Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

Abstract

The recently emerged SARS-CoV-2 Omicron variant encodes 37 amino acid substitutions in the spike protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody-based therapeutics. Here we show that the Omicron RBD binds to human ACE2 with enhanced affinity, relative to the Wuhan-Hu-1 RBD, and binds to mouse ACE2. Marked reductions in neutralizing activity were observed against Omicron compared to the ancestral pseudovirus in plasma from convalescent individuals and from individuals who had been vaccinated against SARS-CoV-2, but this loss was less pronounced after a third dose of vaccine. Most monoclonal antibodies that are directed against the receptor-binding motif lost in vitro neutralizing activity against Omicron, with only 3 out of 29 monoclonal antibodies retaining unaltered potency, including the ACE2-mimicking S2K146 antibody¹. Furthermore, a fraction of broadly neutralizing sarbecovirus monoclonal antibodies neutralized Omicron through recognition of antigenic sites outside the receptor-binding motif, including sotrovimab², S2X259³ and S2H97⁴. The magnitude of Omicron-mediated immune evasion marks a major antigenic shift in SARS-CoV-2. Broadly neutralizing monoclonal antibodies that recognize RBD epitopes that are conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.

Extended Data Fig. 1.. Schematic of mutations landscape in SARS-CoV-2 VOC, VOI and VUM (Variant Under Monitoring).

D, deletion: ins, insertion.

Extended Data Fig. 2.. Amino acid substitutions and their prevalence in the Omicron RBD.

a, SARS-CoV-2 S in fully open conformation (PDB: 7K4N) with positions of mutated residues in Omicron highlighted on one protomer in green or red spheres in or outside the ACE2 footprint (ACE2), respectively. RBM is defined by a 6 Å cutoff in the RBD-ACE2 interface. Not all Omicron mutations are shown. b, Substitutions and their prevalence in Omicron sequences reported in GISAID as of December 20, 2021 (ambiguous amino acid substitutions are indicated with strikethrough cells). Shown are also the substitutions found in other variants. K417N mutation in Delta is found only in a fraction of sequences.

Extended Data Fig. 3.. Amino acid substitutions and their prevalence in the Omicron NTD.

Sequences reported in GIAID as of December 20, 2021; (ambiguous amino acid substitutions are marked with strikethrough cells). Shown are also the substitutions found in other variants.

Extended Data Fig. 4.. Amino acid substitutions and their prevalence in the Omicron S2.

Sequences reported in GIAID as of December 20, 2021; (ambiguous amino acid substitutions are marked with strikethrough cells). Shown are also the substitutions found in other variants.

Extended Data Fig. 5.. Characteristics of emergent mutations of Omicron.

a, Shared mutations of micron with other sarbecovirus and with VOC. b, Since the beginning of the pandemic there is a progressive coalescence of Omicron-defining mutations into non-Omicron haplotypes that may carry as many as 10 of the Omicron-defining mutations. c, Pango lineages (dots) rarely carry more than 10–15 lineage-defining mutations. d, Exceptionally, some non-Omicron haplotypes may carry up to a maximum 19 Omicron-defining mutations. Shown are selected exceptional haplotypes. Spike G142D and Y145del may also be noted as G142del and Y145D.

Extended Data Fig. 6.. SPR analysis of human and mouse ACE2.

a, Full fit results for one representative replicate from each quantifiable SPR dataset with a monomeric analyte (1:1 binding model). b, Single-cycle kinetics SPR analysis of dimeric mouse ACE2 binding to six RBD variants. Dimeric ACE2 is injected successively at 33, 100, 300, and 900 nM. White and gray stripes indicate association and dissociation phases, respectively. The asterisk indicates where high concentrations of dimeric mouse ACE2 is non-specifically binding to the sensor chip surface (Delta experiment was performed separately from the other RBD variants, with a different capture tag and chip surface).

Extended Data Fig. 7.. Neutralization of SARS-CoV-2 Omicron strain by sotrovimab in Vero-TMPRSS2 cells.

a-f, Neutralization curves in Vero-TMPRSS2 cells comparing the sensitivity of SARS-CoV-2 strains with sotrovimab with WA1/2020 D614G and hCoV-19/USA/WI-WSLH-221686/2021 (an infectious clinical isolate of Omicron from a symptomatic individual in the United States). Shown are three independent experiments performed in technical duplicate is shown.

Extended Data Fig. 8.. Neutralization of WT (D614) and Omicron SARS-CoV-2 Spike pseudotyped virus by a panel of 36 mAbs.

a-c, Neutralization of SARS-CoV-2 VSV pseudoviruses carrying wild-type D614 (grey) or Omicron (orange) S protein by NTD-targeting (a) and RBD-targeting (b-c) mAbs (b, site I; c, sites II and V). Data are representative of one independent experiment out of two. Shown is the mean. of 2 technical replicates.

Fig. 1.. Omicron RBD shows increased binding to human ACE2 and gains binding to murine ACE2.

a, Omicron mutations are shown in a primary structure of SARS-CoV-2 S with domains and cleavage sites highlighted. b, Single-cycle kinetics SPR analysis of ACE2 binding to six RBD variants. ACE2 is injected successively at 11, 33, 100, and 300 nM (human) or 33, 100, 300, and 900 nM (mouse). Black curves show fits to a 1:1 binding model. White and gray stripes indicate association and dissociation phases, respectively. c, Quantification of human ACE2 binding data. Reporting average ± standard deviation of three replicates. Asterisks indicate that Delta was measured in a separate experiment with a different chip surface and capture tag; Delta fold-change is calculated relative to affinity of Wuhan-Hu-1 measured in parallel (91 ± 1.6 nM). d, Entry of Wu-Hu-1, Alpha, Beta, Delta, Gamma, Kappa and Omicron VSV pseudoviruses into mouse ACE2 expressing HEK293T cells. Shown are 2 biological replicates (technical triplicates). Lines, geometric mean.

Fig. 2.. Neutralization of Omicron SARS-CoV-2 VSV pseudovirus by plasma from COVID-19 convalescent and vaccinated individuals.

Plasma neutralizing activity in COVID-19 convalescent or vaccinated individuals (mRNA-1273, BNT162b2, AZD1222, Ad26.COV2.S (single dose), Sputnik V and BBIBP-CorV). a, Pairwise neutralizing antibody titers (ID50) against Wuhan-Hu-1 (D614G), Beta, and Omicron VOC, and SARS-CoV. Vero E6-TMPRSS2 used as target cells. Data are geometric mean of n = 3 biologically independent experiments. b, Pairwise neutralizing antibody titers of plasma (ID50) against Wuhan-Hu-1 and Omicron VOC. Data are geometric mean of n = 2 biologically independent experiments. c, Plasma neutralizing activity in dialysis patients who received 3 doses of either BNT162b2 or mRNA-1273 mRNA vaccines. Pairwise neutralizing antibody titers of plasma (ID50) against Wuhan-Hu-1 and Omicron. One representative experiment out of two is shown. Vero E6 used as target cells in b and c. Line, geometric mean of 1/ID50 titers. Shown is the percentage of samples that lost detectable neutralization against Omicron or SARS-CoV. Shown cumulative titer loss not accounting samples with 1/ID50 below the limit of detection. HCW, healthcare workers; Wu, Wuhan-Hu-1; o, Omicron VOC, b, Beta VOC. Enrolled donors’ demographics provided in Extended Data Table 1. Statistical significance is set as P<0.05 and P-values are indicated with asterisks (*=0.033; **=0.002; ***<0.001), using a paired two-sided t test (Wilcoxon rank test).

Fig. 3.. Neutralization of Omicron SARS-CoV-2 VSV pseudovirus by clinical-stage mAbs.

a, RBD sequence of SARS-CoV-2 Wuhan-Hu-1 with highlighted footprints of ACE2 (light blue) and mAbs (colored according to the RBD antigenic site recognized). Omicron RBD is also shown, and amino acid substitutions are boxed. b, Neutralization of SARS-CoV-2 VSV pseudoviruses displaying Wuhan-Hu-1 (white) or Omicron (colored as in Fig. 4b) S proteins by clinical-stage mAbs. Data are representative of one independent experiment out of two. Shown is the mean of 2 technical replicates. c, Geometric mean IC50 values for Omicron (colored as in Fig. 4b) and Wuhan-Hu-1 (white) (top panel), and geometric mean fold change (bottom panel). Vero E6 used as target cells. Shown in blue (right) is neutralization of authentic virus by sotrovimab (WA1/2020 versus hCoV-19/USA/WI-WSLH-221686/2021). Non-neutralizing IC50 titers and fold change were set to 10⁴ and 10³, respectively. Orange dots for sotrovimab indicate neutralization of Omicron VSV pseudovirus carrying R346K. Data are representative of n = 2 biologically independent experiments for most mAbs, for sotrovimab against Omicron VSV n=6 and for Omicron authentic virus n=3.

Fig. 4.. Neutralization of Omicron SARS-CoV-2 VSV pseudovirus by monoclonal antibodies.

a, Mean IC50 values for Omicron (colored as in b) and Wuhan-Hu-1 (white) (top panel), and mean fold change (bottom panel) for 4 NTD mAbs and 32 RBD mAbs. Non-neutralizing IC50 titers and fold change were set to 10⁴ and 10³, respectively. Triangles for S2K146 and S2X259 indicate neutralization of Omicron carrying R346K. Vero E6 used as target cells. Data are representative of n = 2 biologically independent experiments (except for S2K146 and S2X259 where n = 6). b, The RBD sites targeted by 4 mAbs cross-neutralizing Omicron are annotated and representative antibodies (the Fv region) bound to S are shown as a composite. Colored surfaces on the RBD depict the epitopes and the RBM is shown as a black outline.