Table 2.
CRISPR-based diagnostics used in the context of malaria.
| End Point | Method (Cas enzyme, amplification) | Advantages | Limitations | Reference |
|---|---|---|---|---|
| Lateral Flow | SHERLOCK Version 2 (Cas13 RPA) | Similar sensitivity to RT-PCR methods but without the need for expensive thermocyclers; highly specific species delineation capabilities; can perform drug-resistance genotyping; potential for use in mosquitoes as well as in clinical samples | Not yet ready for wide-scale field use; requires higher crRNA concentrations than SHERLOCK in other pathogens; “one-pot” approach not yet achievable; assay design costs are high |
(Gootenberg et al., 2018; Kellner et al., 2019) |
| SHINE Cas13 RPA) | Single step tool with high sensitivity compared to RT-qPCR. Detects virus from unextracted samples. Reduced contamination risk as amplification reaction tubes remain sealed. |
Not yet validated with field samples | (Arizti-Sanz et al., 2020 | |
| STOPCovid (Cas12 LAMP) | Sensitivity of this tool is similar to RT-qPCR Appropriate for low-complexity clinical laboratories. |
Not yet validated with field samples | (Joung et al., 2020 | |
| Fluorescence/ Colorimetry |
SHERLOCK VERSION 1 (Cas9, RPA) | Similar sensitivity to RT-PCR methods but without the need for expensive thermocyclers; highly specific species delineation capabilities; can perform drug-resistance genotyping; potential for use in mosquitoes as well as in clinical samples | Not yet ready for wide-scale field use; requires higher crRNA concentrations than SHERLOCK in other pathogens; “one-pot” approach not yet achievable; assay design costs are high |
(Cunningham et al., 2021 |
| SHERLOCK version 2 (Cas13/RPA) | Multiplexable, portable, rapid, and quantitative detection platform of nucleic acids. | Not yet validated with field samples | (Gootenberg et al., 2018; Kellner et al., 2019) | |
| CARMEN (Cas13, PCR/RPA) | Detects all human-associated viruses with high sensitivity. Enables comprehensive subtyping of some viruses e.g. influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations |
Not yet validated with field samples | (Ackerman et al., 2020 | |
| NASBACC (Cas9/NASBA) | Can discriminate between viral strains with single base resolution | Long turnaround time Not yet validated with field samples Challenge in the sample preparation |
(Pardee et al., 2016 | |
| DETECTR | Higher sensitivity than SHERLOCK; functions in a single tube (“one-pot” approach); isothermal like SHERLOCK; all reaction components can be lyophilized (no need for refrigeration) | Not yet validated with field samples | (Lee et al., 2020 |