CRISPR-Cas based virus detection: Recent advances and perspectives

Abstract

Viral infections are one of the most intimidating threats to human beings. One convincing example is the coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2. Rapid, sensitive, specific and field-deployable identification of causal viruses is critical for disease surveillance, control and treatment. The shortcomings of current methods create an impending need for developing novel biosensing platforms. CRISPR-Cas systems, especially CRISPR-Cas12a and CRISPR-Cas13a, characterized by their sensitivity, specificity, high base resolution and programmability upon nucleic acid recognition, have been repurposed for molecular diagnostics, surging a new path forward in biosensing. They, as the core of some robust diagnostic tools, are revolutionizing the way that virus can be detected. This review focuses on recent advances in virus detection with CRISPR-Cas systems especially CRISPR-Cas12a/Cas13a. We started with a short introduction to CRISPR-Cas systems and the properties of Cas12a and Cas13a effectors, and continued with reviewing the current advances of virus detection utilizing CRISPR-Cas systems. The significance and advantages of such methods were then discussed. Finally, the challenges and perspectives were proposed. We tried to provide readers with a concise profile of emerging and fast-expanding CRISPR-Cas based biosensing technology, and highlighted its potential applications in a range of scenarios with regard to virus detection.

Rapid and Ultrasensitive Detection of Methicillin-Resistant Staphylococcus aureus Based on CRISPR-Cas12a Combined With Recombinase-Aided Amplification

“…In recent years, emerging nucleic acid detection technologies based on CRISPR-Cas developments have opened up new opportunities for pathogen detection (Peng et al, 2020;Zhou et al, 2020;Yin et al, 2021). Compared to traditional assays, the CRISPR-Cas system has low requirements on sample quality and strong anti-interference ability and can be combined with rapid sample pretreatment technology to extract nucleic acids in the field without relying on professional equipment (Ding et al, 2021a).…”

CRISPR‐Cas‐based detection for food safety problems: Current status, challenges, and opportunities

“…More strikingly, apart from human‐to‐human transmission of some contaminants and diseases, the possibility of their transmission from contaminated cold‐chain food samples to humans has also been reported (Pang et al., 2020). Although SARS‐CoV‐2 is not considered a foodborne pathogen, this has led to new challenges in the food industry and food safety detection (Yin, Man, et al., 2021).…”

Applications of surface‐enhanced Raman spectroscopy in environmental detection

“…Currently, the main drawback of CRISPR/Cas biosensing is that samples require pre‐treatment or nucleic acid extraction, which may be difficult for on‐site analysis. Discovering ways to overcome this pre‐treatment step is an avenue for future work 222 . The amplification step, in particular, often requires equipment that is not practical for field work.…”

“…CRISPR/Cas technology, initially developed and popularized as a gene editing tool, has become increasingly common in biosensing due to its high sensitivity down to the level of single nucleic acids residues, and programmability to recognize certain nucleic acids. 222 aM for hepatitis and HPV 224 ). CRISPR/Cas12a has also been used in food authenticity screening, and this avenue in particular is especially promising for the detection of pathogens in environmental samples.…”