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Frequent testing of large population groups combined with contact tracing and isolation measures will be crucial for containing COVID-19 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 ~2.2 molecules/µl at 95% confidence, and near-perfect specificity for SARS-CoV-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 Ct values up to 33, and a specificity of 99.7%, at material cost of 2.73 USD per sample. With a time-to-result less than 24 hours, 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.