Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization

Abstract

The Covid-19 pandemic has ravaged the globe, and its causative agent, SARS-CoV-2, continues to rage. Prospects of ending this pandemic rest on the development of effective interventions. Two monoclonal antibody (mAb) therapeutics have received emergency use authorization, and more are in the pipeline. Furthermore, multiple vaccine constructs have shown promise, including two with ~95% protective efficacy against Covid-19. However, these interventions were directed toward the initial SARS-CoV-2 that emerged in 2019. Considerable viral evolution has occurred since, including variants with a D614G mutation that have become dominant. Viruses with this mutation alone do not appear to be antigenically distinct, however. Recent emergence of new SARS-CoV-2 variants B.1.1.7 in the UK and B.1.351 in South Africa is of concern because of their purported ease of transmission and extensive mutations in the spike protein. We now report that B.1.1.7 is refractory to neutralization by most mAbs to the N-terminal domain (NTD) of spike and relatively resistant to a number of mAbs to the receptor-binding domain (RBD). It is modestly more resistant to convalescent plasma (~3 fold) and vaccinee sera (~2 fold). Findings on B.1.351 are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple potent mAbs to the receptor-binding motif on RBD, largely due to an E484K mutation. Moreover, B.1.351 is markedly more resistant to neutralization by convalescent plasma (~11-33 fold) and vaccinee sera (~6.5-8.6 fold). B.1.351 and emergent variants with similar spike mutations present new challenges for mAb therapy and threaten the protective efficacy of current vaccines.

Fig. 1 |. Emerging SARS-CoV-2 variants identified in the UK and SA.

a, Phylogenetic tree of SARS-CoV-2 variants, with B.1.351 and B.1.1.7 highlighted. b, Mutations in the viral spike identified in B.1.351 (SA) and B.1.1.7 (UK) in addition to D614G.

Fig. 2 |. Susceptibility of UKΔ8 and SAΔ9 pseudoviruses to neutralization by mAbs.

a, Footprints of neutralizing mAbs on the RBD. Left panel, top view of SARS-COV-2 spike with one RBD in the “up” conformation (pdb: 6zgg). RBD and NTD are colored green and peach, respectively. The positions of ‘inner’ and ‘outer’ sides are indicated on the “up” RBD with the ACE2-binding site colored yellow. The three panels to the right show the antibody footprints on RBD. b, Neutralization of UKΔ8, SAΔ9, and WT pseudoviruses by select RBD mAbs. c, Fold-change in IC50 of neutralizing mAbs against UKΔ8 and SAΔ9, as well as single-mutation pseudoviruses, relative to WT. MPI↓ denotes that maximum percent inhibition is substantially reduced, confounding IC50 calculations. d, Neutralization of UKΔ8, SAΔ9, and WT pseudoviruses by NTD-directed mAbs, the footprints of which are delineated by the color tracings in the insert. e, Changes in neutralization IC50 of authorized or investigational therapeutic mAbs against UKΔ8 and SAΔ9. Data in b and d are mean ± SEM of technical triplicates, and represent one of two independent experiments.

Fig. 2 |. Susceptibility of UKΔ8 and SAΔ9 pseudoviruses to neutralization by mAbs.

a, Footprints of neutralizing mAbs on the RBD. Left panel, top view of SARS-COV-2 spike with one RBD in the “up” conformation (pdb: 6zgg). RBD and NTD are colored green and peach, respectively. The positions of ‘inner’ and ‘outer’ sides are indicated on the “up” RBD with the ACE2-binding site colored yellow. The three panels to the right show the antibody footprints on RBD. b, Neutralization of UKΔ8, SAΔ9, and WT pseudoviruses by select RBD mAbs. c, Fold-change in IC50 of neutralizing mAbs against UKΔ8 and SAΔ9, as well as single-mutation pseudoviruses, relative to WT. MPI↓ denotes that maximum percent inhibition is substantially reduced, confounding IC50 calculations. d, Neutralization of UKΔ8, SAΔ9, and WT pseudoviruses by NTD-directed mAbs, the footprints of which are delineated by the color tracings in the insert. e, Changes in neutralization IC50 of authorized or investigational therapeutic mAbs against UKΔ8 and SAΔ9. Data in b and d are mean ± SEM of technical triplicates, and represent one of two independent experiments.

Fig. 2 |. Susceptibility of UKΔ8 and SAΔ9 pseudoviruses to neutralization by mAbs.

a, Footprints of neutralizing mAbs on the RBD. Left panel, top view of SARS-COV-2 spike with one RBD in the “up” conformation (pdb: 6zgg). RBD and NTD are colored green and peach, respectively. The positions of ‘inner’ and ‘outer’ sides are indicated on the “up” RBD with the ACE2-binding site colored yellow. The three panels to the right show the antibody footprints on RBD. b, Neutralization of UKΔ8, SAΔ9, and WT pseudoviruses by select RBD mAbs. c, Fold-change in IC50 of neutralizing mAbs against UKΔ8 and SAΔ9, as well as single-mutation pseudoviruses, relative to WT. MPI↓ denotes that maximum percent inhibition is substantially reduced, confounding IC50 calculations. d, Neutralization of UKΔ8, SAΔ9, and WT pseudoviruses by NTD-directed mAbs, the footprints of which are delineated by the color tracings in the insert. e, Changes in neutralization IC50 of authorized or investigational therapeutic mAbs against UKΔ8 and SAΔ9. Data in b and d are mean ± SEM of technical triplicates, and represent one of two independent experiments.

Fig. 3 |. UKΔ8 and SAΔ9 pseudoviruses are more resistant to neutralization by convalescent plasma from patients.

a, Neutralization results for 20 convalescent plasma samples (P1-P20) against UKΔ8, SAΔ9, and WT. Data represent mean ± SEM of technical triplicates. The panels are arranged by IC50 values against the WT, from low to high. b, Fold change in neutralization IC50 of UKΔ8 and SAΔ9, as well as single-mutation pseudoviruses, relative to the WT presented as a heatmap with darker colors implying greater change. c, Change in reciprocal plasma neutralization IC50 values of convalescent plasma from severe and non-severe patients against UKΔ8 and SAΔ9, relative to the WT. Mean fold changes in IC50 values relative to the WT are written above the p values. Statistical analysis was performed using a two-tailed paired t test.

Fig. 3 |. UKΔ8 and SAΔ9 pseudoviruses are more resistant to neutralization by convalescent plasma from patients.

a, Neutralization results for 20 convalescent plasma samples (P1-P20) against UKΔ8, SAΔ9, and WT. Data represent mean ± SEM of technical triplicates. The panels are arranged by IC50 values against the WT, from low to high. b, Fold change in neutralization IC50 of UKΔ8 and SAΔ9, as well as single-mutation pseudoviruses, relative to the WT presented as a heatmap with darker colors implying greater change. c, Change in reciprocal plasma neutralization IC50 values of convalescent plasma from severe and non-severe patients against UKΔ8 and SAΔ9, relative to the WT. Mean fold changes in IC50 values relative to the WT are written above the p values. Statistical analysis was performed using a two-tailed paired t test.

Fig. 4 |. UKΔ8 and SAΔ9 pseudoviruses are more resistant to neutralization by vaccinee sera.

a, Neutralization profiles for 22 serum samples obtained from persons who received SARS-CoV-2 vaccine made by Moderna (V1-V12) or Pfizer (V13-V22) against UKΔ8, SAΔ9, and WT pseudoviruses. The panels are arranged by IC50 values against the WT, from low to high for each set of vaccinees. Data are mean ± SEM of technical triplicates, and represent one of two independent experiments. b, Fold change in serum neutralization IC50 of UKΔ8 and SAΔ9, as well as single-mutation pseudoviruses, relative to the WT presented as a heatmap with darker colors implying greater change. c, Change in reciprocal serum IC50 values for Moderna and Pfizer vaccinees against UKΔ8 and SAΔ9, relative to the WT. Mean fold change in IC50 relative to the WT is written above the p values. Statistical analysis was performed using a two-tailed paired t test.

Fig. 4 |. UKΔ8 and SAΔ9 pseudoviruses are more resistant to neutralization by vaccinee sera.

a, Neutralization profiles for 22 serum samples obtained from persons who received SARS-CoV-2 vaccine made by Moderna (V1-V12) or Pfizer (V13-V22) against UKΔ8, SAΔ9, and WT pseudoviruses. The panels are arranged by IC50 values against the WT, from low to high for each set of vaccinees. Data are mean ± SEM of technical triplicates, and represent one of two independent experiments. b, Fold change in serum neutralization IC50 of UKΔ8 and SAΔ9, as well as single-mutation pseudoviruses, relative to the WT presented as a heatmap with darker colors implying greater change. c, Change in reciprocal serum IC50 values for Moderna and Pfizer vaccinees against UKΔ8 and SAΔ9, relative to the WT. Mean fold change in IC50 relative to the WT is written above the p values. Statistical analysis was performed using a two-tailed paired t test.