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

COVID-19 / diagnosis COVID-19 Testing / methods Humans Molecular Diagnostic Techniques / methods Nucleic Acid Amplification Techniques / methods

Journal

Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648

Informations de publication

Date de publication:
12 2021
Historique:
received: 20 10 2020
accepted: 26 05 2021
pubmed: 1 7 2021
medline: 24 12 2021
entrez: 30 6 2021
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1038/s41587-021-00966-9 PMID: 34188222 PMC: PMC8678193
pubmed: 34188222
doi: 10.1038/s41587-021-00966-9
pii: 10.1038/s41587-021-00966-9
pmc: PMC8678193
mid: NIHMS1724088
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1556-1562

Subventions

Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : LU-1944/3-1
Organisme : NIMH NIH HHS
ID : R01 MH110049
Pays : United States
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : EXC2151 - 390873048
Organisme : Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)
ID : 01KX2021
Organisme : NHLBI NIH HHS
ID : DP1 HL141201
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG009761
Pays : United States

Commentaires et corrections

Type : ErratumIn

Informations de copyright

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

Références

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Auteurs

Kerstin U Ludwig (KU)

Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.

Ricarda M Schmithausen (RM)

Institute of Hygiene and Public Health, University of Bonn and University Hospital Bonn, Bonn, Germany.
ORCID: 0000-0002-3736-8672

David Li (D)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

Max L Jacobs (ML)

Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany.
Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
ORCID: 0000-0001-5665-9339

Ronja Hollstein (R)

Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.

Katja Blumenstock (K)

Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Jana Liebing (J)

Institute of Experimental Oncology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Mikołaj Słabicki (M)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.
ORCID: 0000-0001-6317-9296

Amir Ben-Shmuel (A)

Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.

Ofir Israeli (O)

Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.

Shay Weiss (S)

Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.

Thomas S Ebert (TS)

Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Nir Paran (N)

Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
ORCID: 0000-0001-5143-9660

Wibke Rüdiger (W)

Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Gero Wilbring (G)

Institute of Hygiene and Public Health, University of Bonn and University Hospital Bonn, Bonn, Germany.
ORCID: 0000-0002-5770-0054

David Feldman (D)

Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.

Bärbel Lippke (B)

Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.

Nina Ishorst (N)

Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.
Institute of Anatomy, Division of Neuroanatomy, University of Bonn and University Hospital Bonn, Bonn, Germany.

Lara M Hochfeld (LM)

Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.
ORCID: 0000-0002-2808-0693

Eva C Beins (EC)

Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.
ORCID: 0000-0002-7779-0210

Ines H Kaltheuner (IH)

Institute of Structural Biology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Maximilian Schmitz (M)

Institute of Structural Biology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Aliona Wöhler (A)

Department of General, Visceral and Thoracic Surgery, Bundeswehr Central Hospital Koblenz, Koblenz, Germany.

Manuel Döhla (M)

Institute of Hygiene and Public Health, University of Bonn and University Hospital Bonn, Bonn, Germany.
Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, Koblenz, Germany.
ORCID: 0000-0001-8029-5264

Esther Sib (E)

Institute of Hygiene and Public Health, University of Bonn and University Hospital Bonn, Bonn, Germany.

Marius Jentzsch (M)

Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Eva-Maria C Moench (EC)

MVZ Laboratory, Dr. Quade and Associates, Cologne, Germany.

Jacob D Borrajo (JD)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

Jonathan Strecker (J)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

Julia Reinhardt (J)

Institute of Experimental Oncology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Brian Cleary (B)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
ORCID: 0000-0003-0825-7129

Matthias Geyer (M)

Institute of Structural Biology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Michael Hölzel (M)

Institute of Experimental Oncology, University of Bonn and University Hospital Bonn, Bonn, Germany.

Rhiannon Macrae (R)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
ORCID: 0000-0002-7850-9056

Markus M Nöthen (MM)

Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.

Per Hoffmann (P)

Institute of Human Genetics, University of Bonn and University Hospital Bonn, Bonn, Germany.
Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.
ORCID: 0000-0002-6573-983X

Martin Exner (M)

Institute of Hygiene and Public Health, University of Bonn and University Hospital Bonn, Bonn, Germany.

Aviv Regev (A)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Klarman Cell Observatory, Massachusetts Institute of Technology, Cambridge, MA, USA.
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA.
Genentech, South San Francisco, CA, USA.
ORCID: 0000-0003-3293-3158

Feng Zhang (F)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA.
ORCID: 0000-0003-0178-7995

Jonathan L Schmid-Burgk (JL)

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA. jonathan.schmid-burgk@ukbonn.de.
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA. jonathan.schmid-burgk@ukbonn.de.
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. jonathan.schmid-burgk@ukbonn.de.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. jonathan.schmid-burgk@ukbonn.de.
Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany. jonathan.schmid-burgk@ukbonn.de.
ORCID: 0000-0003-0988-2487

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Classifications MeSH

Recherchemedicale.com › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › LAMP-Seq enables sensitive, multiplexed...
Recherchemedicale.com › Techniques d'investigation › Techniques de laboratoire clinique › Dépistage de la COVID-19 › LAMP-Seq enables sensitive, multiplexed...
Recherchemedicale.com › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › LAMP-Seq enables sensitive, multiplexed...
Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Techniques de diagnostic moléculaire › LAMP-Seq enables sensitive, multiplexed...
Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Techniques d'amplification d'acides nucléiques › LAMP-Seq enables sensitive, multiplexed...