An engineered CRISPR-Cas12a variant and DNA-RNA hybrid guides enable robust and rapid COVID-19 testing

Kean Hean Ooi, Mengying Mandy Liu, Jie Wen Douglas Tay, Seok Yee Teo, Pornchai Kaewsapsak, Shengyang Jin, Chun Kiat Lee, Jingwen Hou, Sebastian Maurer-Stroh, Weisi Lin, Benedict Yan, Gabriel Yan, Yong-Gui Gao and Meng How Tan ()
Additional contact information
Kean Hean Ooi: Nanyang Technological University
Mengying Mandy Liu: Nanyang Technological University
Jie Wen Douglas Tay: Nanyang Technological University
Seok Yee Teo: Nanyang Technological University
Pornchai Kaewsapsak: Genome Institute of Singapore, Agency for Science Technology and Research
Shengyang Jin: Nanyang Technological University
Chun Kiat Lee: National University Health System
Jingwen Hou: Nanyang Technological University
Sebastian Maurer-Stroh: Bioinformatics Institute, Agency for Science Technology and Research
Weisi Lin: Nanyang Technological University
Benedict Yan: National University Health System
Gabriel Yan: National University Hospital, National University Health System
Yong-Gui Gao: Nanyang Technological University
Meng How Tan: Nanyang Technological University

Nature Communications, 2021, vol. 12, issue 1, 1-23

Abstract: Abstract Extensive testing is essential to break the transmission of SARS-CoV-2, which causes the ongoing COVID-19 pandemic. Here, we present a CRISPR-based diagnostic assay that is robust to viral genome mutations and temperature, produces results fast, can be applied directly on nasopharyngeal (NP) specimens without RNA purification, and incorporates a human internal control within the same reaction. Specifically, we show that the use of an engineered AsCas12a enzyme enables detection of wildtype and mutated SARS-CoV-2 and allows us to perform the detection step with loop-mediated isothermal amplification (LAMP) at 60-65 °C. We also find that the use of hybrid DNA-RNA guides increases the rate of reaction, enabling our test to be completed within 30 minutes. Utilizing clinical samples from 72 patients with COVID-19 infection and 57 healthy individuals, we demonstrate that our test exhibits a specificity and positive predictive value of 100% with a sensitivity of 50 and 1000 copies per reaction (or 2 and 40 copies per microliter) for purified RNA samples and unpurified NP specimens respectively.

Date: 2021
References: Add references at CitEc
Citations: View citations in EconPapers (3)

Downloads: (external link)
https://www.nature.com/articles/s41467-021-21996-6 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21996-6

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-21996-6

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().