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

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Nat Biotechnol


. 2021 Jun 29.
doi: 10.1038/s41587-021-00966-9. Online ahead of print.
LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding


Kerstin U Ludwig ¹ , Ricarda M Schmithausen ² , David Li ^{3 4 5 6} , Max L Jacobs ^{7 8} , Ronja Hollstein ¹ , Katja Blumenstock ⁷ , Jana Liebing ⁹ , Mikołaj Słabicki ^{3 10 11} , Amir Ben-Shmuel ¹² , Ofir Israeli ¹³ , Shay Weiss ¹² , Thomas S Ebert ⁷ , Nir Paran ¹² , Wibke Rüdiger ⁷ , Gero Wilbring ² , David Feldman ¹⁴ , Bärbel Lippke ¹ , Nina Ishorst ^{1 15} , Lara M Hochfeld ¹ , Eva C Beins ¹ , Ines H Kaltheuner ¹⁶ , Maximilian Schmitz ¹⁶ , Aliona Wöhler ¹⁷ , Manuel Döhla ^{2 18} , Esther Sib ² , Marius Jentzsch ⁷ , Jacob D Borrajo ^{3 6} , Jonathan Strecker ^{3 4 5 6} , Julia Reinhardt ⁹ , Brian Cleary ³ , Matthias Geyer ¹⁶ , Michael Hölzel ⁹ , Rhiannon Macrae ^{3 4 5 6} , Markus M Nöthen ¹ , Per Hoffmann ^{1 19} , Martin Exner ² , Aviv Regev ^{3 20 21 22 23 24} , Feng Zhang ^{3 4 5 6 23} , Jonathan L Schmid-Burgk ^{25 26 27 28 29}



Affiliations

• PMID: 34188222
• DOI: 10.1038/s41587-021-00966-9

Abstract

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.