Fig. 6: Detection of SARS-CoV-2 using suboptimal PAM-mediated one-pot reaction.
a, Numbers of canonical PAM (TTTV) and suboptimal PAM (VTTV, TTVV, TCTV) spacers in SARS-CoV-2. b–e, Detection limits of sPAMC (b,d) at 42 °C and STOPCovid.v1 (c,e) at 60 °C on DNA (left) and RNA (right). Fluorescence values at 15 min in sPAMC and 60 min in STOPCovid.v1 are shown in b and c, respectively, and the relevant fluorescence curves were shown in d and e. The numbers of molecules inputted in sPAMC and STOPCovid.v1 were the same. Mean ± s.d. of n = 3 technical replicates for b and c. f, sPAMC results for 204 SARS-CoV-2 nasopharyngeal swab samples (left, 104 positive samples, 48 unextracted samples marked by solid circle and 56 pre-extracted samples marked by hollow circle; right, 100 negative samples). The fluorescence readout was measured at 20 min at 42 °C. The threshold was determined as 3× the average of all samples’ initial fluorescence values, at a signal-to-noise ratio of 3. g, Direct visualization under UV light to detect unextracted SARS-CoV-2 positive samples. The reaction was examined under UV light at 10, 15 and 20 min after incubation at 42 °C. h, Concordance table between sPAMC and RT–qPCR for 204 samples.
