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Marie-Pierre HAYETTE, The RT-PCR diagnostic platform of CHU Liège for the detection of SARS-CoV-2

" The University Hospital of Liège (CHULiège) has developed a diagnostic capability to detect the SARS-CoV-2 by RT-PCR in response to the need for more capacity testing in Belgium from March 2020. Indeed, from February 2020, clinical COVID-19 cases were already detected in Belgium thanks to the Reference laboratory for respiratory viruses in KULeuven (Reflab). However, it appeared rapidly evident that the capacity of the Reflab could not be further enhanced. Therefore Belgian university and non-university hospital laboratories started to develop RT-PCR assays which sensitivity were first validated by the Reflab. CHULiège developed an in house SARS-CoV-2 RT-PCR assay following an adapted version of the Charité Hospital (1) protocol with the aid of the Antwerp University Hospital Microbiology lab and the Reflab. We have chosen to include two targets: the E and RNA-dependent RNA polymerase (RdRP) genes. From the 6th March, we were able to run the test and since this date we run PCR assays every day including Saturday's and Sunday's. However, we rapidly understood that a more automated method would be necessary to absorb much more tests and we chose to contact Roche laboratories and asked for a solution. They proposed the cobas®6800 automated platform that is able to run theoretically more than 1000 tests a day. From the 25th March we use the Roche automate targeting the E and the ORF1ab genes with the CE-IVD cobas SARS-CoV-2 assay. However, due to the pandemic, Roche is obliged to limit the number of tests per laboratory and we can get a maximum of 500 tests per day. In consequence, we run in parallel the Roche method and the manual RT-PCR assay. Until 12th May, we have performed 22805 tests including 16% of positive results with a decrease of the positivity rate from 19% in March to 5% in May (Table 1). Our TAT is mostly within 24h and we are able to perform urgent tests with the Xpert® Xpress SARS-CoV-2 assay for preoperative assessments. Another challenging problem was a great shortage in collection devices, ie ideally nasopharyngeal swabs, in Belgium but also in many countries. In fact, the majority (> 90%) of the swabs used worldwide under different labels, are manufactured by a single Italian firm, Copan Italia, Brescia. In order to find some alternatives, we have been collaborating with Any-Shape SA (Flémalle, Belgium), a company dedicated to Additive Technologies for industry, for the design and development of alternative prototypes to Copan swabs. The technology used is Selective Laser Sintering (SLS) using Nylon. The final selected design, the "Fine Brush" 3D-printed swab has been validated in a clinical study conducted by our laboratory and the CHU of Liege. Their production has been authorized under dispensation from the Minister M.de Block (April 2020; MBD/2020-571391). The hospital Pharmacy of CHULiège sterilizes the swabs individually packed in pouch and prepares AMIES preservative liquid for the transportation of the clinical samples. Volunteers of CIRM research center organize the preparation of PCR kits by assembling one swab and one tube containing the preservative liquid. This is a real human chain that is deployed against the COVID-19 pandemic. We had also a lot of volunteers coming from other laboratories of the Unilab for helping us to run this large amount of PCR tests. Furthermore, the IT services played an essential role in implementing rapid solutions to optimize the reporting results. Regarding the inclusion criteria for PCR testing, they have been changed many times by Sciensano and we run currently PCR tests for hospitalized patients including patients from symptomatic healthcare nurses but also for symptomatic patients sent via their general practitioner. A drive-in, the Depist-Car, has been organized since 5th May on two sites of the CHU Liège, Sart Tilman hospital and Notre-Dame des Bruyères site, in order to receive and screen patients sent by their GP. But many other sampling sites have been opened to facilitate the regional territory covering. This will contribute to the tracing of infected people for whom contact details and symptoms are directly sent by the GP to the e-health platform of the federal Belgian government. All detected people will be contacted by a call center and contacts will be also traced. This will permit the detection of pauci-symptomatic persons that can still disseminate the virus. In conclusion, our laboratory has rapidly answered to the need for more testing capacity since early March 2020 by using an automated platform that allows large testing volumes. Our laboratory technicians are motivated by this new working capacity even if they must work during the week-ends. The COVID-19 pandemic has transformed our personal life but has also provided more flexibility and team working. "
Publication References: 1. Corman V. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eur Surveill 2020. Jan;25(3). doi: 10.2807/1560-7917.ES.2020.25.3.2000045
Contact: Molecular biology laboratory team: Marie-Pierre Hayette, Cécile Meex, Sébastien Bontems, Raphaël Boreux, Pierrette Melin. CHU Liège, Sart Tilman hospital, B-4000 Liège.

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Brussels & Wallonia against COVID19