Mutations accumulated in the Spike of SARS-CoV-2 Omicron allow for more efficient counteraction of the restriction factor BST2/Tetherin

BST2/Tetherin is a restriction factor with broad antiviral activity against enveloped viruses, including coronaviruses. Specifically, BST2 traps nascent particles to membrane compartments, preventing their release and spread. In turn, viruses have evolved multiple mechanisms to counteract BST2. Here, we examined the interactions between BST2 and SARS-CoV-2. Our study shows that BST2 reduces SARS-CoV-2 virion release. However, the virus uses the Spike (S) protein to downregulate BST2. This requires a physical interaction between S and BST2, which routes BST2 for lysosomal degradation in a Clathtin- and ubiquitination-dependent manner. By surveying different SARS-CoV-2 variants of concern (Alpha-Omicron), we found that Omicron is more efficient at counteracting BST2, and that mutations in S account for its enhanced anti-BST2 activity. Mapping analyses revealed that several surfaces in the extracellular region of BST2 are required for an interaction with the Spike, and that the Omicron variant has changed its patterns of association with BST2 to improve its counteraction. Therefore, our study suggests that, besides enhancing receptor binding and evasion of neutralizing antibodies, mutations accumulated in the Spike afford more efficient counteraction of BST2, which highlights that BST2 antagonism is important for SARS-CoV-2 infectivity and spread. BST2/Tetherin is a potent antiviral factor that prevents the egress of multiple enveloped viruses. In turn, viruses have evolved mechanisms to circumvent this block. Here, we found that SARS-CoV-2 primarily uses the Spike protein to promote the lysosomal degradation of BST2, thus, removing it from sites of virion assembly and facilitating virus release. When analyzing several SARS-CoV-2 variants of concern, we found that Omicron is more efficient at counteracting BST2, to the point where its replication is barely impacted by this restriction factor. Subsequent studies identified mutations accumulated in the Omicron Spike as responsible for improving an interaction between Spike and BST2. However, the surfaces in BST2 required for this association differ between Wuhan and Omicron. Remarkably, increased Spike-BST2 binding is associated with enhanced BST2 downregulation. Therefore, these observations suggest that, in addition to enhancing receptor binding and immune evasion, mutations in the Spike afford more efficient counteraction of BST2, highlighting that BST2 antagonism is important for SARS-CoV-2 infectivity.