BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China as the cause of coronavirus disease 2019 in December 2019 and reached Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak . We validated the World Health Organization (WHO) -recommended SARS-CoV-2 assay and analyzed the epidemiology of SARS-CoV-2 and CARVs .
METHODS: Nasopharyngeal/oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by the Basel S-gene and WHO-based E-gene (Roche) assays in parallel using the Basel N-gene assay for confirmation . CARVs were prospectively tested in 2394 NOPS by multiplex nucleic acid testing, including 1816 (75 %) simultaneously for SARS-CoV-2 .
RESULTS: The Basel S-gene and Roche E-gene assays were concordant in 7475 cases (97.5 %) including 825 (11 %) SARS-CoV-2 positives . In 188 (2.5 %) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4 %). Adults were more frequently SARS-CoV-2 positive, whereas children tested more frequently CARV positive . CARV coinfections with SARS-CoV-2 occurred in 1.8% . SARS-CoV-2 replaced CARVs within 3 weeks, reaching 48% of all detected respiratory viruses followed by rhinovirus/enterovirus (13 %), influenza virus (12 %), coronavirus (9 %), respiratory syncytial virus (6 %), and metapneumovirus (6 %).
CONCLUSIONS: Winter CARVs were dominant during the early SARS-CoV-2 pandemic, impacting infection control and treatment decisions, but were rapidly replaced, suggesting competitive infection . We hypothesize that preexisting immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.