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.