BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection
The consecutive emergence and spread of Omicron subvariants BA.1, BA.2, BA.2.12.1, BA.4 and BA.5 poses severe challenges to the efficacy of vaccines and antibody therapeutics. The immune evasiveness of these newly emerging mutants requires urgent and immediate investigation.
To investigate neutralizing antibody (NAb) evasion by the Omicron sublineages, we performed pseudovirus-neutralization assays with plasma samples obtained from individuals who had received three doses of SARS-CoV-2 vaccine, vaccinated individuals who had recovered from BA.1 infection, and vaccinated individuals who had recovered from severe acute respiratory syndrome (SARS). It was found that, BA.2.12.1 and BA.4/BA.5 exhibit stronger neutralization evasion, compared to BA.2, against the plasma of 3-dose vaccinees and, most strikingly, of post-vaccination BA.1 convalescents. The neutralization data indicate that the BA.2.12.1 and BA.4/BA.5 display more potent and distinct humoral immune evasion than BA.1.
The strong antibody evasion capability of new Omicron variants was also validated by the loss of neutralizing efficacy of antibody drugs against these emerging variants. The S371F, D405N, and R408S mutations carried by BA.2/BA.4/BA.5 sublineages would compromise most broad sarbecovirus Nabs, e.g. S309 (sotrovimab), while LY-CoV1404 (Bebtelovimab) and CoV-1230 (Cilgavimab) maintained the neutralizing efficacy against BA.2.12.1 and BA.4/BA.5. Notably, SA55 and SA58 could potently neutralize all Omicron variants as well as sarbecoviruses, such as SARS-CoV-1 and Pangolin-GD. SA55 and SA58 are identified by single-cell V(D)J sequencing by us from individuals who were infected with SARS previously and received SARS-CoV-2 vaccine. The SA55+SA58 antibody paired can confer strong efficacy in both prevention and treatment.
Analyses based on flow cytometry and single-cell V(D)J sequencing (scVDJ-seq) suggested that, BA.1 breakthrough infection mainly recalls the humoral memory induced by wildtype (WT) vaccination and elicits antibodies that bind both WT and BA.1 but respond poorly to the newly emerged variants, consistent with the “original antigenic sin” or “immune imprinting” theory (Fig 3).
To further understand the molecular details of the immune evasion of Omicron variants, we characterized the escaping mutation profiles, epitope distribution, and neutralizing efficacy of 1640 RBD-binding antibodies. Among these antibodies, 614 were from post-vaccination BA.1 convalescent individuals and 411 from vaccinated SARS convalescent individuals. The antibodies were unsupervisedly clustered into 12 epitope groups according to their mutational escaping profiles (Fig 4a). the proportion of antibody of each group varied among WT convalescents/vaccinees, post-vaccination BA.1 breakthrough infection convalescents, and vaccinated SARS convalescents (Fig 4b). Further experiments revealed that the escape hotspots of each epitope group are in line with the binding epitopes of representative antibodies from the same epitope group as shown in complexed Cryo-EM structures (Fig 4f), and antibodies of the same group share similar features in antigen binding and neutralization (Fig 4c-e).
Antibodies cross-reactive to WT and BA.1 RBD enriched on non-ACE2-competing epitopes, such as in Groups E2.1, E2.2, E3 and F1 (Fig 4b, d, e). The neutralizing activity of E3 and F1 is weak, and E2.2 demonstrated moderate neutralizing efficacy (Fig 4e). The neutralizing activity of E2.1 is largely compromised by L452Q carried by BA.2.12.1and L452R carried by BA.4⁄5.The epitopes of BA.1 RBD specific antibodies compete with ACE2 but are largely escaped by BA.2/BA.2.12.1 due to mutations such as D405N, F486V/L452R.
These observations indicate that BA.1-derived vaccine boosters may be no longer ideal for achieving protection against the emerging variants. It’s extremely difficult to achieve herd immunity through Omicron infection because of immune imprinting and fast evolving of immune escaping mutations of viruses.
The study showcased the great potential of high-throughput single-cell sequencing and high-throughput yeast display-based deep mutational screening on antibody characterization as well as understanding immune protection and viral escape on the molecular level. A comprehensive database on the epitopes, escaping mutation profile, and neutralizing activity of SARS-CoV-2 RBD antibodies was established in this work, providing informative data for future development of broad-spectrum vaccines and therapeutic antibodies.