All adult patients hospitalized in a COVID-19 first-line hospital in Paris, France, from January 25, 2020, to April 30, 2020, were included. All patients were tested by systematic mPCR testing if they presented ILI symptoms, according to the eCDC definition, and required hospitalization. The two mPCR assays used during the study period, the QIAstat-Dx SARS-CoV-2 respiratory panel, Qiagen,8 and the BioFire FilmArray RP2+, BioMérieux,9 allow for detecting a wide range of viral and atypical bacterial respiratory targets, including influenza A and B, parainfluenza virus, rhinoviruses/enteroviruses, RSV, metapneumovirus, adenovirus, human coronaviruses (229E, HKU1, OC43, and NL63), Mycoplasma pneumoniae, and Bordetella pertussis. According to the French national definition, a specific SARS-CoV-2 RT-PCR for at-risk patients was performed, starting from March 10, 2020, when systematic testing for SARS-CoV-2 infection began. During this period, three SARS-CoV-2 RT-PCR assays were used: the WHO-recommended in-house RT-PCR assay, the RealStar® SARS-CoV-2 RT-PCR kit, and the Cobas® SARS-CoV-2 assay (Roche Diagnostics). All these assays provided similar performance and limit of detection.

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