Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19

Burrel, Sonia; Hausfater, Pierre; Dres, Martin; Pourcher, Valérie; Luyt, Charles-Edouard; Teyssou, Elisa; Soulié, Cathia; Calvez, Vincent; Marcelin, Anne-Geneviève; Boutolleau, David

OBJECTIVES: We performed a study during the early outbreak period of coronavirus disease 2019 (COVID-19) and the seasonal epidemics of other respiratory viral infections in order to describe the extent of co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses. A second objective consisted in the comparison of the diagnostic performances of URT and LRT samples for SARS-CoV-2 infection and to compare diagnostic performances of upper and lower respiratory tract (URT and LRT) samples for SARS-CoV-2 infection. METHODS: From January 25(th) through March 29(th), 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were tested simultaneously for SARS-CoV-2 and other respiratory viruses. RESULTS: A total of 1423 consecutive patients were tested: 677 (47.6%) males, 746 (52.4%) females, median age of 50 [1-103] years. Twenty-one (1.5%) patients were positive for both SARS-CoV-2 and other respiratory viruses. The detection rate of SARS-CoV-2 was significantly higher in LRT than in URT (53.6% versus 13.4%; P < 0.0001). The analysis of paired samples from 117 (8.2%) patients showed that SARS-CoV-2 load was lower in URT than in LRT samples in 65% of cases. CONCLUSION: The detection of other respiratory viruses in patients during epidemic period cannot rule out SARS-CoV-2 co-infection. Furthermore, LRT samples increases the accuracy of diagnosis of COVID-19.