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Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic preparedness.
Lou, Dan; Meurer, Matthias; Ovchinnikova, Svetlana; Burk, Robin; Denzler, Anna; Herbst, Konrad; Papaioannou, Ioannis A; Duan, Yuanqiang; Jacobs, Max L; Witte, Victoria; Ürge, Daniel; Kirrmaier, Daniel; Krogemann, Michelle; Gubicza, Krisztina; Boerner, Kathleen; Bundschuh, Christian; Weidner, Niklas M; Merle, Uta; Knorr, Britta; Welker, Andreas; Denkinger, Claudia M; Schnitzler, Paul; Kräusslich, Hans-Georg; Dao Thi, Viet Loan; De Allegri, Manuela; Nguyen, Hoa Thi; Deckert, Andreas; Anders, Simon; Knop, Michael.
  • Lou D; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Meurer M; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Ovchinnikova S; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Burk R; Bioquant Center, Heidelberg University, Heidelberg, Germany.
  • Denzler A; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Herbst K; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Papaioannou IA; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Duan Y; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Jacobs ML; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Witte V; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Ürge D; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Kirrmaier D; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Krogemann M; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Gubicza K; German Cancer Research Center (DKFZ), Heidelberg, Germany.
  • Boerner K; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Bundschuh C; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
  • Weidner NM; German Cancer Research Center (DKFZ), Heidelberg, Germany.
  • Merle U; Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany.
  • Knorr B; Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany.
  • Welker A; Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany.
  • Denkinger CM; Department of Gastroenterology, Heidelberg University Hospital, Heidelberg, Germany.
  • Schnitzler P; Landratsamt Rhein-Neckar-Kreis, Gesundheitsamt, Heidelberg, Germany.
  • Kräusslich HG; Landratsamt Rhein-Neckar-Kreis, Gesundheitsamt, Heidelberg, Germany.
  • Dao Thi VL; Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany.
  • De Allegri M; German Center for Infection Research (DZIF), Heidelberg, Germany.
  • Nguyen HT; Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany.
  • Deckert A; Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany.
  • Anders S; German Center for Infection Research (DZIF), Heidelberg, Germany.
  • Knop M; German Center for Infection Research (DZIF), Heidelberg, Germany.
EMBO Rep ; 24(5): e57162, 2023 05 04.
Article in English | MEDLINE | ID: covidwho-2269718
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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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Observational study / Prognostic study Limits: Humans Language: English Journal: EMBO Rep Journal subject: Molecular Biology Year: 2023 Document Type: Article Affiliation country: Embr.202357162

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Observational study / Prognostic study Limits: Humans Language: English Journal: EMBO Rep Journal subject: Molecular Biology Year: 2023 Document Type: Article Affiliation country: Embr.202357162