FnCas9 Editor Linked Uniform Detection Assay for COVID-19

The recent COVID-19 outbreak and pandemic of 2020 and its surveillance were implemented by quickly adapting the existing diagnostic methods to detect the SARS-CoV-2 RNA. While traditional methods for detecting pathogenic DNA and RNA have relied heavily on gold standard quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and sequencing-based methods, their shortcomings under resource-limited settings have emphasized the need of developing point-of-care (POC) diagnostics. Clustered regularly interspaced short palindromic repeats (CRISPR)-based detection systems provide a rapid and accurate alternative. Here, we describe a CRISPR-Cas9-based detection system FnCas9 Editor Linked Uniform Detection Assay (FELUDA) using a lateral flow test that can detect nucleobase and nucleotide sequences depending upon the stoichiometric-based binding of FnCas9 ribonucleoprotein complex (RNP)-target sequences. The assay has been optimized to be conducted within 1 h and shows 100% sensitivity and 97% specificity in clinical samples across a range of viral loads. The lateral strip results are read using the True Outcome Predicted via Strip Evaluation (TOPSE) smartphone application. This assay is versatile and can be optimized and adjusted to target various diseases.

FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip

The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions. During the passage of the virus through affected populations, it has undergone mutations, some of which have recently been linked with increased viral load and prognostic complexities. Several of these variants are point mutations that are difficult to diagnose using the gold standard quantitative real-time PCR (qRT-PCR) method and necessitates widespread sequencing which is expensive, has long turn-around times, and requires high viral load for calling mutations accurately. Here, we repurpose the high specificity of Francisella novicida Cas9 (FnCas9) to identify mismatches in the target for developing a lateral flow assay that can be successfully adapted for the simultaneous detection of SARS-CoV-2 infection as well as for detecting point mutations in the sequence of the virus obtained from patient samples. We report the detection of the S gene mutation N501Y (present across multiple variant lineages of SARS-CoV-2) within an hour using lateral flow paper strip chemistry. The results were corroborated using deep sequencing on multiple wild-type (n = 37) and mutant (n = 22) virus infected patient samples with a sensitivity of 87% and specificity of 97%. The design principle can be rapidly adapted for other mutations (as shown also for E484K and T716I) highlighting the advantages of quick optimization and roll-out of CRISPR diagnostics (CRISPRDx) for disease surveillance even beyond COVID-19. This study was funded by Council for Scientific and Industrial Research, India.

CRISPR Cas9 based genome editing in inherited retinal dystrophies

BACKGROUND

Precision genome engineering, with targeted therapy towards patient-specific mutations is predicted to be the future of personalized medicine. Ophthalmology is in the frontiers of development of targeted therapy since the eye is an accessible organ and has the ease of both delivery as well as monitoring effects of therapy.

MATERIALS AND METHODS

We reviewed literature using keywords CRISPR, precision medicine, genomic editing, retinal dystrophies, retinitis pigmentosa, Usher syndrome, Stargardt's Disease. Further, we collated data on current clinical trials.

RESULTS

There is growing evidence on the role of genomic editing in retinal dystrophies, the various methods used, and stage of development of different therapies have been summarized in this paper.

CONCLUSIONS

The CRISPR-Cas9 system has revolutionized genome editing, and opened avenues in drug discovery. It is important to understand the role of this system along with its applicability in the field of ophthalmology. In this review article, we briefly describe its methodology, the strategies of employing it for making genetic perturbations, and explore its applications in inherited retinal dystrophies.