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

Sonia Burrel (1, 2) , Pierre Hausfater (3, 2, 4) , Martin Dres (5, 2, 2) , Valérie Pourcher (1, 2) , Charles-Edouard Luyt (3, 6, 2) , Elisa Teyssou (1, 2) , Cathia Soulié (1, 2) , Vincent Calvez (1, 2) , Anne-Geneviève Marcelin (1, 2) , David Boutolleau (1, 2)

1 iPLESP - Institut Pierre Louis d'Epidémiologie et de Santé Publique
2 CHU Pitié-Salpêtrière [AP-HP]
3 ICAN - Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases
4 GRC 14 - BIOSFAST - Groupe de recherche clinique Biomarqueurs d’urgence et de réanimation
5 UMRS 1158 - Neurophysiologie Respiratoire Expérimentale et Clinique
6 Institut de cardiologie [CHU Pitié-Salpêtrière]

Objectives: This study was performed 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. It also compared the diagnostic performances of upper respiratory tract (URT) and lower respiratory tract (LRT) samples for SARS-CoV-2 infection. Methods: From 25 January to 29 March 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 simultaneously tested 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 50 (range, 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% vs. 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 this epidemic period could not rule out SARS-CoV-2 co-infection. Furthermore, LRT samples increased the accuracy of diagnosis of COVID-19.

Mots clés: Co-infection; Lower respiratory tract; Other respiratory viruses; SARS-CoV-2

Domaines: Sciences du Vivant [q-bio]

Sonia Burrel, Pierre Hausfater, Martin Dres, Valérie Pourcher, Charles-Edouard Luyt, et al.. Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19. International Journal of Infectious Diseases, 2021, 102, pp.10 - 13. ⟨10.1016/j.ijid.2020.10.040⟩. ⟨hal-03105993⟩