Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant contains extensive sequence changes relative to the earlier-arising B.1, B.1.1, and Delta SARS-CoV-2 variants that have unknown effects on viral infectivity and response to existing vaccines. Using SARS-CoV-2 virus-like particles (VLPs), we examined mutations in all four structural proteins and found that Omicron and Delta showed 4.6-fold higher luciferase delivery overall relative to the ancestral B.1 lineage, a property conferred mostly by enhancements in the S and N proteins, while mutations in M and E were mostly detrimental to assembly. Thirty-eight antisera samples from individuals vaccinated with Pfizer/BioNTech, Moderna, or Johnson & Johnson vaccines and convalescent sera from unvaccinated COVID-19 survivors had 15-fold lower efficacy to prevent cell transduction by VLPs containing the Omicron mutations relative to the ancestral B.1 spike protein. A third dose of Pfizer vaccine elicited substantially higher neutralization titers against Omicron, resulting in detectable neutralizing antibodies in eight out of eight subjects compared to one out of eight preboosting. Furthermore, the monoclonal antibody therapeutics casirivimab and imdevimab had robust neutralization activity against B.1 and Delta VLPs but no detectable neutralization of Omicron VLPs, while newly authorized bebtelovimab maintained robust neutralization across variants. Our results suggest that Omicron has similar assembly efficiency and cell entry compared to Delta and that its rapid spread is due mostly to reduced neutralization in sera from previously vaccinated subjects. In addition, most currently available monoclonal antibodies will not be useful in treating Omicron-infected patients with the exception of bebtelovimab.

Keywords: Omicron; SARS-CoV-2; virus-like particles.

Fig. 1.

Omicron structural gene variants alter infectivity of SC2-VLPs. (A) Sequence differences in genes encoding the structural proteins S, E, M, and N between B.1, B.1.1, Delta, and Omicron viral variants (vertical lines); Omicron-Class 1 and Omicron-Class 3 mutations were created for this study. (B) Workflow for generating SC2-VLPs and testing their ability to transduce ACE2- and TMPRSS2-expressing 293T cells; SC2-VLPs assembled in packaging cells transformed with plasmids encoding S, E, M, and N genes as well as a luciferase mRNA fused to the SARS-CoV-2 packaging signal are tested for receptor-mediated cell transduction using a luciferase detection assay. (C–E) Luminescence measured as a function of VLPs generated with the component protein shown, in a background of B.1 genes (see text for details). (F) Western blot of cell lysates from cells transfected to generate VLPs stained for N, S, and GAPDH as a loading control. (G) Western and Northern blots of particles purified from supernatants by 20% sucrose cushion ultracentrifugation. Staining for N, S, and p24 in the Western blots. Note: lentivirus was added to all supernatants as a loading control for purification. Luc2 mRNA was stained for with a ³²P-labeled probe targeting the luciferase gene. Quantification and statistical comparison of blots in F and G are shown in SI Appendix, Fig. S1.

Fig. 2.

Antiserum neutralization of VLPs generated with different S genes. (A–D) Fifty percent neutralization titers of sera isolated from individuals vaccinated using Pfizer/BioNTech, Moderna, and Johnson & Johnson vaccines or from convalescent COVID-19 patients. Neutralization curves were determined using VLPs with either S-B.1, S-Delta, or S-Omicron. (E–H) Neutralization titers of sera collected before and after third dose vaccination from individuals receiving the Pfizer/BioNTech vaccine. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 evaluated using Friedman’s exact test for repeated measures. ns, not statistically significant.

Fig. 3.

Monoclonal antibody neutralization of VLPs generated with different S genes. Neutralization curves and IC₅₀ values of (A) casirivimab, (B) imdevimab, (C) MM43, (D) Sotrovimab, (E) Bebtelovimab against the S-variants: S-B.1, S-Delta, S-Omicron. (F) IC₅₀ values for each monoclonal antibody.