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BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) protein, one of which removes a beta-strand. Here we investigate its neutralization by a variety of sera from infected and vaccinated individuals and determine its spike (S) ectodomain structure. The BA.2.87.1 receptor binding domain (RBD) is structurally conserved and the RBDs are tightly packed in an "all-down" conformation with a small rotation relative to the trimer axis as compared to the closest previously observed conformation. The N-terminal domain (NTD) maintains a remarkably similar structure overall; however, the rearrangements resulting from the deletions essentially destroy the so-called supersite epitope and eliminate one glycan site, while a mutation creates an additional glycan site, effectively shielding another NTD epitope. BA.2.87.1 is relatively easily neutralized but acquisition of additional mutations in the RBD could increase antibody escape allowing it to become a dominant sub-lineage.

Original publication

DOI

10.1016/j.str.2024.07.020

Type

Journal article

Journal

Structure (London, England : 1993)

Publication Date

10/2024

Volume

32

Pages

1594 - 1602.e6

Addresses

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Centre for Human Genetics, Oxford, UK.

Keywords

PITCH Consortium, Humans, Antibodies, Viral, Epitopes, Sequence Deletion, Binding Sites, Protein Binding, Models, Molecular, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus, Protein Domains, COVID-19, SARS-CoV-2