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Table 1 Pros and cons of CRISPR-based assay for infectious disease. Adapted from James P. Broughton  et. al., 2020, Nature biotechnology, CRISPR–Cas12-based detection of SARS-CoV-2

From: CRISPR-Based Diagnosis of Infectious and Noninfectious Diseases

  SARS-CoV-2
DETECTR, RT–LAMP/Cas12
CDC SARS-CoV-2
qRT–PCR
Target E gene and N genea N gene (three amplicons, N1, N2 and N3)
Sample control RNase P RNase P
LoD 10 copies per μl input 1 copy per μl inputb and 3.2 copies per μl inputc
Assay reaction time (approximate) 30–40 min 120 min
Assay sample-to-result time (approximate) 45 min (with manual RNA extraction) 4 h (including RNA extraction)
Assay results Qualitative Quantitative
Assay components RT–LAMP (62 °C, 20–30 min) Cas12
(37 °C, 10 min) Lateral flow strip (RT, 2 min; no additional time if using
fluorescence readout)
UDG digestion (25 °C, 2 min), reverse transcription (50 °C, 15 min), denature (95 °C, 2 min) amplification, (95 °C, 3 s; 55 °C 30 s; 45 cycles)
Bulky instrumentation
required
No Yes
US FDA EUA approval Pending clinical validation Yes
  1. a: E gene primers target the same amplicon region as in the WHO protocol; N gene primers target the same N2 amplicon region as in the CDC protocol. UDG, uracil-DNA glycosylase
  2. b: Limit of detection confirmation CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel with QIAGEN QIAmp DSP Viral RNA Mini Kit6
  3. C: Limit of detection confirmation of the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel with QIAGEN EZ1 DSP6