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Ludwig KU, Schmithausen RM, Li D, et al. LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding. Nat Biotechnol. 2021;39(12):1556-1562doi: 10.1038/s41587-021-00966-9.
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., Beins, E. C., Kaltheuner, I. H., Schmitz, M., Wöhler, A., Döhla, M., Sib, E., Jentzsch, M., Borrajo, J. D., Strecker, J., Reinhardt, J., Cleary, B., Geyer, M., Hölzel, M., Macrae, R., Nöthen, M. M., Hoffmann, P., Exner, M., Regev, A., Zhang, F., & 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
Ludwig, Kerstin U, et al. "LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding." Nature biotechnology vol. 39,12 (2021): 1556-1562. doi: https://doi.org/10.1038/s41587-021-00966-9
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. LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding. Nat Biotechnol. 2021 Dec;39(12):1556-1562. doi: 10.1038/s41587-021-00966-9. Epub 2021 Jun 29. PMID: 34188222; PMCID: PMC8678193.
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Nat Biotechnol. 2021 Dec;39(12):1556-1562. doi: 10.1038/s41587-021-00966-9. Epub 2021 Jun 29.

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

Nature biotechnology

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

Affiliations

  1. Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.
  2. Institute of Hygiene and Public Health, University of Bonn and University Hospital Bonn, Bonn, Germany.
  3. Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
  4. McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
  5. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
  6. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
  7. Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany.
  8. Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  9. Institute of Experimental Oncology, University of Bonn and University Hospital Bonn, Bonn, Germany.
  10. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  11. Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.
  12. Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  13. Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
  14. Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
  15. Institute of Anatomy, Division of Neuroanatomy, University of Bonn and University Hospital Bonn, Bonn, Germany.
  16. Institute of Structural Biology, University of Bonn and University Hospital Bonn, Bonn, Germany.
  17. Department of General, Visceral and Thoracic Surgery, Bundeswehr Central Hospital Koblenz, Koblenz, Germany.
  18. Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, Koblenz, Germany.
  19. Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.
  20. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
  21. Klarman Cell Observatory, Massachusetts Institute of Technology, Cambridge, MA, USA.
  22. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
  23. Howard Hughes Medical Institute, Cambridge, MA, USA.
  24. Genentech, South San Francisco, CA, USA.
  25. Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
  26. McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
  27. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
  28. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
  29. Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany. [email protected].

PMID: 34188222 PMCID: PMC8678193 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.

© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

References

  1. Nucleic Acids Res. 2000 Jun 15;28(12):E63 - PubMed
  2. Structure. 1997 Jan 15;5(1):95-108 - PubMed
  3. MMWR Morb Mortal Wkly Rep. 2021 Jan 22;70(3):100-105 - PubMed
  4. Chem Biol. 2001 Jan;8(1):1-7 - PubMed
  5. Sci Adv. 2021 Feb 12;7(7): - PubMed
  6. Clin Chem. 2021 Jan 30;67(2):415-424 - PubMed
  7. Chem Commun (Camb). 2014 Apr 11;50(28):3747-9 - PubMed
  8. JAMA. 2020 Apr 14;323(14):1406-1407 - PubMed
  9. Lancet Infect Dis. 2020 May;20(5):533-534 - PubMed
  10. Mol Cell Probes. 2002 Jun;16(3):223-9 - PubMed
  11. BMJ. 2020 Mar 22;368:m1163 - PubMed
  12. Diagn Microbiol Infect Dis. 2018 May;91(1):6-12 - PubMed
  13. J Infect Chemother. 2009 Apr;15(2):62-9 - PubMed
  14. Euro Surveill. 2020 Jan;25(3): - PubMed
  15. Sci Transl Med. 2020 Aug 12;12(556): - PubMed
  16. Science. 2021 Jan 8;371(6525):126-127 - PubMed
  17. Sci Rep. 2020 Dec 10;10(1):21759 - PubMed
  18. Nat Biotechnol. 2020 Jul;38(7):870-874 - PubMed

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