Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529

Abstract

With B.1.1.529 SARS-CoV-2 variant's rapid spread and substantially increased resistance to neutralization by vaccinee and convalescent sera, monoclonal antibodies with potent neutralization are eagerly sought. To provide insight into effective neutralization, we determined cryo-EM structures and evaluated potent receptor-binding domain (RBD) antibodies for their ability to bind and neutralize this new variant. B.1.1.529 RBD mutations altered 16% of the RBD surface, clustering on a ridge of this domain proximal to the ACE2-binding surface and reducing binding of most antibodies. Significant inhibitory activity was retained, however, by select monoclonal antibodies including A19-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309 and LY-CoV1404, which accommodated these changes and neutralized B.1.1.529 with IC50s between 5.1-281 ng/ml, and we identified combinations of antibodies with potent synergistic neutralization. Structure-function analyses delineated the impact of resistance mutations and revealed structural mechanisms for maintenance of potent neutralization against emerging variants.

Combating the SARS-CoV-2 Omicron variant with non-Omicron neutralizing antibodies

“…A panel of control NAbs failed to neutralize the Omicron except S309. S309 neutralized Omicron to a similar degree as previous reports 12 , 13 . GW01 was a cross-NAb that was able to neutralize SARS-CoV and the SARS-related coronaviruses (SARSr-CoVs) RS3367 and WIV1.…”

“…We constructed 34 single mutants of the Omicron variant to identify the key residues that mediate resistance to GW01, 16L9, 4L12, and REGN0987. The S371L mutation, which was found to stabilize the Omicron into a single-RBD-down conformation 12 , greatly decreased the neutralization activities of GW01, 4L12, and REGN10987 ( Table 1 ). The S375F mutation decreased the neutralization activity of GW01 by 16-fold and resulted in resistance to REGN10987.…”

A broad and potent neutralization epitope in SARS-related coronaviruses

“…Omicron is resistant, or has reduced effectiveness, to most current authorized therapeutic monoclonal antibodies as well as cocktails, including LY-CoV555, LY-CoV016, REGN10933, REGN10987, BRII-196, etc. However, neutralization by S309 or its derivative Sotrovimab/VIR-7831 was only reduced by 3-10 fold against Omicron (5,15,16,(25)(26)(27) compared to 40-100 fold reduction for ADG-2/ADG20 against Omicron pseudotyped virus here (Figure 2A) and in another study (16). Importantly, using authentic viruses, only a 20fold reduction of ADG20 neutralization against Omicron was observed compared to Delta, and was the most potent among all the tested therapeutic antibodies (15).…”

The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2

“…The Delta variant S proteins are additions, while other data points are three monomer averages for each of the S protein trimers in subgroups described previously (Lobo and Warwicker, 2021) and open forms (Hong et al, 2022). Reports suggest that for the one RBD up form, this may be due, in part, to enhanced interactions between monomers (S375F-F486) (Zhou et al, 2021). The major thrust of pH dependence predictions for non-Omicron variants is that increased compaction of the spike trimer leads to partial dehydration of some Asp/Glu side chains and a disfavoring of a more compact form at neutral pH, unless balanced by linoleic acid binding to the RBD pocket (Lobo and Warwicker, 2021).…”

“…The major thrust of pH dependence predictions for non-Omicron variants is that increased compaction of the spike trimer leads to partial dehydration of some Asp/Glu side chains and a disfavoring of a more compact form at neutral pH, unless balanced by linoleic acid binding to the RBD pocket (Lobo and Warwicker, 2021). In order to include the Omicron variant spike protein (which may not bind linoleic acid) in this picture, it is necessary to study the one RBD up form since this is the only currently available structure (January 2022) that has a complete set of three RBDs resolved (7tb4) (Zhou et al, 2021). Furthermore, to maintain equivalence between the engineered status of the spike protein ectodomain, analysis is restricted to the 2P (K986P, V987P) stabilized form.…”