A protocol for the detection of SARS-CoV-2 from saliva samples featuring a rapid purification step and a highcontrast colorimetric readout. Saliva is first inactivated using a 100x inactivation reagent consisting of 2.5M TCEP, 100 mM EDTA, 1.2N NaOH solution diluted to approximately 1x final concentration and heated to 95C for 5 minutes. RNA is rapidly purified and concentrated with magnetic beads in a PEG/NaCl-based buffer using a 3Dprinted magnetic stick that enables selective separation of beads without carryover of saliva contaminants. Beads are eluted directly into an RT-LAMP reaction mix, which uses a novel high contrast dye that turns from purple to clear when acidified by nucleic acid amplification products that enables unambiguous identification of successful amplification. This protocol is sensitive down to 1 copy/µl of SARS-CoV-2 in 300 µl of saliva. This degree of sensitivity enables faithful detection of SARS-CoV-2 even in pooled samples.
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