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LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding

View ORCID ProfileJonathan L. Schmid-Burgk, View ORCID ProfileRicarda M. Schmithausen, David Li, Ronja Hollstein, Amir Ben-Shmuel, Ofir Israeli, Shay Weiss, Nir Paran, Gero Wilbring, Jana Liebing, David Feldman, Mikołaj Słabicki, Bärbel Lippke, Esther Sib, Jacob Borrajo, Jonathan Strecker, Julia Reinhardt, Per Hoffmann, Brian Cleary, Michael Hölzel, View ORCID ProfileMarkus M. Nöthen, Martin Exner, Kerstin U. Ludwig, Aviv Regev, Feng Zhang
doi: https://doi.org/10.1101/2020.04.06.025635
Jonathan L. Schmid-Burgk
1Broad Institute of MIT and Harvard Cambridge, MA 02142, USA
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
8Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
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  • ORCID record for Jonathan L. Schmid-Burgk
  • For correspondence: jschmid@broadinstitute.org
Ricarda M. Schmithausen
9Institute of Hygiene and Public Health, University Hospital Bonn, 53127 Bonn, Germany
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  • ORCID record for Ricarda M. Schmithausen
David Li
1Broad Institute of MIT and Harvard Cambridge, MA 02142, USA
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Ronja Hollstein
10Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
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Amir Ben-Shmuel
12Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
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Ofir Israeli
13Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
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Shay Weiss
12Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
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Nir Paran
12Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
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Gero Wilbring
9Institute of Hygiene and Public Health, University Hospital Bonn, 53127 Bonn, Germany
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Jana Liebing
11Institute for Experimental Oncology, University Hospital Bonn, 53127 Bonn, Germany
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David Feldman
14Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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Mikołaj Słabicki
1Broad Institute of MIT and Harvard Cambridge, MA 02142, USA
15Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
16Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
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Bärbel Lippke
10Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
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Esther Sib
9Institute of Hygiene and Public Health, University Hospital Bonn, 53127 Bonn, Germany
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Jacob Borrajo
1Broad Institute of MIT and Harvard Cambridge, MA 02142, USA
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Jonathan Strecker
1Broad Institute of MIT and Harvard Cambridge, MA 02142, USA
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Julia Reinhardt
11Institute for Experimental Oncology, University Hospital Bonn, 53127 Bonn, Germany
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Per Hoffmann
10Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
17Genomics Research Group, Department of Biomedicine, University of Basel, Switzerland
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Brian Cleary
1Broad Institute of MIT and Harvard Cambridge, MA 02142, USA
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Michael Hölzel
11Institute for Experimental Oncology, University Hospital Bonn, 53127 Bonn, Germany
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Markus M. Nöthen
10Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
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  • ORCID record for Markus M. Nöthen
Martin Exner
9Institute of Hygiene and Public Health, University Hospital Bonn, 53127 Bonn, Germany
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Kerstin U. Ludwig
10Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
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Aviv Regev
1Broad Institute of MIT and Harvard Cambridge, MA 02142, USA
5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
6Klarman Cell Observatory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
7Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
18Howard Hughes Medical Institute, Cambridge, MA 02139, USA
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Feng Zhang
1Broad Institute of MIT and Harvard Cambridge, MA 02142, USA
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
18Howard Hughes Medical Institute, Cambridge, MA 02139, USA
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  • Abstract
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Summary

The ongoing SARS-CoV-2 pandemic has already caused devastating losses. Exponential spread can be slowed by social distancing and population-wide isolation measures, but those place a tremendous burden on society, and, once lifted, exponential spread can re-emerge. Regular population-scale testing, combined with contact tracing and case isolation, should help break the cycle of transmission, but current detection strategies are not capable of such large-scale processing. Here we present a protocol for LAMP-Seq, a barcoded Reverse-Transcription Loop-mediated Isothermal Amplification (RT-LAMP) method that is highly scalable. Individual samples are stabilized, inactivated, and amplified in three isothermal heat steps, generating barcoded amplicons that can be pooled and analyzed en masse by sequencing. Using unique barcode combinations per sample from a compressed barcode space enables extensive pooling, potentially further reducing cost and simplifying logistics. We validated LAMP-Seq on 28 clinical samples, empirically optimized the protocol and barcode design, and performed initial safety evaluation. Relying on world-wide infrastructure for next-generation sequencing, and in the context of population-wide sample collection, LAMP-Seq could be scaled to analyze millions of samples per day.

Competing Interest Statement

J.S.-B., D.L., and F.Z. are inventors on a patent application filed by the Broad Institute related to this work with the specific aim of ensuring this technology can be made freely, widely, and rapidly available for research and deployment. F.Z. is a co-founder of Editas Medicine, Beam Therapeutics, Pairwise Plants, Arbor Biotechnologies, and Sherlock Biosciences. A.R. is a founder of Celsius Therapeutics, equity holder in Immunitas, and an SAB member for ThermoFisher Scientific, Syros Pharmaceuticals, Asimov, and Neogene Therapeutics. P.H. and M.M.N. are SAB members of HMG Systems Bioengineering GmbH. M.M.N. served on SABs for Lundbeck Foundation and Robert-Bosch-Stiftung, was reimbursed travel expenses by Shire GmbH, receives salary from and holds shares in Life & Brain GmbH.

Footnotes

  • ↵19 Lead Contact

  • NOTE: This protocol has not been approved for use with clinical samples. To facilitate collaborations with interested parties to jointly advance the fight against the current coronavirus pandemic, we have set up a public forum on www.LAMP-Seq.org.

  • The updated manuscript provides clinical validation data, protocol optimizations, and a novel barcoding scheme.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 08, 2020.
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LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding
Jonathan L. Schmid-Burgk, Ricarda M. Schmithausen, David Li, Ronja Hollstein, Amir Ben-Shmuel, Ofir Israeli, Shay Weiss, Nir Paran, Gero Wilbring, Jana Liebing, David Feldman, Mikołaj Słabicki, Bärbel Lippke, Esther Sib, Jacob Borrajo, Jonathan Strecker, Julia Reinhardt, Per Hoffmann, Brian Cleary, Michael Hölzel, Markus M. Nöthen, Martin Exner, Kerstin U. Ludwig, Aviv Regev, Feng Zhang
bioRxiv 2020.04.06.025635; doi: https://doi.org/10.1101/2020.04.06.025635
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LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding
Jonathan L. Schmid-Burgk, Ricarda M. Schmithausen, David Li, Ronja Hollstein, Amir Ben-Shmuel, Ofir Israeli, Shay Weiss, Nir Paran, Gero Wilbring, Jana Liebing, David Feldman, Mikołaj Słabicki, Bärbel Lippke, Esther Sib, Jacob Borrajo, Jonathan Strecker, Julia Reinhardt, Per Hoffmann, Brian Cleary, Michael Hölzel, Markus M. Nöthen, Martin Exner, Kerstin U. Ludwig, Aviv Regev, Feng Zhang
bioRxiv 2020.04.06.025635; doi: https://doi.org/10.1101/2020.04.06.025635

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