Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants

The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid...

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Published inNature biomedical engineering Vol. 6; no. 8; pp. 932 - 943
Main Authors Arizti-Sanz, Jon, Bradley, A'Doriann, Zhang, Yibin B, Boehm, Chloe K, Freije, Catherine A, Grunberg, Michelle E, Kosoko-Thoroddsen, Tinna-Solveig F, Welch, Nicole L, Pillai, Priya P, Mantena, Sreekar, Kim, Gaeun, Uwanibe, Jessica N, John, Oluwagboadurami G, Eromon, Philomena E, Kocher, Gregory, Gross, Robin, Lee, Justin S, Hensley, Lisa E, MacInnis, Bronwyn L, Johnson, Jeremy, Springer, Michael, Happi, Christian T, Sabeti, Pardis C, Myhrvold, Cameron
Format Journal Article
LanguageEnglish
Published England Nature Publishing Group 01.08.2022
Subjects
Acids
Ambient temperature
Assaying
Cold storage
Coronaviruses
COVID-19 - diagnosis
COVID-19 - virology
COVID-19 Testing
CRISPR-Associated Proteins
Deactivation
Humans
Nucleic Acids
Polymerase chain reaction
Reagents
Reverse transcription
SARS-CoV-2 - classification
SARS-CoV-2 - genetics
SARS-CoV-2 - isolation & purification
Severe acute respiratory syndrome coronavirus 2
Viral diseases
Visual discrimination
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Summary:The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
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J.A.-S. and C.A.F. conceived this study under the guidance of P.C.S. and C.M. J.A.-S., A.B., C.K.B, C.A.F., M.E.G., T.-S.F.K.-T. and G.K. performed initial experiments to improve the SHINE technology. G.K. and R.G. performed viral inactivation experiments under the guidance of L.E.H. J.A-S., A.B., C.K.B. and M.E.G performed experiments and data analysis related to the S gene assay and the development of SHINEv.2. J.N.U., P.E.E. and O.G.J. performed SHINEv.2 experiments in Nigeria under the supervision of C.T.H. J.A.-S., A.B., N.L.W., P.P.P. and S.M. designed and/or tested SHINEv.2 assays for SARS-CoV-2 variant detection. J.S.L. assisted in patient sample collection. J.A.-S. and A.B. performed and analysed experiments with patient samples. Y.B.Z. designed and validated Cas12-based SHINEv.2 assays. L.E.H., B.L.M., J.J., M.S. and C.T.H. provided critical insights on protocols, the experimental results and the work overall. J.A.-S. wrote the paper with guidance from P.C.S. and C.M. P.C.S and C.M. jointly supervised the project. All authors reviewed the manuscript.
Author contributions
ISSN:2157-846X
2157-846X
DOI:10.1038/s41551-022-00889-z