Proteolytic control of the SARS-CoV-2 furin cleavage site defines the phenotypic evolution from the pandemic to endemic state
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The successive emergence of SARS-CoV-2 variants with altered tissue tropism has progressively decoupled transmissibility from lower respiratory tract pathogenicity. Omicron lineages transmit exceptionally well whilst limiting severe lung disease. Here, we demonstrate that this phenotype has evolved through two temporally distinct tissue-specific proteolytic controls at the Spike (S) furin cleavage site (FCS). At the virion level, cell-type-dependent furin-mediated FCS hyper-cleavage depletes S in lung but not nasal epithelial cells. At the infected cell membrane during cell-cell spread, TMPRSS2 mediates S FCS cleavage but is negatively regulated in the presence of ACE2. Tissue-specific solute carriers SLC6A19 and SLC6A20 sequester ACE2, thereby relieving inhibition of TMPRSS2 and enabling S FCS cleavage during cell-cell spread. Critically, whilst all SARS-CoV-2 lineages benefit from this latter pathway, Omicron variants have evolved exclusive dependence on it—a strategic consolidation that focuses S proteolytic activation to TMPRSS2 alone. The combined outcomes of S protein regulation across viral and cell membranes reveal how tissue-specific proteolytic optimisation drives Omicron’s transmission fitness advantage in the upper respiratory tract but at the cost of heavy attenuation in the lower respiratory tract.
Abstract Figure
Graphical Abstract: Dynamics of Spike pools, S FCS cleavage and ACE2 conformations collectively define Omicron Tropism
A & B. Spatial regulation of S protein FCS cleavage. Viral S protein can traffic to two distinct cellular locations: A. virion particles within the trans-Golgi network of infected cells, or B. the plasma membrane of infected cells. Proteolytic cleavage of the FCS at each location is governed by different mechanisms. C. In virion particles, furin plays the dominant role, mediating hyper-FCS cleavage that culminates in S protein depletion in virions generated from cells derived from the lung. Nasal epithelia and other cells permissive to Omicron infections, sustain efficient FCS cleavage without S protein virion depletion. Over time, this phenotype has continued to consolidate from the pandemic to endemic stages of SARS-CoV-2 (Spike depletion relative to Global frequencies of major variants (courtesy of Nextstrain)). The arrival of JN.1 sub-lineages observed the peak of S protein depletion from furin and furin like protease hyper-cleavage. D. From the consequences of S protein depletion, the role of non-FCS cleaved S at the infected cell membrane is revealed. At the infected cell membrane (cells in blue) during cell-cell contact, TMPRSS2 is the primary FCS protease and is present on the recipient cell membrane (cells in green). mportantly, ACE2 negatively regulates TMPRSS2 activity at this location; however, this inhibition is circumvented when ACE2 forms complexes with solute carriers SLC6A19 or SLC6A20. This interaction frees TMPRSS2 from ACE2-mediated inhibition, enabling efficient S1/S2 FCS cleavage at the cell membrane by TMPRSS2. This subsequently exposes S2’ for TMPRSS2 cleavage, driving efficient cell-cell spread via a common protease-gated mechanism. Efficient cell-cell spread is sustained across all SARS-CoV-2 lineages using this pathway, and more recently demonstrated to afford JN.1 sub-lineages a itness advantage relative to XBB.1.5 sub-lineages.
