Rapid detection of SARS-CoV-2 RNA in saliva via Cas13

Publication Date

8-1-2022

Document Type

Article

Publication Title

Nature Biomedical Engineering

Volume

6

Issue

8

DOI

10.1038/s41551-022-00917-y

First Page

944

Last Page

956

Abstract

Rapid nucleic acid testing is central to infectious disease surveillance. Here, we report an assay for rapid COVID-19 testing and its implementation in a prototype microfluidic device. The assay, which we named DISCoVER (for diagnostics with coronavirus enzymatic reporting), involves extraction-free sample lysis via shelf-stable and low-cost reagents, multiplexed isothermal RNA amplification followed by T7 transcription, and Cas13-mediated cleavage of a quenched fluorophore. The device consists of a single-use gravity-driven microfluidic cartridge inserted into a compact instrument for automated running of the assay and readout of fluorescence within 60 min. DISCoVER can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva with a sensitivity of 40 copies μl–1, and was 94% sensitive and 100% specific when validated (against quantitative PCR) using total RNA extracted from 63 nasal-swab samples (33 SARS-CoV-2-positive, with cycle-threshold values of 13–35). The device correctly identified all tested clinical saliva samples (10 SARS-CoV-2-positive out of 13, with cycle-threshold values of 23–31). Rapid point-of-care nucleic acid testing may broaden the use of molecular diagnostics.

Funding Number

N66001-20-2-4033

Funding Sponsor

National Science Foundation

Comments

Full author list: Sita S. Chandrasekaran, Shreeya Agrawal, Alison Fanton, Aditya R. Jangid, Bérénice Charrez, Arturo M. Escajeda, Sungmin Son, Roger Mcintosh, Huyen Tran, Abdul Bhuiya, María Díaz de León Derby, Neil A. Switz, Maxim Armstrong, Andrew R. Harris, Noam Prywes, Maria Lukarska, Scott B. Biering, Dylan C. J. Smock, Amanda Mok, Gavin J. Knott, Qi Dang, Erik Van Dis, Eli Dugan, Shin Kim, Tina Y. Liu, IGI Testing Consortium, Erica A. Moehle, Katherine Kogut, Brenda Eskenazi, Eva Harris, Sarah A. Stanley, Liana F. Lareau, Ming X. Tan, Daniel A. Fletcher, Jennifer A. Doudna, David F. Savage & Patrick D. Hsu

Department

Physics and Astronomy

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