Influenza co-infection associated with severity and mortality in COVID-19 patients

<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>In COVID-19 patients, undetected co-infections may have severe clinical implications associated with increased hospitalization, varied treatment approaches and mortality. Therefore, we investigated the implications of viral and bacterial co-infection in COVID-19 clinical outcomes.</jats:p> </jats:sec><jats:sec> <jats:title>Methods</jats:title> <jats:p>Nasopharyngeal samples were obtained from 48 COVID-19 patients (29% ICU and 71% non-ICU) and screened for the presence of 24 respiratory pathogens using six multiplex PCR panels.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>We found evidence of co-infection in 34 COVID-19 patients (71%). Influenza A H1N1 (n = 17), <jats:italic>Chlamydia pneumoniae</jats:italic> (n = 13) and human adenovirus (n = 10) were the most commonly detected pathogens. Viral co-infection was associated with increased ICU admission (r = 0.1) and higher mortality (OR 1.78, CI = 0.38–8.28) compared to bacterial co-infections (OR 0.44, CI = 0.08–2.45). Two thirds of COVID-19 critically ill patients who died, had a co-infection; and Influenza A H1N1 was the only pathogen for which a direct relationship with mortality was seen (r = 0.2).</jats:p> </jats:sec><jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Our study highlights the importance of screening for co-infecting viruses in COVID-19 patients, that could be the leading cause of disease severity and death. Given the high prevalence of Influenza co-infection in our study, increased coverage of flu vaccination is encouraged to mitigate the transmission of influenza virus during the on-going COVID-19 pandemic and reduce the risk of severe outcome and mortality.</jats:p> </jats:sec>