Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants.

Emergence of new SARS-CoV-2 variants has raised concerns related to the effectiveness of vaccines and antibody therapeutics developed against the unmutated wild-type virus. Here we examined the effect of the 12 most commonly occurring mutations in the receptor binding domain of the Spike protein on its expression, stability, activity, and antibody escape potential. Stability was measured using thermal denaturation, and the activity and antibody escape potential were measured using isothermal titration calorimetry in terms of binding to the human angiotensin-converting enzyme 2 (ACE2) and to neutralizing human antibody CC12.1, respectively. Our results show that mutants differ in their expression levels. Of the 8 best-expressed mutants, 2 (N501Y and K417T/E484K/N501Y) showed stronger affinity to ACE2 compared to the wild-type, while 4 (Y453F, S477N, T478I and S494P) had similar affinity and 2 (K417N and E484K) had weaker affinity than the wild-type. Compared to the wild-type, 4 mutants (K417N, Y453F, N501Y and K417T/E484K/N501Y) had weaker affinity for the CC12.1 antibody, whereas 2 (S477N and S494P) had similar affinity, and 2 (T478I and E484K) had stronger affinity than the wild-type. Mutants also differ in their thermal stability, with the two least stable mutants showing reduced expression. Taken together, these results indicate that multiple factors contribute towards the natural selection of variants, and all these factors need be considered to understand the evolution of the virus. In addition, since not all variants can escape a given neutralizing antibody, antibodies to treat new variants can be chosen based on the specific mutations in that variant.