Multiplex rt-Real Time PCR assays for diagnostic testing of SARS-CoV-2 and seasonal influenza viruses. A challenge of the phase 3 pandemic setting.

BACKGROUND: Pandemic COVID-19 disease represents a challenge for health-care structures and the molecular confirmation of samples from infected individuals is crucial and therefore guides public health decision making. Clusters and possibly increased diffuse transmission could occur in the context of the next influenza season. For this reason, a diagnostic test able to discriminate SARS-CoV-2 from influenza viruses is urgently needed. METHODS: A multiplex rt-Real Time PCR assay was assessed using one laboratory protocol with different Real Time PCR instruments. Overall, 1,000 clinical samples (600 samples SARS-CoV-2 infected patients, 200 samples from influenza infected patients and 200 negative samples) were analyzed. RESULTS: The assay developed was able to detect and discriminate each virus target, and to intercept co-infections. The limit of quantification of each assay ranged between 5 and 10 genomic copy numbers, with a cutoff value of 37.7 and 37.8 for influenza and SARS-CoV-2 viruses, respectively. Only two influenza co-infections were detected in COVID-19 samples. CONCLUSIONS: This study suggests that multiplex assay is a rapid, valid, and accurate method for the detection of SARS-CoV-2 and influenza viruses in clinical samples. The test may be an important diagnostic tool for both diagnostic and surveillance purposes during the seasonal influenza activity period.