Discussion
This work highlights that 6% of SARS-CoV-2-infected patient presented with viral co-infection at our adult ED. This proportion is higher than previously reported for SARS-CoV-2 [6] but at a level similar to the other respiratory viruses[12]. This high prevalence of viral co-infections was observed, despite the limited circulation of other respiratory viruses due to lockdown, curfew, and being in the tail of the season of respiratory viruses [7]. Rhinoviruses, adenoviruses, and other coronaviruses were the most frequently detected viruses with SARS-CoV-2. Adenoviruses and rhinoviruses have already been reported, outside the scope of SARS-CoV-2, as being more frequently involved in viral co-infection, contrary to influenza viruses [13].
In our population, only 6 patients with SARS-CoV-2 were also infected with atypical bacteria. Co-infections can lead to viral interference, one virus limiting or suppressing the replication of the second virus, or to an enhancement of disease severity compared to mono-infection [14]. In our cohort, patients presenting with viral co-infections with SARS-CoV-2 had similar clinical pictures, except for headache and fever, and prognosis than patients solely infected with SARS-CoV-2.
Our study presents several strengths and limitations. It showed a relatively large number of SARS-CoV-2 co-infections compared to previous works [4–7] and linked virological data with detailed clinical data. Syndromic mPCR testing was performed on all patients presenting with ILI during the study period. Thus patients recruited in this observational study are not skewed towards more severe patients and represent all adult patients hospitalised for ILI. However, our study is monocentric, and the SARS-CoV-2 epidemic flared in Ile-de-France when the incidence of most respiratory viruses was waning. Prevalence of viral co-infections with SARS-CoV-2 might be higher in settings with an active circulation of respiratory viruses and/or once social distancing will be over. We also cannot rule out that some specific co-infections might have a deleterious impact, notably SARS-CoV-2/influenza, as only 4 were detected during our study period. Higher severity of SARS-CoV-2/influenza A H1N1pdm2009 has recently been described in golden Syrian hamsters when the two viruses were simultaneously inoculated [15]. We also did not retrieve data on the other pneumonia diagnosis related to pneumococcus or staphylococcus . Thus, although we found that SARS-CoV-2 viral co-infections were rare during the first epidemic wave and did not differ either by their clinical presentation or their outcome from SARS-CoV-2 mono-infections, this reassuring finding must be confirmed in the upcoming months.
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