Comparing the technical performances of three real-time PCRs to counteract the COVID-19 outbreak in Luxembourg

The outbreak of SARS-CoV-2 infections has underlined the critical value of laboratory diagnosis in order to quickly identify infected-patients, to provide optimized care, and to limit coronavirus transmission. Several real-time RT-PCR diagnostic assays were rapidly developed, in particular by pharmaceutical companies which were Conformité Européenne (CE) marked. However, recent data suggest a poor reliability of the diagnostic results that may result from improper or insufficient sample collection, sub-optimal real-time PCR conditions, or personnel operation. The World Health Organization has already warned on PCR assay compatibility that could change overtime in the long run. This is particularly the case for commercially manufactured kits, which may be less likely to have published primer/probe sequences. Since all countries are currently facing reagent shortages that limit the testing capacity, several real-time PCR assays were established to counteract the COVID-19 outbreak by using different techniques and suppliers in Luxembourg. Few of them have been fully evaluated or compared to each other by independent laboratories, especially in various respiratory sample matrice or in alternative sample types such as stool, urine or serum. In addition, minimal handling of the samples will be required to ensure the diagnostic of large cohorts of patients. Optimized Real-Time PCR methods without RNA extraction need therefore to be set-up and validated.
As a response to the currently ongoing pandemic spread, the present COMPARE proposal, which is embedded in WP04 “Diagnostic capacity and large-scale testing strategies for Luxembourg” of the COVID-19 Task Force of Research Luxembourg , aims to:
1) evaluate and compare three real-time PCR techniques established in Luxembourg in terms of sensitivity,specificity, accuracy, and precision
2) evaluate RNA extraction and RT-PCRs for alternative samples considered in diagnostic and research settings
3) develop and validate an assay without RNA extraction to test large cohorts of patients such as for the the Convince and Predi-Covid studies performed in Luxembourg.
The results of this study will provide evidence to the national public health authorities whether the techniques used in the country provide similar technical performances and comparable results as well as to to provide technical evidence for alternative large scale testing strategies.