Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic control

Throughout the current SARS-CoV-2 pandemic, limited diagnostic testing capacity prevented sentinel testing of the population, demonstrating the need for novel testing strategies and infrastructures. Here, we describe the set-up of an alternative testing platform, which allows scalable surveillance testing as an acute pandemic response tool and for pandemic preparedness purposes, exemplified by SARS-CoV-2 diagnostics in an academic environment. The testing strategy involves self-sampling based on gargling saline, pseudonymized sample handling, automated 96-well plate-based RNA extraction, and viral RNA detection using a semi-quantitative multiplexed colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with an analytical sensitivity comparable to RT-quantitative polymerase chain reaction (RT-qPCR). We provide standard operating procedures and an integrated software solution for all workflows, including sample logistics, LAMP assay analysis by colorimetry or by sequencing (LAMP-seq), and communication of results to participants and the health authorities. Using large sample sets including longitudinal sample series we evaluated factors affecting the viral load and the stability of gargling samples as well as the diagnostic sensitivity of the RT-LAMP assay. We performed >35,000 tests during the pandemic, with an average turnover time of fewer than 6 hours from sample arrival at the test station to result announcement. Altogether, our work provides a blueprint for fast, sensitive, scalable, cost- and labor-efficient RT-LAMP diagnostics. As RT-LAMP-based testing requires advanced, but non-specialized laboratory equipment, it is independent of potentially limiting clinical diagnostics supply chains. One-sentence summary A blueprint for scalable RT-LAMP test capacity for the sensitive detection of viral genomes demonstrated by SARS-CoV-2 surveillance testing. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Test development and validation was funded by the Ministry of Science Baden-Wuerttemberg. Testing for the Virusfinder study was embedded in the nationwide research network Applied Surveillance and Testing (Bundesweites Forschungsnetz Angewandte Surveillance und Testing, B-FAST) and the University Medicine Network (Netzwerk Universitaetsmedizin, NUM) for COVID-19 research. The trial was directly financed by the Federal Ministry of Education and Research (Bundesministerium fuer Bildung und Forschung, BMBF). As funding agency, the BMBF had no influence on study design, nor in collection, analysis and interpretation of data. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: For test development and validation, the trial was approved by the ethics committee of the Medical Faculty at the University of Heidelberg file number S-392/2020. For the Virusfinder study, the trial was approved by the ethics committee of the Medical Faculty at the University of Heidelberg on 02/11/2020, amendment 09/11/2020, file number S-790/2020. The study was conducted in accordance with the Declaration of Helsinki ethical standards. Participants provided consent online via the test station web site before sample and data collection. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present work are contained in the manuscript or upon reasonable request to the authors.