Extended Data Fig. 5: Salivary cellular fractions are heterogeneous, but epithelia sustain infection.

a, Salivary epithelial cells were found to heterogeneously express SARS-CoV-2 entry factors in a minority of cells; 1 independent replication. b, Shed cells in saliva display unique TMPRSS family heterogeneity, which we also observed in tissue-specific oral atlases for salivary glands (SG) and mucosa; 1 independent replication. SG express the highest TMPRSS2, and some shed epithelial cells express similar patterns, suggesting they may be shed from the SG ducts; no independent replication. Others express higher TMPRSS4, suggesting these cells may be from the suprabasal mucosa. c, Ciliated cells in saliva are exceedingly rare (α-tubulin + ) but can be present and infected; no independent replication. d, SARS-CoV-2 can be found to be associated with the diverse oral microbiome on shed epithelial cells; 1 independent replication. e, Using a salivary neutrophil atlas from healthy patients, we confirm that virtually no neutrophils express ACE2 or TMPRSS2. f-h, (f) Using cell blocks of heathy saliva from the NIH, we validate our findings that shed salivary epithelial (pan-cytokeratin positive; pCK + ) cells express both ACE2 and TMPRSS2; 1 independent replication. We see minimal to no expression of these SARS-CoV-2 entry factors in pCK⁻negative cells. g, These ACE2 + cells are also infected by SARS-CoV-2 and (h) able to replicate the virus (1 independent replication each). Red arrowheads in (a) indicate SARS-CoV-2 entry factors; in (g) SARS-CoV-2 infection; green arrowheads in (h) represent SARS-CoV-2 replication. Arrowheads in (h) indicate SARS-CoV-2 (red), universal 16 S probe (green) that are co-expressing (yellow); dotted lines (f) represent zoomed-in images. Scale bars: (a,b,d,g) 25 μm, (c,f,h) 10μm.