The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic

Abstract

The rapid spread of the SARS-CoV-2 Omicron variant suggests that the virus might become globally dominant. Further, the high number of mutations in the viral spike protein raised concerns that the virus might evade antibodies induced by infection or vaccination. Here, we report that the Omicron spike was resistant against most therapeutic antibodies but remained susceptible to inhibition by sotrovimab. Similarly, the Omicron spike evaded neutralization by antibodies from convalescent patients or individuals vaccinated with the BioNTech-Pfizer vaccine (BNT162b2) with 12- to 44-fold higher efficiency than the spike of the Delta variant. Neutralization of the Omicron spike by antibodies induced upon heterologous ChAdOx1 (Astra Zeneca-Oxford)/BNT162b2 vaccination or vaccination with three doses of BNT162b2 was more efficient, but the Omicron spike still evaded neutralization more efficiently than the Delta spike. These findings indicate that most therapeutic antibodies will be ineffective against the Omicron variant and that double immunization with BNT162b2 might not adequately protect against severe disease induced by this variant.

Keywords: Omicron; SARS-CoV-2; antibody; immune evasion; neutralization; spike; vaccine.

Graphical abstract

Figure 1

The Omicron spike mediates entry into cell lines with different efficiency as compared with B.1 and Delta spike, binds human ACE2 efficiently, and utilizes a broad range of animal ACE2 orthologues as receptor (A) Epidemiology of SARS-CoV-2 Omicron variant. Purple bars indicate the number of newly reported isolates per day while the blue line shows the cumulative number of isolates as of November 17, 2021. (Based on data deposited in the GISAID database). (B) Global distribution of SARS-CoV-2 Omicron variant. Sequences retrieved from the GISAID database were grouped based on the continent where they were detected (as of November 17, 2021). (C) Schematic overview and domain organization of the S proteins of SARS-CoV-2 Omicron variant. Mutations compared with the SARS-CoV-2 Wuhan-Hu-1 isolate are highlighted in red. (NTD, N-terminal domain; RBD, receptor-binding domain; TD, transmembrane domain). (D) Location of Omicron-specific mutations in the context of the trimeric spike protein. (S1 subunit, light blue; RBD, dark blue; S2 subunit, gray; S1/S2 and S2′ cleavage sites; mutated amino acid residues, red (compared with the S protein of the SARS-CoV-2 Wuhan-Hu-1 isolate). (E) Locations of Omicron-specific mutations in the context of the RBD. (RBD, gray; RBD residues that interact with ACE2, green; ACE2-interacting RBD residues that are mutated in Omicron spike, red: non-ACE2-interacting RBD residues that are mutated in Omicron spike, orange). (F) Particles bearing the indicated S proteins were inoculated onto different cell lines, and S-protein-driven cell entry was analyzed at 16–18 h postinoculation by measuring the activity of virus-encoded firefly luciferase in cell lysates. Presented are the mean from 3 to 12 biological replicates (each conducted with four technical replicates) in which S-protein-driven cell entry was normalized against B.1 (set as 1). (Error bars: SEM). (G) Binding of soluble ACE2 to B.1 or Omicron spike proteins. 293T cells expressing the indicated S protein (or no S protein) following transfection were sequentially incubated with soluble ACE2 harboring a C-terminal Fc-tag derived from human IgG and AlexaFlour-488-conjugated antihuman antibody. Finally, ACE2 binding was analyzed by flow cytometry. Cells incubated with only secondary antibody served as controls. Presented is the mean geometric mean channel fluorescence from six biological replicates (each conducted with single samples). (Error bars: standard deviation). (H) Particles bearing the indicated S proteins or VSV-G were inoculated on BHK-21 cells that were previously transfected to express the indicated ACE2 orthologues or empty vector. S protein-driven cell entry was analyzed as described in (F). Presented are the mean data from three biological replicates (each conducted with four technical replicates) in which signals obtained from particles bearing no viral glycoprotein (indicated by dashed line) were used for normalization (set as 1). (Error bars: SEM). (F–H): statistical significance of differences between individual groups was assessed by two-tailed Students t test: p > 0.05, not significant (ns); ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001.

Figure S1

Cell entry driven by the spike proteins of VOC (related to Figure 1F) Pseudotype entry data presented in Figure 1F normalized against the assay background. Pseudotype entry was normalized against signals obtained from cells inoculated with particles bearing no viral glycoprotein (background, set as 1), and data obtained for particles bearing VSV-G were included. Error bars indicate the SEM.

Figure 2

The Omicron spike evades neutralization by four out of five monoclonal antibodies but is efficiently inhibited by soluble ACE2 (A) Inhibition of S-protein-driven cell entry by soluble ACE2. Particles harboring the indicated S proteins were preincubated (30 min, 37°C) with different dilutions of soluble ACE2 before being inoculated onto Vero cells. S-protein-driven cell entry was analyzed as described in Figure 1F. Presented are the mean data from three biological relocates (each conducted with four technical replicates). (B) Locations of Omicron-specific mutations in the context of the RBD epitopes targeted by casirivimab, imdevimab, bamlanivimab, etesevimab, and sotrovimab. (RBD, gray; epitope targeted by the antibody, blue; Omicron-specific mutations within the epitope, red; Omicron-specific mutations outside the epitope, orange). (C) Omicron spike is resistant against four out of five monoclonal antibodies used for treatment of COVID-19 patients. Particles harboring the indicated S proteins were preincubated (30 min, 37°C) with different concentrations of recombinant monoclonal antibody before being inoculated onto Vero cells. S-protein-driven cell entry was analyzed as described in Figure 1F. Presented are the mean data from three biological replicates (each conducted with four technical replicates). (A and C): statistical significance of differences between individual groups was assessed by two-way analysis of variance with Dunnett’s (A) or Sidak’s (C) post hoc tests: p > 0.05, not significant (ns); ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001.

Figure S2

Individual neutralization data (related to Figure 3) Presented are the individual neutralization results for the data shown in Figure 3. Data represent the mean values of four technical replicates with error bars indicating the standard deviation. The curves were calculated based on a non-linear regression model with variable slope.

Figure 3

The Omicron spike shows high resistance against antibodies elicited upon infection or vaccination (A) Particles bearing the indicated S proteins were preincubated (30 min, 37°C) with different dilutions of convalescent sera/plasma (n = 17) before being inoculated onto Vero cells. S-protein-driven cell entry was analyzed as described in Figure 1F. Black triangles indicate patients with severe disease that required admission to the intensive care unit; all other patients showed mild disease. (B) The experiment was performed as described in (A) but sera from BNT/BNT-vaccinated individuals were analyzed (n = 11). (C) The experiment was performed as described in (A) but sera from AZ/BNT-vaccinated individuals were analyzed (n = 10). (D) The experiment was performed as described in (A) but sera from BNT/BNT/BNT-vaccinated individuals were analyzed (n = 10). (A–D) Patient identifiers are indicated on the x axes. The reciprocal serum/plasma dilution factors that caused a 50% reduction in S protein-driven cell entry (neutralization titer 50, NT50) are shown. Left panels show individual NT50 values clustered per SARS-CoV-2 variant. Black lines and numerical values in brackets indicate median NT50 values, whereas right panels show serum/plasma-specific NT50 values ranked from highest to lowest based on NT50 for B.1. Numerical values indicate the median fold change in neutralization between individual SARS-CoV-2 variants. Dashed lines indicate the lowest serum dilution tested. Statistical significance of differences between individual groups was assessed by Wilcoxon matched-pairs signed rank test: p > 0.05, not significant (ns); ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001).