell responses between groups.

Omicron breakthrough infection, regardless of the prior vaccination type (mRNA or inactivated), resulted in significantly higher NAb levels against various variants compared to Delta breakthrough infection after inactivated vaccination. M-M-o showed substantially higher NAb levels against WT, Delta, and Omicron than I-I-d. Omicron breakthrough infection induced significantly higher NAb levels against Delta than vice versa, suggesting a potential immune barrier against Delta re-infection. M-M-o also induced higher levels of the monoclonal antibodies 13C2 and 08B3, indicating a broader NAb response. Ex vivo T-cell assays showed that M-M-o led to higher numbers of S/M/N/E-specific CD4⁺ T cells and a lower proportion of virus-specific CD45RA⁺CD27⁻CD8⁺ T cells compared to other groups. In vitro assays indicated that breakthrough infection groups showed greater T-cell proliferation and multi-functionality than the I-I-I group.

The findings suggest that Omicron breakthrough infections, irrespective of prior vaccination, generate stronger and broader immune responses than Delta breakthrough infections. The higher NAb levels after Omicron infection might explain the rapid replacement of the Delta variant by Omicron, even under widespread vaccination. The differences in T-cell differentiation and functionality highlight the impact of vaccination-infection patterns on the quality and durability of the immune response. The superior immunogenicity of Omicron may have contributed to its dominance. These results have implications for vaccine development and deployment, emphasizing the need for strategies that enhance the breadth and durability of immunity against emerging variants.

This study demonstrated that Omicron breakthrough infections elicit stronger and broader neutralizing antibody and T cell responses compared to Delta breakthrough infections, potentially explaining Omicron's dominance. mRNA vaccination followed by Omicron infection generated particularly robust immunity. The findings highlight the impact of vaccination-infection patterns on immune imprinting and underscore the importance of developing effective vaccination strategies that provide durable and broad protection against emerging SARS-CoV-2 variants. Future research could focus on strategies to optimize vaccination schedules and vaccine design to enhance protection against a wider range of variants.

The study's retrospective nature and reliance on existing datasets might limit the generalizability of the findings. The sample sizes for some groups, particularly those involving mRNA vaccination followed by Omicron infection, were relatively small. Further research with larger and more diverse cohorts is warranted to confirm and extend these findings.