Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
Chang-Chun D. Lee,
Nicholas C Wu,
Abigail M. Jackson,
Marit van Gils,
Rogier W. Sanders,
Dennis R. Burton,
S Momsen Reincke,
Andrew B. Ward,
Ian A. Wilson
Posted 17 Feb 2021
bioRxiv DOI: 10.1101/2021.02.16.430500
Posted 17 Feb 2021
The protective efficacy of neutralizing antibodies (nAbs) elicited during natural infection with SARS-CoV-2 and by vaccination based on its spike protein has been compromised with emergence of the recent SARS-CoV-2 variants. Residues E484 and K417 in the receptor-binding site (RBS) are both mutated in lineages first described in South Africa (B.1.351) and Brazil (B.18.104.22.168). The nAbs isolated from SARS-CoV-2 patients are preferentially encoded by certain heavy-chain germline genes and the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2) can each bind the RBS in two different binding modes. However, their binding and neutralization are abrogated by either the E484K or K417N mutation, whereas nAbs to the cross-reactive CR3022 and S309 sites are largely unaffected. This structural and functional analysis illustrates why mutations at E484 and K417 adversely affect major classes of nAbs to SARS-CoV-2 with consequences for next-generation COVID-19 vaccines.
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