S2 Table -

A) CT values from COVID-19 patient NP swabs or non-COVID-19 patient NP swabs following direct RT-qPCR versus standard RT-qPCR for SARS-CoV-2 RNA detection that included RNA extraction. A total of 90 NP swab samples representing low SARS-CoV-2 RNA loads (CT values of 27 to 36) or non-detected (i.e., negative) SARS-COV-2 RNA as determined by clinical RT-qPCR at UW in Seattle (labeled “original clinical RT-qPCR”) were analyzed by the indicated methods to establish the limit of detection and specificity of the direct RT-qPCR method. Direct RT-qPCR was performed on 3 µl of NP swab diluent after heating for 10 minutes at 95°C. In parallel, RNA was extracted from 200 µl of NP swab diluent (per the UW standard clinical protocol) that had been previously heated at 95°C, and RNA representing 20 µl of the original diluent was used in RT-qPCR. Samples below the limit of detection (CT of 40 or more) are designated “NEG.” These data are linked to Fig 3. B) CT values from COVID-19 patient NP swabs or non-COVID-19 patient NP swabs following direct RT-qPCR versus standard RT-qPCR for EXO RNA that was spiked into the swab diluent. A total of 90 NP swab samples representing low SARS-CoV-2 RNA loads (CT values of 27 to 36) or non-detected (i.e., negative) SARS-COV-2 RNA as determined by clinical RT-qPCR at UW in Seattle were analyzed by the indicated methods. For the donors indicated, an aliquot of swab diluent was spiked with 4 × 104 copies of EXO control RNA prior to RNA extraction or direct addition of sample to the RT-qPCR reaction for subsequent detection with an EXO primer/probe set. Direct RT-qPCR was performed on 3 µl of NP swab diluent after heating for 10 minutes at 95°C. In parallel, RNA was also extracted from 200 µl of NP swab diluent (per the UW standard clinical protocol) that had been previously heated at 95°C for 10 minutes, and RNA representing 20 µl of the original diluent was used in RT-qPCR. Samples below the limit of detection (CT of 40 or more) are designated “NEG.” EXO, EXO primer/probe set; N2, 2019-nCoV_N2 primer/probe set.
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