Cryptic-site-specific antibodies to the SARS-CoV-2 receptor binding domain can retain functional binding affinity to spike variants

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has accumulated more than 700 million infection cases and 6.9 million deaths. New variants have affected antibody interaction with the surface spike protein. We defined the domain specificities and measured hexa-proline stabilized spike protein (HexaPro) binding kinetics of a large panel of antibodies sourced by the Coronavirus Immunotherapeutics Consortium. Epitope binning analysis of antibodies competing for HexaPro binding separated the fine specificities of the majority of antibodies to four regions: top, outer, mesa/valley, or cryptic site of receptor binding domain (RBD). Most of the top-RBD-specific antibodies showed >3-fold loss of binding and authentic-virus neutralization activity for the B.1.351 variant. Remarkably, among RBD mesa/valley-specific or cryptic-site-specific antibodies, 55% showed >3-fold stronger affinities, and at least 60% maintained neutralization activity for the B.1.351 variant. These data also highlighted the diversity of SARS-CoV-2-specific antibodies that retain high spike affinities and antiviral functions across variants.