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The Host Interactome of Spike Expands the Tropism of SARS-CoV-2

Casimir Bamberger, Sandra Pankow, Salvador Martínez-Bartolomé, Jolene Diedrich, Robin Park, and John Yates III 

Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA.

In humans, SARS-CoV-2 primarily infects lung epithelial cells through the host entry receptor Angiotensin Converting Enzyme 2 (ACE2), but it can spread to multiple other tissues, even those that are negative for ACE2. However, the molecular mechanisms that underlie this potentially ACE2-independent cell entry remain unknown. Here, we determined the host interactome of the Spike protein and additional SARS-CoV-2 ORFs in disease-relevant human bronchial epithelial cells (16HBEo–). Because the relative abundance of Spike proteoforms can impact the tropism of SARS-CoV-2, we compared the host interactome of a D614 Spike strain of the virus with that of the more rapidly spreading D614G mutated Spike strain. A juxtaposition of the host interactomes revealed that more D614 than G614 Spike is retained in the endoplasmic reticulum (ER) by quality control proteins FBX2, UGGT1, Calnexin, HSP7C and GRP78/BiP.  Thrombospondin and Laminin, which are two glycoproteins that may function as restriction factors or co-receptors in an alternative virus entry, were bound more by D614 than G614. To further delineate cell types that might be susceptible to SARS-CoV-2 infection we developed a novel proteomic cell type set enrichment analysis (pCtSEA). pCtSEA analysis of the host interactome of Spike revealed a broad virus tropism, from mucous epithelial cells to macrophages, monocytes, and epithelial cells in the nephron. Because the N-terminal S1 domain of Furin-cleaved D614 but not G614 Spike is preferentially degraded by the endoplasmatic reticulum-associated protein degradation (ERAD) and the C-terminal S2 cleavage product remains available for integration into Spike trimers, we conclude that endoproteolytic cleavage of Spike may enable an alternative co-receptor dependent cell entry into ACE2-negative cell types. This interpretation may provide a molecular explanation for a severe progression of disease in select COVID-19 patients and suggest that drugs for COVID-19 should include a ‘S2-only’ proteoform in addition to full length Spike protein as antigen.