Blueprint for a Pop-up SARS-CoV-2 Testing Lab

Jennifer A. Doudna

is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.04.11.20061424 doi: medRxiv preprint Supplementary Figure 3 . Clinical validation assay using leftover samples from Kaiser Permanente -one of duplicate PCR plates. The results from the corresponding duplicate PCR plate are shown in Figure 5 . Undetermined Ct values are plotted as Ct = 0. A : Ten known positive and ten known negative patient samples in UTM leftover from Kaiser Permanente's clinical testing facility were delivered to Sarah Stanley's BSL-3 lab at UC Berkeley where they were inactivated by diluting 1:1 in 2X DNA/RNA Shield. Decontaminated tubes were delivered to IGIB where they entered our testing pipeline, starting with arraying into 96-deep-well plates using the Hamilton STARlet robot. B : Assay quality controls. Full workflow controls were processed starting at RNA extraction in the 96-well plates. RNA extraction control is composed of Thermo Fisher's MS2 control in 1X DNA/RNA shield and PBS. Human RNA controls are composed of 200 ng/ml purified RNA from 293T cells in 1X DNA/RNA shield and PBS. PCR controls were processed starting at assembling RT-qPCR reactions and include a water control, and the Thermo Fisher kit positive SARS-CoV-2 RNA control (without MS2). The second RNA extract control from the left returned two high Ct values and one undetermined value for SARS-CoV-2. Based on our decision matrix criteria for resulting (Table 2) , this control returns a NEG result (positive for only 1 SARS-CoV-2 gene). While this meets our acceptance criteria, we expect that there may have been some cross contamination from neighboring wells during sealing and unsealing of the plate during an unexpected instrument calibration step.