Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies

Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike. Mutations in spike impacting antibody and/or ACE2 binding are appearing worldwide, imposing the need to monitor SARS-CoV2 evolution and dynamics in the population. Determining signatures in SARS-CoV-2 that render the virus resistant to neutralizing antibodies is critical. We engineered 25 spike-pseudotyped lentiviruses containing individual and combined mutations in the spike protein, including all defining mutations in the variants of concern, to identify the effect of single and synergic amino acid substitutions in promoting immune escape. We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y. Our analysis of synergic mutations provides a signature for hotspots for immune evasion and for targets of therapies, vaccines and diagnostics. Author summary For a SARS-CoV-2 virion to enter a cell, the spike protein displayed at its surface must be recognized by the host ACE2 receptor. Serum neutralizing antibodies, shown to develop upon natural SARS-CoV-2 infection or vaccination, bind spike protein preventing the recognition by ACE2 and, consequently, infection. However, SARS-CoV-2 virus is constantly evolving, and can acquire mutations in spike that render this protein resistant to neutralizing antibodies and make vaccines ineffective. In this paper, we tested how single and a combination of mutations naturally occurring in spike, including in variants of concern, would synergize to affect antibody neutralizing capacity. We then integrated these findings with in silico analyses of amino acids binding to ACE2 and antibodies, and distributed them in a grid as amino acids important for binding to ACE2 or antibodies, or both. We found that changes in amino such as E484 and S494, which frequently interact with antibodies but not with ACE2, promptly evolve immune escape mutants, elicited by infection or vaccination, if the mutation severely alters the binding specificity of the antibody. Our work also suggests that the combination of these mutations with others promoting ACE2 binding, such as N501Y, increases their ability to escape neutralizing-antibody responses.