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

Abstract

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.

Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections

“…While E484K only mildly increases the affinity of the RBD for ACE2 receptor, N501Y appears to substantially enhance it by allowing it to engage the receptor for longer (71)(72)(73). This is in agreement with an observation of pseudotyped viruses carrying N501Y mutation demonstrating a higher infectivity in vitro than those carrying E484K mutation (68).…”

SARS-CoV-2 Infection: New Molecular, Phylogenetic, and Pathogenetic Insights. Efficacy of Current Vaccines and the Potential Risk of Variants

“…However, it is important to point out that mutations at position 477 have not been identified as being important with convalescent plasma [ 203 ]. A recent report also identified E484 and S494 mutations, which are capable of interacting with nAbs but not with ACE2, as determinant for promptly evolved immune escape mutants [ 204 ]. In addition, it has also been reported that the combination of these mutations with others promoting ACE2 binding, such as N501Y, increases their ability to escape nAb responses.…”

“…In addition, it has also been reported that the combination of these mutations with others promoting ACE2 binding, such as N501Y, increases their ability to escape nAb responses. The mutation at position 494 also deserves attention, either alone or combined with synergetic mutations, as it seems to reduce the neutralization competency of convalescent sera, thereby facilitating nAb escape, and thus facilitating antibody escape without modifying the affinity for ACE2 [ 204 ].…”

Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC)

“…The first reported mutation of the Spike protein was D614G mutation, which was found to enhance the SARS-CoV-2 transmission [13]. The N501Y mutation increased the affinity of the Spike protein for its receptor, Angiotensin Converting Enzyme 2 (ACE2), thereby increasing the chances of viral transmission [14]. Mutation E484K is known to contribute to the evasion of antibody neutralization [15].…”