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.