LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding.

Ludwig, Kerstin U; Schmithausen, Ricarda M; Li, David; Jacobs, Max L; Hollstein, Ronja; Blumenstock, Katja; Liebing, Jana; Słabicki, Mikołaj; Ben-Shmuel, Amir; Israeli, Ofir; Weiss, Shay; Ebert, Thomas S; Paran, Nir; Rüdiger, Wibke; Wilbring, Gero; Feldman, David; Lippke, Bärbel; Ishorst, Nina; Hochfeld, Lara M; Beins, Eva C; Kaltheuner, Ines H; Schmitz, Maximilian; Wöhler, Aliona; Döhla, Manuel; Sib, Esther; Jentzsch, Marius; Borrajo, Jacob D; Strecker, Jonathan; Reinhardt, Julia; Cleary, Brian; Geyer, Matthias; Hölzel, Michael; Macrae, Rhiannon; Nöthen, Markus M; Hoffmann, Per; Exner, Martin; Regev, Aviv; Zhang, Feng; Schmid-Burgk, Jonathan L

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 ~2.2 molecules per µl 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.