Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction

Several new variants of SARS-CoV-2 have emerged since fall 2020 which have multiple mutations in the receptor-binding domain (RBD) of the spike protein. It is unclear which mutations affect receptor affinity versus immune recognition.

We produced wild type RBD, RBD with single mutations (E484K, K417N, or N501Y) or with all three mutations combined and tested their binding to ACE2 by biolayer interferometry (BLI). The ability of convalescent sera to recognize RBDs and block their interaction with ACE2 was tested as well.

We demonstrated that single mutation N501Y increased binding affinity to ACE2 but did not strongly affect its recognition by convalescent sera. In contrast, single mutation E484K had almost no impact on the binding kinetics, but essentially abolished recognition of RBD by convalescent sera. Interestingly, combining mutations E484K, K417N, and N501Y resulted in a RBD with both features: enhanced receptor binding and abolished immune recognition.

Our data demonstrate that single mutations either affect receptor affinity or immune recognition while triple mutant RBDs combine both features.