Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants

Author:

Ke ZunlongORCID,Peacock Thomas P.ORCID,Brown Jonathan C.ORCID,Sheppard Carol M.ORCID,Croll Tristan I.ORCID,Kotecha AbhayORCID,Goldhill Daniel H.ORCID,Barclay Wendy S.ORCID,Briggs John A.G.ORCID

Abstract

AbstractThe evolution of SARS-CoV-2 variants with increased fitness has been accompanied by structural changes in the spike (S) proteins that are the major target for the adaptive immune response. Single-particle cryo-EM analysis of soluble S from SARS-CoV-2 variants has revealed this structural adaptation at high-resolution. The analysis of S trimers in situ on intact virions has the potential to provide more functionally relevant insights into S structure and virion morphology. Here, we characterized B.1, Alpha, Beta, Gamma, Delta, Kappa, and Mu variants by cryo-electron microscopy and tomography, assessing S cleavage, virion morphology, S incorporation, “in-situ” high-resolution S structures and the range of S conformational states. We found no evidence for adaptive changes in virion morphology, but describe multiple different positions in the S protein where amino acid changes alter local protein structure. Considered together, our data is consistent with a model where amino acid changes at multiple positions from the top to the base of the spike cause structural changes that can modulate the conformational dynamics of S.

Publisher

Cold Spring Harbor Laboratory

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