3.3 The Omicron variant cross-recognizing feature of ancestral SARS-CoV-2-specific T cell and antibody
We also explored whether the Omicron variant immune evasion exists for the antibodies and T cell responses induced by the inactivated vaccine inoculated 2-year convalescents. We performed a competitive ELISA assay to further evaluate the S protein RBD-binding neutralizing antibodies against the WT strain as well as Delta and Omicron (BA.1, BA.2, and BA.4/5). When comparing the titers at three time points, i.e. 6 months, 1 year and 2 years, neutralizing capacities of sera showed a decreasing trend between 6-month and 1-year cohorts against the WT as well as other variants (Figure 5A). The inhibition rates of NAb to each strain were markedly raised in the vaccinated 2-year convalescents compared to their unvaccinated time points at 6 months and 1 year, with median inhibition rates against five strains (WT, Delta, BA.1, BA.2, and BA.4/5) in the 2-year visit that were 1.3, 1.4, 4.5, 2.0, and 2.9 times those for the 1-year visit (Figure 5A). None of the individuals had detectable neutralizing antibodies in the unvaccinated cohort (Figure 5B). In the sera of 2-year convalescents with vaccination, the median NAb inhibition rates against the WT, Delta, BA.1, BA.2, and BA.4/5 strains (94.5, 90.9, 39.3, 47.8, and 37.6%), were much higher than in healthy controls with vaccination against these strains (74.7, 54.7, 11.8, 16.7, and 14.0%) (Figure 5B). The median anti-RBD NAb inhibition levels against WT, Delta, BA.1, BA.2, and BA.4/5 strains were higher by 1.3-, 1.7-, 3.3-, 2.9, 2.7-fold, respectively, in the vaccinated 2-year convalescents as compared to the vaccinated healthy controls (Figure 5B). The Nab inhibition against WT and other variants was directly compared within 2-year convalescents and healthy controls after vaccination (Figure 5C, D). The positive proportions of vaccinated 2-year convalescents sera against BA.1 (70.6%), BA.2 (78.4%), and BA.4/5 (82.4%) variants were lower than WT (94.1%) and Delta (94.1%) but mostly above the detection threshold (Figure 5C and Supplementary Table 3). However, we found statistical differences among all five strains, except for BA.1 and BA.4/5 strains (p < 0.001, Figure 5C). For the 2-year convalescents who had a history of vaccination, non-reduction in the median ratio of neutralizing activity of Delta, a 2.4-fold reduction of BA.1, a 2.0-fold reduction of BA.2, and a 2.5-fold reduction of BA.4/5 was shown, compared with the neutralization of WT strain (Figure 5C). Even lower proportions of healthy controls after vaccinations showed positive neutralization responses against BA.1 (34.3%), BA.2 (37.1%) as well as BA.4/5 (34.3%), and a markedly drop in comparison with WT (85.7%) and Delta (80.0%) was observed (Figure 5D and Supplementary Table 3). Notably, in the healthy controls, the cross-neutralizing antibodies were much lower than that for 2-year convalescents after vaccination. The drop level of NAb inhibition rates against Delta, BA.1, BA.2, and BA.4/5 was 1.4-, 6.3-, 4.5-, and 5.3-fold respectively, compared to WT (Figure 5D).
Comparing the geometric mean ratio of four SARS-CoV-2 variants NAb inhibition rates normalized WT, these data indicate that 2-year vaccinated convalescents lead to more broadly cross-neutralization of BA.1 and BA.4/5 as compared with healthy individuals with vaccination, but not for Delta and BA.2 (Figure 5E). We also calculated the seropositivity rates of NAb against all four SARS-CoV-2 strains, regarding cross-protection of neutralizing antibodies. We observed a higher proportion of antibodies neutralized overall stains in the convalescent participants (68.6%) compared to the healthy controls following vaccination (28.6%) (p = 0.001, Figure 5F). These data show that 2-year COVID-19 convalescents with vaccination have more tolerance to the Omicron variant than healthy controls after vaccination, though both groups were inoculated with the inactivated vaccine for the WT strain.
Furthermore, we assessed the T cell responses from 2-year convalescents and healthy controls after vaccination to WT and Omicron BA.1 peptide pools (RBD, S1, and S2) (Figure 6A). T cell reactivities in 2-year convalescents after inoculated inactivated vaccines were significantly higher than in healthy controls against WT and BA.1 peptide pools (p <0.001) (Figure 6B). Notably, we found no remarkable difference in IFN-γ levels between WT and BA.1 for 2-year convalescents (median 150 SFU/106 PBMCs for WT S1; median 130 SFU/106 PBMCs for BA.1 S1) and healthy controls following immunization (Figure 6B). Based on the profile of cytokine expression (IFN-γ, IL-2, TNF-α) after stimulation with either WT or BA.1 S1/S2 antigens among the 2-year convalescents and healthy controls after vaccination, we demonstrated that high cross-CD4+ and CD8+ T cell responses retained against BA.1 in both 2-year convalescents and healthy controls after vaccination (Figure 6C, D). In conclusion, the spike-specific T cell reactivity produced by vaccination and/or previous infection is vastly preserved against Omicron BA.1.