Scalable RT‐LAMP‐based SARS‐CoV‐2 testing for infection surveillance with applications in pandemic preparedness

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.

Democratizing nucleic acid-based molecular diagnostic tests for infectious diseases at resource-limited settings – from point of care to extreme point of care

“…Lou et al performed more than 35 000 such tests, establishing its capability to run amidst challenged supply chains. 154 Kundrod et al developed a quantitative sample-to-answer RT-LAMP test for detecting SARS-CoV-2 from saliva, nasal, or nasopharyngeal swabs, using an extraction-free simple lysis and sample deactivation protocol. 155 The authors piloted a University-wide surveillance testing program covering upto 400 human subjects per day.…”

Simple but powerful interactive data analysis in R with R/LinekdCharts

“…In this project, a colorimetric assay based on loop-mediated DNA amplification (LAMP, [35]) was carried out on microtiter plates. The app allowed lab technicians to inspect the measured change in pH as function of incubation time, to link curves to wells and to patients, to compare replicates, and to check and, if needed, amend automatic result calling (see [33] for details). Such continuous quality control is vital for reliable medical diagnostics and has to be offered in an easy-to-use manner and quick-to-grasp to avoid mistakes from repetition and fatigue.…”

“…Fig. 8 A screenshot of an app that was used as a GUI to perform manual inspection and classification of LAMP testing for SARS-CoV-2 viral RNA [32,33]. The app was used during our SARS-CoV-2 surveillance study [34] and for voluntary testing for COVID-19 infection on campus (University of Heidelberg) in 2020/2021.…”

Development of an extraction-free LAMP method for the generic detection of Orthopoxvirus and for the specific detection of Mpox virus

“…LAMP diagnostic assays have also been successfully used as a point-of-care diagnostic tool during the SARS-CoV-2 pandemic [20][21][22].…”