Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

Abstract

Transmission of SARS-CoV-2 is uncontrolled in many parts of the world; control is compounded in some areas by the higher transmission potential of the B.1.1.7 variant¹, which has now been reported in 94 countries. It is unclear whether the response of the virus to vaccines against SARS-CoV-2 on the basis of the prototypic strain will be affected by the mutations found in B.1.1.7. Here we assess the immune responses of individuals after vaccination with the mRNA-based vaccine BNT162b2². We measured neutralizing antibody responses after the first and second immunizations using pseudoviruses that expressed the wild-type spike protein or a mutated spike protein that contained the eight amino acid changes found in the B.1.1.7 variant. The sera from individuals who received the vaccine exhibited a broad range of neutralizing titres against the wild-type pseudoviruses that were modestly reduced against the B.1.1.7 variant. This reduction was also evident in sera from some patients who had recovered from COVID-19. Decreased neutralization of the B.1.1.7 variant was also observed for monoclonal antibodies that target the N-terminal domain (9 out of 10) and the receptor-binding motif (5 out of 31), but not for monoclonal antibodies that recognize the receptor-binding domain that bind outside the receptor-binding motif. Introduction of the mutation that encodes the E484K substitution in the B.1.1.7 background to reflect a newly emerged variant of concern (VOC 202102/02) led to a more-substantial loss of neutralizing activity by vaccine-elicited antibodies and monoclonal antibodies (19 out of 31) compared with the loss of neutralizing activity conferred by the mutations in B.1.1.7 alone. The emergence of the E484K substitution in a B.1.1.7 background represents a threat to the efficacy of the BNT162b2 vaccine.

Extended Data Figure 1. Immune responses three weeks after first dose of Pfizer SARS-CoV-2 vaccine BNT162b2

a, Serum IgG responses against N protein, Spike and the Spike Receptor Binding Domain (RBD) from first vaccine participants (green), recovered COVID-19 cases (red), 3 convalescent plasma units and healthy controls (grey) as measured by a flow cytometry based Luminex assay. MFI, mean fluorescence intensity. Geometric mean titre (GMT with standard deviation (s.d) of two technical repeats presented. b, Relationship between serum IgG responses as measured by flow cytometry and serum neutralisation ID50. c, Relationship between serum neutralisation ID50 and T cell responses against SARS-CoV-2 by IFN gamma ELISpot. SFU: spot forming units. d, Relationship between serum IgG responses and T cell responses. Simple linear regression is presented with Pearson correlation (r), P-value (p) and regression coefficient/slope (β).

Extended data Fig 2. Neutralization by first dose BNT162b2 vaccine and convalescent sera against wild type and mutant (N501Y, A570D, ΔH69/V70) SARS-CoV-2 pseudotyped viruses

(a-b) Vaccine sera dilution for 50% neutralization against WT and Spike mutant with N501Y, A570D, ΔH69/V70. Geometric mean titre (GMT) + s.d of two independent experiments with two technical repeats presented. (c-d) Convalescent sera dilution for 50% neutralization against WT and Spike mutant with N501Y, A570D, Δ H69/V70. GMT + s.d of representative experiment with two technical repeats presented. e, Representative curves of convalescent serum log₁₀ inverse dilution against % neutralization for WT v N501Y, A570D, ΔH69/V70. Where a curve is shifted to the right this indicates the virus is less sensitive to the neutralizing antibodies in the serum. Data are means of technical replicates and error bars represent standard error of the mean. Data are representative of 2 independent experiments. Limit of detection for 50% neutralization set at 10.

Extended Data Fig. 3. Representative neutralization curves of BNT162b2 vaccine sera against pseudovirus virus bearing eight Spike mutations present in B.1.1.7 versus wild type (all In Spike D614G background).

Indicated is serum log₁₀ inverse dilution against % neutralization. Where a curve is shifted to the right this indicates the virus is less sensitive to the neutralizing antibodies in the serum. Data are for first dose of vaccine (D1). Data points represent means of technical replicates and error bars represent standard error of the mean. Limit of detection for 50% neutralization set at 10.

Extended Data Fig. 4. Representative neutralization curves of convalescent sera against wild type and B.1.1.7 Spike mutant SARS-CoV-2 pseudoviruses.

Indicated is serum log₁₀ inverse dilution against % neutralization. Where a curve is shifted to the right this indicates the virus is less sensitive to the neutralizing antibodies in the serum. Data points represent means of technical replicates and error bars represent standard error of the mean. Limit of detection for 50% neutralization set at 10.

Extended Data Fig. 5. Neutralisation of WT (D614G), B.1.1.7 and TM (N501Y, E484K, K417N) SARS-CoV-2 Spike pseudotyped virus by a panel of 57 monoclonal antibodies (mAbs).

a-c, Neutralisation of WT (black), B.1.1.7 (blue) and TM (red) SARS-CoV-2-MLV by 9 NTD-targeting (a), 29 RBM-targeting (b) and 19 non-RBM-targeting (c) mAbs.

Extended Data Fig. 6. Kinetics of binding to WT and N501Y SARS-CoV-2 RBD of 43 RBD-specific mAbs.

a-b, Binding to WT (black) and N501Y (blue) RBD by 22 RBM-targeting (a) and 21 non-RBM-targeting (b) mAbs. An antibody of irrelevant specificity was included as negative control. mAbs: monoclonal antibodies

Extended Data Fig. 7. Kinetics of binding to WT and E484K SARS-CoV-2 RBD of 46 RBD-specific mAbs.

a-b, Binding to WT (black) and E484K (red) RBD by 27 RBM-targeting (a) and 19 non-RBM-targeting (b) mAbs. An antibody of irrelevant specificity was included as negative control. mAbs: monoclonal antibodies

Extended Data Fig. 8. Binding of human ACE2 to SARS-CoV-2 WT, N501Y, TM (N501Y, E484K, K417N) RBDs.

a-b. BLI binding analysis of the human ACE2 ectodomain (residues 1-615) to immobilized SARS-CoV-2 WT RBD (a) and B.1.1.7 RBD (b). Black lines correspond to a global fit of the data using a 1:1 binding model. RBD: receptor binding domain.

Figure 1. Neutralization by first and second dose mRNA vaccine sera against wild type and B.1.1.7 Spike mutant SARS-CoV-2 pseudotyped viruses.

a, Spike in open conformation with a single erect RBD (PDB: 6ZGG) in trimer axis vertical view with the locations of mutated residues highlighted in red spheres and labelled on the monomer with erect RBD. Vaccine first dose (b-c, n=37), second dose (d-e, n=21) and convalescent sera, Conv. (f-g,n=27) against WT and B.1.1.7 Spike mutant with N501Y, A570D, ΔH69/V70, Δ144/145, P681H, T716I, S982A and D1118H. GMT with s.d presented of two independent experiments each with two technical repeats. Wilcoxon matched-pairs signed rank test p-values * <0.05, ** <0.01, ***<0.001, **** <0.0001, ns not significant HS – human AB serum control. Limit of detection for 50% neutralization set at 10.

Figure 2. E484K appearing in background of B.1.1.7 with evidence of transmission

a. Representation of Spike RBM:ACE2 interface (PDB: 6M0J) with residues E484, N501 and K417 highlighted as spheres coloured by element b. Maximum likelihood phylogeny of a subset of sequences from the United Kingdom bearing the E484K mutation (green) and lineage B.1.1.7 (blue), with background sequences without RBD mutations in black. As of 11^th Feb 2021, 30 sequences from the B.1.1.7 lineage (one cluster of 25 at top of phylogenetic tree) have acquired the E484K mutation (red). c. Sequence accumulation over time in GISAID for UK sequences with B.1.1.7 and E484K. RBD – receptor binding domain; NTD – N terminal domain.

Figure 3

Neutralization potency of mRNA vaccine sera and convalescent sera (pre SARS-CoV-2 B.1.1.7) against pseudotyped virus bearing Spike mutations in the B1.1.7 lineage with and without E484K in the receptor binding domain (all In Spike D614G background). a, Example neutralization curves for vaccinated individuals. Data points represent mean of technical replicates with standard error and are representative of two independent experiments (b-g). 50% neutralisation titre for each virus against sera derived (b,c, n=37) following first vaccination (d,e, n=21) following second vaccination and (f,g, n=20) convalescent sera (CS) expressed as fold change relative to WT. Data points are mean fold change of technical replicates and are representative of two independent experiments. Central bar represents mean with outer bars representing s.d. Wilcoxon matched-pairs signed rank test p-values *<0.05, **<0.01, ***<0.001, ****<0.0001; ns not significant. Limit of detection for 50% neutralization set at 10.

Figure 4. Neutralization and binding by a panel of NTD- and RBD-specific mAbs against WT, B.1.1.7 and RBD mutant SARS-CoV-2 viruses.

a, Neutralization of WT D614G (black), B.1.1.7 (blue) and a triple mutant (TM, carrying RBD mutations K417N/E484K/N501Y) (red) pseudotyped SARS-CoV-2-MLVs by 3 selected mAbs (S2E12, S2X333 and S2H14) from one representative experiment. Shown is the mean ± s.d. of 2 technical replicates. b, Neutralization of WT (D614G), B.1.1.7 and TM SARS-CoV-2-MLVs by 60 mAbs targeting NTD (n=10), RBM (n=31) and non-RBM sites in the RBD (n=19). Shown are the mean IC50 values (ng/ml) of n=2 independent experiments. c-e, Neutralization shown as mean IC50 values (upper panel) and mean fold change of B.1.1.7 (blue) or TM (red) relative to WT (lower panel) of NTD (c), RBM (d) and non-RBM (e) mAbs. Lower panel shows IC50 values from 2 independent experiments. f-h, Kinetics of binding of mAbs to WT (black), N501Y (blue) and E484K (red) RBD as measured by bio-layer interferometry (BLI). Shown in (f) are the 4 RBM-targeting mAbs with no reduced binding to N501Y or E484K RBD. Area under the curve (AUC) (g) and AUC fold change (h) of 50 mAbs tested against WT, N501Y and E484K RBD. mAbs with a >1.3 AUC fold change shown in blue and red. mAbs: monoclonal antibodies. NTD: N-terminal domain