How to Make the Most in Molecular Monitoring of Key Respiratory Viruses in Patients Cared in a Regional University Hospital, from the Period of COVID-19 Emergence

Author(s): Yasmina Sayed, Antoine Kimmoun, Véronique Venard, Eliane Albuisson, Raphaël E. Duval, Evelyne Schvoerer

For patients with lower respiratory tract infections, optimized molecular monitoring of key respiratory viruses along with the COVID-19 emergence is needed. The aims of this retrospective study were to investigate (i) epidemiological viral patterns among patients hospitalized for acute respiratory failure, (ii) the use of multiplex infectious respiratory PCR panel along with COVID-19, (iii) exemplary clinical scenarios within a subgroup of 18 patients in intensive care unit (ICU). From January 2021 to June 2022, during the very high SARS-CoV-2 circulation in France, 2,383 respiratory samples from 1,614 patients who underwent multiplex PCR were retrospectively analyzed in a regional university hospital, either a panel for upper respiratory tract samples (19 viruses/4 bacteria) or for the lower respiratory tract samples (8 viruses/18 bacteria). The ‘upper panel’ detected viruses in 45.5% of 990 samples, including enterovirus/rhinovirus (n=168) and SARS-CoV-2 (n=99), while the ‘lower panel’ showed positivity in 60.4% of 1,393 samples, including 9.6% that were positive for viruses alone. For the 18 well documented ICU patients with at least one virus in the lower panel, seven received direct antiviral treatment, mainly against influenza viruses. The main findings showed (i) the frequency of entero/rhinovirus infections, with severe clinical forms; (ii) the interest in expanded molecular detection of viral respiratory infections along with the SARS-CoV-2 emergence to learn about co-circulation of viruses in patients and their dissemination; (iii) the usefulness of syndromic panel-based assays in an exemplary ICU for adapted direct antiviral treatment.