Processing and analysis of Respiratory Samples
Respiratory samples were inactivated by incubation with a lysis buffer containing guanidinium thiocyanate in a biological safety cabinet for 10 minutes prior to analysis.  SARS-CoV-2 RNA testing was performed on the cobas SARS-CoV-2 6800 (Roche Molecular Systems, Branchburg, NJ) in accordance with the manufacturer’s instructions. A 0·6 mL aliquot of each sample was loaded onto the cobas 6800 where it was combined with the cobas SARS-CoV-2 master mix containing an internal RNA control primers, and probes targeting the ORF1/a nonstructural region that is specific for SARS-CoV-2 (target 1), as well as the conserved, structural protein envelope E gene that is shared by the Sarbecovirus subgenus (target 2).  Results were reported by the cobas SARS-CoV-2 test as either “detected” (targets 1 and 2 detected), “presumptive positive” (target 1 not detected; target 2 detected), or “not detected.”