FLUORESCENCE IN SITU HYBRIDIZATION

Fluorescence in situ hybridization (FISH) was performed as we described previously¹ using the fixed frozen tissue protocol for the RNAscope Multiplex Fluorescent Detection Reagents v2 kit (Cat# 323110, Advanced Cell Diagnostics). Cataloged RNAscope probes were from Advanced Cell Diagnostics (Table S5). The probes to SARS-CoV-2 spike (S) antisense detecting the presence of the viral particles and open reading frame 1ab (ORF1ab) sense detecting the replicating virus were validated on sections from healthy fungiform papillae biopsied before March 2020, which showed no amplification or fluorescence.¹ Sections incubated with the positive control probes targeting RNA polymerase II subunit A (POLR2A), peptidylprolyl isomerase B (PPIB), and ubiquitin C (UBC) and the negative control probe targeting the bacterial gene bacillus subtilis dihydrodipicolinate reductase (Dapb) from Advanced Cell Diagnostics were included in each FISH experiment.