Fig. 1

LAMP-BEAC: RT-LAMP assayed using molecular beacons. a Product from a LAMP reaction is depicted emphasizing its loop region which forms single-stranded loops during amplification along with an example molecular beacon in its annealed hairpin form, which is quenched. Binding of the beacon to the target complementary sequence LAMP amplicon separates the fluorescent group and the quencher, allowing detection of fluorescence. The red loops on the beacon indicate locked nucleic acids used to increase binding affinity. b A genome map of SARS-CoV-2 showing the locations of primer binding sites for the LAMP primer sets used in this study. c Example of visual detection of LAMP-BEAC fluorescence using an orange filter with blue illumination. Multiplexed SARS-CoV-2-targeted Penn and human control STATH primer sets were used to amplify samples consisting of water or inactivated saliva with or without synthetic SARS-CoV-2 RNA (10,000 copies per reaction). Molecular beacons Penn_LF_S1 conjugated to a FAM fluorophore fluorescing green and Stath_LB_S2 conjugated to Cy3 fluorescing yellow were included in the reaction. The image was captured using the “Night Sight” mode of a Google Pixel 2 cell phone