ABSTRACT
The lack of preparedness for detecting and responding to the SARS-CoV-2 pathogen (i.e. COVID-19) has caused enormous harm to public health and the economy. Testing strategies deployed on a population scale at ‘Day Zero', i.e., the time of the first reported case, would be of significant value. Next Generation Sequencing (NGS) has such capabilities;however, it has limited detection sensitivity for low copy number pathogens. Here we leverage the CRISPR-Cas9 system to effectively remove abundant sequences not contributing to pathogen detection and show that NGS detection sensitivity of SARS-CoV-2 approaches that of RT-qPCR. The resulting sequence data can also be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single molecular and analysis workflow. This NGS workflow is pathogen agnostic and, therefore, has the potential to transform how large-scale pandemic response and focused clinical infectious disease testing are pursued in the future. Graphical Next generation sequencing could provide ‘Day Zero' testing for pandemic preparedness however, abundant uninformative sequences mask the signal from low level pathogens. Chan et al. establish a method using the CRISPR-Cas system to remove uninformative sequences in vitro to achieve sensitivity and specificity of pathogen detection comparable to RT-qPCR.