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.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Amino Acid Substitution / genetics
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Angiotensin-Converting Enzyme 2 / genetics
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Angiotensin-Converting Enzyme 2 / immunology
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Antibodies, Monoclonal / immunology
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Antibodies, Neutralizing / immunology*
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Antibodies, Viral / immunology
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COVID-19 / immunology
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COVID-19 / virology*
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Cell Line
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Humans
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Immune Evasion
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Mutation / genetics
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Protein Binding
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SARS-CoV-2 / genetics
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SARS-CoV-2 / immunology*
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Spike Glycoprotein, Coronavirus / genetics
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Spike Glycoprotein, Coronavirus / immunology*
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Spike Glycoprotein, Coronavirus / metabolism
Substances
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Antibodies, Monoclonal
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Antibodies, Neutralizing
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Antibodies, Viral
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Spike Glycoprotein, Coronavirus
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spike protein, SARS-CoV-2
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Angiotensin-Converting Enzyme 2
Grants and funding
This project is supported by the grants PTDC/CCI-BIO/28200/2017 awarded to DF; FCT RESEARCH4COVID 19 (Refs 580 and 644) awarded by the Fundação para a Ciência e a Tecnologia (FCT, Portugal,
https://www.fct.pt/index.phtml.en) to MJA and also by COVID-19 emergency funds 2020 from Fundação Calouste Gulbenkian - Instituto Gulbenkian de Ciência (FCG-IGC, Portugal,
https://gulbenkian.pt/ciencia/) to MJA. The work of JD benefited from COVID-19 emergency funds 2020 from Fundação Gulbenkian de Ciência and from Câmara Municipal de Oeiras (
https://www.oeiras.pt). The work of HS was supported by ESCMID (
https://www.escmid.org) and by Gilead Génese (PGG/009/2017,
https://gileadgenese.pt) grants. MJA is funded by FCT 2020.02373.CEECIND; FF is supported by the FCT grant PTDC/BIA-CEL/32211/2017; JG and HS are supported by Fundação para a Ciência e Tecnologia (FCT) through PD/BD/128343/2017 and CEECIND/01049/2020.