Journal
NATURE BIOTECHNOLOGY
Volume 39, Issue 12, Pages 1556-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41587-021-00966-9
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Funding
- Deutsche Forschungsgemeinschaft (DFG) [EXC2151 -390873048]
- DFG [GE 976/9-2, LU1944/3-1]
- Federal Ministry for Education and Research [01KX2021]
- Klarman Incubator
- National Institutes of Health [1R01-HG009761, 1R01-MH110049, 1DP1-HL141201]
- Harold G. and Leila Mathers Foundation
- Patrick J. McGovern Foundation
- Open Philanthropy Project
- Poitras Center for Psychiatric Disorders Research at MIT
- Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT
- Phillips family
- Howard Hughes Medical Institute
- Howard Hughes Medical Institute Gilliam Fellowship
- Edward Mallinckrodt, Jr. Foundation
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Frequent and fast testing with high sensitivity and specificity, low cost, and easy deployment make LAMP-Seq a promising tool for integrated public health surveillance programs in containing COVID-19 outbreaks.
Frequent testing of large population groups combined with contact tracing and isolation measures will be crucial for containing Coronavirus Disease 2019 outbreaks. Here we present LAMP-Seq, a modified, highly scalable reverse transcription loop-mediated isothermal amplification (RT-LAMP) method. Unpurified biosamples are barcoded and amplified in a single heat step, and pooled products are analyzed en masse by sequencing. Using commercial reagents, LAMP-Seq has a limit of detection of similar to 2.2 molecules per mu l at 95% confidence and near-perfect specificity for severe acute respiratory syndrome coronavirus 2 given its sequence readout. Clinical validation of an open-source protocol with 676 swab samples, 98 of which were deemed positive by standard RT-qPCR, demonstrated 100% sensitivity in individuals with cycle threshold values of up to 33 and a specificity of 99.7%, at a very low material cost. With a time-to-result of fewer than 24 h, low cost and little new infrastructure requirement, LAMP-Seq can be readily deployed for frequent testing as part of an integrated public health surveillance program.
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