A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

Better understanding of antibody cross-reactivity will benefit therapeutic and vaccine designs. Wu et al. used the highly neutralizing monoclonal antibody CR3022, which was isolated from a recovered SARS patient, to probe the antigenic variation between SARS-CoV and SARS-CoV-2. CR3022 recognises a 28-residue epitope which is largely conserved between the strains, but has a much greater affinity to SARS-CoV and cannot neutralise SARS-CoV-2. P384A mutation of SARS-CoV-2 increases CR3022’s binding affinity and promotes neutralisation, with similar potency to that of SARS-CoV. Further analysis demonstrated that there is considerable flexibility in the binding of CR3022 and SARS-CoV RBD.  

Research Highlights

1. Of the 4/28 residues within CR3022’s epitope that are not conserved between SARS-CoV and SARS-CoV-2, only mutation at residue 384 (P -> A) increased the antibody’s affinity for SARS-CoV-2 spike protein (KD = 1.4 nM) from WT (KD = 68 nM). 

2. P384A mutation promoted CR3022-mediated neutralisation of SARS-CoV-2 pseudovirus (IC50 – 3.2 μg/ml) which was similar to SARS-CoV (IC50 – 5.2 μg/ml). 

3. Neutralisation of P384A mutant was similar at both IgG and Fab formulation. 

4. Amino acid substitution at 384 alters the number of hydrogen bonds formed between the RBD and VH S96 of CR3022 (A = 3, P = 1). This may impact the differences in CR3022 binding to SARS-CoV and SARS-CoV-2 RBD.  

5. Structural analysis revealed that 3 CR3022 Fabs could simultaneously bind to one SARS-CoV S protein, whilst all three RBDs were in the “up” conformation. In addition, CR3022 could make quaternary contacts with the N-terminal domain during interaction.  

Impact for COVID-19 research:  

• Understanding antibody-epitope interactions, and the possibility of cross reactivity between antibodies, will better aid designs of therapeutics and vaccine candidates.  

Methodologies: 

• Study Type: in vitro, in silico  

• Important cell lines/viral models used: SARS-CoV and SARS-CoV-2 pseudovirus 

• Key Techniques: crystallography, negative-strain electron microscopy, cryo-EM, biolayer interferometry for binding assays, neutralisation assay 

Limitations: 

• Suggest differences in binding affinity could be caused by less hydrogen bonds between CR3022 and RBD at residue 384. This mutation is discussed in isolation and does not consider the impact the differences at other non-conserved residues (372, 420, 519) would have on structural interaction.  

• No statistics for both binding affinity and neutralisation assays.  

• Figure 1 – results are representative of only two replicates.