Identification of an IGHV3-53-Encoded RBD-Targeting Cross-Neutralizing Antibody from an Early COVID-19 Convalescent

Area of Science:

• Immunology
• Virology
• Structural Biology

Background:

• Omicron variants of SARS-CoV-2 have become dominant, diminishing the efficacy of current neutralizing antibodies.
• There is an urgent need for novel therapeutic neutralizing antibodies (NAbs) effective against evolving Omicron sublineages.

Purpose of the Study:

• To isolate and characterize a potent cross-neutralizing antibody targeting the SARS-CoV-2 receptor binding domain (RBD).
• To evaluate the neutralizing activity of the identified antibody against various Omicron variants.

Main Methods:

• Isolation of receptor binding domain (RBD)-specific single memory B cells from a COVID-19 convalescent using flow cytometry.
• Amplification and cloning of antibody variable region genes (heavy and light chains).
• Expression, ELISA screening, and neutralizing activity detection of antibodies; structural analysis of antibody-RBD interaction.

Main Results:

• An IGHV3-53-encoded antibody, D6, targeting the RBD was identified, originating from IGKV1-9*01 germlines.
• D6 demonstrated potent neutralization (IC50 < 0.04 μg/mL) against Omicron variants BA.1, BA.2, BA.4/5, and BF.7, with reduced but effective activity against XBB.
• D6 exhibited high affinity binding (KD < 1.0 × 10^-12 M) to prototype and BA.1 RBDs; structural analysis revealed interaction with the RBD external subdomain.

Conclusions:

• The antibody D6 exhibits broad cross-neutralizing activity against key Omicron variants.
• The structural basis for D6's potent cross-neutralization involves deep interaction of its HCDR3 and LCDR3 with the RBD.
• mAb D6 represents a promising candidate for developing next-generation anti-COVID-19 therapeutic reagents.