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

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

doi:10.1038/s41587-021-00966-9

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

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

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58 Scopus citations

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.

Original language	English
Pages (from-to)	1556-1562
Number of pages	7
Journal	Nature Biotechnology
Volume	39
Issue number	12
DOIs	https://doi.org/10.1038/s41587-021-00966-9
State	Published - 1 Dec 2021
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Biomedical Engineering
Molecular Medicine

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41587-021-00966-9

Cite this

Ludwig, K. U., Schmithausen, R. M., Li, D., Jacobs, M. L., Hollstein, R., Blumenstock, K., Liebing, J., Słabicki, M., Ben-Shmuel, A., Israeli, O., Weiss, S., Ebert, T. S., Paran, N., Rüdiger, W., Wilbring, G., Feldman, D., Lippke, B., Ishorst, N., Hochfeld, L. M., ... Schmid-Burgk, J. L. (2021). LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding. Nature Biotechnology, 39(12), 1556-1562. https://doi.org/10.1038/s41587-021-00966-9

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title = "LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding",

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 \textasciitilde{}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.",

author = "Ludwig, \{Kerstin U.\} and Schmithausen, \{Ricarda M.\} and David Li and Jacobs, \{Max L.\} and Ronja Hollstein and Katja Blumenstock and Jana Liebing and Miko{\l}aj S{\l}abicki and Amir Ben-Shmuel and Ofir Israeli and Shay Weiss and Ebert, \{Thomas S.\} and Nir Paran and Wibke R{\"u}diger and Gero Wilbring and David Feldman and B{\"a}rbel Lippke and Nina Ishorst and Hochfeld, \{Lara M.\} and Beins, \{Eva C.\} and Kaltheuner, \{Ines H.\} and Maximilian Schmitz and Aliona W{\"o}hler and Manuel D{\"o}hla and Esther Sib and Marius Jentzsch and Borrajo, \{Jacob D.\} and Jonathan Strecker and Julia Reinhardt and Brian Cleary and Matthias Geyer and Michael H{\"o}lzel and Rhiannon Macrae and N{\"o}then, \{Markus M.\} and Per Hoffmann and Martin Exner and Aviv Regev and Feng Zhang and Schmid-Burgk, \{Jonathan L.\}",

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.",

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doi = "10.1038/s41587-021-00966-9",

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Ludwig, KU, Schmithausen, RM, Li, D, Jacobs, ML, Hollstein, R, Blumenstock, K, Liebing, J, Słabicki, M, Ben-Shmuel, A, Israeli, O, Weiss, S, Ebert, TS, Paran, N, Rüdiger, W, Wilbring, G, Feldman, D, Lippke, B, Ishorst, N, Hochfeld, LM, Beins, EC, Kaltheuner, IH, Schmitz, M, Wöhler, A, Döhla, M, Sib, E, Jentzsch, M, Borrajo, JD, Strecker, J, Reinhardt, J, Cleary, B, Geyer, M, Hölzel, M, Macrae, R, Nöthen, MM, Hoffmann, P, Exner, M, Regev, A, Zhang, F & Schmid-Burgk, JL 2021, 'LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding', Nature Biotechnology, vol. 39, no. 12, pp. 1556-1562. https://doi.org/10.1038/s41587-021-00966-9

TY - JOUR

T1 - LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding

AU - Ludwig, Kerstin U.

AU - Schmithausen, Ricarda M.

AU - Li, David

AU - Jacobs, Max L.

AU - Hollstein, Ronja

AU - Blumenstock, Katja

AU - Liebing, Jana

AU - Słabicki, Mikołaj

AU - Ben-Shmuel, Amir

AU - Israeli, Ofir

AU - Weiss, Shay

AU - Ebert, Thomas S.

AU - Paran, Nir

AU - Rüdiger, Wibke

AU - Wilbring, Gero

AU - Feldman, David

AU - Lippke, Bärbel

AU - Ishorst, Nina

AU - Hochfeld, Lara M.

AU - Beins, Eva C.

AU - Kaltheuner, Ines H.

AU - Schmitz, Maximilian

AU - Wöhler, Aliona

AU - Döhla, Manuel

AU - Sib, Esther

AU - Jentzsch, Marius

AU - Borrajo, Jacob D.

AU - Strecker, Jonathan

AU - Reinhardt, Julia

AU - Cleary, Brian

AU - Geyer, Matthias

AU - Hölzel, Michael

AU - Macrae, Rhiannon

AU - Nöthen, Markus M.

AU - Hoffmann, Per

AU - Exner, Martin

AU - Regev, Aviv

AU - Zhang, Feng

AU - Schmid-Burgk, Jonathan L.

PY - 2021/12/1

Y1 - 2021/12/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85109300289

U2 - 10.1038/s41587-021-00966-9

DO - 10.1038/s41587-021-00966-9

M3 - Article

C2 - 34188222

AN - SCOPUS:85109300289

SN - 1087-0156

VL - 39

SP - 1556

EP - 1562

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 12

ER -

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

Abstract

ASJC Scopus subject areas

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