Abstract: The invention describes a kit for detection of a target polynucleotide using a CRISPR effector system that comprises CAS9 from Francisella novicida, a synthetic sgRNA and a detection scheme based on binding and subsequent enzymatic cleavage of the target polynucleotide. The invention also describes a method for detection of a target polynucleotide using the kit. The kit can be el applied to both pathogenic and non-pathogenic polynucleotides and can be used to distinguish polynucleotides different by a single mismatch without the need for sequencing. The kit can also be used for detection of COVID-19. The kit is economical, easy to assemble and provides a robust and rapid readout that can be appropriately adapted for point of care applications.