Tetherin restricts SARS-CoV-2 replication despite antagonistic effects of Spike and ORF7a

Abstract

SARS-CoV-2 infection induces interferon-stimulated genes, one of which encodes Tetherin, a transmembrane protein inhibiting the release of various enveloped viruses from infected cells. Previous studies revealed that SARS-CoV encodes two Tetherin antagonists: the Spike protein (S) inducing lysosomal degradation of Tetherin, and ORF7a altering its glycosylation. SARS-CoV-2 ORF7a has also been shown to antagonize Tetherin. Therefore, we here investigated whether SARS-CoV-2 S is also a Tetherin antagonist and compared the abilities and mechanisms of S and ORF7a in counteracting Tetherin. SARS-CoV and SARS-CoV-2 S reduced Tetherin cell surface levels in a cell type-dependent manner, possibly related to the basal protein levels of Tetherin. In HEK293T cells, under conditions of high exogenous Tetherin expression, SARS-CoV-2 S and ORF7a reduced total Tetherin levels much more efficiently than the respective counterparts derived from SARS-CoV. Nevertheless, ORF7a from both strains was able to alter Tetherin glycosylation. The ability to decrease total protein levels of Tetherin was conserved among S proteins from different SARS-CoV-2 variants (D614G, Cluster 5, , {gamma}, {delta}, o). While SARS-CoV-2 S and ORF7a both colocalized with Tetherin, only ORF7a directly interacted with the restriction factor. Despite the presence of two Tetherin antagonists, however, SARS-CoV-2 replication in Caco-2 cells was further enhanced upon Tetherin knockout. Altogether, our data show that endogenous Tetherin restricts SARS-CoV-2 replication, and that the antiviral activity of Tetherin is partially counteracted by two viral antagonists with differential and complementary modes of action, S and ORF7a. IMPORTANCEViruses have adopted multiple strategies to cope with innate antiviral immunity. They blunt signaling and encode proteins that counteract antiviral host factors. One such factor is Tetherin, that tethers nascent virions to the cell membrane and interferes with virus release. For SARS-CoV, the viral glycoprotein Spike (S) and the accessory protein ORF7a are Tetherin antagonists. For pandemic SARS-CoV-2, such activity has only been shown for ORF7a. We therefore analyzed whether SARS-CoV-2 S is a Tetherin-counteracting protein and whether there are differences in the abilities of the viral proteins to antagonize Tetherin. Of note, the efficiency of Tetherin antagonism was more pronounced for S and ORF7a from SARS-CoV-2 compared to their SARS-CoV orthologs. Still, Tetherin was able to restrict SARS-CoV-2 replication. Our results highlight the fundamental importance of the innate immune response in the context of SARS-CoV-2 control and the evolutionary pressure on pathogenic viruses to withhold efficient Tetherin antagonism.