Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic

Variants of SARS-CoV-2, defined mainly by mutations in the spike glycoprotein, have emerged throughout the COVID-19 pandemic and will undoubtedly continue to emerge in the future. Spike strongly influences virus phenotype, and it is therefore critical to understand the evolution of this viral protein during distinct phases of the pandemic. Here, we generated a panel of recombinant viruses carrying spike from 27 of the most significant variants, circulating between 2020 and 2024, within an otherwise identical genomic backbone. We systematically assessed phenotypic traits of these viruses both in vitro and in vivo in hamsters. Overall, we determined distinct phenotypic trajectories of spike among and between the variants circulating before (“pre-Omicron") and after (“post-Omicron”) the emergence of Omicron. Spillover of SARS-CoV-2 in the human population was followed by a period of adaptation and fine-tuning to the host in the pre-Omicron variants. Omicron simultaneously “reset” several established phenotypes of previously circulating variants. Since then, spike of post-Omicron variants maintained its enhanced tropism for the nasal epithelium but displayed over time several phenotypic traits typical of the pre-Omicron variants. These data suggest that it may be possible for spike with phenotypic features of both pre- and post-Omicron variants to emerge in the future.