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Lou D, Meurer M, Ovchinnikova S, Burk R, Denzler A, Herbst K, Papaioannou IA, Duan Y, Jacobs ML, Witte V, Ürge D, Kirrmaier D, Krogemann M, Gubicza K, Boerner K, Bundschuh C, Weidner NM, Merle U, Knorr B, Welker A, Denkinger CM, Schnitzler P, Kräusslich HG, Dao Thi VL, De Allegri M, Nguyen HT, Deckert A, Anders S, Knop M. Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic preparedness. EMBO Rep 2023; 24:e57162. [PMID: 36951170 PMCID: PMC10157315 DOI: 10.15252/embr.202357162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/24/2023] Open
Abstract
Throughout the SARS-CoV-2 pandemic, limited diagnostic capacities prevented sentinel testing, demonstrating the need for novel testing infrastructures. Here, we describe the setup of a cost-effective platform that can be employed in a high-throughput manner, which allows surveillance testing as an acute pandemic control and preparedness tool, exemplified by SARS-CoV-2 diagnostics in an academic environment. The strategy involves self-sampling based on gargling saline, pseudonymized sample handling, automated RNA extraction, and viral RNA detection using a semiquantitative multiplexed colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with an analytical sensitivity comparable with RT-qPCR. We provide standard operating procedures and an integrated software solution for all workflows, including sample logistics, analysis by colorimetry or sequencing, and communication of results. We evaluated factors affecting the viral load and the stability of gargling samples as well as the diagnostic sensitivity of the RT-LAMP assay. In parallel, we estimated the economic costs of setting up and running the test station. We performed > 35,000 tests, with an average turnover time of < 6 h from sample arrival to result announcement. Altogether, our work provides a blueprint for fast, sensitive, scalable, cost- and labor-efficient RT-LAMP diagnostics, which is independent of potentially limiting clinical diagnostics supply chains.
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Affiliation(s)
- Dan Lou
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Matthias Meurer
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Svetlana Ovchinnikova
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Robin Burk
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Anna Denzler
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Konrad Herbst
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | | | - Yuanqiang Duan
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Max L Jacobs
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Victoria Witte
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Daniel Ürge
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Daniel Kirrmaier
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle Krogemann
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Krisztina Gubicza
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kathleen Boerner
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Christian Bundschuh
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Niklas M Weidner
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Uta Merle
- Department of Gastroenterology, Heidelberg University Hospital, Heidelberg, Germany
| | - Britta Knorr
- Landratsamt Rhein-Neckar-Kreis, Gesundheitsamt, Heidelberg, Germany
| | - Andreas Welker
- Landratsamt Rhein-Neckar-Kreis, Gesundheitsamt, Heidelberg, Germany
| | - Claudia M Denkinger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Paul Schnitzler
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Viet Loan Dao Thi
- German Center for Infection Research (DZIF), Heidelberg, Germany
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Manuela De Allegri
- Heidelberg Institute of Global Health, University Hospital and Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Hoa Thi Nguyen
- Heidelberg Institute of Global Health, University Hospital and Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Andreas Deckert
- Heidelberg Institute of Global Health, University Hospital and Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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