Results
3768 patients were included during the study period, 1906 from the ED and 1862 other inpatients. Overall, 806 (21%), 755 (20%), and 28 (1%) samples were positive for SARS-CoV-2, any other respiratory viruses, or atypical bacteria, respectively. The SARS-CoV-2 wave struck from February to April with a peak incidence between mid-March and early-April. At this time, rhinoviruses, human coronaviruses, adenoviruses, or parainfluenza viruses were still circulating, but most of the seasonal respiratory virus epidemic was already gone, especially influenza (cf Figure 1). Among the 806 SARS-CoV-2-positive patients, 42 (5%), 7 (1%), and 6 (1%) also presented one, two other viruses and atypical bacteria, respectively, and 61 (8%) non-SARS-CoV-2 patients positive by mPCR showed viral co-infections. Most frequently associated viruses were rhinoviruses (17), common human coronaviruses (15), adenoviruses (7), parainfluenza (5), metapneumoviruses (4), influenza (4), and RSV (2) and other pathogens (7). The temporal distribution of pathogens is depicted below (Figure). When comparing ED patients with SARS-CoV-2 either alone (n= 249) or associated (n=33) , they presented similar age, symptoms, vital signs measurements, or comorbidities, except for fever (p=0.013) and headaches (p=0.048). Among those co-infected patients, 0 (0%) were hospitalized in ICU at day 1 versus 64/249 (26%) patients with only a SARS-CoV2 infection, p=0.78. 5 (2%) among the co-infected patients died during hospitalization, and 49 (20%) with only a SARS-CoV2 infection, p=0.78.