SARS-Cov-2 variants of concern decelerate the dynamics of spike open conformation as an evolutionary strategy

SARS-CoV-2 variants of concern harbor mutations in the Spike (S) protein that confer more efficient transmission and reduce the efficacy of COVID-19 vaccines and antibody therapies. S mediates virus entry and is the primary target for antibody responses. S is a trimer in which the receptor-binding domain of each protomer engages the cellular receptor human Angiotensin-Converting Enzyme 2 (hACE2). Structural studies of soluble-form S variants have revealed an increased propensity to sample more hACE2-accessible conformations. However, real-time observations of conformational dynamics that govern the structural equilibriums of the S variants have been lacking. Here, we report single-molecule FÃrster Resonance Energy Transfer (smFRET) studies of S variants containing critical mutations such as D614G and E484K in the context of virus particles. S containing these mutations predominantly occupied the more open hACE2-accessible conformations, agreeing with previous structural work on soluble trimers. Importantly, they exhibited decelerated transitions from hACE2-bound conformations, indicating that increased stability of S in its receptor-bound state is part of the SARS-Cov-2 adaptation strategy to the human population. Our findings provide a new perspective of SARS-CoV-2 evolution, thus informing intervention adjustment to control the dynamic pandemic.