The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom

Abstract

To determine whether the neutralization activity of monoclonal antibodies, convalescent sera and vaccine-elicited sera was affected by the top five epidemic SARS-CoV-2 variants in the UK, including D614G+L18F+A222V, D614G+A222V, D614G+S477N, VOC-202012/01(B.1.1.7) and D614G+69-70del+N439K, a pseudovirus-neutralization assay was performed to evaluate the relative neutralization titers against the five SARS-CoV-2 variants and 12 single deconvolution mutants based on the variants. In this study, 18 monoclonal antibodies, 10 sera from convalescent COVID-19 patients, 10 inactivated-virus vaccine-elicited sera, 14 mRNA vaccine-elicited sera, nine RBD-immunized mouse sera, four RBD-immunized horse sera, and four spike-encoding DNA-immunized guinea pig sera were tested and analyzed. The N501Y, N439K, and S477N mutations caused immune escape from nine of 18 mAbs. However, the convalescent sera, inactivated virus vaccine-elicited sera, mRNA vaccine-elicited sera, spike DNA-elicited sera, and recombinant RBD protein-elicited sera could still neutralize these variants (within three-fold changes compared to the reference D614G variant). The neutralizing antibody responses to different types of vaccines were different, whereby the response to inactivated-virus vaccine was similar to the convalescent sera.

Keywords: B.1.1.7; monoclonal antibody; mutation; neutralization; pseudotyped virus; vaccine.

Figure 1

Analysis of mutations and epidemic variants of SARS-CoV-2. (A) The numbers of each mutation in the spike protein of SARS-CoV-2 with a frequency above 1% worldwide and in the UK were tracked in GISAID from March 1st 2020 to Jan 13th 2021. The 17 mutations are listed in order of global frequency. (B) The percentage of UK epidemic variants on Jan 13th 2021 on GISAID.

Figure 2

The neutralization activity of mAbs against 16 SARS-CoV-2 variants and mutations. (A) Monoclonal antibodies were serially diluted and mixed with equal amounts of the five different SARS-CoV-2 variants and those containing a single mutation. After pre-incubation at 37°C for 1 h, trypsinized Huh 7 cells were added. After cultivation for 24 h, the luminescence of the target cells was measured. The neutralization inhibition rate of the antibody and ID₅₀ was calculated using the Reed–Muench method. The data represent the ID₅₀ ratio of each variant to that of D614G. The neutralization ability of 19 different monoclonal antibodies (x axis) against 16 SARS-CoV-2 variants and mutations (y axis) are shown as heatmap. Red represents an increase in neutralization capacity, while blue represents a decrease in neutralization capacity. Four-fold changes were considered statistically significant. (B) Structure modeling of the mutation N501Y in S1 and S982A in S2 based on “6VXX”.

Figure 3

The neutralization activity of polyclonal Abs against the five epidemic variants. Sera were serially diluted and the other procedures were the same as described for Figure 2A . Scatter plot of (A–F) showing the neutralization ID₅₀ ratio of each variant to that of D614G. Each point represents a single result, and the dashed line represents the mean value. The results are a summary of at least three repeated experiments. The dotted line represents 4-fold changes. (D) showed the animal immunization scheme.