02716nas a2200313   4500008004100000022001400041245011400055210006900169260000900238300001100247490000700258520169700265100001701962700001801979700002201997700002002019700002202039700001602061700002002077700002202097700002002119700002002139700003302159700001502192700001902207700001802226700002702244856013102271       2021                        eng d  a2050-084X00aFnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip0 aFnCas9based CRISPR diagnostic for rapid and accurate detection o  cJUN   ae671300 v103 aThe 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.1 aKumar, Manoj1 aGulati, Sneha1 aAnsari, Asgar, H.1 aPhutela, Rhythm1 aAcharya, Sundaram1 aAzhar, Mohd1 aMurthy, Jayaram1 aKathpalia, Poorti1 aKanakan, Akshay1 aMaurya, Ranjeet1 aVasudevan, Janani, Srinivasa1 aAparna, S.1 aPandey, Rajesh1 aMaiti, Souvik1 aChakraborty, Debojyoti  uhttps://library.ncl.res.in/content/fncas9-based-crispr-diagnostic-rapid-and-accurate-detection-major-sars-cov-2-variants-paper