SARS-CoV-2 RT-PCR
The test was performed on the DiaSorin Molecular Simplexa COVID-19 Direct (https://www.fda.gov/media/136286/download) under an FDA EUA for BAL samples. Fifty microliters of the sample were directly analyzed, without a separate extraction step, for 2 different targets - SARS-CoV-2 orf1a/b  and S  genes. The instrument provides the Ct value (number of PCR cycles required to amplify the targeted viral material to a detectable level). We used the Ct value as surrogate for the amount of virus present in BAL specimens. Tests were run on fresh BAL samples immediately after the bronchoscopy, except for three subjects who had their samples frozen at -800C prior to testing.