Colorimetric RT-LAMP and LAMP-sequencing forDetecting SARS-CoV-2 RNA in Clinical Samples

Konrad Herbst; Matthias Meurer; Daniel Kirrmaier; Simon Anders; Michael Knop; Viet Loan Dao Thi

doi:10.21769/BioProtoc.3964

Colorimetric RT-LAMP and LAMP-sequencing forDetecting SARS-CoV-2 RNA in Clinical Samples

Bio Protoc. 2021 Mar 20;11(6):e3964. doi: 10.21769/BioProtoc.3964.

Authors

Konrad Herbst¹, Matthias Meurer¹, Daniel Kirrmaier², Simon Anders¹, Michael Knop^{1

2

3}, Viet Loan Dao Thi⁴

Affiliations

¹ Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
² German Cancer Research Center (DKFZ), Heidelberg, Germany.
³ DKFZ-ZMBH Alliance, Heidelberg, Germany.
⁴ Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany.

Abstract

During pandemics, such as the one caused by SARS-CoV-2 coronavirus, simple methods to rapidly test large numbers of people are needed. As a faster and less resource-demanding alternative to detect viral RNA by conventional qPCR, we used reverse transcription loop-mediated isothermal amplification (RT-LAMP). We previously established colorimetric RT-LAMP assays on both purified and unpurified SARS-CoV-2 clinical specimens and further developed a multiplexed sequencing protocol (LAMP-sequencing) to analyze the outcome of many RT-LAMP reactions at the same time (Dao Thi et al., 2020). Extending on this work, we hereby provide step-by-step protocols for both RT-LAMP assays and read-outs.

Keywords: LAMP-sequencing; RT-LAMP; SARS-CoV-2 detection; Tn5 tagmentation; colorimetric assay.