Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Abstract

On the 24 ^th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.

Figure 1. Sarbecovirus RBD sequence analysis.

Shown with Alpha, Beta, Delta and Omicron variants (the latter repeated on the lower line to clarify the Omicron changes. Binding sites for the early pandemic potent antibodies (Dejnirattisai et al., 2021a) and the potent Beta antibodies ((Liu et al., 2021b) are depicted using iron heat colours (grey > straw > blue > glowing red > yellow > white) to indicate relative levels of antibody contact and commercial antibody contacts are depicted with the pairs of antibodies in red or blue with purple denoting interactions with the same residue). Totally conserved residues are boxed on a red background on the upper rows, whilst on the final row the Omicron mutations are boxed in red. Secondary elements are denoted above the alignment. The figure was produced in part using Espript (Robert and Gouet, 2014).

Figure 2. Distribution of Omicron changes.

(A) Trimeric S model depicted as a grey surface with one monomer highlighted in pale blue, ACE2 binding site in green and changes in Omicron shown in red, left side view, right top view. (B) RBD depicted as a grey surface with the ACE2 footprint in dark grey and changes in Omicron in red, left: top view, right: front and back views. Epitopes are labelled according to the torso analogy and mutations labelled. (C,D,E,F) Top view of RBD depicted as a grey surface with (C), ACE2 binding site in green (D), Alpha change in yellow (E), Beta changes in cyan (F), Delta changes in purple. Figure produced using chimera X (Pettersen et al., 2021).

Figure 3.. Neutralization assays against Omicron.

FRNT50 values for the indicated viruses using serum from convalescent subjects previously infected with A) Early pandemic virus (n=32), (B) Alpha (n=18), (C) Beta (n=14), (D) Gamma (n=16), (E) Delta (n=19), (F) Delta before vaccination or Delta after vaccination (n=17), (G) Before and after the third dose of AZD1222 (n=41), (H) 4 weeks, 6 months after the second dose, before the third and after the third dose of BNT162b2 (n=20). In A-E comparison is made with neutralization titres to Victoria, Alpha, Beta and Gamma and Delta previously reported in (Dejnirattisai et al., 2021a; Supasa et al., 2021; Zhou et al., 2021; Dejnirattisai et al., 2021b; Liu et al., 2021b), in G the data points for BNT162b2 are taken from (Flaxman et al., 2021). Geometric mean titres are shown above each column. The Wilcoxon matched-pairs signed rank test was used for the analysis and two-tailed P values were calculated.

Figure 4. mAb Neutralization curves.

FRNT curves for mAb from (A) Early pandemic, (B) Beta infected cases or (C) Commercial sources. Omicron neutralization is compared with curves for Victoria, Alpha, Beta, Gamma and Delta which have been previously reported (Dejnirattisai et al., 2021a; Supasa et al., 2021; Zhou et al., 2021; Dejnirattisai et al., 2021b; Liu et al., 2021b). Neutralization titres are reported in Table S1.

Figure 5.. Relative Antibody Contact.

RBD surface rendered in PyMOL exported and rendered in mabscape using iron heat colours (grey > straw > blue > glowing red > yellow > white) to indicate relative levels of antibody contact. Antibody contact is calculated for each surface vertex as the number of antibodies within a 10 Å radius by their known or predicted positions from earlier mapping studies (Dejnirattisai et al., 2021a; Liu et al., 2021b). Outward facing cones are placed at the nearest vertex to each mutated residue Calpha atom on the RBD surface. Drawn back and front views for (A) all RBD-reactive antibodies isolated from early pandemic or strongly neutralizing (< 100 ng/ml) (B) strongly neutralising antibodies isolated from Beta-infected sera (C) potent antibodies isolated from Beta infected cases (D) therapeutic antibodies for clinical use (from PDB: 7BEP, 6XDG, 7L7E, 7KMG, 7KMH). (A,B,C) Front (left) and back (right) views of the RBD drawn as a grey surface with Omicron changes highlighted in magenta and glycans drawn as sticks. (E) Outline footprints of a selection of early pandemic mAbs: 58, 88, 222, 253, 278 are shown by balls representing the centroid of interacting loops for LC (blues), HC (reds) and joined by yellow lines. (F) As for A, showing a selection of Beta antibodies:27, 47, 49, 53. Substituted residues in magenta are labelled. (G) As for A showing the footprints of a selection of commercial antibodies: REGN10933, REGN10987, S309, AZD1061, AZD8895, LY-CoV555, LY-CoV016.

Figure 6.. Affinity driving mutations in Omicron RBD have previously been identified by in vitro evolution for tighter binding.

(A) Analysis of the occurrence and prevalence of Omicron variant mutations. The background is coloured according to S-protein functional domains: NTD domain (AA 12 – 306; orange), RBD domain (AA 318 – 514; green), Furin cleavage site and its proximity (AA 655 – 701; blue). The four positions critical for the high affinity of RBD-62 are highlighted in bold. Mutation frequencies within individual lineages are denoted in green (100–75 %), blue (75–50 %) and magenta (50–25 %). Information about the distribution and frequency of S-protein mutations and the spatiotemporal characterization of SARS-CoV-2 lineages was retrieved from www.outbreak.info (Mullen et al., 2020) and Gisaid database (Elbe and Buckland-Merrett, 2017).* Same evolutionary origin, a Number of evolutionary non-related lineages with given or similar mutation (Zahradnik et al., 2021c), b log(10) number of the observed Omicron mutation at the given position as determined on 14.11.2021, c same as b but total log(10) number of changes at the given position. d fold-change in binding as determined by yeast-surface display. (B) Comparison of fold change in binding affinity among selected mutations and their combinations as determined by titrating ACE2 on yeast surface displayed RBD mutations. Values are fold-change relative to the original strain. For Omicron, yeast titration is denoted in violet, SPR (this study) is black, SPR as determined in (Cameroni et al., 2021) is grey and ELISA as determined in (Schubert et al., 2021) is in orange. Data denoted by black dots have been reported previously (Zahradnik et al., 2021b). (C) RBD-62 (blue)/ACE2 (green) structure (PDB: 7BH9) overlaid on Omicron RBD structure (orange) as determined bound to Beta 55. All Omicron mutations are shown, overlaid on relevant RBD-62 mutations. (D) Electrostatic potential surface depictions calculated using the APBS plugin in PyMol for left to right: early pandemic Victoria RBD showing the ACE2 interacting surface, ACE2 showing surface that binds the RBD, Beta RBD ACE2 interacting surface, RBD-62 ACE2 interacting surface, Omicron RBD ACE2 interacting surface. Blue is positive and red negative potential (scale bar shown above).

Figure 7. Antigenic map from neutralization data for omicron.

(A) neutralization data (log titres) showing sera as columns against challenge variants as rows. Sera are grouped into blocks according to the eliciting variant. The reference neutralization titre for each block is calculated as the average of all self-challenge titres, i.e. when challenged with the same variant as which elicited the serum. In the case of vaccine sera this was taken as the average of all best neutralisation titres. Colours within a single block therefore express the relative neutralization titre with respect to this reference. (B) shows an example of the equivalent model generated from one run of antigenic map refinement using the same reference offsets as calculated for (A). (C) shows three-dimensional view of the antigenic map for variants of concern. The distance between two points corresponds to the drop-off in neutralisation titre used to generate value for (B). (D) same antigenic space as (C), but rotated to look down from the point of view of the Omicron position on the remaining variants. (E) Overlay of the X-ray structure of Omicron (red) on the early pandemic (Wuhan) RBD (grey) and the predicted model of the Omicron RBD in black, drawn as cartoons. The structural change effected by the S371L, S373P and S375F mutations is shown enlarged see inset. (F) X-ray structure of ternary complex of Omicron RBD with Beta 55 and EY6A Fabs. The Omicron RBD is shown as a grey semi-transparent surface with the mutated residues in magenta. The Fabs are drawn as cartoons, heavy chain in magenta and light chain in blue.