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