Table 1.

Various CRISPR-associated protein-based diagnostic platforms for virus diagnosis and their mode of detection.

Nuclease	Platform	Primary amplification method	Detection method	Mechanism	References
Cas9	NASBACC	NASBA	Electronic optical reader	PAM recognition and cleavage to activate Toehead switch	(Pardee et al., 2016)
	CRISDA	PCR	Fluorescence spectrophotometer	Cas9 creates nicks at the border and the target gene amplifies through external primers	(Zhou W. et al., 2018)
	CAS-EXPAR	EXPAR	Real-time fluoresces monitoring	Cas9 creates nicks and NEase produces ssDNA internal primers cyclically	(Huang et al., 2018)
	CASLFA	PCR	Paper-based LF device	Cas9/sgRNA complexes with target DNA and detected through AuNP-DNA probes	(Wang et al., 2020)
	FELUDA	RPA/PCR	Paper-based LF device	gRNA-dFnCas9 RNP complexes with target DNA and detected colorimetric LF device	(Azhar et al., 2020)
Cas12	DETECTR	LAMP	Paper-based LF device	Cas12a-crRNA complex binds and cleaves a dsDNA and detects fluorescence in collateral cleaved probe DNA	(Broughton et al., 2020)
	HOLMES	PCR	Fluorescence spectrophotometer	Cas12a-crRNA complex binds and cleaves a dsDNA and detects fluorescence in collateral cleaved probe DNA	(Li et al., 2018)
	HOLMESv2	LAMP	Fluorescence spectrophotometer	HOLMES upgraded; LAMP and Cas12b trans-cleavage integrated into one step	(Li et al., 2019)
	AIOD-CRISPR	PCR	LED blue light illuminator	One-pot collateral cleavage reaction system and colorimetric detection	(Ding et al., 2020)
	iSCAN	LAMP	Fluorescence visualization in UV light and LF device	CRISPR-Cas12a-based collateral cleavage and fluorescence-based detection	(Ali et al., 2020)
Cas13	SHERLOCK	RPA	Fluorescence spectrophotometer/ Paper based LF device	crRNA/Cas13 targets an ssRNA and cleaved fluorescent ssRNA probe collaterally	(Gootenberg et al., 2017; Kellner et al., 2020)
	SHERLOCKv2	RPA	LF device	Upgraded SHERLOCK; High quantification and sensitivity	(Gootenberg et al., 2018)
	CREST	RPA/PCR	Fluorescence spectrophotometer/Paper based LF device		(Rauch et al., 2020)
	CARMEN	PCR	Fluorescence spectrophotometer	SHERLOCK method in one array enables more than 4,500 nucleic acids.	(Ackerman et al., 2020)
	CARVER	PCR	Fluorescence spectrophotometer	Most advanced system to diagnose a sample using the SHERLOCK method, treat a viral infection, and measure the effectiveness of the treatment	(Freije et al., 2019)

CARMEN, Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids; CARVER, Cas13-assisted restriction of viral expression and readout; CREST, Cas13-based, Rugged, Equitable, Scalable Testing; CRISDA, CRISPR/Cas9-triggered nicking endonuclease-mediated strand displacement amplification; CRISPR, clustered regularly interspaced short palindromic repeats; DETECTR, DNA Endonuclease Targeted CRISPR Trans Reporter; FELUDA, FNCAS9 Editor-Linked Uniform Detection Assay; HOLMES, one-HOur Low-cost Multipurpose highly Efficient System; LAMP, loop-mediated isothermal amplification; PAM, protospacer adjacent motif; RNP, ribonucleoprotein; RPA, recombinase polymerase amplification; SHERLOCK, specific high-sensitivity enzymatic reporter unlocking.