Affinities of the nanobody repertoire against SARS-CoV-2 variants.
(A) Each nanobody is plotted against their affinity (KD) for SARS-CoV-2 Spike S1 from wild-type, delta and omicron BA.1, BA.4, XBB and BQ.1.1 strains. Kinetic values are summarized in Table 1. Nanobodies are characterized into their respective epitope groups as described previousl (Mast, Fridy et al. 2021). (B) Displayed are the structures of the RBD of spike delta (PDB ID: 7SBO), omicron BA.1 (PDB ID: 7T9K), omicron BA.4 RBD (modeled using AlphaFold), omicron XBB (PDB ID: 8IOU) and omicron BQ.1.1 (PDB ID: 8FXC. The structures feature heat-mapped epitopes of binding, ranging from pale white (weak binding to SARS-CoV-2) to dark red (strong binding to SARS-CoV-2). In the grey box, mutations specific to each variant are highlighted in blue. The nanobodies that contributed to epitope mapping are in bold in panel A. The color bar scale indicates each epitope’s binding affinity strength, represented as the normalized -log ratio of nanobody binding (KD) of variant versus wild-type SARS-CoV-2 Spike S1. For groups with multiple nanobodies, the average −log10 (KD) for the nanobodies within that group were calculated, then normalized to an affinity score ranging from 0–100 using the min and max average −log10 (KD) for that group. Higher −log10 ratios indicates stronger binding of the nanobody to the variant versus wild type. S1-RBD-16 bound omicron BA.1 and BA.4/5 in ELISA. S1-RBD-11 was not tested against omicron BA.4. S1-65 was not tested against BA.1. Only S1-1, S1-RBD-22, S1-RBD-9, S1-4, S1-35, S1-39, S1-RBD-6, S1-RBD-5, S1-23, S1-RBD-40, S1-RBD-46 and S1-46 were tested against omicron XBB and omicron BQ.1.1. All structure representations were generated using ChimeraX (Pettersen, Goddard et al. 2021).