Unless working in a BSL-3 laboratory, COVID-19 patient samples should be treated to inactivate any potential viral contamination prior to working with them in a BSL-2 lab.  There are several validated virus inactivation methods reported in the literature, including heating at 56 oC for an hour, or treatment with certain chemical detergents.  Effective virus inactivation should be verified for whatever method is utilized.  The samples used in our assay were inactive with 4% Triton X-100 at RT for 5-10 min.  After sample collection, the iQue instrument automatically cleans itself by default after each run and at shutdown.  As with any flow cytometry system, the waste generated should be treated with a proper decontamination solution before disposal, and waste disposal should be done according to local regulations.