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

Keith Pardee; Alexander A Green; Melissa K Takahashi; Dana Braff; Guillaume Lambert; Jeong Wook Lee; Tom Ferrante; Duo Ma; Nina Donghia; Melina Fan; Nichole M Daringer; Irene Bosch; Dawn M Dudley; David H O'Connor; Lee Gehrke; James J Collins

doi:10.1016/j.cell.2016.04.059

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

Cell. 2016 May 19;165(5):1255-1266. doi: 10.1016/j.cell.2016.04.059. Epub 2016 May 6.

Authors

Affiliations

¹ Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.
² Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ 85287, USA.
³ Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁴ Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
⁵ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
⁶ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
⁷ Addgene, Cambridge, MA 02139, USA.
⁸ Wisconsin National Primate Research Center and Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53706, USA.
⁹ Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA.
¹⁰ Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: jimjc@mit.edu.

PMID: 27160350
DOI: 10.1016/j.cell.2016.04.059

Abstract

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. PAPERCLIP.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Blood / virology
Clustered Regularly Interspaced Short Palindromic Repeats
Computer Simulation
Dengue / diagnosis
Dengue / virology
Genetic Techniques
Macaca mulatta
Molecular Diagnostic Techniques / economics
Molecular Diagnostic Techniques / methods*
RNA, Viral / isolation & purification
Zika Virus / classification
Zika Virus / genetics
Zika Virus / isolation & purification*
Zika Virus Infection / diagnosis*
Zika Virus Infection / virology

Substances

RNA, Viral

Abstract

Publication types

MeSH terms

Substances

Grants and funding