SARS-CoV-2 Omicron XBB Lineage Spike Structures, Conformations, Antigenicity, and Receptor Recognition

Abstract

A recombinant lineage of the SARS-CoV-2 Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryo-EM structures of XBB.1.5, XBB.1.16, EG.5 and EG.5.1 spike (S) ectodomains to reveal reinforced 3-RBD-down receptor inaccessible closed states mediated by interprotomer receptor binding domain (RBD) interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters including stability, receptor binding and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.

Note:
Funding Information: Cryo-EM data were collected at the Duke Krios at the Duke University Shared Materials Instrumentation Facility (SMIF), a member of the North Carolina Research Triangle Nanotechnology Network (RTNN), which is supported by the National Science Foundation (award number ECCS-2025064) as part of the National Nanotechnology Coordinated Infrastructure (NNCI). This study utilized the computational resources offered by Duke Research Computing (http://rc.duke.edu; NIH 1S10OD018164-01) at Duke University. This work was supported by NIH R01 AI165947 (P.A. and R.H.), R01 AI 165147 (P.A. and W.B.W.), NIH, NIAID, DMID grant P01 AI158571 (B.F.H.).

Declaration of Interests: B.F.H., K.O.S., R.J.E., S.M-C.G., and P.A. are named in patents submitted on the SARS-CoV-2 monoclonal antibodies studied in this paper. Other authors declare no competing interests.

Keywords: XBB.1.5, XBB.1.16, EG.5, vaccine booster, conformational change, virus evolution, allostery, Receptor Binding Domain, thermostability, Cryo-EM