Complementarity determining regions in SARS-CoV-2 hybrid immunity

Abstract

Pre-vaccination SARS-CoV-2 infection can boost protection elicited by COVID-19 vaccination and post-vaccination breakthrough SARS-CoV-2 infection can boost existing immunity conferred by COVID-19 vaccination. Such 'hybrid immunity' is effective against SARS-CoV-2 variants. In order to understand 'hybrid immunity' at the molecular level we studied the complementarity determining regions (CDR) of anti-RBD (receptor binding domain) antibodies isolated from individuals with 'hybrid immunity' as well as from 'naive' (not SARS-CoV-2 infected) vaccinated individuals. CDR analysis was done by liquid chromatography/mass spectrometry-mass spectrometry. Principal component analysis and partial least square differential analysis showed that COVID-19 vaccinated people share CDR profiles and that pre-vaccination SARS-CoV-2 infection or breakthrough infection further shape the CDR profile, with a CDR profile in hybrid immunity that clustered away from the CDR profile in vaccinated people without infection. Thus, our results show a CDR profile in hybrid immunity that is distinct from the vaccination-induced CDR profile.

Keywords: COVID-19; SARS-CoV-2; complementary determining region; hybrid immunity; vaccination.

Figure 1

CDR profile and IgG anti-S antibodies before and after two doses of the BN162b2 vaccine [6 weeks (40-45 days) after first dose, three weeks after the second dose] in naïve individuals and in individuals that had been infected with SARS-CoV-2 before vaccination (determined by a positive SARS-CoV-2 PCR on a respiratory sample or presence of IgG anti-S and/or IgG anti-N in serum before infection) (experiment #1). The figure shows the anti-S antibody levels (A), the PCA analysis (B), heat map after hierarchical clustering of the CDR features (C) and age and gender distribution of the included individuals (D). The heat map indicates the variance (from -2 to 2) compared to the mean (0) for each peptide feature. The included vaccination/infection-induced CDR-derived peptides were those that revealed discriminative by sPLS-DA analysis. The green-labeled CDR-derived peptides were also revealed discriminative by sPLS-DA analysis in experiment #2 ( Extended Data Figure 2 ). The median [25^th-75^th percentile] anti-S antibody levels (AU/mL) were 2 [1.8-3.3], 8483 [7028-18901], 122 [86-243], and 26771 [18235-30021] pre-vaccination naïve, post-vaccination naïve, pre-vaccination infected and post-vaccination infected, respectively.

Figure 2

CDR profile and anti-S antibodies before, 3 months and 10 months after BN162b2 vaccination (two doses) in naive individuals and in individuals that experienced a breakthrough infection between 3 and 10 months after vaccination (experiment #3). The figure shows the anti-S antibody levels (A), the PCA analysis (B), heat map after hierarchical clustering of the CDR features (C) and age and gender distribution with timing of the breakthrough infection of the included individuals (D). The heat map indicates the variance (from -2 to 2) compared to the mean (0) for each peptide feature. The included vaccination/infection-induced CDR-derived peptides were those that revealed discriminative by sPLS-DA analysis. The green-labeled CDR-derived peptides were also revealed discriminative by sPLS-DA analysis in experiment #4 ( Extended Data Figure 4 ). The median [25^th-75^th percentile] anti-S antibody levels (AU/mL) were 2 [0.2-3.47], 2914 [2453-10717] and 374 [278-531], 2 [0.5-2.7], 3621 [2152-7819], 66209 [26454-79519], pre-vaccination no breakthrough, post-vaccination 3 months no breakthrough, post-vaccination no breakthrough, pre-vaccination breakthrough, post-vaccination 3 months breakthrough, post-vaccination breakthrough, respectively.