S1 Table -

A) CT values from 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 150 NP swab samples representing high (CT values less than 20), intermediate (CT values of 20–30), or low (CT values of more than 30) SARS-CoV-2 RNA loads as determined by clinical RT-qPCR at UW in Seattle (labeled “original clinical RT-qPCR”) were analyzed by the indicated methods. Direct RT-qPCR was performed on 3 µl of NP swab diluent after heating for 10 minutes at 95°C or not. In parallel, RNA was extracted from 30 µl of NP swab diluent that had been previously heated at 95°C for 10 minutes or not, and RNA representing 3 µl of the original diluent was used in RT-qPCR to allow a head-to-head comparison with direct RT-qPCR on the same quantity of NP swab diluent. For selected samples (n = 100), 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 or not, 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.” Three separate experiments (50 NP swabs per experiment, 150 different samples total) were performed and are indicated. A subset of this data is linked to Fig 2. B) CT values from 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 150 NP swab samples representing high (CT values less than 20), intermediate (CT values of 20–30), or low (CT values of more than 30) SARS-CoV-2 RNA loads as determined by clinical RT-qPCR at UW in Seattle (labeled “original clinical RT-qPCR”) 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 or not. In parallel, RNA was extracted from 30 µl of NP swab diluent that had been previously heated at 95°C for 10 minutes or not, and RNA representing 3 µl of the original diluent was used in RT-qPCR to allow a head-to-head comparison with direct RT-qPCR on the same quantity of NP swab diluent. For selected samples (n = 100), 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 or not, 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.” Three separate experiments (50 NP swabs per experiment, 150 different samples total) were performed and are indicated. EXO, EXO primer/probe set; N1, 2019-nCoV_N1 primer/probe set; N2, 2019-nCoV_N2 primer/probe set; nd, not done.
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