Detect and destroy: CRISPR-based technologies for the response against viruses

Abstract

Despite numerous viral outbreaks in the last decade, including a devastating global pandemic, diagnostic and therapeutic technologies remain severely lacking. CRISPR-Cas systems have the potential to address these critical needs in the response against infectious disease. Initially discovered as the bacterial adaptive immune system, these systems provide a unique opportunity to create programmable, sequence-specific technologies for detection of viral nucleic acids and inhibition of viral replication. This review summarizes how CRISPR-Cas systems—in particular the recently discovered DNA-targeting Cas12 and RNA-targeting Cas13, both possessing a unique trans -cleavage activity—are being harnessed for viral diagnostics and therapies. We further highlight the numerous technologies whose development has accelerated in response to the COVID-19 pandemic.

Biosafety materials: Ushering in a new era of infectious disease diagnosis and treatment with the CRISPR/Cas system

“…Cas13a is an RNA-guided RNA enzyme with CRISPR RNA (crRNA)-guided single-stranded RNA (ssRNA) cleavage activity [18] , [19] . In 2016, Cas13a was found to have target RNA triggering “side-chain cleavage” activity [20] .…”

Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses

“…With no HNH domain, Cas12a performs dsDNA cleavage using the endonuclease ability of the RuvC domain [ 254 ]. In addition to target cleavage, Cas12, unlike Cas9, also provides collateral cleavage activity (also referred to as trans -cleavage) on any ssDNA in the sample, a useful property in nucleic acid-based detection [ 255 ]. It enables a ssDNA reporter probe modified with fluorophore and quencher groups to be used to monitor an assay ( Fig.…”

“…Therefore, the Cas12a enzyme appears to be a better enzyme for amplification methods with lower operating temperatures, such as RPA [ 263 ], while Cas12b is suitable for LAMP [ 223 ]-based CRISPR/Cas systems. However, these subtypes and other enzymes and their thermal activity and performance largely depend on the microorganisms from which they are derived; thus, their operating temperatures and suitability for different isothermal amplifications can vary [ 255 , 269 , [272] , [273] , [274] ].…”

Structural principles of CRISPR-Cas enzymes used in nucleic acid detection

“…Such an immunity is achieved in a three-stage process: adaptation to infection by incorporation of new spacers derived from MGEs, processing of CRISPR RNA (crRNA) to yield mature guide RNA and interference against target DNA/RNA by CRISPR-Cas nucleases ( Barrangou, 2015 ; Sorek et al, 2013 ; Wright et al, 2016 ; Barrangou and Marraffini, 2014 ). The extraordinary programmability of the CRISPR-Cas effectors through crRNA has found convenient applications in genome editing, therapeutics and more recently, specific nucleic acid detections ( Barrangou and Doudna, 2016 ; Zhang, 2019 ; Freije and Sabeti, 2021 ; Wang et al, 2020 ).…”