A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness

Cell Rep Methods. 2023 Apr 18;3(5):100463. doi: 10.1016/j.crmeth.2023.100463. eCollection 2023 May 22.

Abstract

The lack of preparedness for detecting and responding to the severe acute respiratory syndrome coronavirus 2 (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 work flow 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.

Keywords: CRISPR; NGS; infectious disease; metatranscriptomics; pathogen detection.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • COVID-19* / diagnosis
  • Communicable Diseases*
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Pandemics
  • SARS-CoV-2 / genetics