Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components

Keith Pardee et al. Cell, Volume 165, Issue 5, p1255–1266, 19 May 2016

Highlights

• A portable, low-cost diagnostic platform for the detection of Zika virus
• Discrimination of viral strains at single-base resolution using a CRISPR-based tool
• Low femtomolar detection of Zika virus from infected monkey plasma
• Programmable sensor development workflow for rapid responses to global epidemics 

Summary

The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises.