Structural and functional characterization of a conserved cryptic epitope on SARS-CoV-2 spike S2 subunit

Area of Science:

• Virology
• Immunology
• Structural Biology

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolves, necessitating broad-spectrum vaccines and therapeutics.
• The conserved S2 subunit of the SARS-CoV-2 spike protein is a potential target for universal coronavirus countermeasures.
• Understanding the S2 antigenic landscape is crucial for developing effective vaccines against variants of concern (VOCs).

Purpose of the Study:

• To identify and characterize antibodies targeting the S2 subunit of the SARS-CoV-2 spike protein.
• To investigate the binding properties and neutralization capabilities of S2-specific antibodies.
• To explore the potential of S2 as a target for broadly protective vaccines.

Main Methods:

• Yeast surface display was used to isolate S2-specific antibodies from COVID-19 convalescent donors.
• Biophysical characterization and cryo-electron microscopy were employed to define antibody epitopes and binding preferences.
• Neutralization assays with pseudoviruses and authentic SARS-CoV-2, along with a mouse challenge model, were used to assess antibody efficacy.

Main Results:

• S2-targeted antibodies preferentially bound to open spike conformations and a stabilized S2 construct, not the closed prefusion spike.
• Cryo-EM revealed a cryptic epitope on S2, conserved among sarbecoviruses but occluded in the closed spike conformation.
• These antibodies demonstrated weak pseudovirus neutralization, failed to neutralize authentic SARS-CoV-2, and offered no protection in a mouse model.

Conclusions:

• A non-neutralizing epitope on the SARS-CoV-2 S2 subunit elicits antibodies during human infection.
• These S2-specific antibodies can serve as valuable tools for studying S2 conformational dynamics.
• The findings provide insights for optimizing S2-based antigens for future vaccine development against sarbecoviruses.