Analysis of a SARS-CoV-2 convalescent cohort identified a common strategy for escape of vaccine-induced anti-RBD antibodies by Beta and Omicron variants

Abstract

Background: Evolutionary pressure has led to the emergence of SARS-CoV-2 variants, with the most recent Omicron variant containing an unparalleled 30 mutations in the spike protein. Many of these mutations are expected to increase immune evasion, thus making breakthrough cases and re-infection more common.

Methods: From June 2020 to December 2021 serial blood samples (initial post recovery, 6 months, 12 months) were collected from a COVID-19 convalescent cohort in Boston, MA. Plasma was isolated for use in Mesoscale Discovery based antibody binding assays. Unvaccinated donors or those vaccinated prior to the primary blood draw were excluded from this analysis, as were those who did not have at least two blood draws. Wilcoxon signed rank tests were used to compare pre- and post-vaccination titers and antibody response against different variants, while McNemar tests were used to compare the proportions of achieving ≥ 4 fold increases against different variants.

Findings: Forty-eight COVID convalescent donors with post-infection vaccination (hybrid immunity) were studied to evaluate the levels of cross-reactive antibodies pre- and post- vaccination against various SARS-CoV-2 Spike and receptor binding domain (RBD) proteins. Vaccination with BNT162b2, mRNA-1273 or Ad26.COV2.S led to a 6·3 to 7·8 fold increase in anti-Spike antibody titers and a 7·0 to 7·4 fold increase in anti-WT, Alpha and Delta RBD antibody. However, a lower response was observed for Beta and Omicron RBDs with only 7/48 (15%) and 15/48 (31%) donors having a ≥4 fold increase in post-vaccination titers against Beta and Omicron RBDs. Structural analysis of the Beta and Omicron RBDs reveal a shared immune escape strategy involving residues K417-E484-N501 that is exploited by these variants of concern.

Interpretation: Through mutations of the K417-E484-N501 triad, SARS-CoV-2 has evolved to evade neutralization by the class I/II anti-RBD antibody fraction of hybrid immunity plasma as the polyclonal antibody response post-vaccination shows limitations in the ability to solve the structural requirements to bind the mutant RBDs.

Funding: Massachusetts Consortium on Pathogen Readiness (280870.5116709.0016) and the National Institute of Allergy and Infectious Diseases (1R01AI161152-01A1).

Keywords: COVID-19; Hybrid immunity; Neutralization escape mutations; Omicron variant; SARS-CoV-2; Vaccine induced antibody titers.

Figure 1

Antibody responses to full-length Spike and RBD proteins from various SARS-CoV-2 variants of concern using samples from 48 donors. Titers were measured by MSD ELISA at 1:200 dilution against full length spike (a–e) or RBD (f–j) proteins. (k) GMTR for each variant with 95% CI and number of donors who displayed a ≥ 4 fold increase in antibody titer post vaccination. P values represent a comparison of GMTR between WT and the indicated variants using Wilcoxon signed rank test. (l) Plasma titers against indicated Spike or RBD protein post vaccination. P values for statistical comparison in (l) is found in Table S6. Dots indicate individual donors and error bar represents overall Geometric Mean with 95% CI. All samples were performed in triplicate. Statistical analysis for a–j was performed using Wilcoxon Signed-Rank tests for paired data.

Figure 2

COVID-19 vaccination induced waning antibody responses to the RBD domains of Beta and Omicron spike variants using samples from 47 donors. The intervals between the completion of vaccination and final sample collection were calculated and segregated as < 6 months (short interval, red bars) and > 6 months (long interval, blue bars). Full length spike (a–e) and RBD (f–j) antibody titers for donors in different interval groups is shown. The titers were measured by MSD ELISA at 1:200 dilution, each sample was performed in triplicate. k) GMTR with 95% CI comparing pre and post vaccination for each group is shown. Dots represent individual donors and error bars indicate Geometric Mean with 95% CI. Statistical analysis was performed by Kruskal-Wallis rank sum test.

Figure 3

RBD sequence alignment of Wuhan-Hu-1 (WT), Alpha (B.1.1.7), Delta (B.1.617.2), Beta (B.1.351), and Omicron (B.1.1.529). (a) Amino acid sequence alignment is shown with K417-E484-N501 highlighted. (b) Surface representation of WT, Beta, and Omicron RBD is shown with their respective residues 417, 484, and 501 highlighted in red (top). Electrostatic potential of surface residues for each RBD is also shown (bottom). PDB files used WT: 7CH5, Beta: 7LYN, Omicron: 7T9L.