SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) exhibit escape from neutralizing antibodies, causing concern about vaccine effectiveness. However, while non-neutralizing cytotoxic functions of antibodies are associated with improved disease outcome and vaccine protection, Fc effector function escape from VOCs is poorly defined. Furthermore, whether VOCs trigger Fc functions with altered specificity, as has been reported for neutralization, is unknown. Here, we demonstrate that the Beta VOC partially evades Fc effector activity in individuals infected with the original (D614G) variant. However, not all functions are equivalently affected, suggesting differential targeting by antibodies mediating distinct Fc functions. Furthermore, Beta and Delta infection trigger responses with significantly improved Fc cross-reactivity against global VOCs compared with D614G-infected or Ad26.COV2.S-vaccinated individuals. This suggests that, as for neutralization, the infecting spike sequence affects Fc effector function. These data have important implications for vaccine strategies that incorporate VOCs, suggesting these may induce broader Fc effector responses.

Keywords: Ad26.COV2.S; Beta; Delta; Fc effector function; SARS-CoV-2; variant of concern.

Graphical abstract

Figure 1

Binding and neutralization of plasma from hospitalized SARS-CoV-2 convalescent individuals sampled in waves driven by distinct viral lineages (A) The number of SARS-CoV-2 cases in South Africa per epidemiological week from March 2020 to November 2021 (right y axis) is represented by bars, with black bars indicating the period that the wave 1 (n = 27), wave 2 (n = 21), and wave 3 (n = 22) samples were obtained. The percentage of total SARS-CoV-2 sequences over time (left y axis) is shown as a line plot where the proportions of the original D614G, Alpha, Beta, Gamma, Delta, Eta, Kappa, and C.1.2 lineages are shown. (B and C) (B) IgA and (C) IgG-binding levels by ELISA of wave 1 or wave 2 samples against the original (D614G) (white) or Beta (red) spike. (D) Neutralization of original (D614G) or Beta pseudoviruses by wave 1 and 2 plasma. Limits of detection are shown with dotted lines, geometric mean titers are shown, and fold change decrease in black and fold change increase in red below the graph. All results are the mean of two independent experiments. Statistical significance between variants was calculated using Wilcoxon paired t test: ∗∗p < 0.01; ∗∗∗∗p < 0.0001.

Figure 2

Fc effector function is largely preserved against Beta (A) Fc effector functions of wave 1 and wave 2 plasma against either original (white) and Beta (red) spike protein or spike-expressing cells. ADCP is represented as the percentage of monocytic cells that take up spike-coated beads multiplied by their geometric mean fluorescence intensity (MFI). ADCC shown as relative light units (RLU) signaling through FcγRIIIa expressing cells. ADCD is shown as the MFI of C3 deposition on spike-coated beads and ADCT represented as the relative proportion of biotinylated spike-expressing cell membrane on carboxyfluorescein succinimidyl ester (CFSE)-positive monocytic cells. Dotted lines indicate the limit of detection and all samples are represented following the subtraction of background. Median values of all functions are shown above the graphs and fold change decrease in black and fold change increase in red below the graph. Results are representative of two independent experiments. Statistical significance between variants is calculated using Wilcoxon paired t test; ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001; and ns = non-significant. (B) Fold difference of functions against Beta relative to the original variant for wave 1 and 2 samples where the dotted line indicates no change between variants (red = Beta > D614G; white = D614G < Beta). The median of the fold changes is indicated by lines

Figure 3

ADCC targets the RBD and NTD and is partially escaped by Beta (A) ADCC of monoclonal antibodies CR3022, P2B-2FB, and palivizumab shown as RLU of signaling through FcγRIIIa expressing cells and crosslinking of original (white) or Beta (red) (K417N, E484K, and N501Y) RBD protein. Error bars indicate standard deviation of the mean of two independent experiments. (B) ADCC of monoclonal antibodies 4A8 and palivizumab against original (white) or Beta (red; L18F, D80A, D215G, 242–244 del) NTD protein. (C and D) Wave 1 and wave 2 plasma against original (white) or Beta (red) (C) RBD or (D) NTD protein. All plots are representative of a minimum of two independent experiments. Median values of all functions are shown above the graphs with fold change decrease in black and fold change increase in red below the graph. Statistical significance between variants was calculated using Wilcoxon paired t test; ∗∗∗∗p < 0.0001 and ns = non-significant

Figure 4

Beta and Ad26.COV.2.S-elicited ADCC responses are cross-reactive against variants of concern (A–D) ADCC of (A) wave 1, (B) wave 2, (C) wave 3, (D) Ad26.COV.2.S vaccinee plasma (day 28) against the original, VOC, and SARS-CoV-1 representative of two independent experiments. Bars indicate the median, represented below the graphs with squares indicating the ADCC against the autologous variant and circles indicating ADCC against the heterologous variants. Statistical significance was calculated using the Friedman test, with Dunn’s multiple test comparisons, where gray lines indicate significance between SARS-CoV-2 and SARS-CoV-1 and black lines between SARS-CoV-2 variants. (E) Fold difference represented as ADCC activity against the variant for wave 1, wave 2, wave 3, or vaccine plasma relative to the original. The dotted line represents no fold difference, while lines indicate the median. Statistical differences between waves and vaccine responses were calculated using the Kruskal-Wallis test with Dunn’s multiple test comparisons. ∗p < 0.05, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, and ns = non-significant.