Field-deployable viral diagnostics using CRISPR-Cas13

Cameron Myhrvold; Catherine A Freije; Jonathan S Gootenberg; Omar O Abudayyeh; Hayden C Metsky; Ann F Durbin; Max J Kellner; Amanda L Tan; Lauren M Paul; Leda A Parham; Kimberly F Garcia; Kayla G Barnes; Bridget Chak; Adriano Mondini; Mauricio L Nogueira; Sharon Isern; Scott F Michael; Ivette Lorenzana; Nathan L Yozwiak; Bronwyn L MacInnis; Irene Bosch; Lee Gehrke; Feng Zhang; Pardis C Sabeti

doi:10.1126/science.aas8836

Field-deployable viral diagnostics using CRISPR-Cas13

Science. 2018 Apr 27;360(6387):444-448. doi: 10.1126/science.aas8836.

Authors

Cameron Myhrvold^{1

2}, Catherine A Freije^{1

2

3}, Jonathan S Gootenberg^{4

5

6

7

8}, Omar O Abudayyeh^{4

6

7

8

9}, Hayden C Metsky^{4

10}, Ann F Durbin^{3

11}, Max J Kellner⁴, Amanda L Tan¹², Lauren M Paul¹², Leda A Parham¹³, Kimberly F Garcia¹³, Kayla G Barnes^{4

2

14}, Bridget Chak^{4

2}, Adriano Mondini¹⁵, Mauricio L Nogueira¹⁶, Sharon Isern¹², Scott F Michael¹², Ivette Lorenzana¹³, Nathan L Yozwiak^{4

2}, Bronwyn L MacInnis^{4

14}, Irene Bosch^{11

17}, Lee Gehrke^{3

11

18}, Feng Zhang^{4

6

7

8}, Pardis C Sabeti^{1

2

3

14

19}

Affiliations

¹ Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. pardis@broadinstitute.org cmyhrvol@broadinstitute.org cfreije@broadinstitute.org.
² Center for Systems Biology, Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
³ Ph.D. Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA.
⁴ Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.
⁵ Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
⁶ McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA.
⁷ Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA.
⁸ Department of Biological Engineering, MIT, Cambridge, MA 02139, USA.
⁹ Department of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA.
¹⁰ Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA.
¹¹ Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA.
¹² Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA.
¹³ Centro de Investigaciones Genética, Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras.
¹⁴ Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA.
¹⁵ Araraquara Laboratory of Public Health, School of Pharmaceutical Sciences, São Paulo State University, São Paulo, Brazil.
¹⁶ Laboratorio de Pesquisas em Virologia, Faculdade de Medicina de Sao Jose do Rio Preto, São Paulo, Brazil.
¹⁷ Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA.
¹⁸ Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
¹⁹ Howard Hughes Medical Institute (HHMI), Chevy Chase, MD 20815, USA.

Abstract

Mitigating global infectious disease requires diagnostic tools that are sensitive, specific, and rapidly field deployable. In this study, we demonstrate that the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015-2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms.

Publication types

Evaluation Study
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adaptation, Physiological / genetics
Bacterial Proteins / chemistry*
CRISPR-Associated Proteins / chemistry*
Dengue / diagnosis*
Dengue Virus / genetics
Dengue Virus / isolation & purification*
Endonucleases / chemistry*
Enzyme Assays*
Humans
Microcephaly / diagnosis
Microcephaly / virology
Polymorphism, Single Nucleotide
RNA, Viral / analysis*
Zika Virus / genetics
Zika Virus / isolation & purification*
Zika Virus Infection / diagnosis*

Substances

Bacterial Proteins
CRISPR-Associated Proteins
RNA, Viral
Endonucleases

Abstract

Publication types

MeSH terms

Substances

Grants and funding